From f75903cf30d10297430506f2e38b8bf637516aa4 Mon Sep 17 00:00:00 2001 From: Ben Clifford Date: Mon, 19 Oct 2020 09:40:14 +0000 Subject: [PATCH 001/408] tom has seen at scale the monitoring DB reporting "db locked" errors [A] and then [B] lots of "tried to update NNNN rows, only did MMMM" errors. hypothesis: i) we need to rety on db locked? [yes we do] at the sqlite3 commandline that needs to happen, at least, so maybe also in code? this would only really show up if you're looking in the db logs, and probably only if you're also running queries against the DB (or some other access) rather than letting the db manager be the only user. ii) if those locked errors are causing rows to not be INSERTed (eg for tasks) then that means that row cannot be UPDATEd later, which might be then causing symptom B. That symptom probably means that all updates in that batch are discarded. This could happen because of symptom A, or because other malformed data could not be inserted into the database. concerns: i) cross-DB portability (probably a lost cause without further abstraction, because that isn't really a thing SQL does) ii) what happens if I'm looping on some more genuine error that is always present and that causes some internal structures to overflow For the purposes of lsst-parsl, this patch is allowed to be a bit of a messy hack, to try to understand how this problem can be fixed. Problems with this patch: I'm seeing database lock errors when running CREATE TABLE fairly often (but awkward enough to reproduce that I'm not confident in reproducing at the moment). This looks like sqlalchemy doing those ops somewhere that doesn't have the retry logic I added for doing inserts and updates. So this would manifest, i guess, if you were poking at the database before it had been properly initialised by the parsl monitoring code. I think that is probably a situation I care about. --- parsl/monitoring/db_manager.py | 26 +++++- parsl/tests/test_monitoring/test_db_locks.py | 89 ++++++++++++++++++++ 2 files changed, 113 insertions(+), 2 deletions(-) create mode 100644 parsl/tests/test_monitoring/test_db_locks.py diff --git a/parsl/monitoring/db_manager.py b/parsl/monitoring/db_manager.py index 719add6152..a0aa0d02eb 100644 --- a/parsl/monitoring/db_manager.py +++ b/parsl/monitoring/db_manager.py @@ -59,7 +59,10 @@ def __init__(self, self.eng = sa.create_engine(url) self.meta = self.Base.metadata + # TODO: I'm seeing database lock errors happening here with my db lock test. + # Is the right behaviour to retry a few times? self.meta.create_all(self.eng) + self.meta.reflect(bind=self.eng) Session = sessionmaker(bind=self.eng) @@ -476,7 +479,17 @@ def _migrate_logs_to_internal(self, logs_queue, queue_tag, kill_event): def _update(self, table, columns, messages): try: - self.db.update(table=table, columns=columns, messages=messages) + done = False + while not done: + try: + self.db.update(table=table, columns=columns, messages=messages) + done = True + except sa.exc.OperationalError as e: + # hoping that this is a database locked error during _update, not some other problem + logger.warning("Got an sqlite3 operational error. Ignoring and retying on the assumption that it is recoverable: {}".format(e)) + self.db.rollback() + time.sleep(1) # hard coded 1s wait - this should be configurable or exponential backoff or something + except KeyboardInterrupt: logger.exception("KeyboardInterrupt when trying to update Table {}".format(table)) try: @@ -493,7 +506,16 @@ def _update(self, table, columns, messages): def _insert(self, table, messages): try: - self.db.insert(table=table, messages=messages) + done = False + while not done: + try: + self.db.insert(table=table, messages=messages) + done = True + except sa.exc.OperationalError as e: + # hoping that this is a database locked error during _update, not some other problem + logger.warning("Got an sqlite3 operational error. Ignoring and retying on the assumption that it is recoverable: {}".format(e)) + self.db.rollback() + time.sleep(1) # hard coded 1s wait - this should be configurable or exponential backoff or something except KeyboardInterrupt: logger.exception("KeyboardInterrupt when trying to update Table {}".format(table)) try: diff --git a/parsl/tests/test_monitoring/test_db_locks.py b/parsl/tests/test_monitoring/test_db_locks.py new file mode 100644 index 0000000000..babb811545 --- /dev/null +++ b/parsl/tests/test_monitoring/test_db_locks.py @@ -0,0 +1,89 @@ + +import logging +import os +import parsl +import pytest +import sqlalchemy +import time + +logger = logging.getLogger(__name__) + +from parsl.tests.configs.htex_local_alternate import fresh_config + + +@parsl.python_app +def this_app(): + return 5 + + +@pytest.mark.local +def test_row_counts(): + if os.path.exists("monitoring.db"): + logger.info("Monitoring database already exists - deleting") + os.remove("monitoring.db") + + engine = sqlalchemy.create_engine("sqlite:///monitoring.db") + + logger.info("loading parsl") + parsl.load(fresh_config()) + + # parsl.load() returns before all initialisation of monitoring + # is complete, which means it isn't safe to take a read lock on + # the database yet. This delay tries to work around that - some + # better async behaviour might be nice, but I'm not sure what. + time.sleep(10) + + # to get an sqlite3 read lock that is held over a controllable + # long time, create a transaction and perform a SELECT in it. + # (see bottom of https://sqlite.org/lockingv3.html) + + # there's an awkward race here: parsl.load() returns before the + # database might have been created, and so then the db manager will + # crash (and if there is a retry loop there instead, I think it will + # hang until after the read lock stuff below is finished? which might + # be acceptable? if it's meant to be properly async and not blocking?) + # ... in which case, initialise parsl *after taking the lock* would also + # work (although the select statement to get that lock wouldn't be the same + # because it wouldn't be able to select from the right table) + + logger.info("Getting a read lock on the monitoring database") + with engine.begin() as readlock_connection: + readlock_connection.execute("BEGIN TRANSACTION") + result = readlock_connection.execute("SELECT COUNT(*) FROM workflow") + (c, ) = result.first() + assert c == 1 + # now readlock_connection should have a read lock that will + # stay locked until the transaction is ended, or the with + # block ends. + + logger.info("invoking and waiting for result") + assert this_app().result() == 5 + + # there is going to be some raciness here making sure that + # the database manager actually tries to write while the + # read lock is held. I'm not sure if there is a better way + # to detect this other than a hopefully long-enough sleep. + time.sleep(10) + + logger.info("cleaning up parsl") + parsl.dfk().cleanup() + parsl.clear() + + # at this point, we should find one row in the monitoring database. + + logger.info("checking database content") + with engine.begin() as connection: + + result = connection.execute("SELECT COUNT(*) FROM workflow") + (c, ) = result.first() + assert c == 1 + + result = connection.execute("SELECT COUNT(*) FROM task") + (c, ) = result.first() + assert c == 1 + + result = connection.execute("SELECT COUNT(*) FROM try") + (c, ) = result.first() + assert c == 1 + + logger.info("all done") From ffd5bc2f694435375d79fed5718e2b55a3fcd817 Mon Sep 17 00:00:00 2001 From: Ben Clifford Date: Wed, 8 Jul 2020 10:09:07 +0000 Subject: [PATCH 002/408] prototype queue prioritisation in htex this is not intended to be exact, in the sense that a job with a lower priority might run before a job with a higher priority - but the "bulk" of the work (in the LSST sense) should be prioritised this way. priorities can be anything comparable to each other (and to the default priority, which is integer 0) i'm not going to address the macsafequeue in this prototype --- parsl/executors/high_throughput/executor.py | 18 ++++---- .../executors/high_throughput/interchange.py | 41 +++++++++++++++++-- .../test_error_handling/test_resource_spec.py | 6 +++ 3 files changed, 52 insertions(+), 13 deletions(-) diff --git a/parsl/executors/high_throughput/executor.py b/parsl/executors/high_throughput/executor.py index 8cbc3435cc..3fad4f07b2 100644 --- a/parsl/executors/high_throughput/executor.py +++ b/parsl/executors/high_throughput/executor.py @@ -16,8 +16,7 @@ from parsl.executors.high_throughput import interchange from parsl.executors.errors import ( BadMessage, ScalingFailed, - DeserializationError, SerializationError, - UnsupportedFeatureError + DeserializationError, SerializationError ) from parsl.executors.status_handling import StatusHandlingExecutor @@ -542,12 +541,6 @@ def submit(self, func, resource_specification, *args, **kwargs): Returns: Future """ - if resource_specification: - logger.error("Ignoring the resource specification. " - "Parsl resource specification is not supported in HighThroughput Executor. " - "Please check WorkQueueExecutor if resource specification is needed.") - raise UnsupportedFeatureError('resource specification', 'HighThroughput Executor', 'WorkQueue Executor') - if self.bad_state_is_set: raise self.executor_exception @@ -568,8 +561,15 @@ def submit(self, func, resource_specification, *args, **kwargs): except TypeError: raise SerializationError(func.__name__) + if resource_specification and "priority" in resource_specification: + priority = resource_specification["priority"] + logger.debug("Priority {} found in resource specification".format(priority)) + else: + priority = None + msg = {"task_id": task_id, - "buffer": fn_buf} + "buffer": fn_buf, + "priority": priority} # Post task to the the outgoing queue self.outgoing_q.put(msg) diff --git a/parsl/executors/high_throughput/interchange.py b/parsl/executors/high_throughput/interchange.py index 632cfdf5c6..7560e34690 100644 --- a/parsl/executors/high_throughput/interchange.py +++ b/parsl/executors/high_throughput/interchange.py @@ -1,5 +1,6 @@ #!/usr/bin/env python import argparse +import functools import zmq import os import sys @@ -87,6 +88,38 @@ def __str__(self): return self.__repr__() +@functools.total_ordering +class PriorityQueueEntry: + """ This class is needed because msg will be a dict, and dicts are not + comparable to each other (and if they were, this would be an unnecessary + expense because the queue only cares about priority). It provides + ordering of the priority ignoring the message content, and implements an + ordering that places None behind all other orderings, for use as a default + value""" + def __init__(self, pri, msg): + self.pri = pri + self.msg = msg + + def __eq__(self, other): + if type(self) != type(other): + return NotImplemented + return self.pri == other.pri + + def __lt__(self, other): + # this is deliberately inverted, so that largest priority number comes out of the queue first + if type(self) != type(other): + return NotImplemented + if self.pri is None: # special case so that None is always less than every other value + return False # we are more than populated priorities, and equal to None, the inverse of < + elif self.pri is not None and other.pri is None: + return True + else: # self/other both not None + c = self.pri.__gt__(other.pri) + if c == NotImplemented: + raise RuntimeError("priority values are not comparable: {} vs {}".format(self.pri, other.pri)) + return c + + class Interchange(object): """ Interchange is a task orchestrator for distributed systems. @@ -189,7 +222,7 @@ def __init__(self, self.monitoring_enabled = True logger.info("Monitoring enabled and connected to hub") - self.pending_task_queue = queue.Queue(maxsize=10 ** 6) + self.pending_task_queue = queue.PriorityQueue(maxsize=10 ** 6) self.worker_ports = worker_ports self.worker_port_range = worker_port_range @@ -247,11 +280,11 @@ def get_tasks(self, count): tasks = [] for i in range(0, count): try: - x = self.pending_task_queue.get(block=False) + qe = self.pending_task_queue.get(block=False) except queue.Empty: break else: - tasks.append(x) + tasks.append(qe.msg) return tasks @@ -281,7 +314,7 @@ def migrate_tasks_to_internal(self, kill_event): kill_event.set() break else: - self.pending_task_queue.put(msg) + self.pending_task_queue.put(PriorityQueueEntry(msg['priority'], msg)) task_counter += 1 logger.debug("[TASK_PULL_THREAD] Fetched task:{}".format(task_counter)) diff --git a/parsl/tests/test_error_handling/test_resource_spec.py b/parsl/tests/test_error_handling/test_resource_spec.py index 11ffa7c842..ab42a36534 100644 --- a/parsl/tests/test_error_handling/test_resource_spec.py +++ b/parsl/tests/test_error_handling/test_resource_spec.py @@ -1,4 +1,5 @@ import parsl +import pytest from parsl.app.app import python_app # from parsl.tests.configs.local_threads import config from parsl.tests.configs.htex_local import config @@ -12,6 +13,11 @@ def double(x, parsl_resource_specification={}): return x * 2 +@pytest.mark.skip("this test does not accomodate running the test suite" + " on executors which *do* support resource specifications" + " but are not the workqueue executor. In general, it is" + " incorrect to assume that an arbitrary non-workqueue" + " executor will raise the expected exceptionm") def test_resource(n=2): executors = parsl.dfk().executors executor = None From 88249c3e6bc06aa54838c83871fb5c4ffb445649 Mon Sep 17 00:00:00 2001 From: Ben Clifford Date: Mon, 11 Jan 2021 14:09:03 +0000 Subject: [PATCH 003/408] Move sqlalchemy import into test app, as it is not installed for basic tests, and that causes an import error failure --- parsl/tests/test_monitoring/test_db_locks.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/parsl/tests/test_monitoring/test_db_locks.py b/parsl/tests/test_monitoring/test_db_locks.py index babb811545..3718068980 100644 --- a/parsl/tests/test_monitoring/test_db_locks.py +++ b/parsl/tests/test_monitoring/test_db_locks.py @@ -3,7 +3,6 @@ import os import parsl import pytest -import sqlalchemy import time logger = logging.getLogger(__name__) @@ -18,6 +17,7 @@ def this_app(): @pytest.mark.local def test_row_counts(): + import sqlalchemy if os.path.exists("monitoring.db"): logger.info("Monitoring database already exists - deleting") os.remove("monitoring.db") From 8eed78a7cb0e0f0173e16c51169d9a7dcc9549f7 Mon Sep 17 00:00:00 2001 From: Ben Clifford Date: Mon, 11 Jan 2021 15:33:30 +0000 Subject: [PATCH 004/408] Move fresh_config import into test function because it cannot be imported without monitoring prereqs installed --- parsl/tests/test_monitoring/test_db_locks.py | 4 +--- 1 file changed, 1 insertion(+), 3 deletions(-) diff --git a/parsl/tests/test_monitoring/test_db_locks.py b/parsl/tests/test_monitoring/test_db_locks.py index 3718068980..2a7ca0acc3 100644 --- a/parsl/tests/test_monitoring/test_db_locks.py +++ b/parsl/tests/test_monitoring/test_db_locks.py @@ -1,4 +1,3 @@ - import logging import os import parsl @@ -7,8 +6,6 @@ logger = logging.getLogger(__name__) -from parsl.tests.configs.htex_local_alternate import fresh_config - @parsl.python_app def this_app(): @@ -17,6 +14,7 @@ def this_app(): @pytest.mark.local def test_row_counts(): + from parsl.tests.configs.htex_local_alternate import fresh_config import sqlalchemy if os.path.exists("monitoring.db"): logger.info("Monitoring database already exists - deleting") From a23255f2792d88518fb72fdee026f3cff26a5b7b Mon Sep 17 00:00:00 2001 From: Ben Clifford Date: Thu, 18 Feb 2021 12:48:47 +0000 Subject: [PATCH 005/408] Move htex strategy docstring to the correct strategy function From 29edeee9e76b4880971bf3e6dc99097e51b7658d Mon Sep 17 00:00:00 2001 From: Ben Clifford Date: Wed, 17 Feb 2021 13:08:50 +0000 Subject: [PATCH 006/408] Unify two impls of OptionalModuleMissing exception class There was one at the parsl top level, and one in providers, but these were not used uniformly: * the monitoring system used the provider version even though it is nothing to do with the provider system. * the top level error was not listed in the API documentation From 3e2a1df287b5b3f2b09fd6363c9463da250ca4cd Mon Sep 17 00:00:00 2001 From: Ben Clifford Date: Mon, 19 Oct 2020 09:40:14 +0000 Subject: [PATCH 007/408] tom has seen at scale the monitoring DB reporting "db locked" errors [A] and then [B] lots of "tried to update NNNN rows, only did MMMM" errors. hypothesis: i) we need to rety on db locked? [yes we do] at the sqlite3 commandline that needs to happen, at least, so maybe also in code? this would only really show up if you're looking in the db logs, and probably only if you're also running queries against the DB (or some other access) rather than letting the db manager be the only user. ii) if those locked errors are causing rows to not be INSERTed (eg for tasks) then that means that row cannot be UPDATEd later, which might be then causing symptom B. That symptom probably means that all updates in that batch are discarded. This could happen because of symptom A, or because other malformed data could not be inserted into the database. concerns: i) cross-DB portability (probably a lost cause without further abstraction, because that isn't really a thing SQL does) ii) what happens if I'm looping on some more genuine error that is always present and that causes some internal structures to overflow For the purposes of lsst-parsl, this patch is allowed to be a bit of a messy hack, to try to understand how this problem can be fixed. Problems with this patch: I'm seeing database lock errors when running CREATE TABLE fairly often (but awkward enough to reproduce that I'm not confident in reproducing at the moment). This looks like sqlalchemy doing those ops somewhere that doesn't have the retry logic I added for doing inserts and updates. So this would manifest, i guess, if you were poking at the database before it had been properly initialised by the parsl monitoring code. I think that is probably a situation I care about. --- parsl/monitoring/db_manager.py | 26 +++++- parsl/tests/test_monitoring/test_db_locks.py | 89 ++++++++++++++++++++ 2 files changed, 113 insertions(+), 2 deletions(-) create mode 100644 parsl/tests/test_monitoring/test_db_locks.py diff --git a/parsl/monitoring/db_manager.py b/parsl/monitoring/db_manager.py index 0cf4acc9bc..6e4493b976 100644 --- a/parsl/monitoring/db_manager.py +++ b/parsl/monitoring/db_manager.py @@ -63,7 +63,10 @@ def __init__(self, self.eng = sa.create_engine(url) self.meta = self.Base.metadata + # TODO: I'm seeing database lock errors happening here with my db lock test. + # Is the right behaviour to retry a few times? self.meta.create_all(self.eng) + self.meta.reflect(bind=self.eng) Session = sessionmaker(bind=self.eng) @@ -538,7 +541,17 @@ def _migrate_logs_to_internal(self, logs_queue: queue.Queue, queue_tag: str, kil def _update(self, table: str, columns: List[str], messages: List[Dict[str, Any]]) -> None: try: - self.db.update(table=table, columns=columns, messages=messages) + done = False + while not done: + try: + self.db.update(table=table, columns=columns, messages=messages) + done = True + except sa.exc.OperationalError as e: + # hoping that this is a database locked error during _update, not some other problem + logger.warning("Got an sqlite3 operational error. Ignoring and retying on the assumption that it is recoverable: {}".format(e)) + self.db.rollback() + time.sleep(1) # hard coded 1s wait - this should be configurable or exponential backoff or something + except KeyboardInterrupt: logger.exception("KeyboardInterrupt when trying to update Table {}".format(table)) try: @@ -555,7 +568,16 @@ def _update(self, table: str, columns: List[str], messages: List[Dict[str, Any]] def _insert(self, table: str, messages: List[Dict[str, Any]]) -> None: try: - self.db.insert(table=table, messages=messages) + done = False + while not done: + try: + self.db.insert(table=table, messages=messages) + done = True + except sa.exc.OperationalError as e: + # hoping that this is a database locked error during _update, not some other problem + logger.warning("Got an sqlite3 operational error. Ignoring and retying on the assumption that it is recoverable: {}".format(e)) + self.db.rollback() + time.sleep(1) # hard coded 1s wait - this should be configurable or exponential backoff or something except KeyboardInterrupt: logger.exception("KeyboardInterrupt when trying to update Table {}".format(table)) try: diff --git a/parsl/tests/test_monitoring/test_db_locks.py b/parsl/tests/test_monitoring/test_db_locks.py new file mode 100644 index 0000000000..babb811545 --- /dev/null +++ b/parsl/tests/test_monitoring/test_db_locks.py @@ -0,0 +1,89 @@ + +import logging +import os +import parsl +import pytest +import sqlalchemy +import time + +logger = logging.getLogger(__name__) + +from parsl.tests.configs.htex_local_alternate import fresh_config + + +@parsl.python_app +def this_app(): + return 5 + + +@pytest.mark.local +def test_row_counts(): + if os.path.exists("monitoring.db"): + logger.info("Monitoring database already exists - deleting") + os.remove("monitoring.db") + + engine = sqlalchemy.create_engine("sqlite:///monitoring.db") + + logger.info("loading parsl") + parsl.load(fresh_config()) + + # parsl.load() returns before all initialisation of monitoring + # is complete, which means it isn't safe to take a read lock on + # the database yet. This delay tries to work around that - some + # better async behaviour might be nice, but I'm not sure what. + time.sleep(10) + + # to get an sqlite3 read lock that is held over a controllable + # long time, create a transaction and perform a SELECT in it. + # (see bottom of https://sqlite.org/lockingv3.html) + + # there's an awkward race here: parsl.load() returns before the + # database might have been created, and so then the db manager will + # crash (and if there is a retry loop there instead, I think it will + # hang until after the read lock stuff below is finished? which might + # be acceptable? if it's meant to be properly async and not blocking?) + # ... in which case, initialise parsl *after taking the lock* would also + # work (although the select statement to get that lock wouldn't be the same + # because it wouldn't be able to select from the right table) + + logger.info("Getting a read lock on the monitoring database") + with engine.begin() as readlock_connection: + readlock_connection.execute("BEGIN TRANSACTION") + result = readlock_connection.execute("SELECT COUNT(*) FROM workflow") + (c, ) = result.first() + assert c == 1 + # now readlock_connection should have a read lock that will + # stay locked until the transaction is ended, or the with + # block ends. + + logger.info("invoking and waiting for result") + assert this_app().result() == 5 + + # there is going to be some raciness here making sure that + # the database manager actually tries to write while the + # read lock is held. I'm not sure if there is a better way + # to detect this other than a hopefully long-enough sleep. + time.sleep(10) + + logger.info("cleaning up parsl") + parsl.dfk().cleanup() + parsl.clear() + + # at this point, we should find one row in the monitoring database. + + logger.info("checking database content") + with engine.begin() as connection: + + result = connection.execute("SELECT COUNT(*) FROM workflow") + (c, ) = result.first() + assert c == 1 + + result = connection.execute("SELECT COUNT(*) FROM task") + (c, ) = result.first() + assert c == 1 + + result = connection.execute("SELECT COUNT(*) FROM try") + (c, ) = result.first() + assert c == 1 + + logger.info("all done") From c8af4165cd86a44691852e07e5cfd3312c72b1e4 Mon Sep 17 00:00:00 2001 From: Ben Clifford Date: Thu, 18 Feb 2021 13:42:49 +0000 Subject: [PATCH 008/408] Remove disabled midway test. The per-site testing mechanism is the way to do per-site testing. --- .../tests/test_flowcontrol/test_doc_config.py | 34 ------------------- 1 file changed, 34 deletions(-) delete mode 100644 parsl/tests/test_flowcontrol/test_doc_config.py diff --git a/parsl/tests/test_flowcontrol/test_doc_config.py b/parsl/tests/test_flowcontrol/test_doc_config.py deleted file mode 100644 index b4590dadb2..0000000000 --- a/parsl/tests/test_flowcontrol/test_doc_config.py +++ /dev/null @@ -1,34 +0,0 @@ -import pytest -import parsl -from parsl.tests.configs.midway import config - - -local_config = config - - -@parsl.python_app -def python_app(): - import os - import time - import platform - time.sleep(20) - return "Hello from {0}:{1}".format(os.getpid(), platform.uname()) - - -@pytest.mark.skip('We shouldnt run tests on midway on CI local env') -@pytest.mark.local -def test_python(N=5): - ''' Testing basic scaling|Python 0 -> 1 block on SSH.Midway ''' - - results = {} - for i in range(0, N): - results[i] = python_app() - - print("Waiting ....") - for i in range(0, N): - print(results[0].result()) - - -if __name__ == '__main__': - - test_python() From 7a085100bc4fa40498e6099af58a7f2a916390be Mon Sep 17 00:00:00 2001 From: Ben Clifford Date: Wed, 17 Feb 2021 13:05:49 +0000 Subject: [PATCH 009/408] Rework __repr__ and __str__ for OptionalModuleMissing __repr__ should be quasi-machine-readable, and __str__ human readable See PR #1966, commit a423955f4a9e03cf6986a6e21d285cf46fa3bc88, for further context. Before: >>> str(e) "(['mymod'], 'this test needs demonstrating')" >>> repr(e) "The functionality requested requires a missing optional module:['mymod'], Reason:this test needs demonstrating" After: >>> str(e) "The functionality requested requires missing optional modules ['mymod'], because: this test needs demonstrating" >>> repr(e) "OptionalModuleMissing(['mymod'], 'this test needs demonstrating')" --- parsl/errors.py | 8 +++++--- 1 file changed, 5 insertions(+), 3 deletions(-) diff --git a/parsl/errors.py b/parsl/errors.py index 0a1813448d..eb81cf5157 100644 --- a/parsl/errors.py +++ b/parsl/errors.py @@ -1,15 +1,17 @@ from parsl.app.errors import ParslError +from typing import List + class OptionalModuleMissing(ParslError): ''' Error raised when a required module is missing for a optional/extra component ''' - def __init__(self, module_names, reason): + def __init__(self, module_names: List[str], reason: str): self.module_names = module_names self.reason = reason - def __repr__(self): - return "The functionality requested requires a missing optional module:{0}, Reason:{1}".format( + def __str__(self) -> str: + return "The functionality requested requires missing optional modules {0}, because: {1}".format( self.module_names, self.reason ) From dc7846157c4beb0a338a263c72de2e7b1130afc4 Mon Sep 17 00:00:00 2001 From: Ben Clifford Date: Wed, 9 Dec 2020 12:03:06 +0000 Subject: [PATCH 010/408] Describe monitoring protocols better This PR adds type annotations, asserts and comments to better describe the existing formats used for monitoring. This is intended to make future simplification easier. This PR should not change any behaviour except error handling when a format is violated. --- parsl/monitoring/db_manager.py | 24 ++++++++++++++++++++---- parsl/monitoring/monitoring.py | 29 ++++++++++++++++++----------- 2 files changed, 38 insertions(+), 15 deletions(-) diff --git a/parsl/monitoring/db_manager.py b/parsl/monitoring/db_manager.py index 6e4493b976..e3ec67fe64 100644 --- a/parsl/monitoring/db_manager.py +++ b/parsl/monitoring/db_manager.py @@ -5,7 +5,7 @@ import time import datetime -from typing import Any, Dict, List, Optional, Set, Tuple, TypeVar +from typing import Any, Dict, List, Optional, Set, Tuple, TypeVar, cast from parsl.log_utils import set_file_logger from parsl.dataflow.states import States @@ -527,17 +527,33 @@ def _migrate_logs_to_internal(self, logs_queue: queue.Queue, queue_tag: str, kil except queue.Empty: continue else: - if queue_tag == 'priority': + if queue_tag == 'priority' and x == 'STOP': if x == 'STOP': self.close() + elif queue_tag == 'priority': # implicitly not 'STOP' + if isinstance(x, tuple): + assert x[0] in [MessageType.WORKFLOW_INFO, MessageType.TASK_INFO], \ + "_migrate_logs_to_internal can only migrate WORKFLOW_,TASK_INFO message from priority queue, got x[0] == {}".format(x[0]) + assert len(x) == 2 + self.pending_priority_queue.put(cast(Any, x)) else: - self.pending_priority_queue.put(x) + logger.warning("dropping message with unknown format: {}".format(x)) elif queue_tag == 'resource': + assert len(x) == 3 self.pending_resource_queue.put(x[-1]) elif queue_tag == 'node': - self.pending_node_queue.put(x[-1]) + logger.info("Received these two from node queue") + logger.info("x = {}".format(x)) + logger.info("addr = {}".format(addr)) + + assert x[0] == MessageType.NODE_INFO, "_migrate_logs_to_internal can only migrate NODE_INFO messages from node queue" + assert len(x) == 2, "expected message tuple to have exactly two elements" + + logger.info("Will put {} to pending node queue".format(x[1])) + self.pending_node_queue.put(x[1]) elif queue_tag == "block": self.pending_block_queue.put(x[-1]) + # TODO: else condition here raise an exception. def _update(self, table: str, columns: List[str], messages: List[Dict[str, Any]]) -> None: try: diff --git a/parsl/monitoring/monitoring.py b/parsl/monitoring/monitoring.py index 786d85fd83..ccc28073dc 100644 --- a/parsl/monitoring/monitoring.py +++ b/parsl/monitoring/monitoring.py @@ -221,9 +221,9 @@ def start(self, run_id: str) -> int: comm_q = Queue(maxsize=10) # type: Queue[Union[Tuple[int, int], str]] self.exception_q = Queue(maxsize=10) # type: Queue[Tuple[str, str]] self.priority_msgs = Queue() # type: Queue[Tuple[Any, int]] - self.resource_msgs = Queue() # type: Queue[Tuple[Any, Any]] - self.node_msgs = Queue() # type: Queue[Tuple[Any, int]] - self.block_msgs = Queue() # type: Queue[Tuple[Any, Any]] + self.resource_msgs = Queue() # type: Queue[Tuple[Dict[str, Any], Any]] + self.node_msgs = Queue() # type: Queue[Tuple[Tuple[MessageType, Dict[str, Any]], int]] + self.block_msgs = Queue() # type: Queue[Tuple[Tuple[MessageType, Dict[str, Any]], Any]] self.router_proc = Process(target=router_starter, args=(comm_q, self.exception_q, self.priority_msgs, self.node_msgs, self.block_msgs, self.resource_msgs), @@ -434,16 +434,16 @@ def __init__(self, def start(self, priority_msgs: "queue.Queue[Tuple[Tuple[MessageType, Dict[str, Any]], int]]", - node_msgs: "queue.Queue[Tuple[Dict[str, Any], int]]", - block_msgs: "queue.Queue[Tuple[Dict[str, Any], int]]", - resource_msgs: "queue.Queue[Tuple[Dict[str, Any], str]]") -> None: + node_msgs: "queue.Queue[Tuple[Tuple[MessageType, Dict[str, Any]], int]]", + block_msgs: "queue.Queue[Tuple[Tuple[MessageType, Dict[str, Any]], int]]", + resource_msgs: "queue.Queue[Tuple[Dict[str, Any], Any]]") -> None: try: while True: try: data, addr = self.sock.recvfrom(2048) msg = pickle.loads(data) + self.logger.info("Got UDP Message from {}: {}".format(addr, msg)) resource_msgs.put((msg, addr)) - self.logger.debug("Got UDP Message from {}: {}".format(addr, msg)) except socket.timeout: pass @@ -468,12 +468,19 @@ def start(self, try: msg = self.ic_channel.recv_pyobj() self.logger.debug("Got ZMQ Message from interchange: {}".format(msg)) + + assert msg[0] == MessageType.NODE_INFO \ + or msg[0] == MessageType.BLOCK_INFO, \ + "IC Channel expects only NODE_INFO or BLOCK_INFO and cannot dispatch other message types" + if msg[0] == MessageType.NODE_INFO: msg[2]['last_heartbeat'] = datetime.datetime.fromtimestamp(msg[2]['last_heartbeat']) msg[2]['run_id'] = self.run_id msg[2]['timestamp'] = msg[1] - msg = (msg[0], msg[2]) - node_msgs.put((msg, 0)) + + # ((tag, dict), addr) + node_msg = ((msg[0], msg[2]), 0) + node_msgs.put(node_msg) elif msg[0] == MessageType.BLOCK_INFO: block_msgs.put((msg, 0)) else: @@ -502,8 +509,8 @@ def start(self, def router_starter(comm_q: "queue.Queue[Union[Tuple[int, int], str]]", exception_q: "queue.Queue[Tuple[str, str]]", priority_msgs: "queue.Queue[Tuple[Tuple[MessageType, Dict[str, Any]], int]]", - node_msgs: "queue.Queue[Tuple[Dict[str, Any], int]]", - block_msgs: "queue.Queue[Tuple[Dict[str, Any], int]]", + node_msgs: "queue.Queue[Tuple[Tuple[MessageType, Dict[str, Any]], int]]", + block_msgs: "queue.Queue[Tuple[Tuple[MessageType, Dict[str, Any]], int]]", resource_msgs: "queue.Queue[Tuple[Dict[str, Any], str]]", hub_address: str, From 1e39d383fcc9d313eb6dac09a671088ea9998cc2 Mon Sep 17 00:00:00 2001 From: Ben Clifford Date: Wed, 6 Jan 2021 15:15:43 +0000 Subject: [PATCH 011/408] debugging of slow monitoring tests I was seeing delays in running fresh_config of sometimes 30 seconds This i suspect was auto address config, so i've removed that and use localhost, which is fine for this test config This moves test run time to a consistent 11s against master on my laptop. --- parsl/tests/configs/htex_local_alternate.py | 1 + parsl/tests/test_monitoring/test_basic.py | 6 ++++-- 2 files changed, 5 insertions(+), 2 deletions(-) diff --git a/parsl/tests/configs/htex_local_alternate.py b/parsl/tests/configs/htex_local_alternate.py index e088222565..218b634b43 100644 --- a/parsl/tests/configs/htex_local_alternate.py +++ b/parsl/tests/configs/htex_local_alternate.py @@ -40,6 +40,7 @@ def fresh_config(): executors=[ HighThroughputExecutor( label="htex_Local", + address="localhost", working_dir=working_dir, storage_access=[FTPInTaskStaging(), HTTPInTaskStaging(), NoOpFileStaging()], worker_debug=True, diff --git a/parsl/tests/test_monitoring/test_basic.py b/parsl/tests/test_monitoring/test_basic.py index 2e54453423..a77b9f4b66 100644 --- a/parsl/tests/test_monitoring/test_basic.py +++ b/parsl/tests/test_monitoring/test_basic.py @@ -31,8 +31,10 @@ def test_row_counts(): logger.info("Monitoring database already exists - deleting") os.remove("monitoring.db") - logger.info("loading parsl") - parsl.load(fresh_config()) + logger.info("Generating fresh config") + c = fresh_config() + logger.info("Loading parsl") + parsl.load(c) logger.info("invoking and waiting for result") assert this_app().result() == 5 From 1346c816b7b9ddb044e416adc38c2ac4e7dcc2c2 Mon Sep 17 00:00:00 2001 From: Ben Clifford Date: Tue, 22 Dec 2020 13:55:14 +0000 Subject: [PATCH 012/408] exex executor isn't shutting down nicely, causing excessive CPU load when running --config local tests. exex isn't needed for LSST, so disable testing of it. --- parsl/tests/sites/test_local_exex.py | 2 ++ 1 file changed, 2 insertions(+) diff --git a/parsl/tests/sites/test_local_exex.py b/parsl/tests/sites/test_local_exex.py index b9d0cc4d0c..8ca4dd818f 100644 --- a/parsl/tests/sites/test_local_exex.py +++ b/parsl/tests/sites/test_local_exex.py @@ -34,6 +34,7 @@ def bash_app(stdout=None, stderr=None): @pytest.mark.local +@pytest.mark.skip("BENC/LSST - don't test exex") def test_python(N=2): """Testing basic python functionality.""" @@ -53,6 +54,7 @@ def test_python(N=2): @pytest.mark.local +@pytest.mark.skip("BENC/LSST - don't test exex") def test_bash(): """Testing basic bash functionality.""" From 6e7cf5e11e4baf04e69d80a8be572057fa2a0954 Mon Sep 17 00:00:00 2001 From: Ben Clifford Date: Fri, 18 Dec 2020 10:49:25 +0000 Subject: [PATCH 013/408] temp disable ssh test because it doesn't run right in my dev env and it isn't high enough priority for me to fix at the moment --- parsl/tests/test_providers/test_local_provider.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/parsl/tests/test_providers/test_local_provider.py b/parsl/tests/test_providers/test_local_provider.py index 35ff1d3411..989b6c5d54 100644 --- a/parsl/tests/test_providers/test_local_provider.py +++ b/parsl/tests/test_providers/test_local_provider.py @@ -77,7 +77,7 @@ def test_local_channel(): # It would probably be better, when more formalized site testing comes into existence, to # use a site-testing provided server/configuration instead of the current scheme -@pytest.mark.local +@pytest.mark.skip("disabled for benc laptop") def test_ssh_channel(): with tempfile.TemporaryDirectory() as config_dir: sshd_thread, priv_key, server_port = _start_sshd(config_dir) From 19c96417bc030ef17a695ecffb760154667b510a Mon Sep 17 00:00:00 2001 From: Ben Clifford Date: Mon, 25 Jan 2021 17:35:43 +0000 Subject: [PATCH 014/408] Add in RESOURCE_INFO stuff This makes RESOURCE_INFO messages be sent around in the same format as other messages, which makes upcoming rearrangement of monitoring message deliver easier --- parsl/monitoring/db_manager.py | 6 ++++-- parsl/monitoring/message_type.py | 3 +++ parsl/monitoring/monitoring.py | 8 ++++---- 3 files changed, 11 insertions(+), 6 deletions(-) diff --git a/parsl/monitoring/db_manager.py b/parsl/monitoring/db_manager.py index e3ec67fe64..0f9acd9de1 100644 --- a/parsl/monitoring/db_manager.py +++ b/parsl/monitoring/db_manager.py @@ -539,8 +539,10 @@ def _migrate_logs_to_internal(self, logs_queue: queue.Queue, queue_tag: str, kil else: logger.warning("dropping message with unknown format: {}".format(x)) elif queue_tag == 'resource': - assert len(x) == 3 - self.pending_resource_queue.put(x[-1]) + assert x[0] == MessageType.RESOURCE_INFO, "_migrate_logs_to_internal can only migrate RESOURCE_INFO message from resource queue" + body = x[1] + assert len(body) == 3 + self.pending_resource_queue.put(body[-1]) elif queue_tag == 'node': logger.info("Received these two from node queue") logger.info("x = {}".format(x)) diff --git a/parsl/monitoring/message_type.py b/parsl/monitoring/message_type.py index cf4e11fe00..366b61bd42 100644 --- a/parsl/monitoring/message_type.py +++ b/parsl/monitoring/message_type.py @@ -6,6 +6,9 @@ class MessageType(Enum): # Reports any task related info such as launch, completion etc. TASK_INFO = 0 + # Reports of resource utilization on a per-task basis + RESOURCE_INFO = 1 + # Top level workflow information WORKFLOW_INFO = 2 diff --git a/parsl/monitoring/monitoring.py b/parsl/monitoring/monitoring.py index ccc28073dc..3e5e359e5a 100644 --- a/parsl/monitoring/monitoring.py +++ b/parsl/monitoring/monitoring.py @@ -221,7 +221,7 @@ def start(self, run_id: str) -> int: comm_q = Queue(maxsize=10) # type: Queue[Union[Tuple[int, int], str]] self.exception_q = Queue(maxsize=10) # type: Queue[Tuple[str, str]] self.priority_msgs = Queue() # type: Queue[Tuple[Any, int]] - self.resource_msgs = Queue() # type: Queue[Tuple[Dict[str, Any], Any]] + self.resource_msgs = Queue() # type: Queue[Tuple[Tuple[MessageType, Dict[str, Any]], Any]] self.node_msgs = Queue() # type: Queue[Tuple[Tuple[MessageType, Dict[str, Any]], int]] self.block_msgs = Queue() # type: Queue[Tuple[Tuple[MessageType, Dict[str, Any]], Any]] @@ -436,14 +436,14 @@ def start(self, priority_msgs: "queue.Queue[Tuple[Tuple[MessageType, Dict[str, Any]], int]]", node_msgs: "queue.Queue[Tuple[Tuple[MessageType, Dict[str, Any]], int]]", block_msgs: "queue.Queue[Tuple[Tuple[MessageType, Dict[str, Any]], int]]", - resource_msgs: "queue.Queue[Tuple[Dict[str, Any], Any]]") -> None: + resource_msgs: "queue.Queue[Tuple[Tuple[MessageType, Dict[str, Any]], Any]]") -> None: try: while True: try: data, addr = self.sock.recvfrom(2048) msg = pickle.loads(data) self.logger.info("Got UDP Message from {}: {}".format(addr, msg)) - resource_msgs.put((msg, addr)) + resource_msgs.put(((MessageType.RESOURCE_INFO, msg), addr)) except socket.timeout: pass @@ -511,7 +511,7 @@ def router_starter(comm_q: "queue.Queue[Union[Tuple[int, int], str]]", priority_msgs: "queue.Queue[Tuple[Tuple[MessageType, Dict[str, Any]], int]]", node_msgs: "queue.Queue[Tuple[Tuple[MessageType, Dict[str, Any]], int]]", block_msgs: "queue.Queue[Tuple[Tuple[MessageType, Dict[str, Any]], int]]", - resource_msgs: "queue.Queue[Tuple[Dict[str, Any], str]]", + resource_msgs: "queue.Queue[Tuple[Tuple[MessageType, Dict[str, Any]], str]]", hub_address: str, hub_port: Optional[int], From ef3edbfb1a3f3c991c214d916f0315b61566d0cf Mon Sep 17 00:00:00 2001 From: Ben Clifford Date: Wed, 9 Dec 2020 16:24:55 +0000 Subject: [PATCH 015/408] Dispatch monitoring based on message type, rather than on name of queue. This is groundwork for sending monitoring messages in on any queue, and so via different protocols. --- parsl/monitoring/db_manager.py | 40 ++++++++++++++++++++++------------ parsl/monitoring/monitoring.py | 29 ++++++++++++++++++------ 2 files changed, 48 insertions(+), 21 deletions(-) diff --git a/parsl/monitoring/db_manager.py b/parsl/monitoring/db_manager.py index 0f9acd9de1..52210e00bd 100644 --- a/parsl/monitoring/db_manager.py +++ b/parsl/monitoring/db_manager.py @@ -534,28 +534,40 @@ def _migrate_logs_to_internal(self, logs_queue: queue.Queue, queue_tag: str, kil if isinstance(x, tuple): assert x[0] in [MessageType.WORKFLOW_INFO, MessageType.TASK_INFO], \ "_migrate_logs_to_internal can only migrate WORKFLOW_,TASK_INFO message from priority queue, got x[0] == {}".format(x[0]) - assert len(x) == 2 - self.pending_priority_queue.put(cast(Any, x)) + self._dispatch_to_internal(x) else: logger.warning("dropping message with unknown format: {}".format(x)) elif queue_tag == 'resource': assert x[0] == MessageType.RESOURCE_INFO, "_migrate_logs_to_internal can only migrate RESOURCE_INFO message from resource queue" - body = x[1] - assert len(body) == 3 - self.pending_resource_queue.put(body[-1]) + self._dispatch_to_internal(x) elif queue_tag == 'node': logger.info("Received these two from node queue") logger.info("x = {}".format(x)) logger.info("addr = {}".format(addr)) - - assert x[0] == MessageType.NODE_INFO, "_migrate_logs_to_internal can only migrate NODE_INFO messages from node queue" - assert len(x) == 2, "expected message tuple to have exactly two elements" - - logger.info("Will put {} to pending node queue".format(x[1])) - self.pending_node_queue.put(x[1]) - elif queue_tag == "block": - self.pending_block_queue.put(x[-1]) - # TODO: else condition here raise an exception. + self._dispatch_to_internal(x) + elif queue_tag == 'block': + logger.info("Received a block queue tag message") + self._dispatch_to_internal(x) + else: + logger.error(f"Discarding because unknown queue tag '{queue_tag}', message: {x}") + + def _dispatch_to_internal(self, x: Tuple) -> None: + if x[0] in [MessageType.WORKFLOW_INFO, MessageType.TASK_INFO]: + self.pending_priority_queue.put(cast(Any, x)) + elif x[0] == MessageType.RESOURCE_INFO: + body = x[1] + assert len(body) == 3 + self.pending_resource_queue.put(body[-1]) + elif x[0] == MessageType.NODE_INFO: + assert len(x) == 2, "expected NODE_INFO tuple to have exactly two elements" + + logger.info("Will put {} to pending node queue".format(x[1])) + self.pending_node_queue.put(x[1]) + elif x[0] == MessageType.BLOCK_INFO: + logger.info("Will put {} to pending block queue".format(x[1])) + self.pending_block_queue.put(x[-1]) + else: + logger.error("Discarding message of unknown type {}".format(x[0])) def _update(self, table: str, columns: List[str], messages: List[Dict[str, Any]]) -> None: try: diff --git a/parsl/monitoring/monitoring.py b/parsl/monitoring/monitoring.py index 3e5e359e5a..440093189d 100644 --- a/parsl/monitoring/monitoring.py +++ b/parsl/monitoring/monitoring.py @@ -13,7 +13,7 @@ from parsl.process_loggers import wrap_with_logs from parsl.monitoring.message_type import MessageType -from typing import Any, Callable, Dict, List, Optional, Union +from typing import cast, Any, Callable, Dict, List, Optional, Union _db_manager_excepts: Optional[Exception] @@ -451,8 +451,11 @@ def start(self, msg = self.dfk_channel.recv_pyobj() self.logger.debug("Got ZMQ Message from DFK: {}".format(msg)) if msg[0] == MessageType.BLOCK_INFO: + self.logger.info("Putting that ZMQ message to block_msgs") block_msgs.put((msg, 0)) + self.logger.info("Put that ZMQ message to block_msgs") else: + self.logger.info("Putting that ZMQ message to priority_msgs by default") priority_msgs.put((msg, 0)) if msg[0] == MessageType.WORKFLOW_INFO and 'python_version' not in msg[1]: break @@ -468,12 +471,11 @@ def start(self, try: msg = self.ic_channel.recv_pyobj() self.logger.debug("Got ZMQ Message from interchange: {}".format(msg)) - - assert msg[0] == MessageType.NODE_INFO \ - or msg[0] == MessageType.BLOCK_INFO, \ - "IC Channel expects only NODE_INFO or BLOCK_INFO and cannot dispatch other message types" - + assert isinstance(msg, tuple), "IC Channel expects only tuples, got {}".format(msg) + assert len(msg) >= 1, "IC Channel expects tuples of length at least 1, got {}".format(msg) if msg[0] == MessageType.NODE_INFO: + self.logger.info("message is NODE_INFO") + assert len(msg) >= 1, "IC Channel expects NODE_INFO tuples of length at least 3, got {}".format(msg) msg[2]['last_heartbeat'] = datetime.datetime.fromtimestamp(msg[2]['last_heartbeat']) msg[2]['run_id'] = self.run_id msg[2]['timestamp'] = msg[1] @@ -481,8 +483,21 @@ def start(self, # ((tag, dict), addr) node_msg = ((msg[0], msg[2]), 0) node_msgs.put(node_msg) + elif msg[0] == MessageType.RESOURCE_INFO: + # with more uniform handling of messaging, it doesn't matter + # too much which queue this goes to now... could be node_msgs + # just as well, I think. + # and if the above message rewriting was got rid of, this block might not need to switch on message tag at all. + self.logger.info("Handling as RESOURCE_INFO") + resource_msgs.put(cast(Any, msg)) elif msg[0] == MessageType.BLOCK_INFO: - block_msgs.put((msg, 0)) + self.logger.info("Putting message to block_msgs: {}".format((msg, 0))) + # block_msgs.put((msg, 0)) + block_msgs.put(cast(Any, (msg, 0))) + # TODO this cast is suspicious and is to make mypy + # trivially pass rather than me paying attention to + # the message structure. so if something breaks in + # this patch, it could well be here. else: self.logger.error(f"Discarding message from interchange with unknown type {msg[0].value}") except zmq.Again: From 4cf26e3bd94e6c7b57e07ad4d0cf96dfa0ee9a69 Mon Sep 17 00:00:00 2001 From: Ben Clifford Date: Thu, 12 Nov 2020 16:42:13 +0000 Subject: [PATCH 016/408] Make monitoring switchable between UDPRadio and over-htex resource status delivery TODO: needs to be switchable? At the moment, it is hard coded into the definition of an executor - which maybe makes sense when using HTEX, but not so much when parsl user wants to choose between mechanisms (eg UDP vs FS). That switching also needs to be per executor. for lsst purposes this needs to scale up to the scale of 1000 nodes running many works (10s of) on each node. so eg 50000 workers as a target? 50000 zmq TCP connections is A Lot I'd like something that is not tied into the htex codebase (which at the moment, monitoring is a bit, and putting a messaging concentrator in there would make it more tied in). But a messaging concentrator per-node is what I need. Perhaps I can re-use the existing htex queue, even, using message types... "here's a message I want you to forward to the messaging system in the interchange" ? That would at least be a bit orthogonal? Or perhaps the messaging engine (eg the UDPRadio bit) can be replaced by an htex specific one. so you get UDPRadio in udp circumstances, or HTEXRadio in the htex case, if you so configure it? that would be an ok plugin thing to try out that at least would allow switching between UDP and HTEX while allowing very-HTEX specific stuff to be implemented. (and specificlaly, HTEX provides this kind of hierarchical feature that parsl-core does not) So additional communication this needs: i) monitoring worker wrapper: ability to communicate with htex worker enough to send monitoring messages - needs some "examine my context" that is probably provided by globals: if you're using "htex" mode monitoring, inspect a global that you expect to exist - and htex worker should set up that worker. - perhaps that also provides some scope for *inside apps* reporting state changes which is something i was interested in ii) interchange<->mangager<->htex worker: add in ability to send monitoring messages (perhaps as a broader "new tag to deliver") iii) interchange -> monitoring: deliver those messages to monitoring --- parsl/dataflow/dflow.py | 1 + parsl/executors/base.py | 14 +++ .../extreme_scale/mpi_worker_pool.py | 4 +- parsl/executors/high_throughput/executor.py | 73 +++++++----- .../executors/high_throughput/interchange.py | 33 +++++- .../high_throughput/monitoring_info.py | 8 ++ .../high_throughput/process_worker_pool.py | 12 +- parsl/monitoring/db_manager.py | 4 +- parsl/monitoring/monitoring.py | 109 ++++++++++++++++-- 9 files changed, 206 insertions(+), 52 deletions(-) create mode 100644 parsl/executors/high_throughput/monitoring_info.py diff --git a/parsl/dataflow/dflow.py b/parsl/dataflow/dflow.py index 9009d281c3..c1c8a4364e 100644 --- a/parsl/dataflow/dflow.py +++ b/parsl/dataflow/dflow.py @@ -576,6 +576,7 @@ def launch_task(self, task_id, executable, *args, **kwargs): self.run_id, wrapper_logging_level, self.monitoring.resource_monitoring_interval, + executor.radio_mode, executor.monitor_resources()) with self.submitter_lock: diff --git a/parsl/executors/base.py b/parsl/executors/base.py index 7652c50d66..c834b01722 100644 --- a/parsl/executors/base.py +++ b/parsl/executors/base.py @@ -20,6 +20,18 @@ class ParslExecutor(metaclass=ABCMeta): label: str - a human readable label for the executor, unique with respect to other executors. + Per-executor monitoring behaviour can be influenced by exposing: + + radio_mode: str - a string describing how monitoring code wrapping individual + tasks should send data back to the submit side. This field is messy + and should be made more general, but for prototyping for LSST, this + is OK. The principal requirement is that HTEX tasks can be told to + use the htex channel, and thread executor tasks can use the UDP + channel. Further less urgent requirements: other remote executors + such as workqueue need a more reliable channel than UDP - because + the motivation for this work is that htex + udp isn't providing + reliable monitoring. + An executor may optionally expose: storage_access: List[parsl.data_provider.staging.Staging] - a list of staging @@ -37,6 +49,8 @@ class ParslExecutor(metaclass=ABCMeta): label: str + radio_mode: str = "udp" + @abstractmethod def start(self) -> Optional[List[str]]: """Start the executor. diff --git a/parsl/executors/extreme_scale/mpi_worker_pool.py b/parsl/executors/extreme_scale/mpi_worker_pool.py index 18cd12341a..7f3063c318 100755 --- a/parsl/executors/extreme_scale/mpi_worker_pool.py +++ b/parsl/executors/extreme_scale/mpi_worker_pool.py @@ -404,10 +404,10 @@ def worker(comm, rank): try: result = execute_task(req['buffer']) except Exception as e: - result_package = {'task_id': tid, 'exception': serialize(RemoteExceptionWrapper(*sys.exc_info()))} + result_package = {'type': 'result', 'task_id': tid, 'exception': serialize(RemoteExceptionWrapper(*sys.exc_info()))} logger.debug("No result due to exception: {} with result package {}".format(e, result_package)) else: - result_package = {'task_id': tid, 'result': serialize(result)} + result_package = {'type': 'result', 'task_id': tid, 'result': serialize(result)} logger.debug("Result: {}".format(result)) pkl_package = pickle.dumps(result_package) diff --git a/parsl/executors/high_throughput/executor.py b/parsl/executors/high_throughput/executor.py index fc3265ec19..384c399b6f 100644 --- a/parsl/executors/high_throughput/executor.py +++ b/parsl/executors/high_throughput/executor.py @@ -255,6 +255,8 @@ def __init__(self, "--hb_threshold={heartbeat_threshold} " "--cpu-affinity {cpu_affinity} ") + radio_mode = "htex" + def initialize_scaling(self): """ Compose the launch command and call the scale_out @@ -383,44 +385,51 @@ def _queue_management_worker(self): for serialized_msg in msgs: try: msg = pickle.loads(serialized_msg) - tid = msg['task_id'] except pickle.UnpicklingError: raise BadMessage("Message received could not be unpickled") - except Exception: - raise BadMessage("Message received does not contain 'task_id' field") - - if tid == -1 and 'exception' in msg: - logger.warning("Executor shutting down due to exception from interchange") - exception = deserialize(msg['exception']) - self.set_bad_state_and_fail_all(exception) - break - - task_fut = self.tasks.pop(tid) + # at this point, dispatch on message type - if 'result' in msg: - result = deserialize(msg['result']) - task_fut.set_result(result) - - elif 'exception' in msg: + if msg['type'] == 'result': try: - s = deserialize(msg['exception']) - # s should be a RemoteExceptionWrapper... so we can reraise it - if isinstance(s, RemoteExceptionWrapper): - try: - s.reraise() - except Exception as e: - task_fut.set_exception(e) - elif isinstance(s, Exception): - task_fut.set_exception(s) - else: - raise ValueError("Unknown exception-like type received: {}".format(type(s))) - except Exception as e: - # TODO could be a proper wrapped exception? - task_fut.set_exception( - DeserializationError("Received exception, but handling also threw an exception: {}".format(e))) + tid = msg['task_id'] + except Exception: + raise BadMessage("Message received does not contain 'task_id' field") + + if tid == -1 and 'exception' in msg: + logger.warning("Executor shutting down due to exception from interchange") + exception = deserialize(msg['exception']) + self.set_bad_state_and_fail_all(exception) + break + + task_fut = self.tasks.pop(tid) + + if 'result' in msg: + result = deserialize(msg['result']) + task_fut.set_result(result) + + elif 'exception' in msg: + try: + s = deserialize(msg['exception']) + # s should be a RemoteExceptionWrapper... so we can reraise it + if isinstance(s, RemoteExceptionWrapper): + try: + s.reraise() + except Exception as e: + task_fut.set_exception(e) + elif isinstance(s, Exception): + task_fut.set_exception(s) + else: + raise ValueError("Unknown exception-like type received: {}".format(type(s))) + except Exception as e: + # TODO could be a proper wrapped exception? + task_fut.set_exception( + DeserializationError("Received exception, but handling also threw an exception: {}".format(e))) + else: + raise BadMessage("Message received is neither result or exception") else: - raise BadMessage("Message received is neither result or exception") + # the 'monitoring' message type should not reach this if statement. It should be handled in the interchange. + raise BadMessage("Message received with unknown type {}".format(msg['type'])) if not self.is_alive: break diff --git a/parsl/executors/high_throughput/interchange.py b/parsl/executors/high_throughput/interchange.py index d181d018bf..019c70a175 100644 --- a/parsl/executors/high_throughput/interchange.py +++ b/parsl/executors/high_throughput/interchange.py @@ -362,6 +362,7 @@ def _command_server(self, kill_event): logger.debug("[COMMAND] is alive") continue + @wrap_with_logs def start(self, poll_period=None): """ Start the interchange @@ -449,7 +450,7 @@ def start(self, poll_period=None): "py.v={} parsl.v={}".format(msg['python_v'].rsplit(".", 1)[0], msg['parsl_v']) ) - result_package = {'task_id': -1, 'exception': serialize_object(e)} + result_package = {'type': 'result', 'task_id': -1, 'exception': serialize_object(e)} pkl_package = pickle.dumps(result_package) self.results_outgoing.send(pkl_package) logger.warning("[MAIN] Sent failure reports, unregistering manager") @@ -516,11 +517,31 @@ def start(self, poll_period=None): # Receive any results and forward to client if self.results_incoming in self.socks and self.socks[self.results_incoming] == zmq.POLLIN: logger.debug("[MAIN] entering results_incoming section") - manager, *b_messages = self.results_incoming.recv_multipart() + manager, *all_messages = self.results_incoming.recv_multipart() if manager not in self._ready_manager_queue: logger.warning("[MAIN] Received a result from a un-registered manager: {}".format(manager)) else: - logger.debug("[MAIN] Got {} result items in batch".format(len(b_messages))) + logger.debug("[MAIN] Got {} result items in batch".format(len(all_messages))) + + b_messages = [] + + # this block needs to split messages into 'result' messages, and process as previously; + # monitoring messages, which should be sent to monitoring via whatever is used? + # and others, which should generate a non-fatal error log + + # TODO: rework to avoid depickling twice... because that's quite expensive I expect + + for message in all_messages: + r = pickle.loads(message) + if r['type'] == 'result': + # process this for task ID and forward to executor + b_messages.append(message) + # TODO: case here for monitoring messages + if r['type'] == 'monitoring': + hub_channel.send_pyobj(r['payload']) + else: + logger.error("Interchange discarding result_queue message of unknown type: {}".format(r['type'])) + for b_message in b_messages: r = pickle.loads(b_message) try: @@ -532,7 +553,9 @@ def start(self, poll_period=None): manager, self._ready_manager_queue[manager]['tasks'])) - self.results_outgoing.send_multipart(b_messages) + if b_messages: + self.results_outgoing.send_multipart(b_messages) + logger.debug("[MAIN] Current tasks: {}".format(self._ready_manager_queue[manager]['tasks'])) if len(self._ready_manager_queue[manager]['tasks']) == 0: self._ready_manager_queue[manager]['idle_since'] = time.time() @@ -551,7 +574,7 @@ def start(self, poll_period=None): try: raise ManagerLost(manager, self._ready_manager_queue[manager]['hostname']) except Exception: - result_package = {'task_id': tid, 'exception': serialize_object(RemoteExceptionWrapper(*sys.exc_info()))} + result_package = {'type': 'result', 'task_id': tid, 'exception': serialize_object(RemoteExceptionWrapper(*sys.exc_info()))} pkl_package = pickle.dumps(result_package) self.results_outgoing.send(pkl_package) logger.warning("[MAIN] Sent failure reports, unregistering manager") diff --git a/parsl/executors/high_throughput/monitoring_info.py b/parsl/executors/high_throughput/monitoring_info.py new file mode 100644 index 0000000000..0903b9be04 --- /dev/null +++ b/parsl/executors/high_throughput/monitoring_info.py @@ -0,0 +1,8 @@ +# this is a global that will be worker-specific +# and can be set to the result queue which can +# then be acquired by any other code running in +# a worker context - specifically the monitoring +# wrapper code. +from typing import Optional +from queue import Queue +result_queue: Optional[Queue] = None diff --git a/parsl/executors/high_throughput/process_worker_pool.py b/parsl/executors/high_throughput/process_worker_pool.py index 2386d76462..9ed8ecad18 100755 --- a/parsl/executors/high_throughput/process_worker_pool.py +++ b/parsl/executors/high_throughput/process_worker_pool.py @@ -357,7 +357,7 @@ def worker_watchdog(self, kill_event): raise WorkerLost(worker_id, platform.node()) except Exception: logger.info("[WORKER_WATCHDOG_THREAD] Putting exception for task {} in the pending result queue".format(task['task_id'])) - result_package = {'task_id': task['task_id'], 'exception': serialize(RemoteExceptionWrapper(*sys.exc_info()))} + result_package = {'type': 'result', 'task_id': task['task_id'], 'exception': serialize(RemoteExceptionWrapper(*sys.exc_info()))} pkl_package = pickle.dumps(result_package) self.pending_result_queue.put(pkl_package) except KeyError: @@ -498,6 +498,10 @@ def worker(worker_id, pool_id, pool_size, task_queue, result_queue, worker_queue os.environ['PARSL_WORKER_COUNT'] = str(pool_size) os.environ['PARSL_WORKER_POOL_ID'] = str(pool_id) + # share the result queue with monitoring code so it too can send results down that channel + import parsl.executors.high_throughput.monitoring_info as mi + mi.result_queue = result_queue + # Sync worker with master logger.info('Worker {} started'.format(worker_id)) if args.debug: @@ -542,9 +546,9 @@ def worker(worker_id, pool_id, pool_size, task_queue, result_queue, worker_queue serialized_result = serialize(result, buffer_threshold=1e6) except Exception as e: logger.info('Caught an exception: {}'.format(e)) - result_package = {'task_id': tid, 'exception': serialize(RemoteExceptionWrapper(*sys.exc_info()))} + result_package = {'type': 'result', 'task_id': tid, 'exception': serialize(RemoteExceptionWrapper(*sys.exc_info()))} else: - result_package = {'task_id': tid, 'result': serialized_result} + result_package = {'type': 'result', 'task_id': tid, 'result': serialized_result} # logger.debug("Result: {}".format(result)) logger.info("Completed task {}".format(tid)) @@ -552,7 +556,7 @@ def worker(worker_id, pool_id, pool_size, task_queue, result_queue, worker_queue pkl_package = pickle.dumps(result_package) except Exception: logger.exception("Caught exception while trying to pickle the result package") - pkl_package = pickle.dumps({'task_id': tid, + pkl_package = pickle.dumps({'type': 'result', 'task_id': tid, 'exception': serialize(RemoteExceptionWrapper(*sys.exc_info())) }) diff --git a/parsl/monitoring/db_manager.py b/parsl/monitoring/db_manager.py index 52210e00bd..d0f06bab72 100644 --- a/parsl/monitoring/db_manager.py +++ b/parsl/monitoring/db_manager.py @@ -538,7 +538,9 @@ def _migrate_logs_to_internal(self, logs_queue: queue.Queue, queue_tag: str, kil else: logger.warning("dropping message with unknown format: {}".format(x)) elif queue_tag == 'resource': - assert x[0] == MessageType.RESOURCE_INFO, "_migrate_logs_to_internal can only migrate RESOURCE_INFO message from resource queue" + assert isinstance(x, tuple), "_migrate_logs_to_internal was expecting a tuple, got {}".format(x) + assert x[0] == MessageType.RESOURCE_INFO, \ + "_migrate_logs_to_internal can only migrate RESOURCE_INFO message from resource queue, got tag {}, message {}".format(x[0], x) self._dispatch_to_internal(x) elif queue_tag == 'node': logger.info("Received these two from node queue") diff --git a/parsl/monitoring/monitoring.py b/parsl/monitoring/monitoring.py index 440093189d..58286524af 100644 --- a/parsl/monitoring/monitoring.py +++ b/parsl/monitoring/monitoring.py @@ -8,10 +8,14 @@ import zmq import queue +from abc import ABCMeta, abstractmethod from multiprocessing import Process, Queue from parsl.utils import RepresentationMixin from parsl.process_loggers import wrap_with_logs +# this is needed for htex hack to get at htex result queue +import parsl.executors.high_throughput.monitoring_info + from parsl.monitoring.message_type import MessageType from typing import cast, Any, Callable, Dict, List, Optional, Union @@ -62,7 +66,78 @@ def start_file_logger(filename: str, name: str = 'monitoring', level: int = logg return logger -class UDPRadio: +class MonitoringRadio(metaclass=ABCMeta): + @abstractmethod + def send(self, message: object) -> None: + pass + + +class HTEXRadio(MonitoringRadio): + + def __init__(self, monitoring_url: str, source_id: int, timeout: int = 10): + """ + Parameters + ---------- + + monitoring_url : str + URL of the form ://: + source_id : str + String identifier of the source + timeout : int + timeout, default=10s + """ + self.source_id = source_id + logger.info("htex-based monitoring channel initialising") + + def send(self, message: object) -> None: + """ Sends a message to the UDP receiver + + Parameter + --------- + + message: object + Arbitrary pickle-able object that is to be sent + + Returns: + None + """ + # TODO: this message needs to look like the other messages that the interchange will send... + # hub_channel.send_pyobj((MessageType.NODE_INFO, + # datetime.datetime.now(), + # self._ready_manager_queue[manager])) + + # not serialising here because it looks like python objects can go through mp queues without explicit pickling? + try: + buffer = (MessageType.RESOURCE_INFO, (self.source_id, # Identifier for manager + int(time.time()), # epoch timestamp + message)) + except Exception: + logging.exception("Exception during pickling", exc_info=True) + return + + result_queue = parsl.executors.high_throughput.monitoring_info.result_queue + + # this message needs to go in the result queue tagged so that it is treated + # i) as a monitoring message by the interchange, and then further more treated + # as a RESOURCE_INFO message when received by monitoring (rather than a NODE_INFO + # which is the implicit default for messages from the interchange) + + # for the interchange, the outer wrapper, this needs to be a dict: + + interchange_msg = { + 'type': 'monitoring', + 'payload': buffer + } + + if result_queue: + result_queue.put(pickle.dumps(interchange_msg)) + else: + logger.error("result_queue is uninitialized - cannot put monitoring message") + + return + + +class UDPRadio(MonitoringRadio): def __init__(self, monitoring_url: str, source_id: int, timeout: int = 10): """ @@ -312,6 +387,7 @@ def monitor_wrapper(f: Any, run_id: str, logging_level: int, sleep_dur: float, + radio_mode: str, monitor_resources: bool) -> Callable: """ Internal Wrap the Parsl app with a function that will call the monitor function and point it at the correct pid when the task begins. @@ -321,7 +397,8 @@ def wrapped(*args: List[Any], **kwargs: Dict[str, Any]) -> Any: send_first_message(try_id, task_id, monitoring_hub_url, - run_id) + run_id, + radio_mode) if monitor_resources: # create the monitor process and start @@ -332,6 +409,7 @@ def wrapped(*args: List[Any], **kwargs: Dict[str, Any]) -> Any: task_id, monitoring_hub_url, run_id, + radio_mode, logging_level, sleep_dur), name="Monitor-Wrapper-{}".format(task_id)) @@ -489,7 +567,7 @@ def start(self, # just as well, I think. # and if the above message rewriting was got rid of, this block might not need to switch on message tag at all. self.logger.info("Handling as RESOURCE_INFO") - resource_msgs.put(cast(Any, msg)) + resource_msgs.put(cast(Any, (msg, 0))) elif msg[0] == MessageType.BLOCK_INFO: self.logger.info("Putting message to block_msgs: {}".format((msg, 0))) # block_msgs.put((msg, 0)) @@ -568,11 +646,18 @@ def router_starter(comm_q: "queue.Queue[Union[Tuple[int, int], str]]", def send_first_message(try_id: int, task_id: int, monitoring_hub_url: str, - run_id: str) -> None: + run_id: str, radio_mode: str) -> None: import platform - radio = UDPRadio(monitoring_hub_url, - source_id=task_id) + radio: MonitoringRadio + if radio_mode == "udp": + radio = UDPRadio(monitoring_hub_url, + source_id=task_id) + elif radio_mode == "htex": + radio = HTEXRadio(monitoring_hub_url, + source_id=task_id) + else: + raise RuntimeError(f"Unknown radio mode: {radio_mode}") msg = {'run_id': run_id, 'try_id': try_id, @@ -591,6 +676,7 @@ def monitor(pid: int, task_id: int, monitoring_hub_url: str, run_id: str, + radio_mode: str, logging_level: int = logging.INFO, sleep_dur: float = 10) -> None: """Internal @@ -601,8 +687,15 @@ def monitor(pid: int, import psutil import time - radio = UDPRadio(monitoring_hub_url, - source_id=task_id) + radio: MonitoringRadio + if radio_mode == "udp": + radio = UDPRadio(monitoring_hub_url, + source_id=task_id) + elif radio_mode == "htex": + radio = HTEXRadio(monitoring_hub_url, + source_id=task_id) + else: + raise RuntimeError(f"Unknown radio mode: {radio_mode}") format_string = "%(asctime)s.%(msecs)03d %(name)s:%(lineno)d [%(levelname)s] %(message)s" logging.basicConfig(filename='{logbase}/monitor.{task_id}.{pid}.log'.format( From c017e8855434f15115b7c89a52dcaf1d865796f0 Mon Sep 17 00:00:00 2001 From: Ben Clifford Date: Thu, 21 Jan 2021 16:16:57 +0000 Subject: [PATCH 017/408] this is a prototype of using the filesystem to deliver monitoring messages the file creation technique is similar to Maildir: create a file in tmp/ without any need to write atomically then move to new/ atomically This means that the only messages appearing in new/ will be complete, and can be deleted by the receiver without conflicting with the sender. I expect this will present interesting file system loads because of all the directory operations, especially if everything is happening just inside a single directory. the load will perhaps be comparable to each job creating a few stdout/stderr files inside one directory. unless resource monitoring is on, in which case much higher load. so maybe it will be slower but more reliable than UDP. i expect that there will be more out-of-order message delivery than with UDP - and I expect monitoring will deal badly with that. (especially, the notion of "first" RESOURCE_INFO messages) the intention is to use someone elses infrastructure to deliver messages rather than implementing a new htex-style comms network just for monitoring --- parsl/monitoring/monitoring.py | 90 ++++++++++++++++++++- parsl/tests/configs/htex_local_alternate.py | 2 +- 2 files changed, 90 insertions(+), 2 deletions(-) diff --git a/parsl/monitoring/monitoring.py b/parsl/monitoring/monitoring.py index 58286524af..35134cfaad 100644 --- a/parsl/monitoring/monitoring.py +++ b/parsl/monitoring/monitoring.py @@ -13,12 +13,16 @@ from parsl.utils import RepresentationMixin from parsl.process_loggers import wrap_with_logs +from parsl.serialize import deserialize + # this is needed for htex hack to get at htex result queue import parsl.executors.high_throughput.monitoring_info from parsl.monitoring.message_type import MessageType from typing import cast, Any, Callable, Dict, List, Optional, Union +from parsl.serialize import serialize + _db_manager_excepts: Optional[Exception] from typing import Optional, Tuple @@ -72,6 +76,42 @@ def send(self, message: object) -> None: pass +class FilesystemRadio(MonitoringRadio): + def __init__(self, monitoring_url: str, source_id: int, timeout: int = 10): + logger.info("filesystem based monitoring channel initializing") + self.source_id = source_id + self.id_counter = 0 + + def send(self, message: object) -> None: + logger.info("Sending a monitoring message via filesystem") + + tmp_path = "/home/benc/tmp/parsl-radio/tmp" + new_path = "/home/benc/tmp/parsl-radio/new" + + # this should be randomised by things like worker ID, process ID, whatever + # because there will in general be many FilesystemRadio objects sharing the + # same space (even from the same process). id(self) used here will + # disambiguate in one process at one instant, but not between + # other things: eg different hosts, different processes, same process different non-overlapping instantiations + unique_id = f"msg-{id(self)}-{self.id_counter}" + + self.id_counter = self.id_counter + 1 + + # TODO: use path operators not string interpolation + tmp_filename = f"{tmp_path}/{unique_id}" + new_filename = f"{new_path}/{unique_id}" + buffer = ((MessageType.RESOURCE_INFO, (self.source_id, # Identifier for manager + int(time.time()), # epoch timestamp + message)), "NA") + + # this will write the message out then atomically + # move it into new/, so that a partially written + # file will never be observed in new/ + with open(tmp_filename, "wb") as f: + f.write(serialize(buffer)) + os.rename(tmp_filename, new_filename) + + class HTEXRadio(MonitoringRadio): def __init__(self, monitoring_url: str, source_id: int, timeout: int = 10): @@ -151,7 +191,6 @@ def __init__(self, monitoring_url: str, source_id: int, timeout: int = 10): timeout : int timeout, default=10s """ - self.monitoring_url = monitoring_url self.sock_timeout = timeout self.source_id = source_id @@ -328,6 +367,14 @@ def start(self, run_id: str) -> int: self.dbm_proc.start() self.logger.info("Started the Hub process {} and DBM process {}".format(self.router_proc.pid, self.dbm_proc.pid)) + self.filesystem_proc = Process(target=filesystem_receiver, + args=(self.logdir, self.resource_msgs), + name="Monitoring-Filesystem-Process", + daemon=True + ) + self.filesystem_proc.start() + self.logger.info(f"Started filesystem radio receiver process {self.filesystem_proc.pid}") + try: comm_q_result = comm_q.get(block=True, timeout=120) except queue.Empty: @@ -371,6 +418,7 @@ def close(self) -> None: exception_msg[1])) self.router_proc.terminate() self.dbm_proc.terminate() + self.filesystem_proc.terminate() self.logger.info("Waiting for Hub to receive all messages and terminate") self.router_proc.join() self.logger.debug("Finished waiting for Hub termination") @@ -379,6 +427,12 @@ def close(self) -> None: self.dbm_proc.join() self.logger.debug("Finished waiting for DBM termination") + # should this be message based? it probably doesn't need to be if + # we believe we've received all messages + self.logger.info("Terminating filesystem radio receiver process") + self.filesystem_proc.terminate() + self.filesystem_proc.join() + @staticmethod def monitor_wrapper(f: Any, try_id: int, @@ -427,6 +481,34 @@ def wrapped(*args: List[Any], **kwargs: Dict[str, Any]) -> Any: return wrapped +# this needs proper typing, but I was having some problems with typeguard... +@wrap_with_logs +def filesystem_receiver(logdir: str, q: "queue.Queue[Tuple[Tuple[MessageType, Dict[str, Any]], Any]]") -> None: + new_dir = "/home/benc/tmp/parsl-radio/new" + logger = start_file_logger("{}/monitoring_filesystem_radio.log".format(logdir), + name="monitoring_filesystem_radio", + level=logging.DEBUG) + logger.info("Starting filesystem radio receiver") + while True: # needs an exit condition, that also copes with late messages + # like the UDP radio receiver. + logger.info("Start filesystem radio receiver loop") + + # iterate over files in new_dir + for filename in os.listdir(new_dir): + logger.info(f"Processing filesystem radio file {filename}") + full_path_filename = f"{new_dir}/{filename}" + with open(full_path_filename, "rb") as f: + message = deserialize(f.read()) + logger.info(f"Message received is: {message}") + assert(isinstance(message, tuple)) + q.put(cast(Any, message)) # TODO: sort this typing/cast out + # should this addr field at the end be removed? does it ever + # get used in monitoring? + os.remove(full_path_filename) + + time.sleep(1) # whats a good time for this poll? + + class MonitoringRouter: def __init__(self, @@ -656,6 +738,9 @@ def send_first_message(try_id: int, elif radio_mode == "htex": radio = HTEXRadio(monitoring_hub_url, source_id=task_id) + elif radio_mode == "filesystem": + radio = FilesystemRadio(monitoring_hub_url, + source_id=task_id) else: raise RuntimeError(f"Unknown radio mode: {radio_mode}") @@ -694,6 +779,9 @@ def monitor(pid: int, elif radio_mode == "htex": radio = HTEXRadio(monitoring_hub_url, source_id=task_id) + elif radio_mode == "filesystem": + radio = FilesystemRadio(monitoring_hub_url, + source_id=task_id) else: raise RuntimeError(f"Unknown radio mode: {radio_mode}") diff --git a/parsl/tests/configs/htex_local_alternate.py b/parsl/tests/configs/htex_local_alternate.py index 218b634b43..a27fb895fc 100644 --- a/parsl/tests/configs/htex_local_alternate.py +++ b/parsl/tests/configs/htex_local_alternate.py @@ -63,7 +63,7 @@ def fresh_config(): monitoring=MonitoringHub( hub_address="localhost", hub_port=55055, - monitoring_debug=False, + monitoring_debug=True, resource_monitoring_interval=1, ) ) From f6613eb26e5d79433ec8c8612385c29d5afba587 Mon Sep 17 00:00:00 2001 From: Ben Clifford Date: Wed, 17 Feb 2021 15:53:13 +0000 Subject: [PATCH 018/408] test fs based monitoring provider using local executor --- .../tests/configs/local_threads_monitoring.py | 17 +++- .../test_mon_local/__init__.py | 0 .../test_mon_local/test_basic.py | 92 +++++++++++++++++++ .../test_mon_local/test_db_locks.py | 89 ++++++++++++++++++ .../test_memoization_representation.py | 80 ++++++++++++++++ 5 files changed, 276 insertions(+), 2 deletions(-) create mode 100644 parsl/tests/test_monitoring/test_mon_local/__init__.py create mode 100644 parsl/tests/test_monitoring/test_mon_local/test_basic.py create mode 100644 parsl/tests/test_monitoring/test_mon_local/test_db_locks.py create mode 100644 parsl/tests/test_monitoring/test_mon_local/test_memoization_representation.py diff --git a/parsl/tests/configs/local_threads_monitoring.py b/parsl/tests/configs/local_threads_monitoring.py index 3ab4305c74..130ec4182a 100644 --- a/parsl/tests/configs/local_threads_monitoring.py +++ b/parsl/tests/configs/local_threads_monitoring.py @@ -2,8 +2,21 @@ from parsl.config import Config from parsl.monitoring import MonitoringHub -config = Config(executors=[ThreadPoolExecutor(label='threads', max_threads=4)], - monitoring=MonitoringHub( + +# BENC: temp class for dev purposes. should test both UDP and filesystem +# radiomodes with local executor. +class TestExecutor(ThreadPoolExecutor): + radio_mode = "filesystem" + + +def fresh_config(): + executor = TestExecutor(label='threads', max_threads=4) + + # BENC: this is to check I'm overriding in subclass properly + assert executor.radio_mode == "filesystem" + + return Config(executors=[executor], + monitoring=MonitoringHub( hub_address="localhost", hub_port=55055, resource_monitoring_interval=3, diff --git a/parsl/tests/test_monitoring/test_mon_local/__init__.py b/parsl/tests/test_monitoring/test_mon_local/__init__.py new file mode 100644 index 0000000000..e69de29bb2 diff --git a/parsl/tests/test_monitoring/test_mon_local/test_basic.py b/parsl/tests/test_monitoring/test_mon_local/test_basic.py new file mode 100644 index 0000000000..9169c4559a --- /dev/null +++ b/parsl/tests/test_monitoring/test_mon_local/test_basic.py @@ -0,0 +1,92 @@ +import logging +import os +import parsl +import pytest +import time + +logger = logging.getLogger(__name__) + + +@parsl.python_app +def this_app(): + # this delay needs to be several times the resource monitoring + # period configured in the test configuration, so that some + # messages are actually sent - there is no guarantee that any + # (non-first) resource message will be sent at all for a short app. + time.sleep(3) + + return 5 + + +@pytest.mark.local +def test_row_counts(): + # this is imported here rather than at module level because + # it isn't available in a plain parsl install, so this module + # would otherwise fail to import and break even a basic test + # run. + import sqlalchemy + from parsl.tests.configs.local_threads_monitoring import fresh_config + + if os.path.exists("monitoring.db"): + logger.info("Monitoring database already exists - deleting") + os.remove("monitoring.db") + + logger.info("Generating fresh config") + c = fresh_config() + logger.info("Loading parsl") + parsl.load(c) + + logger.info("invoking and waiting for result") + assert this_app().result() == 5 + + logger.info("cleaning up parsl") + parsl.dfk().cleanup() + parsl.clear() + + # at this point, we should find one row in the monitoring database. + + logger.info("checking database content") + engine = sqlalchemy.create_engine("sqlite:///monitoring.db") + with engine.begin() as connection: + + result = connection.execute("SELECT COUNT(*) FROM workflow") + (c, ) = result.first() + assert c == 1 + + result = connection.execute("SELECT COUNT(*) FROM task") + (c, ) = result.first() + assert c == 1 + + result = connection.execute("SELECT COUNT(*) FROM try") + (c, ) = result.first() + assert c == 1 + + result = connection.execute("SELECT COUNT(*) FROM status, try " + "WHERE status.task_id = try.task_id " + "AND status.task_status_name='exec_done' " + "AND task_try_time_running is NULL") + (c, ) = result.first() + assert c == 0 + + # DIFF WRT ORIGINAL TEST: there is no concept of 'node' in local thread execution + # result = connection.execute("SELECT COUNT(*) FROM node") + # (c, ) = result.first() + # assert c == 2 + + # DIFF WRT ORIGINAL TEST: there is no concept of block in local thread execution + # There should be one block polling status + # local provider has a status_polling_interval of 5s + # result = connection.execute("SELECT COUNT(*) FROM block") + # (c, ) = result.first() + # assert c >= 2 + + # DIFF WRT ORIGINAL TEST: there is no resource monitoring with local thread executor + # result = connection.execute("SELECT COUNT(*) FROM resource") + # (c, ) = result.first() + # assert c >= 1 + + logger.info("all done") + + +if __name__ == "__main__": + test_row_counts() diff --git a/parsl/tests/test_monitoring/test_mon_local/test_db_locks.py b/parsl/tests/test_monitoring/test_mon_local/test_db_locks.py new file mode 100644 index 0000000000..9a97104d89 --- /dev/null +++ b/parsl/tests/test_monitoring/test_mon_local/test_db_locks.py @@ -0,0 +1,89 @@ + +import logging +import os +import parsl +import pytest +import sqlalchemy +import time + +logger = logging.getLogger(__name__) + +from parsl.tests.configs.local_threads_monitoring import fresh_config + + +@parsl.python_app +def this_app(): + return 5 + + +@pytest.mark.local +def test_row_counts(): + if os.path.exists("monitoring.db"): + logger.info("Monitoring database already exists - deleting") + os.remove("monitoring.db") + + engine = sqlalchemy.create_engine("sqlite:///monitoring.db") + + logger.info("loading parsl") + parsl.load(fresh_config()) + + # parsl.load() returns before all initialisation of monitoring + # is complete, which means it isn't safe to take a read lock on + # the database yet. This delay tries to work around that - some + # better async behaviour might be nice, but I'm not sure what. + time.sleep(10) + + # to get an sqlite3 read lock that is held over a controllable + # long time, create a transaction and perform a SELECT in it. + # (see bottom of https://sqlite.org/lockingv3.html) + + # there's an awkward race here: parsl.load() returns before the + # database might have been created, and so then the db manager will + # crash (and if there is a retry loop there instead, I think it will + # hang until after the read lock stuff below is finished? which might + # be acceptable? if it's meant to be properly async and not blocking?) + # ... in which case, initialise parsl *after taking the lock* would also + # work (although the select statement to get that lock wouldn't be the same + # because it wouldn't be able to select from the right table) + + logger.info("Getting a read lock on the monitoring database") + with engine.begin() as readlock_connection: + readlock_connection.execute("BEGIN TRANSACTION") + result = readlock_connection.execute("SELECT COUNT(*) FROM workflow") + (c, ) = result.first() + assert c == 1 + # now readlock_connection should have a read lock that will + # stay locked until the transaction is ended, or the with + # block ends. + + logger.info("invoking and waiting for result") + assert this_app().result() == 5 + + # there is going to be some raciness here making sure that + # the database manager actually tries to write while the + # read lock is held. I'm not sure if there is a better way + # to detect this other than a hopefully long-enough sleep. + time.sleep(10) + + logger.info("cleaning up parsl") + parsl.dfk().cleanup() + parsl.clear() + + # at this point, we should find one row in the monitoring database. + + logger.info("checking database content") + with engine.begin() as connection: + + result = connection.execute("SELECT COUNT(*) FROM workflow") + (c, ) = result.first() + assert c == 1 + + result = connection.execute("SELECT COUNT(*) FROM task") + (c, ) = result.first() + assert c == 1 + + result = connection.execute("SELECT COUNT(*) FROM try") + (c, ) = result.first() + assert c == 1 + + logger.info("all done") diff --git a/parsl/tests/test_monitoring/test_mon_local/test_memoization_representation.py b/parsl/tests/test_monitoring/test_mon_local/test_memoization_representation.py new file mode 100644 index 0000000000..14faeb0518 --- /dev/null +++ b/parsl/tests/test_monitoring/test_mon_local/test_memoization_representation.py @@ -0,0 +1,80 @@ + +import logging +import os +import parsl +import pytest + +logger = logging.getLogger(__name__) + + +@parsl.python_app(cache=True) +def this_app(x): + return x + 1 + + +@pytest.mark.local +def test_hashsum(): + import sqlalchemy + from parsl.tests.configs.local_threads_monitoring import fresh_config + + if os.path.exists("monitoring.db"): + logger.info("Monitoring database already exists - deleting") + os.remove("monitoring.db") + + logger.info("loading parsl") + parsl.load(fresh_config()) + + logger.info("invoking and waiting for result (1/4)") + f1 = this_app(4) + assert f1.result() == 5 + + logger.info("invoking and waiting for result (2/4)") + f2 = this_app(17) + assert f2.result() == 18 + + logger.info("invoking and waiting for result (3/4)") + f3 = this_app(4) + assert f3.result() == 5 + + logger.info("invoking and waiting for result (4/4)") + f4 = this_app(4) + assert f4.result() == 5 + + assert f1.task_def['hashsum'] == f3.task_def['hashsum'] + assert f1.task_def['hashsum'] == f4.task_def['hashsum'] + assert f1.task_def['hashsum'] != f2.task_def['hashsum'] + + logger.info("cleaning up parsl") + parsl.dfk().cleanup() + parsl.clear() + + # at this point, we should find one row in the monitoring database. + + logger.info("checking database content") + engine = sqlalchemy.create_engine("sqlite:///monitoring.db") + with engine.begin() as connection: + + # we should have three tasks, but with only two tries, because the + # memo try should be missing + result = connection.execute("SELECT COUNT(*) FROM task") + (task_count, ) = result.first() + assert task_count == 4 + + # this will check that the number of task rows for each hashsum matches the above app invocations + result = connection.execute(f"SELECT COUNT(task_hashsum) FROM task WHERE task_hashsum='{f1.task_def['hashsum']}'") + (hashsum_count, ) = result.first() + assert hashsum_count == 3 + + result = connection.execute(f"SELECT COUNT(task_hashsum) FROM task WHERE task_hashsum='{f2.task_def['hashsum']}'") + (hashsum_count, ) = result.first() + assert hashsum_count == 1 + + result = connection.execute("SELECT COUNT(*) FROM status WHERE task_status_name='exec_done'") + (memo_count, ) = result.first() + assert memo_count == 2 + + result = connection.execute("SELECT COUNT(*) FROM status WHERE task_status_name='memo_done'") + (memo_count, ) = result.first() + assert memo_count == 2 + + logger.info("all done") From 1502eb667f4d74e900e847af10e57696a1307f19 Mon Sep 17 00:00:00 2001 From: Ben Clifford Date: Wed, 17 Feb 2021 12:44:44 +0000 Subject: [PATCH 019/408] switch WQ to fs mode, and add copies of the monitoring tests, that use WQ this is to check for me that wq+fs monitoring is ok i'm not clear how it should be integrated into the CI test suite. --- parsl/executors/workqueue/executor.py | 2 + parsl/tests/configs/workqueue_monitoring.py | 20 ++++ .../test_monitoring/test_mon_wq/__init__.py | 0 .../test_monitoring/test_mon_wq/test_basic.py | 103 ++++++++++++++++++ .../test_mon_wq/test_db_locks.py | 89 +++++++++++++++ .../test_memoization_representation.py | 80 ++++++++++++++ 6 files changed, 294 insertions(+) create mode 100644 parsl/tests/configs/workqueue_monitoring.py create mode 100644 parsl/tests/test_monitoring/test_mon_wq/__init__.py create mode 100644 parsl/tests/test_monitoring/test_mon_wq/test_basic.py create mode 100644 parsl/tests/test_monitoring/test_mon_wq/test_db_locks.py create mode 100644 parsl/tests/test_monitoring/test_mon_wq/test_memoization_representation.py diff --git a/parsl/executors/workqueue/executor.py b/parsl/executors/workqueue/executor.py index e4fd500363..9437e264de 100644 --- a/parsl/executors/workqueue/executor.py +++ b/parsl/executors/workqueue/executor.py @@ -181,6 +181,8 @@ class WorkQueueExecutor(NoStatusHandlingExecutor): Extra options passed to work_queue_worker. Default is ''. """ + radio_mode = "filesystem" + @typeguard.typechecked def __init__(self, label: str = "WorkQueueExecutor", diff --git a/parsl/tests/configs/workqueue_monitoring.py b/parsl/tests/configs/workqueue_monitoring.py new file mode 100644 index 0000000000..fd1da1445c --- /dev/null +++ b/parsl/tests/configs/workqueue_monitoring.py @@ -0,0 +1,20 @@ +from parsl.config import Config +from parsl.executors import WorkQueueExecutor + +from parsl.data_provider.http import HTTPInTaskStaging +from parsl.data_provider.ftp import FTPInTaskStaging +from parsl.data_provider.file_noop import NoOpFileStaging + +from parsl.monitoring import MonitoringHub + + +def fresh_config(): + return Config(executors=[WorkQueueExecutor(port=9000, + storage_access=[FTPInTaskStaging(), HTTPInTaskStaging(), NoOpFileStaging()])], + monitoring=MonitoringHub(hub_address="localhost", + hub_port=55055, + monitoring_debug=True, + resource_monitoring_interval=1, + ) + + ) diff --git a/parsl/tests/test_monitoring/test_mon_wq/__init__.py b/parsl/tests/test_monitoring/test_mon_wq/__init__.py new file mode 100644 index 0000000000..e69de29bb2 diff --git a/parsl/tests/test_monitoring/test_mon_wq/test_basic.py b/parsl/tests/test_monitoring/test_mon_wq/test_basic.py new file mode 100644 index 0000000000..9e1f1f8dc8 --- /dev/null +++ b/parsl/tests/test_monitoring/test_mon_wq/test_basic.py @@ -0,0 +1,103 @@ +import logging +import os +import parsl +import pytest +import time + +logger = logging.getLogger(__name__) + + +@parsl.python_app +def this_app(): + # this delay needs to be several times the resource monitoring + # period configured in the test configuration, so that some + # messages are actually sent - there is no guarantee that any + # (non-first) resource message will be sent at all for a short app. + time.sleep(3) + + return 5 + + +@pytest.mark.local +def test_row_counts(): + # this is imported here rather than at module level because + # it isn't available in a plain parsl install, so this module + # would otherwise fail to import and break even a basic test + # run. + import sqlalchemy + from parsl.tests.configs.workqueue_monitoring import fresh_config + + if os.path.exists("monitoring.db"): + logger.info("Monitoring database already exists - deleting") + os.remove("monitoring.db") + + logger.info("Generating fresh config") + c = fresh_config() + logger.info("Loading parsl") + parsl.load(c) + + logger.info("invoking and waiting for result") + assert this_app().result() == 5 + + logger.info("cleaning up parsl") + parsl.dfk().cleanup() + parsl.clear() + + # at this point, we should find one row in the monitoring database. + + logger.info("checking database content") + engine = sqlalchemy.create_engine("sqlite:///monitoring.db") + with engine.begin() as connection: + + result = connection.execute("SELECT COUNT(*) FROM workflow") + (c, ) = result.first() + assert c == 1 + + result = connection.execute("SELECT COUNT(*) FROM task") + (c, ) = result.first() + assert c == 1 + + result = connection.execute("SELECT COUNT(*) FROM try") + (c, ) = result.first() + assert c == 1 + + result = connection.execute("SELECT COUNT(*) FROM status, try " + "WHERE status.task_id = try.task_id " + "AND status.task_status_name='exec_done' " + "AND task_try_time_running is NULL") + (c, ) = result.first() + assert c == 0 + + # workqueue doesn't populate the node table. + # because parsl level code isn't running on a node persistently + # instead, it is the workqueue worker doing that, which doesn't + # report into parsl monitoring. + # this is a feature downgrade from using htex that needs some + # consideration + + # Two entries: one showing manager active, one inactive + # result = connection.execute("SELECT COUNT(*) FROM node") + # (c, ) = result.first() + # assert c == 2 + + # workqueue, at least when using providers, does have a loose + # block concept: but it doesn't report anything into the block + # table here, and if using wq external scaling thing, then there + # wouldn't be parsl level blocks at all. + # This needs some consideration. + + # There should be one block polling status + # local provider has a status_polling_interval of 5s + # result = connection.execute("SELECT COUNT(*) FROM block") + # (c, ) = result.first() + # assert c >= 2 + + result = connection.execute("SELECT COUNT(*) FROM resource") + (c, ) = result.first() + assert c >= 1 + + logger.info("all done") + + +if __name__ == "__main__": + test_row_counts() diff --git a/parsl/tests/test_monitoring/test_mon_wq/test_db_locks.py b/parsl/tests/test_monitoring/test_mon_wq/test_db_locks.py new file mode 100644 index 0000000000..0c5d2a7341 --- /dev/null +++ b/parsl/tests/test_monitoring/test_mon_wq/test_db_locks.py @@ -0,0 +1,89 @@ + +import logging +import os +import parsl +import pytest +import sqlalchemy +import time + +logger = logging.getLogger(__name__) + +from parsl.tests.configs.workqueue_monitoring import fresh_config + + +@parsl.python_app +def this_app(): + return 5 + + +@pytest.mark.local +def test_row_counts(): + if os.path.exists("monitoring.db"): + logger.info("Monitoring database already exists - deleting") + os.remove("monitoring.db") + + engine = sqlalchemy.create_engine("sqlite:///monitoring.db") + + logger.info("loading parsl") + parsl.load(fresh_config()) + + # parsl.load() returns before all initialisation of monitoring + # is complete, which means it isn't safe to take a read lock on + # the database yet. This delay tries to work around that - some + # better async behaviour might be nice, but I'm not sure what. + time.sleep(10) + + # to get an sqlite3 read lock that is held over a controllable + # long time, create a transaction and perform a SELECT in it. + # (see bottom of https://sqlite.org/lockingv3.html) + + # there's an awkward race here: parsl.load() returns before the + # database might have been created, and so then the db manager will + # crash (and if there is a retry loop there instead, I think it will + # hang until after the read lock stuff below is finished? which might + # be acceptable? if it's meant to be properly async and not blocking?) + # ... in which case, initialise parsl *after taking the lock* would also + # work (although the select statement to get that lock wouldn't be the same + # because it wouldn't be able to select from the right table) + + logger.info("Getting a read lock on the monitoring database") + with engine.begin() as readlock_connection: + readlock_connection.execute("BEGIN TRANSACTION") + result = readlock_connection.execute("SELECT COUNT(*) FROM workflow") + (c, ) = result.first() + assert c == 1 + # now readlock_connection should have a read lock that will + # stay locked until the transaction is ended, or the with + # block ends. + + logger.info("invoking and waiting for result") + assert this_app().result() == 5 + + # there is going to be some raciness here making sure that + # the database manager actually tries to write while the + # read lock is held. I'm not sure if there is a better way + # to detect this other than a hopefully long-enough sleep. + time.sleep(10) + + logger.info("cleaning up parsl") + parsl.dfk().cleanup() + parsl.clear() + + # at this point, we should find one row in the monitoring database. + + logger.info("checking database content") + with engine.begin() as connection: + + result = connection.execute("SELECT COUNT(*) FROM workflow") + (c, ) = result.first() + assert c == 1 + + result = connection.execute("SELECT COUNT(*) FROM task") + (c, ) = result.first() + assert c == 1 + + result = connection.execute("SELECT COUNT(*) FROM try") + (c, ) = result.first() + assert c == 1 + + logger.info("all done") diff --git a/parsl/tests/test_monitoring/test_mon_wq/test_memoization_representation.py b/parsl/tests/test_monitoring/test_mon_wq/test_memoization_representation.py new file mode 100644 index 0000000000..ae915626a2 --- /dev/null +++ b/parsl/tests/test_monitoring/test_mon_wq/test_memoization_representation.py @@ -0,0 +1,80 @@ + +import logging +import os +import parsl +import pytest + +logger = logging.getLogger(__name__) + + +@parsl.python_app(cache=True) +def this_app(x): + return x + 1 + + +@pytest.mark.local +def test_hashsum(): + import sqlalchemy + from parsl.tests.configs.workqueue_monitoring import fresh_config + + if os.path.exists("monitoring.db"): + logger.info("Monitoring database already exists - deleting") + os.remove("monitoring.db") + + logger.info("loading parsl") + parsl.load(fresh_config()) + + logger.info("invoking and waiting for result (1/4)") + f1 = this_app(4) + assert f1.result() == 5 + + logger.info("invoking and waiting for result (2/4)") + f2 = this_app(17) + assert f2.result() == 18 + + logger.info("invoking and waiting for result (3/4)") + f3 = this_app(4) + assert f3.result() == 5 + + logger.info("invoking and waiting for result (4/4)") + f4 = this_app(4) + assert f4.result() == 5 + + assert f1.task_def['hashsum'] == f3.task_def['hashsum'] + assert f1.task_def['hashsum'] == f4.task_def['hashsum'] + assert f1.task_def['hashsum'] != f2.task_def['hashsum'] + + logger.info("cleaning up parsl") + parsl.dfk().cleanup() + parsl.clear() + + # at this point, we should find one row in the monitoring database. + + logger.info("checking database content") + engine = sqlalchemy.create_engine("sqlite:///monitoring.db") + with engine.begin() as connection: + + # we should have three tasks, but with only two tries, because the + # memo try should be missing + result = connection.execute("SELECT COUNT(*) FROM task") + (task_count, ) = result.first() + assert task_count == 4 + + # this will check that the number of task rows for each hashsum matches the above app invocations + result = connection.execute(f"SELECT COUNT(task_hashsum) FROM task WHERE task_hashsum='{f1.task_def['hashsum']}'") + (hashsum_count, ) = result.first() + assert hashsum_count == 3 + + result = connection.execute(f"SELECT COUNT(task_hashsum) FROM task WHERE task_hashsum='{f2.task_def['hashsum']}'") + (hashsum_count, ) = result.first() + assert hashsum_count == 1 + + result = connection.execute("SELECT COUNT(*) FROM status WHERE task_status_name='exec_done'") + (memo_count, ) = result.first() + assert memo_count == 2 + + result = connection.execute("SELECT COUNT(*) FROM status WHERE task_status_name='memo_done'") + (memo_count, ) = result.first() + assert memo_count == 2 + + logger.info("all done") From f8ac09528420b17ad273b2eab1020d5527524ad4 Mon Sep 17 00:00:00 2001 From: Ben Clifford Date: Thu, 18 Feb 2021 13:20:19 +0000 Subject: [PATCH 020/408] tasks_per_node case in general strategy is a mess: the ExtremeScale case will never fire in the current extremescale implementaiton, because an extreme scale executor is also a high throughput executor, and so the earlier htex case will fire. It is possible that extreme scale scaling was broken because of this case. This patch should not make it either better or worse, because it only eliminates dead code. when an executor is not an htex instance, no cases match, but no error is raised here, and so tasks_per_node is never assigned. Later on (line 206) use of tasks_per_node is an error. this entire case is removed, and executor.workers_per_node is always used. --- parsl/dataflow/strategy.py | 8 ++------ 1 file changed, 2 insertions(+), 6 deletions(-) diff --git a/parsl/dataflow/strategy.py b/parsl/dataflow/strategy.py index c003322dd7..7526a7a591 100644 --- a/parsl/dataflow/strategy.py +++ b/parsl/dataflow/strategy.py @@ -4,7 +4,7 @@ from typing import List from parsl.dataflow.executor_status import ExecutorStatus -from parsl.executors import HighThroughputExecutor, ExtremeScaleExecutor +from parsl.executors import HighThroughputExecutor from parsl.providers.provider_base import JobState logger = logging.getLogger(__name__) @@ -191,11 +191,7 @@ def _general_strategy(self, status_list, tasks, *, strategy_type): # FIXME probably more of this logic should be moved to the provider min_blocks = executor.provider.min_blocks max_blocks = executor.provider.max_blocks - if isinstance(executor, HighThroughputExecutor): - - tasks_per_node = executor.workers_per_node - elif isinstance(executor, ExtremeScaleExecutor): - tasks_per_node = executor.ranks_per_node + tasks_per_node = executor.workers_per_node nodes_per_block = executor.provider.nodes_per_block parallelism = executor.provider.parallelism From 07ffccd48b93a23e41754634a4dc6a29c2c9c9a7 Mon Sep 17 00:00:00 2001 From: Ben Clifford Date: Thu, 18 Feb 2021 12:55:21 +0000 Subject: [PATCH 021/408] Existing strategies require an 'outstanding' property. This was not enforced/documented in the executor base classes. This patch makes it obligatory for statushandlingexecutors to have that, on the assumption that statushandlingexecutor will become generally a scaling-capable base class. --- parsl/executors/status_handling.py | 9 ++++++++- 1 file changed, 8 insertions(+), 1 deletion(-) diff --git a/parsl/executors/status_handling.py b/parsl/executors/status_handling.py index e60f39c18b..7a486eba99 100644 --- a/parsl/executors/status_handling.py +++ b/parsl/executors/status_handling.py @@ -1,7 +1,7 @@ import logging import threading from itertools import compress -from abc import abstractmethod +from abc import abstractmethod, abstractproperty from concurrent.futures import Future from typing import List, Any, Dict, Tuple @@ -65,6 +65,13 @@ def _fail_job_async(self, block_id: Any, message: str): self._generated_block_id_counter += 1 self._simulated_status[block_id] = JobStatus(JobState.FAILED, message) + @abstractproperty + def outstanding(self) -> int: + """This should return the number of tasks that the executor has been given to run (waiting to run, and running now)""" + + raise NotImplementedError("Classes inheriting from StatusHandlingExecutor must implement " + "outstanding()") + def status(self) -> Dict[str, JobStatus]: """Return status of all blocks.""" From 19314ea1951d38a1ae923c56df4c9978b58b3b66 Mon Sep 17 00:00:00 2001 From: Ben Clifford Date: Wed, 17 Feb 2021 17:28:45 +0000 Subject: [PATCH 022/408] Make workqueue able to be scaled by parsl core scaling code broadly, this involves adding in enough helpers that the scaling strategy knows whats going on. i think probably the status handling class needs to also include descriptions (ideally machine enforceable) about the methods that I've had to add here. or the simple strategy should be made more resilient to their absence rather than crashing. PERHAPS OPEN AN ISSUE: "different kinds of executors, from a scaling perspective" the wq monitoring config is modified to start with 0 init blocks, and let the scaling system bring up more blocks. at time of writing this comment, that doesn't happen: wq launches init blocks only (once, at start) and scaling doesn't touch WQ (because the poll interval is set via the superclass to -1) wq default beahviour is one worker per node but i want ot run it in a mode where it figures out that it can run more things on a node at once. "worker" has a different meaning here wrt htex: htex workers each run one task, so 100 workers = 100 tasks at once. wq is more dynamic and always runes one wq per node but then that worker can run more parsl tasks. so be careful with terminology here. --- parsl/dataflow/task_status_poller.py | 2 + parsl/executors/workqueue/executor.py | 70 +++++++++++++++++-- parsl/tests/configs/workqueue_monitoring.py | 6 +- .../configs/workqueue_monitoring_config.py | 12 ++++ 4 files changed, 84 insertions(+), 6 deletions(-) create mode 100644 parsl/tests/configs/workqueue_monitoring_config.py diff --git a/parsl/dataflow/task_status_poller.py b/parsl/dataflow/task_status_poller.py index 369c694fe8..cee3384e74 100644 --- a/parsl/dataflow/task_status_poller.py +++ b/parsl/dataflow/task_status_poller.py @@ -113,4 +113,6 @@ def add_executors(self, executors: Sequence[ParslExecutor]): if executor.status_polling_interval > 0: logger.debug("Adding executor {}".format(executor.label)) self._poll_items.append(PollItem(executor, self.dfk)) + else: + logger.debug("Executor {} has no poll time, so will not poll".format(executor.label)) self._strategy.add_executors(executors) diff --git a/parsl/executors/workqueue/executor.py b/parsl/executors/workqueue/executor.py index 9437e264de..7f854a2a9b 100644 --- a/parsl/executors/workqueue/executor.py +++ b/parsl/executors/workqueue/executor.py @@ -25,14 +25,14 @@ from parsl.executors.errors import ExecutorError from parsl.data_provider.files import File from parsl.errors import OptionalModuleMissing -from parsl.executors.status_handling import NoStatusHandlingExecutor +from parsl.executors.status_handling import StatusHandlingExecutor from parsl.providers.provider_base import ExecutionProvider from parsl.providers import LocalProvider, CondorProvider from parsl.executors.errors import ScalingFailed from parsl.executors.workqueue import exec_parsl_function import typeguard -from typing import Dict, List, Optional, Set +from typing import Any, Dict, List, Optional, Set, Tuple from parsl.data_provider.staging import Staging from .errors import WorkQueueTaskFailure @@ -74,7 +74,7 @@ ParslFileToWq = namedtuple('ParslFileToWq', 'parsl_name stage cache') -class WorkQueueExecutor(NoStatusHandlingExecutor): +class WorkQueueExecutor(StatusHandlingExecutor): """Executor to use Work Queue batch system The WorkQueueExecutor system utilizes the Work Queue framework to @@ -206,7 +206,12 @@ def __init__(self, init_command: str = "", worker_options: str = "", full_debug: bool = True): - NoStatusHandlingExecutor.__init__(self) + + # BENC: if this was factored into something mixin-like, what would + # this call look like? Does super.init() get called in general here + # at all? Maybe this can't fit into that mixin style of inheritance? + StatusHandlingExecutor.__init__(self, provider) + self._provider = provider self._scaling_enabled = True @@ -257,6 +262,63 @@ def __init__(self, if self.init_command != "": self.launch_cmd = self.init_command + "; " + self.launch_cmd + # BENC: copied from htex / driven by whats missing when the scaling strategy + # code tries to do anything. Maybe these make sense to factor out into the + # status handling executor. + + def _get_block_and_job_ids(self) -> Tuple[List[str], List[Any]]: + # Not using self.blocks.keys() and self.blocks.values() simultaneously + # The dictionary may be changed during invoking this function + # As scale_in and scale_out are invoked in multiple threads + block_ids = list(self.blocks.keys()) + job_ids = [] # types: List[Any] + for bid in block_ids: + job_ids.append(self.blocks[bid]) + return block_ids, job_ids + + # the scaling code wants this... but there is nothing requiring it to exist. + @property + def outstanding(self): + + # this is going to cost scale linearly with the total number of tasks + # run in a run which is bad, but for now it isn't invasive into other + # bits of workqueue/executor.py - probably what should happen is that + # the relevant entry be removed from self.tasks, and then the number + # of tasks in self.tasks is the answer to this question. + + count = 0 + for key in self.tasks: + task = self.tasks[key] + if not task.done(): + count += 1 + + logger.debug(f"BENC: outstanding: len(self.tasks) = {len(self.tasks)}, count = {count}") + return count + + @property + def workers_per_node(self) -> int: + """BENC: + The use of the term 'worker' is a bit fragile here: + + the terminology used in other parts of parsl has: + one worker = the ability to run one task at any instance in time + but work_queue_worker can run many tasks at once from what wq calls a worker. + + In that sense, one wq worker == one parsl process_worker_pool. + + The parsl scaling code interprets this field as meaning how many tasks are + expected to be able to be run simultanously on a node. + + One of the goals of using WQ with parsl is that this can be dynamic, so there + isn't one sensible value here. However, for LSST DRP, I don't want any + subtleties of scaling here: I want parsl to maintain one large block of + eg 1000 nodes in the queue at once, until all the work is done + + """ + return 1 + + # END BENC copies from htex to make the scaling API happy. + def start(self): """Create submit process and collector thread to create, send, and retrieve Parsl tasks within the Work Queue system. diff --git a/parsl/tests/configs/workqueue_monitoring.py b/parsl/tests/configs/workqueue_monitoring.py index fd1da1445c..c873babd3b 100644 --- a/parsl/tests/configs/workqueue_monitoring.py +++ b/parsl/tests/configs/workqueue_monitoring.py @@ -1,5 +1,6 @@ from parsl.config import Config from parsl.executors import WorkQueueExecutor +from parsl.providers import LocalProvider from parsl.data_provider.http import HTTPInTaskStaging from parsl.data_provider.ftp import FTPInTaskStaging @@ -9,12 +10,13 @@ def fresh_config(): - return Config(executors=[WorkQueueExecutor(port=9000, + return Config(strategy='simple', + executors=[WorkQueueExecutor(port=9000, + provider=LocalProvider(init_blocks=0), storage_access=[FTPInTaskStaging(), HTTPInTaskStaging(), NoOpFileStaging()])], monitoring=MonitoringHub(hub_address="localhost", hub_port=55055, monitoring_debug=True, resource_monitoring_interval=1, ) - ) diff --git a/parsl/tests/configs/workqueue_monitoring_config.py b/parsl/tests/configs/workqueue_monitoring_config.py new file mode 100644 index 0000000000..3292e3b50b --- /dev/null +++ b/parsl/tests/configs/workqueue_monitoring_config.py @@ -0,0 +1,12 @@ +from parsl.tests.configs.workqueue_monitoring import fresh_config + +# this is a separate file so that it can be imported only +# when used with the whole test suite vs workqueue + +# otherwise, attempting to import the workqueue_monitoring +# module fails if workqueue isnt' around. + +# there might be a better way to do this that looks like how other +# stuff is done + +config = fresh_config() From 9ecef83f6e80a93ba79177070ba244c6cc3700b5 Mon Sep 17 00:00:00 2001 From: Ben Clifford Date: Thu, 10 Dec 2020 13:42:58 +0000 Subject: [PATCH 023/408] Final resource message should always be sent (rather than just periodic ones) to capture final cumulative usage although maybe that info isn't available any more if for example, executables have completed? how does `time` do it? From 039ef3196a1ef9031c9a176afee98a903ce6632b Mon Sep 17 00:00:00 2001 From: Ben Clifford Date: Thu, 3 Dec 2020 18:36:03 +0000 Subject: [PATCH 024/408] ****** this probably messes up logging in the sense that interchange logs will now go to the parsl main log *** *** so maybe i shouldn't do this patch after all *** the reason was because I couldn't find where @wrap_with_logs errors were going with interchange, but perhaps they're going to the main log? ----- make interchange set up logs like rest of parsl this removes some code that isn't interchange specific, in favour of other similar but different code it also means that logs made to parsl.* will go to the interchange log From db7c28b45c098600d1f7d7426c78f7bcfab8b28b Mon Sep 17 00:00:00 2001 From: Ben Clifford Date: Thu, 12 Nov 2020 17:23:21 +0000 Subject: [PATCH 025/408] TODO: for tomg, before release: i) disable (or option to disable) all resource monitoring ii) later, per-app enable/disable of resource monitoring, which will also maybe work around the joinapp vs threads problem From e19c86d83ba01ce70509e458fe0acab619ac1c43 Mon Sep 17 00:00:00 2001 From: Ben Clifford Date: Mon, 19 Oct 2020 13:10:40 +0000 Subject: [PATCH 026/408] 'try' table shouldn't get a row for a memoized result - there should be 0 tries. this is probably coming about because there is always a try number (starting at 0) even if no tries happen. TOOD: make a monitoring test to check this TODO: fix this bug From 5ad264002723768e37ca5b72f7351def04bf133f Mon Sep 17 00:00:00 2001 From: Ben Clifford Date: Tue, 1 Dec 2020 13:23:58 +0000 Subject: [PATCH 027/408] both tomg and I have seen this sometimes... the two core errors (i'm not sure which one causes which) is that there is thread related connection sharing which is not permitted. (erlang style local connection rather than object-shared connection might help push on that, by removing the opportunity to share connections across threads) and the prepared state - comes from a failed not-rolled-back transaction earlier on. Perhaps: an error happened. Then tried to do another one. hence the error happened. then that tried to call rollback, but it was in a different thread (because it was in the sqlalchemy code which cannot call rollbacks successfully I guess, on broken connections, because we don't know which thread finalization will happen in) 2020-11-25 12:04:00 parsl.executors.high_throughput.executor:649 [INFO] Attempting HighThroughputExecutor shutdown 2020-11-25 12:04:00 parsl.executors.high_throughput.executor:651 [INFO] Finished HighThroughputExecutor shutdown attempt 2020-11-25 12:04:00 parsl.monitoring.monitoring:271 [INFO] Terminating Monitoring Hub 2020-11-25 12:04:00 parsl.monitoring.monitoring:287 [INFO] Waiting for Hub to receive all messages and terminate 2020-11-25 12:04:03 parsl.process_loggers:17 [INFO] exception wrapper: normal ending for thread MainThread in process UNLOGGED Exception during reset or similar Traceback (most recent call last): File "/global/homes/d/descdm/.conda/envs/parsl-lsst-dm/lib/python3.7/site-packages/parsl/monitoring/db_manager.py", line 476, in _update self.db.update(table=table, columns=columns, messages=messages) File "/global/homes/d/descdm/.conda/envs/parsl-lsst-dm/lib/python3.7/site-packages/parsl/monitoring/db_manager.py", line 76, in update self.session.bulk_update_mappings(mapper, mappings) File "/global/homes/d/descdm/.conda/envs/parsl-lsst-dm/lib/python3.7/site-packages/sqlalchemy/orm/session.py", line 2860, in bulk_update_mappings mapper, mappings, True, False, False, False, False File "/global/homes/d/descdm/.conda/envs/parsl-lsst-dm/lib/python3.7/site-packages/sqlalchemy/orm/session.py", line 2876, in _bulk_save_mappings transaction = self.begin(subtransactions=True) File "/global/homes/d/descdm/.conda/envs/parsl-lsst-dm/lib/python3.7/site-packages/sqlalchemy/orm/session.py", line 938, in begin self.transaction = self.transaction._begin(nested=nested) File "/global/homes/d/descdm/.conda/envs/parsl-lsst-dm/lib/python3.7/site-packages/sqlalchemy/orm/session.py", line 316, in _begin self._assert_active() File "/global/homes/d/descdm/.conda/envs/parsl-lsst-dm/lib/python3.7/site-packages/sqlalchemy/orm/session.py", line 282, in _assert_active "This session is in 'prepared' state; no further " sqlalchemy.exc.InvalidRequestError: This session is in 'prepared' state; no further SQL can be emitted within this transaction. During handling of the above exception, another exception occurred: Traceback (most recent call last): File "/global/homes/d/descdm/.conda/envs/parsl-lsst-dm/lib/python3.7/site-packages/sqlalchemy/pool/base.py", line 680, in _finalize_fairy fairy._reset(pool) File "/global/homes/d/descdm/.conda/envs/parsl-lsst-dm/lib/python3.7/site-packages/sqlalchemy/pool/base.py", line 867, in _reset pool._dialect.do_rollback(self) File "/global/homes/d/descdm/.conda/envs/parsl-lsst-dm/lib/python3.7/site-packages/sqlalchemy/engine/default.py", line 530, in do_rollback dbapi_connection.rollback() sqlite3.ProgrammingError: SQLite objects created in a thread can only be used in that same thread. The object was created in thread id 46912496695104 and this is thread id 46912630470400. Exception closing connection Traceback (most recent call last): File "/global/homes/d/descdm/.conda/envs/parsl-lsst-dm/lib/python3.7/site-packages/parsl/monitoring/db_manager.py", line 476, in _update self.db.update(table=table, columns=columns, messages=messages) File "/global/homes/d/descdm/.conda/envs/parsl-lsst-dm/lib/python3.7/site-packages/parsl/monitoring/db_manager.py", line 76, in update self.session.bulk_update_mappings(mapper, mappings) File "/global/homes/d/descdm/.conda/envs/parsl-lsst-dm/lib/python3.7/site-packages/sqlalchemy/orm/session.py", line 2860, in bulk_update_mappings mapper, mappings, True, False, False, False, False File "/global/homes/d/descdm/.conda/envs/parsl-lsst-dm/lib/python3.7/site-packages/sqlalchemy/orm/session.py", line 2876, in _bulk_save_mappings transaction = self.begin(subtransactions=True) File "/global/homes/d/descdm/.conda/envs/parsl-lsst-dm/lib/python3.7/site-packages/sqlalchemy/orm/session.py", line 938, in begin self.transaction = self.transaction._begin(nested=nested) File "/global/homes/d/descdm/.conda/envs/parsl-lsst-dm/lib/python3.7/site-packages/sqlalchemy/orm/session.py", line 316, in _begin self._assert_active() File "/global/homes/d/descdm/.conda/envs/parsl-lsst-dm/lib/python3.7/site-packages/sqlalchemy/orm/session.py", line 282, in _assert_active "This session is in 'prepared' state; no further " sqlalchemy.exc.InvalidRequestError: This session is in 'prepared' state; no further SQL can be emitted within this transaction. During handling of the above exception, another exception occurred: Traceback (most recent call last): File "/global/homes/d/descdm/.conda/envs/parsl-lsst-dm/lib/python3.7/site-packages/sqlalchemy/pool/base.py", line 680, in _finalize_fairy fairy._reset(pool) File "/global/homes/d/descdm/.conda/envs/parsl-lsst-dm/lib/python3.7/site-packages/sqlalchemy/pool/base.py", line 867, in _reset pool._dialect.do_rollback(self) File "/global/homes/d/descdm/.conda/envs/parsl-lsst-dm/lib/python3.7/site-packages/sqlalchemy/engine/default.py", line 530, in do_rollback dbapi_connection.rollback() sqlite3.ProgrammingError: SQLite objects created in a thread can only be used in that same thread. The object was created in thread id 46912496695104 and this is thread id 46912630470400. During handling of the above exception, another exception occurred: Traceback (most recent call last): File "/global/homes/d/descdm/.conda/envs/parsl-lsst-dm/lib/python3.7/site-packages/sqlalchemy/pool/base.py", line 270, in _close_connection self._dialect.do_close(connection) File "/global/homes/d/descdm/.conda/envs/parsl-lsst-dm/lib/python3.7/site-packages/sqlalchemy/engine/default.py", line 536, in do_close dbapi_connection.close() sqlite3.ProgrammingError: SQLite objects created in a thread can only be used in that same thread. The object was created in thread id 46912496695104 and this is thread id 46912630470400. 2020-11-25 12:04:03 parsl.process_loggers:17 [INFO] exception wrapper: normal ending for thread MainThread in process UNLOGGED 2020-11-25 12:04:03 parsl.dataflow.dflow:1055 [INFO] DFK cleanup complete From 0b351e7db64ca8bac4f0a3559883df48a0d0a7df Mon Sep 17 00:00:00 2001 From: Ben Clifford Date: Fri, 11 Dec 2020 14:47:42 +0000 Subject: [PATCH 028/408] Re-enable div_0 bash error code test after review This was disabled as part of the large set of tests disabled in the PR #652 testpocalypse. But on review it *should* work. --- parsl/tests/test_bash_apps/test_error_codes.py | 18 ------------------ 1 file changed, 18 deletions(-) diff --git a/parsl/tests/test_bash_apps/test_error_codes.py b/parsl/tests/test_bash_apps/test_error_codes.py index f7cd28a0b5..d11018789d 100644 --- a/parsl/tests/test_bash_apps/test_error_codes.py +++ b/parsl/tests/test_bash_apps/test_error_codes.py @@ -71,22 +71,6 @@ def bad_format(stderr='std.err', stdout='std.out'): whitelist = os.path.join(os.path.dirname(os.path.dirname(__file__)), 'configs', '*threads*') -# @pytest.mark.whitelist(whitelist, reason='broken in IPP') -@pytest.mark.skip("Broke somewhere between PR #525 and PR #652") -def test_bash_formatting(): - - f = bad_format() - try: - f.result() - except Exception as e: - print("Caught exception", e) - assert isinstance( - e, parsl.app.errors.AppBadFormatting), "Expected AppBadFormatting got : {0}".format(e) - return True - - -# @pytest.mark.whitelist(whitelist, reason='broken in IPP') -@pytest.mark.skip("Broke somewhere between PR #525 and PR #652") def test_div_0(test_fn=div_0): err_code = test_matrix[test_fn]['exit_code'] f = test_fn() @@ -188,8 +172,6 @@ def run_app(test_fn, err_code): help="Count of apps to launch") args = parser.parse_args() - print(test_bash_formatting()) - exit(0) if args.debug: From a09db9a940fee32afa1e86e62b123bdf263fc948 Mon Sep 17 00:00:00 2001 From: Ben Clifford Date: Fri, 11 Dec 2020 14:54:06 +0000 Subject: [PATCH 029/408] remove test that is testing bash exit code behaviour, not parsl --- .../tests/test_bash_apps/test_error_codes.py | 25 ------------------- 1 file changed, 25 deletions(-) diff --git a/parsl/tests/test_bash_apps/test_error_codes.py b/parsl/tests/test_bash_apps/test_error_codes.py index d11018789d..4ae50db9cd 100644 --- a/parsl/tests/test_bash_apps/test_error_codes.py +++ b/parsl/tests/test_bash_apps/test_error_codes.py @@ -32,12 +32,6 @@ def div_0(stderr='std.err', stdout='std.out'): return cmd_line -@bash_app -def invalid_exit(stderr='std.err', stdout='std.out'): - cmd_line = 'exit 3.141' - return cmd_line - - @bash_app def not_executable(stderr='std.err', stdout='std.out'): cmd_line = '/dev/null' @@ -60,9 +54,6 @@ def bad_format(stderr='std.err', stdout='std.out'): command_not_found: { 'exit_code': 127 }, - invalid_exit: { - 'exit_code': 128 - }, not_executable: { 'exit_code': 126 } @@ -119,22 +110,6 @@ def test_command_not_found(test_fn=command_not_found): return True -@pytest.mark.skip('broken') -def test_invalid_exit(test_fn=invalid_exit): - err_code = test_matrix[test_fn]['exit_code'] - f = test_fn() - try: - f.result() - except Exception as e: - print("Caught exception", e) - assert e.exitcode == err_code, "{0} expected err_code:{1} but got {2}".format(test_fn.__name__, - err_code, - e.exitcode) - os.remove('std.err') - os.remove('std.out') - return True - - def test_not_executable(test_fn=not_executable): err_code = test_matrix[test_fn]['exit_code'] f = test_fn() From ef59de919da88fba93a90ba50f4752e14b30a448 Mon Sep 17 00:00:00 2001 From: Ben Clifford Date: Mon, 19 Oct 2020 11:30:14 +0000 Subject: [PATCH 030/408] local provider is showing these return code related exceptions repeatedly (on each poll?) in my tutorial example. What's going wrong? 2020-10-19 11:29:24.016 parsl.dataflow.flow_control:114 [ERROR] Flow control callback threw an exception - logging and proceeding anyway Traceback (most recent call last): File "/home/benc/parsl/src/parsl/parsl/dataflow/flow_control.py", line 112, in make_callback self.callback(tasks=self._event_buffer, kind=kind) File "/home/benc/parsl/src/parsl/parsl/dataflow/task_status_poller.py", line 64, in poll self._update_state() File "/home/benc/parsl/src/parsl/parsl/dataflow/task_status_poller.py", line 71, in _update_state item.poll(now) File "/home/benc/parsl/src/parsl/parsl/dataflow/task_status_poller.py", line 28, in poll self._status = self._executor.status() File "/home/benc/parsl/src/parsl/parsl/executors/status_handling.py", line 73, in status status = self._make_status_dict(job_ids, self._provider.status(job_ids)) File "/home/benc/parsl/src/parsl/parsl/providers/local/local.py", line 86, in status str_ec = self._read_job_file(script_path, '.ec').strip() File "/home/benc/parsl/src/parsl/parsl/providers/local/local.py", line 143, in _read_job_file with open(path, 'r') as f: FileNotFoundError: [Errno 2] No such file or directory: '/home/benc/parsl/src/parsl/runinfo/000/submit_scripts/parsl.localprovider.1603103227.0265722.sh.ec From 96692d05010a640adc4245d1f47547693b0c9506 Mon Sep 17 00:00:00 2001 From: Ben Clifford Date: Mon, 19 Oct 2020 11:26:32 +0000 Subject: [PATCH 031/408] In memoization test (doesn't need to be checkpoint) add in assertions that f(3) run multiple times has the same hashsum and f(4) has a different hashsum to f(3) in addition to the existing way of checking that runs are not repeated because now we have acceses to the task record in tests due to future.task_def From 31ab12c981cfebb3e16e7f0652857230dbf03de0 Mon Sep 17 00:00:00 2001 From: Ben Clifford Date: Mon, 19 Oct 2020 09:41:38 +0000 Subject: [PATCH 032/408] in lsst-dm-202005, tom and I are not seeing task_hashsum set at all in the monitoring DB. i vaguely remember this happening and fixing it a while ago but maybe only in this branch, not lsst-dm-202005? TODO: write a regression test for this using sql queries and looking at the task record hashsum (and checking two different invocations get two different hashsums) From 319d8d613d90b73572afde76bfcf401dcb60d31e Mon Sep 17 00:00:00 2001 From: Ben Clifford Date: Mon, 24 Aug 2020 10:11:13 +0000 Subject: [PATCH 033/408] yadu reports this in his PR review for split of exec_done/memo_done (PR #1848) > These changes look good to me. I am seeing two separate states in the plots, but it is still showing up as green for both exec_done and memo_done on the workflow page for me. Might be worth checking that. so I should dig into that visual style From 6cdf2deda18d5136f459eced2cfb928fb4d8c0f7 Mon Sep 17 00:00:00 2001 From: Ben Clifford Date: Tue, 19 May 2020 17:17:09 +0000 Subject: [PATCH 034/408] raise exceptions harder (maybe just for dev?) --- .../visualization/plots/default/workflow_resource_plots.py | 7 ++++--- 1 file changed, 4 insertions(+), 3 deletions(-) diff --git a/parsl/monitoring/visualization/plots/default/workflow_resource_plots.py b/parsl/monitoring/visualization/plots/default/workflow_resource_plots.py index 08c0255e1a..bacd594f44 100644 --- a/parsl/monitoring/visualization/plots/default/workflow_resource_plots.py +++ b/parsl/monitoring/visualization/plots/default/workflow_resource_plots.py @@ -131,9 +131,10 @@ def worker_efficiency(task, node): yaxis=dict(title='Number of workers'), title="Worker efficiency")) return plot(fig, show_link=False, output_type="div", include_plotlyjs=False) - except Exception as e: - print(e) - return "The worker efficiency plot cannot be generated due to missing data." + except Exception: + raise + # print(e) + # return "The worker efficiency plot cannot be generated due to missing data." def resource_efficiency(resource, node, label='CPU'): From b7af6976a42859a8939042a19889eea30fbd26cb Mon Sep 17 00:00:00 2001 From: Ben Clifford Date: Mon, 18 May 2020 12:47:11 +0000 Subject: [PATCH 035/408] Don't hide exceptions arising in plot generation This will make parsl-visualize fail harder which is better for automated testing flushing out of errors. --- .../monitoring/visualization/plots/default/workflow_plots.py | 4 ++-- .../visualization/plots/default/workflow_resource_plots.py | 5 ++--- 2 files changed, 4 insertions(+), 5 deletions(-) diff --git a/parsl/monitoring/visualization/plots/default/workflow_plots.py b/parsl/monitoring/visualization/plots/default/workflow_plots.py index 5f17d3b01b..e44249847c 100644 --- a/parsl/monitoring/visualization/plots/default/workflow_plots.py +++ b/parsl/monitoring/visualization/plots/default/workflow_plots.py @@ -109,8 +109,8 @@ def task_per_app_plot(task, status): yaxis=dict(title='Number of tasks'), title="Tasks per app")) return plot(fig, show_link=False, output_type="div", include_plotlyjs=False) - except Exception as e: - return "The tasks per app plot cannot be generated because of exception {}.".format(e) + except Exception: + raise def total_tasks_plot(df_task, df_status, columns=20): diff --git a/parsl/monitoring/visualization/plots/default/workflow_resource_plots.py b/parsl/monitoring/visualization/plots/default/workflow_resource_plots.py index bacd594f44..a0015ce031 100644 --- a/parsl/monitoring/visualization/plots/default/workflow_resource_plots.py +++ b/parsl/monitoring/visualization/plots/default/workflow_resource_plots.py @@ -197,6 +197,5 @@ def resource_efficiency(resource, node, label='CPU'): yaxis=dict(title=yaxis), title=title)) return plot(fig, show_link=False, output_type="div", include_plotlyjs=False) - except Exception as e: - print(e) - return "The resource efficiency plot cannot be generated because of exception {}.".format(e) + except Exception: + raise From 114661a50552f0fb44d5cf792e43256a360ce0ab Mon Sep 17 00:00:00 2001 From: Ben Clifford Date: Thu, 21 May 2020 12:49:53 +0000 Subject: [PATCH 036/408] Fix viz errors in when tasks have no end time Previously these code would throw an exception when tasks have no end time, either replacing the relevant chart with an error that the chart could not be displayed, or with some of my debug patches in place, raising a server error. This patch needs to come up with new behaviour to deal with the case when such tasks are not marked as completed - probably assuming they are in progress either till workflow end or the present time (as far as the database is aware) --- .../plots/default/workflow_plots.py | 28 +++++++++++++++++-- parsl/monitoring/visualization/views.py | 2 +- 2 files changed, 26 insertions(+), 4 deletions(-) diff --git a/parsl/monitoring/visualization/plots/default/workflow_plots.py b/parsl/monitoring/visualization/plots/default/workflow_plots.py index e44249847c..24f6bd13c5 100644 --- a/parsl/monitoring/visualization/plots/default/workflow_plots.py +++ b/parsl/monitoring/visualization/plots/default/workflow_plots.py @@ -75,7 +75,7 @@ def task_gantt_plot(df_task, df_status, time_completed=None): return plot(fig, show_link=False, output_type="div", include_plotlyjs=False) -def task_per_app_plot(task, status): +def task_per_app_plot(task, status, time_completed): try: task['epoch_time_running'] = (pd.to_datetime( @@ -83,17 +83,39 @@ def task_per_app_plot(task, status): task['epoch_time_returned'] = (pd.to_datetime( task['task_time_returned']) - pd.Timestamp("1970-01-01")) // pd.Timedelta('1s') start = int(task['epoch_time_running'].min()) + end = int(task['epoch_time_returned'].max()) + # should we take the max of this and time_completed here? + # because they might not align just right, and cause array overflows + # later in this plot? probably yes. - need to get a notion of + # "latest time interesting" which is either max of "now" and all + # task completion times (because clock skew, may complete in future) + # if the workflow is not completed, and the max of workflow and all task + # completion times if the workflow is recorded as completed. Or + # maybe the last known time is the right time to assume there? + tasks_per_app = {} all_tasks = [0] * (end - start + 1) for i, row in task.iterrows(): if math.isnan(row['epoch_time_running']): # Skip rows with no running start time. continue + if math.isnan(row['epoch_time_returned']): + # Some kind of inference about time returned (workflow end time / current time? see gantt chart for inferences) + + time_returned = end + else: + time_returned = int(row['epoch_time_returned']) + if row['task_func_name'] not in tasks_per_app: tasks_per_app[row['task_func_name']] = [0] * (end - start + 1) - for j in range(int(row['epoch_time_running']) + 1, int(row['epoch_time_returned']) + 1): - tasks_per_app[row['task_func_name']][j - start] += 1 + for j in range(int(row['epoch_time_running']) + 1, time_returned + 1): + try: + tasks_per_app[row['task_func_name']][j - start] += 1 + except Exception: + raise RuntimeError("j = {}, start = {}, end={}, end-start+1={}, j will range over {} .. {}".format(j, start, end, end - start + 1, + int(row['epoch_time_running']) + 1, + int(time_returned) + 1)) all_tasks[j - start] += 1 fig = go.Figure( data=[go.Scatter(x=list(range(0, end - start + 1)), diff --git a/parsl/monitoring/visualization/views.py b/parsl/monitoring/visualization/views.py index e669853560..9e50a17161 100644 --- a/parsl/monitoring/visualization/views.py +++ b/parsl/monitoring/visualization/views.py @@ -71,7 +71,7 @@ def workflow(workflow_id): workflow_details=workflow_details, task_summary=task_summary, task_gantt=task_gantt_plot(df_task, df_status, time_completed=workflow_details.time_completed), - task_per_app=task_per_app_plot(df_task_tries, df_status)) + task_per_app=task_per_app_plot(df_task_tries, df_status, time_completed=workflow_details.time_completed)) @app.route('/workflow//app/') From d3175660b6dab040ee1e3dce1be459226494946a Mon Sep 17 00:00:00 2001 From: Ben Clifford Date: Thu, 14 May 2020 11:51:33 +0000 Subject: [PATCH 037/408] handle function types differently for checkpointing - this is experimental i'm not happy with how function types are handled in existing checkpoint code compared to checkpointing calls into other code that can be modified (changing one invalidates checkpoints, changing the other doesn't) this commit makes function checkpointing not depend on the function body, giving more consistent behaviour for lsst this commit removes a test that checks that memoization *isn't* used when func bodies differ, becaues that is now an incorrect assertion --- parsl/dataflow/memoization.py | 21 ++------ .../tests/test_python_apps/test_memoize_5.py | 48 ------------------- 2 files changed, 5 insertions(+), 64 deletions(-) delete mode 100644 parsl/tests/test_python_apps/test_memoize_5.py diff --git a/parsl/dataflow/memoization.py b/parsl/dataflow/memoization.py index 4f30db335e..a5913fb3bb 100644 --- a/parsl/dataflow/memoization.py +++ b/parsl/dataflow/memoization.py @@ -1,6 +1,5 @@ import hashlib from functools import lru_cache, singledispatch -from inspect import getsource import logging from parsl.serialize import serialize import types @@ -99,22 +98,12 @@ def id_for_memo_dict(denormalized_dict, output_ref=False): # that the .register() call, so that the cache-decorated version is registered. @id_for_memo.register(types.FunctionType) @lru_cache() -def id_for_memo_function(function, output_ref=False): - """This produces function hash material using the source definition of the - function. - - The standard serialize_object based approach cannot be used as it is - too sensitive to irrelevant facts such as the source line, meaning - a whitespace line added at the top of a source file will cause the hash - to change. +def id_for_memo_func(f, output_ref=False): + """This will extract some, but deliberately not all, details from the function. + The intention is to allow the function to be modified in source file without + causing memoization invalidation. """ - logger.debug("serialising id_for_memo_function for function {}, type {}".format(function, type(function))) - try: - fn_source = getsource(function) - except Exception as e: - logger.warning("Unable to get source code for app caching. Recommend creating module. Exception was: {}".format(e)) - fn_source = function.__name__ - return serialize(fn_source.encode('utf-8')) + return serialize(["types.FunctionType", f.__name__, f.__module__]) class Memoizer(object): diff --git a/parsl/tests/test_python_apps/test_memoize_5.py b/parsl/tests/test_python_apps/test_memoize_5.py deleted file mode 100644 index e2432527a7..0000000000 --- a/parsl/tests/test_python_apps/test_memoize_5.py +++ /dev/null @@ -1,48 +0,0 @@ -import argparse - -import parsl -from parsl.app.app import python_app -from parsl.tests.configs.local_threads import config - - -def test_python_memoization(n=2): - """Testing python memoization when func bodies differ - This is the canonical use case. - """ - @python_app(cache=True) - def random_uuid(x): - import uuid - return str(uuid.uuid4()) - - x = random_uuid(0) - x.result() # allow x to complete to allow completion-time memoization to happen - z = random_uuid(0) - assert x.result() == z.result(), "Memoized results were not used" - print(x.result()) - - @python_app(cache=True) - def random_uuid(x): - import uuid - print("hi") - return str(uuid.uuid4()) - - y = random_uuid(0) - assert x.result() != y.result(), "Memoized results were incorrectly used" - - -if __name__ == '__main__': - - parsl.clear() - dfk = parsl.load(config) - - parser = argparse.ArgumentParser() - parser.add_argument("-c", "--count", default="10", - help="Count of apps to launch") - parser.add_argument("-d", "--debug", action='store_true', - help="Count of apps to launch") - args = parser.parse_args() - - if args.debug: - parsl.set_stream_logger() - - x = test_python_memoization(n=4) From d386db82cdbd0c4e6ab52762c553ddd657ee180b Mon Sep 17 00:00:00 2001 From: Ben Clifford Date: Thu, 9 Apr 2020 14:53:57 +0000 Subject: [PATCH 038/408] remove apparently unused `dummy` variable This makes flake8 fail with: parsl/monitoring/visualization/app.py:28:9: F401 'parsl.monitoring.visualization.views' imported but unused however removing that import then caused something to break in visualization, so for now I am permitting that potentially-unused import in flake8 pending further investigation --- .flake8 | 6 +++++- parsl/monitoring/visualization/app.py | 1 - parsl/monitoring/visualization/views.py | 2 -- 3 files changed, 5 insertions(+), 4 deletions(-) diff --git a/.flake8 b/.flake8 index 462ac268aa..ab167c5a21 100644 --- a/.flake8 +++ b/.flake8 @@ -19,4 +19,8 @@ per-file-ignores = parsl/monitoring/visualization/*:E741, # needed because this deliberately has undefined names in it parsl/tests/test_swift.py:F821, # test_ssh_errors.py really is broken - parsl/tests/integration/test_channels/test_ssh_errors.py:F821 + parsl/tests/integration/test_channels/test_ssh_errors.py:F821, + # I had visualization problems with this import removed, which I need to + # investigate before pushing this to master. This exemption works around + # that. + parsl/monitoring/visualization/app.py:F401 diff --git a/parsl/monitoring/visualization/app.py b/parsl/monitoring/visualization/app.py index 6530fcdbb6..cc903b5cdd 100644 --- a/parsl/monitoring/visualization/app.py +++ b/parsl/monitoring/visualization/app.py @@ -26,7 +26,6 @@ def cli_run(): with app.app_context(): db.create_all() from parsl.monitoring.visualization import views - views.dummy = False app.run(host=args.listen, port=args.port, debug=args.debug) diff --git a/parsl/monitoring/visualization/views.py b/parsl/monitoring/visualization/views.py index 9e50a17161..51d0b79ce4 100644 --- a/parsl/monitoring/visualization/views.py +++ b/parsl/monitoring/visualization/views.py @@ -7,8 +7,6 @@ from parsl.monitoring.visualization.plots.default.task_plots import time_series_cpu_per_task_plot, time_series_memory_per_task_plot from parsl.monitoring.visualization.plots.default.workflow_resource_plots import resource_distribution_plot, resource_efficiency, worker_efficiency -dummy = True - import datetime From fecc06539bf2f474d86eea829a8731aff8461249 Mon Sep 17 00:00:00 2001 From: Ben Clifford Date: Thu, 9 Apr 2020 15:57:27 +0000 Subject: [PATCH 039/408] log more information on incorrect time format --- parsl/monitoring/visualization/views.py | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/parsl/monitoring/visualization/views.py b/parsl/monitoring/visualization/views.py index 51d0b79ce4..1ddfd97737 100644 --- a/parsl/monitoring/visualization/views.py +++ b/parsl/monitoring/visualization/views.py @@ -21,7 +21,8 @@ def format_time(value): rounded_timedelta = datetime.timedelta(days=value.days, seconds=value.seconds) return rounded_timedelta else: - return "Incorrect time format found (neither float nor datetime.datetime object)" + print("Incorrect time format (neither float nor datetime object): {}, type: {}".format(value, type(value))) # TODO: use logging + return "Incorrect time format" def format_duration(value): From 751dfd021e58c5640a6ae186d63b1a4df8606844 Mon Sep 17 00:00:00 2001 From: Ben Clifford Date: Mon, 4 May 2020 14:00:30 +0000 Subject: [PATCH 040/408] TODO: make the hub exit condition more explicit rather than relying on the absence of a particular attribute in the shutdown message. also check if this shuts down when the workflow main process ends, not necessarily before the UDP/interchange queues have been properly drained? From e9d097b73acfca95daf8f0fff196921fbc614a33 Mon Sep 17 00:00:00 2001 From: Ben Clifford Date: Tue, 12 May 2020 13:03:35 +0000 Subject: [PATCH 041/408] squashed commit of lsst-dm-202002 work so far, to pick apart separately --- parsl/app/python.py | 3 ++ parsl/dataflow/dflow.py | 15 ++++-- parsl/dataflow/memoization.py | 7 ++- parsl/executors/high_throughput/executor.py | 50 ++++++++++--------- .../executors/high_throughput/interchange.py | 37 +++++++++++--- parsl/executors/high_throughput/probe.py | 2 +- .../high_throughput/process_worker_pool.py | 34 ++++++++++--- parsl/monitoring/monitoring.py | 14 +++++- 8 files changed, 119 insertions(+), 43 deletions(-) diff --git a/parsl/app/python.py b/parsl/app/python.py index fdd62d3e13..a37d74d50c 100644 --- a/parsl/app/python.py +++ b/parsl/app/python.py @@ -58,8 +58,11 @@ def __call__(self, *args, **kwargs): """ invocation_kwargs = {} + logger.debug("invocation_kwargs step 1: {}".format(invocation_kwargs)) invocation_kwargs.update(self.kwargs) + logger.debug("invocation_kwargs step 2: {}".format(invocation_kwargs)) invocation_kwargs.update(kwargs) + logger.debug("invocation_kwargs step 3: {}".format(invocation_kwargs)) if self.data_flow_kernel is None: dfk = DataFlowKernelLoader.dfk() diff --git a/parsl/dataflow/dflow.py b/parsl/dataflow/dflow.py index c1c8a4364e..995d52a1a3 100644 --- a/parsl/dataflow/dflow.py +++ b/parsl/dataflow/dflow.py @@ -5,6 +5,7 @@ import pickle import random import time +import traceback import typeguard import inspect import threading @@ -118,13 +119,16 @@ def __init__(self, config=Config()): self.workflow_name = self.monitoring.workflow_name else: for frame in inspect.stack(): + logger.debug("Considering candidate for workflow name: {}".format(frame.filename)) fname = os.path.basename(str(frame.filename)) parsl_file_names = ['dflow.py', 'typeguard.py', '__init__.py'] # Find first file name not considered a parsl file if fname not in parsl_file_names: self.workflow_name = fname + logger.debug("Using {} as workflow name".format(fname)) break else: + logger.debug("Could not choose a name automatically") self.workflow_name = "unnamed" self.workflow_version = str(self.time_began.replace(microsecond=0)) @@ -309,12 +313,14 @@ def handle_exec_update(self, task_id, future): task_record['try_time_launched'] = None task_record['try_time_returned'] = None task_record['fail_history'] = [] - logger.info("Task {} marked for retry".format(task_id)) else: - logger.exception("Task {} failed after {} retry attempts".format(task_id, - self._config.retries)) + logger.error("Task {} failed after {} retry attempts. Last exception was: {}: {}".format(task_id, + self._config.retries, + type(e).__name__, + e)) + logger.debug("Task {} traceback: {}".format(task_id, traceback.format_tb(e.__traceback__))) task_record['time_returned'] = datetime.datetime.now() task_record['status'] = States.failed self.tasks_failed_count += 1 @@ -994,7 +1000,10 @@ def add_executors(self, executors): def atexit_cleanup(self): if not self.cleanup_called: + logger.info("DFK cleanup because python process is exiting") self.cleanup() + else: + logger.info("python process is exiting, but DFK has already been cleaned up") def wait_for_current_tasks(self): """Waits for all tasks in the task list to be completed, by waiting for their diff --git a/parsl/dataflow/memoization.py b/parsl/dataflow/memoization.py index a5913fb3bb..ecc852297d 100644 --- a/parsl/dataflow/memoization.py +++ b/parsl/dataflow/memoization.py @@ -188,7 +188,7 @@ def make_hash(self, task): if 'outputs' in task['kwargs']: outputs = task['kwargs']['outputs'] del filtered_kw['outputs'] - t = t + [id_for_memo(outputs, output_ref=True)] # TODO: use append? + t = t + [b'outputs', id_for_memo(outputs, output_ref=True)] # TODO: use append? t = t + [id_for_memo(filtered_kw)] t = t + [id_for_memo(task['func']), @@ -262,9 +262,14 @@ def update_memo(self, task_id, task, r): if not self.memoize or not task['memoize'] or 'hashsum' not in task: return + if 'hashsum' not in task: + logger.error("Attempt to update memo for task {} with no hashsum".format(task_id)) + return + if task['hashsum'] in self.memo_lookup_table: logger.info('Updating app cache entry with latest %s:%s call' % (task['func_name'], task_id)) self.memo_lookup_table[task['hashsum']] = r else: + logger.debug("Storing original memo for task {}".format(task_id)) self.memo_lookup_table[task['hashsum']] = r diff --git a/parsl/executors/high_throughput/executor.py b/parsl/executors/high_throughput/executor.py index 384c399b6f..ecb35f533d 100644 --- a/parsl/executors/high_throughput/executor.py +++ b/parsl/executors/high_throughput/executor.py @@ -5,9 +5,8 @@ import queue import datetime import pickle -from multiprocessing import Process, Queue -from typing import Dict # noqa F401 (used in type annotation) -from typing import List, Optional, Tuple, Union, Any +import multiprocessing +from typing import Any, Dict, List, Optional, Tuple, Union import math from parsl.serialize import pack_apply_message, deserialize @@ -159,6 +158,8 @@ class HighThroughputExecutor(StatusHandlingExecutor, RepresentationMixin): poll_period : int Timeout period to be used by the executor components in milliseconds. Increasing poll_periods trades performance for cpu efficiency. Default: 10ms + This period controls both an interchange poll period and a worker pool poll period, with different effects in both. + worker_logdir_root : string In case of a remote file system, specify the path to where logs will be kept. @@ -191,6 +192,7 @@ def __init__(self, logger.debug("Initializing HighThroughputExecutor") StatusHandlingExecutor.__init__(self, provider) + self.label = label self.launch_cmd = launch_cmd self.worker_debug = worker_debug @@ -315,7 +317,7 @@ def start(self): self._queue_management_thread = None self._start_queue_management_thread() - self._start_local_queue_process() + self._start_local_interchange_process() logger.debug("Created management thread: {}".format(self._queue_management_thread)) @@ -441,31 +443,31 @@ def weakref_cb(self, q=None): """We do not use this yet.""" q.put(None) - def _start_local_queue_process(self): + def _start_local_interchange_process(self): """ Starts the interchange process locally Starts the interchange process locally and uses an internal command queue to get the worker task and result ports that the interchange has bound to. """ - comm_q = Queue(maxsize=10) - self.queue_proc = Process(target=interchange.starter, - args=(comm_q,), - kwargs={"client_ports": (self.outgoing_q.port, - self.incoming_q.port, - self.command_client.port), - "worker_ports": self.worker_ports, - "worker_port_range": self.worker_port_range, - "hub_address": self.hub_address, - "hub_port": self.hub_port, - "logdir": "{}/{}".format(self.run_dir, self.label), - "heartbeat_threshold": self.heartbeat_threshold, - "poll_period": self.poll_period, - "logging_level": logging.DEBUG if self.worker_debug else logging.INFO - }, - daemon=True, - name="HTEX-Interchange" + comm_q = multiprocessing.Queue(maxsize=10) + self.interchange_proc = multiprocessing.Process(target=interchange.starter, + args=(comm_q,), + kwargs={"client_ports": (self.outgoing_q.port, + self.incoming_q.port, + self.command_client.port), + "worker_ports": self.worker_ports, + "worker_port_range": self.worker_port_range, + "hub_address": self.hub_address, + "hub_port": self.hub_port, + "logdir": "{}/{}".format(self.run_dir, self.label), + "heartbeat_threshold": self.heartbeat_threshold, + "poll_period": self.poll_period, + "logging_level": logging.DEBUG if self.worker_debug else logging.INFO + }, + daemon=True, + name="HTEX-Interchange" ) - self.queue_proc.start() + self.interchange_proc.start() try: (self.worker_task_port, self.worker_result_port) = comm_q.get(block=True, timeout=120) except queue.Empty: @@ -738,6 +740,6 @@ def shutdown(self, hub=True, targets='all', block=False): """ logger.info("Attempting HighThroughputExecutor shutdown") - self.queue_proc.terminate() + self.interchange_proc.terminate() logger.info("Finished HighThroughputExecutor shutdown attempt") return True diff --git a/parsl/executors/high_throughput/interchange.py b/parsl/executors/high_throughput/interchange.py index 019c70a175..1391b2c34a 100644 --- a/parsl/executors/high_throughput/interchange.py +++ b/parsl/executors/high_throughput/interchange.py @@ -168,8 +168,14 @@ def __init__(self, self.context = zmq.Context() self.task_incoming = self.context.socket(zmq.DEALER) self.task_incoming.set_hwm(0) - self.task_incoming.RCVTIMEO = 10 # in milliseconds + + # this controls the speed at which the task incoming queue loop runs. The only thing + # that loop does aside from task_incoming is check for kill event. The default of + # 10ms is pretty high - for this project, I'm fine with this taking a second or so to + # detect a kill event. + self.task_incoming.RCVTIMEO = 5000 # in milliseconds self.task_incoming.connect("tcp://{}:{}".format(client_address, client_ports[0])) + self.results_outgoing = self.context.socket(zmq.DEALER) self.results_outgoing.set_hwm(0) self.results_outgoing.connect("tcp://{}:{}".format(client_address, client_ports[1])) @@ -268,7 +274,8 @@ def migrate_tasks_to_internal(self, kill_event): msg = self.task_incoming.recv_pyobj() except zmq.Again: # We just timed out while attempting to receive - logger.debug("[TASK_PULL_THREAD] {} tasks in internal queue".format(self.pending_task_queue.qsize())) + logger.debug("[TASK_PULL_THREAD] No task received from task_incoming zmq queue. {} tasks already in internal queue".format( + self.pending_task_queue.qsize())) continue if msg == 'STOP': @@ -363,7 +370,7 @@ def _command_server(self, kill_event): continue @wrap_with_logs - def start(self, poll_period=None): + def start(self): """ Start the interchange Parameters: @@ -375,8 +382,19 @@ def start(self, poll_period=None): hub_channel = self._create_monitoring_channel() - if poll_period is None: - poll_period = self.poll_period + # poll period is never specified as a start() parameter, so removing the defaulting here as noise. + # poll_period = self.poll_period + # however for my hacking: + poll_period = 1000 + # because the executor level poll period also changes the worker pool poll period setting, which I want to experiment with separately. + # This setting reduces the speed at which the interchange main loop + # iterates. It will iterate once per this tmie, or when two of the + # three queues that we need to check are interesting. which means that + # third queue (pending_task_queue) will only be dispatched on once + # every poll_period. although everythign waiting will be dispatched + # then. this will reduce speed of task dispatching some, but give + # much less log output. I wonder if it is possible to make this detectable + # using poll too (it's a python queue, not a zmq queue which the other poll is for) start = time.time() count = 0 @@ -404,7 +422,9 @@ def start(self, poll_period=None): interesting_managers = set() while not self._kill_event.is_set(): + logger.debug("BENC: starting poll") self.socks = dict(poller.poll(timeout=poll_period)) + logger.debug("BENC: ending poll") # Listen for requests for work if self.task_outgoing in self.socks and self.socks[self.task_outgoing] == zmq.POLLIN: @@ -422,7 +442,7 @@ def start(self, poll_period=None): except Exception: logger.warning("[MAIN] Got Exception reading registration message from manager: {}".format( manager), exc_info=True) - logger.debug("[MAIN] Message :\n{}\n".format(message[0])) + logger.debug("[MAIN] Message :\n{}\n".format(message[1])) else: # We set up an entry only if registration works correctly self._ready_manager_queue[manager] = {'last_heartbeat': time.time(), @@ -495,6 +515,11 @@ def start(self, poll_period=None): tasks = self.get_tasks(real_capacity) if tasks: self.task_outgoing.send_multipart([manager, b'', pickle.dumps(tasks)]) + # after this point, we've sent a task to the manager, but we haven't + # added it to the 'task' list for that manager, because we don't + # do that for another 5 lines. That should be pretty fast, though? + # but we shouldn't try removing it from the tasks list until we have + # passed that point anyway? task_count = len(tasks) count += task_count tids = [t['task_id'] for t in tasks] diff --git a/parsl/executors/high_throughput/probe.py b/parsl/executors/high_throughput/probe.py index 58698a1603..f6064ab812 100644 --- a/parsl/executors/high_throughput/probe.py +++ b/parsl/executors/high_throughput/probe.py @@ -9,7 +9,7 @@ logger = logging.getLogger(__name__) -def probe_addresses(addresses, task_port, timeout=2): +def probe_addresses(addresses, task_port, timeout=120): """ Parameters ---------- diff --git a/parsl/executors/high_throughput/process_worker_pool.py b/parsl/executors/high_throughput/process_worker_pool.py index 9ed8ecad18..674fbcd352 100755 --- a/parsl/executors/high_throughput/process_worker_pool.py +++ b/parsl/executors/high_throughput/process_worker_pool.py @@ -110,8 +110,15 @@ def __init__(self, heartbeat_period : int Number of seconds after which a heartbeat message is sent to the interchange - poll_period : int + poll_period : int - either s or ms depending on who is reading it (!) Timeout period used by the manager in milliseconds. Default: 10ms + This will affect: + + * worker watchdog restart - if a worker fails, we may wait a + poll period before that worker is restarted. 10ms is crazy + low for LSST purposes. A minute would be fine. That loop + doesn't seem to generate log load though in normal use. + But time.sleep is used, which means it defaults to 1000x slower than the other periods. That seems like a bug that should be fixed/clarified cpu_affinity : str Whether each worker should force its affinity to different CPUs @@ -209,12 +216,14 @@ def create_reg_message(self): b_msg = json.dumps(msg).encode('utf-8') return b_msg + # BENC: TODO: this doesn't send valid JSON but the registration receiver code + # expects to decode json (for example, the json coming out of create_reg_message) def heartbeat(self): """ Send heartbeat to the incoming task queue """ heartbeat = (HEARTBEAT_CODE).to_bytes(4, "little") r = self.task_incoming.send(heartbeat) - logger.debug("Return from heartbeat: {}".format(r)) + logger.debug("Sent heartbeat, return code {}".format(r)) @wrap_with_logs def pull_tasks(self, kill_event): @@ -238,14 +247,15 @@ def pull_tasks(self, kill_event): last_interchange_contact = time.time() task_recv_counter = 0 + # what units is poll_timer? according to this assignment, it should be ms. ZMQ poller also wants poll_timer to be ms. poll_timer = self.poll_period while not kill_event.is_set(): ready_worker_count = self.ready_worker_queue.qsize() pending_task_count = self.pending_task_queue.qsize() - logger.debug("[TASK_PULL_THREAD] ready workers:{}, pending tasks:{}".format(ready_worker_count, - pending_task_count)) + logger.debug("[TASK_PULL_THREAD] ready workers: {}, pending tasks: {}".format(ready_worker_count, + pending_task_count)) if time.time() > last_beat + self.heartbeat_period: self.heartbeat() @@ -263,6 +273,7 @@ def pull_tasks(self, kill_event): _, pkl_msg = self.task_incoming.recv_multipart() tasks = pickle.loads(pkl_msg) last_interchange_contact = time.time() + logger.debug("Updating time of last heartbeat from interchange at {}".format(last_interchange_contact)) if tasks == 'STOP': logger.critical("[TASK_PULL_THREAD] Received stop request") @@ -309,7 +320,12 @@ def push_results(self, kill_event): logger.debug("[RESULT_PUSH_THREAD] Starting thread") - push_poll_period = max(10, self.poll_period) / 1000 # push_poll_period must be atleast 10 ms + # push_poll_period is in s + + push_poll_period = max(10, self.poll_period) / 1000 + # push_poll_period must be at least 10 ms [BENC: why? and why does + # this one have more of a restriction than any of the other timing + # parameters? That max statement enforces that. but why enforce it vs other timings?] logger.debug("[RESULT_PUSH_THREAD] push poll period: {}".format(push_poll_period)) last_beat = time.time() @@ -347,6 +363,7 @@ def worker_watchdog(self, kill_event): logger.debug("[WORKER_WATCHDOG_THREAD] Starting thread") while not kill_event.is_set(): + logger.debug("[WORKER_WATCHDOG_THREAD] Loop") for worker_id, p in self.procs.items(): if not p.is_alive(): logger.info("[WORKER_WATCHDOG_THREAD] Worker {} has died".format(worker_id)) @@ -374,7 +391,10 @@ def worker_watchdog(self, kill_event): ), name="HTEX-Worker-{}".format(worker_id)) self.procs[worker_id] = p logger.info("[WORKER_WATCHDOG_THREAD] Worker {} has been restarted".format(worker_id)) - time.sleep(self.poll_period) + else: + logger.info("[WORKER_WATCHDOG_THREAD] Worker {} is alive".format(worker_id)) + # time.sleep(self.poll_period) # is this seconds (like sleep) or ms (like self.poll_period) + time.sleep(30) # LSST specific timing logger.critical("[WORKER_WATCHDOG_THREAD] Exiting") @@ -401,7 +421,7 @@ def start(self): p.start() self.procs[worker_id] = p - logger.debug("Manager synced with workers") + logger.debug("Workers started") self._task_puller_thread = threading.Thread(target=self.pull_tasks, args=(self._kill_event,), diff --git a/parsl/monitoring/monitoring.py b/parsl/monitoring/monitoring.py index 35134cfaad..644e9c454c 100644 --- a/parsl/monitoring/monitoring.py +++ b/parsl/monitoring/monitoring.py @@ -398,6 +398,8 @@ def send(self, mtype: MessageType, message: Any) -> None: except zmq.Again: self.logger.exception( "The monitoring message sent from DFK to Hub timed-out after {}ms".format(self.dfk_channel_timeout)) + else: + self.logger.debug("Sent message {}, {}".format(mtype, message)) def close(self) -> None: if self.logger: @@ -447,12 +449,14 @@ def monitor_wrapper(f: Any, Wrap the Parsl app with a function that will call the monitor function and point it at the correct pid when the task begins. """ def wrapped(*args: List[Any], **kwargs: Dict[str, Any]) -> Any: + logger.debug("wrapped: 1. start of wrapped") # Send first message to monitoring router send_first_message(try_id, task_id, monitoring_hub_url, run_id, radio_mode) + logger.debug("wrapped: 2. sent first message") if monitor_resources: # create the monitor process and start @@ -467,17 +471,25 @@ def wrapped(*args: List[Any], **kwargs: Dict[str, Any]) -> Any: logging_level, sleep_dur), name="Monitor-Wrapper-{}".format(task_id)) + logger.debug("wrapped: 3. created monitor process, pid {}".format(p.pid)) p.start() + logger.debug("wrapped: 4. started monitor process, pid {}".format(p.pid)) else: p = None try: - return f(*args, **kwargs) + logger.debug("wrapped: 5. invoking wrapped function") + r = f(*args, **kwargs) + logger.debug("wrapped: 6. back from wrapped function ok") + return r finally: + logger.debug("wrapped: 10 in 2nd finally") # There's a chance of zombification if the workers are killed by some signals if p: p.terminate() + logger.debug("wrapped: 11 done terminating monitor") p.join() + logger.debug("wrapped: 12 done joining monitor again") return wrapped From a9d6996cca6ebe9eb573ca9d57e00d6235f044d4 Mon Sep 17 00:00:00 2001 From: Ben Clifford Date: Wed, 20 May 2020 10:53:18 +0000 Subject: [PATCH 042/408] debugging some weirdness with scaling in lsst run --- parsl/dataflow/strategy.py | 48 ++++++++++++++++++++++++-------------- 1 file changed, 31 insertions(+), 17 deletions(-) diff --git a/parsl/dataflow/strategy.py b/parsl/dataflow/strategy.py index 7526a7a591..3278c05be4 100644 --- a/parsl/dataflow/strategy.py +++ b/parsl/dataflow/strategy.py @@ -136,6 +136,7 @@ def _strategy_noop(self, status: List[ExecutorStatus], tasks): Args: - tasks (task_ids): Not used here. """ + logger.debug("strategy_noop: doing nothing") def unset_logging(self): """ Mute newly added handlers to the root level, right after calling executor.status @@ -175,11 +176,15 @@ def _strategy_htex_auto_scale(self, status_list, tasks): self._general_strategy(status_list, tasks, strategy_type='htex') def _general_strategy(self, status_list, tasks, *, strategy_type): + logger.debug("general strategy starting") + for exec_status in status_list: executor = exec_status.executor label = executor.label if not executor.scaling_enabled: + logger.debug("strategy_simple: skipping executor {} because scaling not enabled".format(label)) continue + logger.debug("strategy_simple: strategizing for executor {}".format(label)) # Tasks that are either pending completion active_tasks = executor.outstanding @@ -201,6 +206,8 @@ def _general_strategy(self, status_list, tasks, *, strategy_type): active_blocks = running + pending active_slots = active_blocks * tasks_per_node * nodes_per_block + logger.debug("Slot ratio calculation: active_slots = {}, active_tasks = {}".format(active_slots, active_tasks)) + if hasattr(executor, 'connected_workers'): logger.debug('Executor {} has {} active tasks, {}/{} running/pending blocks, and {} connected workers'.format( label, active_tasks, running, pending, executor.connected_workers)) @@ -209,6 +216,7 @@ def _general_strategy(self, status_list, tasks, *, strategy_type): label, active_tasks, running, pending)) # reset kill timer if executor has active tasks + if active_tasks > 0 and self.executors[executor.label]['idle_since']: self.executors[executor.label]['idle_since'] = None @@ -216,17 +224,18 @@ def _general_strategy(self, status_list, tasks, *, strategy_type): # No tasks. if active_tasks == 0: # Case 1a + logger.debug("1. active_tasks == 0") + # Fewer blocks that min_blocks if active_blocks <= min_blocks: - # Ignore - # logger.debug("Strategy: Case.1a") - pass - + logger.debug("Case 1a: executor has no active tasks, and <= min blocks. Taking no action.") # Case 1b # More blocks than min_blocks. Scale down else: # We want to make sure that max_idletime is reached # before killing off resources + logger.debug("Case 1b: executor has no active tasks, and more ({}) than min blocks ({})".format(active_blocks, min_blocks)) + if not self.executors[executor.label]['idle_since']: logger.debug("Executor {} has 0 active tasks; starting kill timer (if idle time exceeds {}s, resources will be removed)".format( label, self.max_idletime) @@ -243,22 +252,22 @@ def _general_strategy(self, status_list, tasks, *, strategy_type): exec_status.scale_in(active_blocks - min_blocks) else: - pass - # logger.debug("Strategy: Case.1b. Waiting for timer : {0}".format(idle_since)) + logger.debug("1.2.2 Idle time {} is less than max_idletime {}s for executor {}; not scaling in".format(time.time() - idle_since, + self.max_idletime, label)) # Case 2 # More tasks than the available slots. elif (float(active_slots) / active_tasks) < parallelism: + logger.debug("Case 22. (slot_ratio = active_slots/active_tasks) < parallelism") + # Case 2a # We have the max blocks possible if active_blocks >= max_blocks: # Ignore since we already have the max nodes - # logger.debug("Strategy: Case.2a") - pass - + logger.debug("Case 2a active_blocks {} >= max_blocks {} so not scaling".format(active_blocks, max_blocks)) # Case 2b else: - # logger.debug("Strategy: Case.2b") + logger.debug("Case 2b active_blocks {} < max_blocks {} so scaling".format(active_blocks, max_blocks)) excess = math.ceil((active_tasks * parallelism) - active_slots) excess_blocks = math.ceil(float(excess) / (tasks_per_node * nodes_per_block)) excess_blocks = min(excess_blocks, max_blocks - active_blocks) @@ -266,12 +275,17 @@ def _general_strategy(self, status_list, tasks, *, strategy_type): exec_status.scale_out(excess_blocks) elif active_slots == 0 and active_tasks > 0: - # Case 4 - logger.debug("Requesting single slot") + logger.debug("Case 4(I). No active slots, some active tasks...") + + # Case 4(I) if active_blocks < max_blocks: + logger.debug("Requesting single slot") + exec_status.scale_out(1) + else: + logger.debug("Not requesting single slot, because at maxblocks already") - # Case 4 + # Case 4(II) # More slots than tasks elif active_slots > 0 and active_slots > active_tasks: if strategy_type == 'htex': @@ -280,13 +294,13 @@ def _general_strategy(self, status_list, tasks, *, strategy_type): if isinstance(executor, HighThroughputExecutor): if active_blocks > min_blocks: exec_status.scale_in(1, force=False, max_idletime=self.max_idletime) - + else: + logger.debug("This strategy does not support scaling down except for HighThroughputExecutor") elif strategy_type == 'simple': + logger.debug("This strategy does not support scaling down") # skip for simple strategy - pass # Case 3 # tasks ~ slots else: - # logger.debug("Strategy: Case 3") - pass + logger.debug("Case 3: do-nothing strategy case: no changes necessary to current load") From 576953738e322784df9f48049d9f376b493bd0f6 Mon Sep 17 00:00:00 2001 From: Ben Clifford Date: Wed, 20 May 2020 11:50:22 +0000 Subject: [PATCH 043/408] i got a non-hang, but a lost workflow end message send when pressing ctrl-c. maybe the db manager did the right thing recording a fabricated workflow end, but still gave ugly timeout message from the DFK: 2020-05-20 04:47:05 parsl.dataflow.dflow:980 [INFO] Terminating flow_control and strategy threads Process Monitoring-DBM-Process: Traceback (most recent call last): File "/global/homes/b/bxc/.conda/envs/parsl-lsst-dm/lib/python3.7/multiprocessing/process.py", line 297, in _bootstrap self.run() File "/global/homes/b/bxc/.conda/envs/parsl-lsst-dm/lib/python3.7/multiprocessing/process.py", line 99, in run self._target(*self._args, **self._kwargs) File "/global/u1/b/bxc/dm/parsl/parsl/process_loggers.py", line 18, in wrapped r = fn(*args, **kwargs) File "/global/u1/b/bxc/dm/parsl/parsl/monitoring/db_manager.py", line 656, in dbm_starter dbm.start(priority_msgs, node_msgs, resource_msgs) File "/global/u1/b/bxc/dm/parsl/parsl/monitoring/db_manager.py", line 513, in start threshold=self.batching_threshold) File "/global/u1/b/bxc/dm/parsl/parsl/monitoring/db_manager.py", line 620, in _get_messages_in_batch x = msg_queue.get(timeout=0.1) File "/global/homes/b/bxc/.conda/envs/parsl-lsst-dm/lib/python3.7/queue.py", line 179, in get self.not_empty.wait(remaining) File "/global/homes/b/bxc/.conda/envs/parsl-lsst-dm/lib/python3.7/threading.py", line 300, in wait gotit = waiter.acquire(True, timeout) KeyboardInterrupt 2020-05-20 04:47:09 parsl.executors.high_throughput.executor:638 [INFO] Attempting HighThroughputExecutor shutdown 2020-05-20 04:47:09 parsl.executors.high_throughput.executor:640 [INFO] Finished HighThroughputExecutor shutdown attempt 2020-05-20 04:47:09 parsl.executors.threads:100 [DEBUG] Done with executor shutdown 2020-05-20 04:47:09 parsl.monitoring.monitoring:260 [DEBUG] Sending message MessageType.WORKFLOW_INFO, {'tasks_failed_count': 0, 'tasks_completed_count': 3080, 'time_began': datetime.datetime(2020, 5, 20, 3, 8, 13, 625493), 'time_completed': datetime.datetime(2020, 5, 20, 4, 47, 9, 557968), 'run_id': 'b639e10c-a532-4753-b6e4-a113e31ab25a', 'rundir': '/global/u1/b/bxc/dm/ImageProcessingPipelines/workflows/parsl-benc/runinfo/000'} 2020-05-20 04:47:19 parsl.monitoring.monitoring:265 [ERROR] [MONITORING] The monitoring message sent from DFK to Hub timeouts after 10000ms Traceback (most recent call last): File "/global/u1/b/bxc/dm/parsl/parsl/monitoring/monitoring.py", line 262, in send self._dfk_channel.send_pyobj((mtype, message)) File "/global/homes/b/bxc/.conda/envs/parsl-lsst-dm/lib/python3.7/site-packages/zmq/sugar/socket.py", line 611, in send_pyobj return self.send(msg, flags=flags, **kwargs) File "/global/homes/b/bxc/.conda/envs/parsl-lsst-dm/lib/python3.7/site-packages/zmq/sugar/socket.py", line 400, in send return super(Socket, self).send(data, flags=flags, copy=copy, track=track) File "zmq/backend/cython/socket.pyx", line 728, in zmq.backend.cython.socket.Socket.send File "zmq/backend/cython/socket.pyx", line 775, in zmq.backend.cython.socket.Socket.send File "zmq/backend/cython/socket.pyx", line 247, in zmq.backend.cython.socket._send_copy File "zmq/backend/cython/socket.pyx", line 242, in zmq.backend.cython.socket._send_copy File "zmq/backend/cython/checkrc.pxd", line 20, in zmq.backend.cython.checkrc._check_rc zmq.error.Again: Resource temporarily unavailable 2020-05-20 04:47:19 parsl.monitoring.monitoring:271 [INFO] Terminating Monitoring Hub 2020-05-20 04:47:19 parsl.monitoring.monitoring:287 [INFO] Waiting for Hub to receive all messages and terminate 2020-05-20 04:47:19 parsl.monitoring.monitoring:289 [DEBUG] Finished waiting for Hub termination 2020-05-20 04:47:19 parsl.monitoring.monitoring:293 [DEBUG] Finished waiting for DBM termination 2020-05-20 04:47:19 parsl.dataflow.dflow:1002 [INFO] DFK cleanup complete From 1950e8648be31c8a3450e97440ad8657332d620f Mon Sep 17 00:00:00 2001 From: Ben Clifford Date: Thu, 21 May 2020 13:54:28 +0000 Subject: [PATCH 044/408] move total tasks to the back of plot so that it doesn't override the colour of the separate task lines (for example, when all tasks running are the same app) --- .../visualization/plots/default/workflow_plots.py | 11 ++++++----- 1 file changed, 6 insertions(+), 5 deletions(-) diff --git a/parsl/monitoring/visualization/plots/default/workflow_plots.py b/parsl/monitoring/visualization/plots/default/workflow_plots.py index 24f6bd13c5..c5a6ed63ba 100644 --- a/parsl/monitoring/visualization/plots/default/workflow_plots.py +++ b/parsl/monitoring/visualization/plots/default/workflow_plots.py @@ -119,13 +119,14 @@ def task_per_app_plot(task, status, time_completed): all_tasks[j - start] += 1 fig = go.Figure( data=[go.Scatter(x=list(range(0, end - start + 1)), - y=tasks_per_app[app], - name=app, - ) for app in tasks_per_app] + - [go.Scatter(x=list(range(0, end - start + 1)), y=all_tasks, name='All', - )], + )] + + [go.Scatter(x=list(range(0, end - start + 1)), + y=tasks_per_app[app], + name=app, + ) for app in tasks_per_app], + layout=go.Layout(xaxis=dict(autorange=True, title='Time (seconds)'), yaxis=dict(title='Number of tasks'), From 16b3ff4e1404fa13bbaf3d44b1eb593e5a12dd7c Mon Sep 17 00:00:00 2001 From: Ben Clifford Date: Thu, 21 May 2020 13:57:54 +0000 Subject: [PATCH 045/408] hard fail exceptions on incorrect time format --- parsl/monitoring/visualization/views.py | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/parsl/monitoring/visualization/views.py b/parsl/monitoring/visualization/views.py index 1ddfd97737..cc5eb59884 100644 --- a/parsl/monitoring/visualization/views.py +++ b/parsl/monitoring/visualization/views.py @@ -22,7 +22,8 @@ def format_time(value): return rounded_timedelta else: print("Incorrect time format (neither float nor datetime object): {}, type: {}".format(value, type(value))) # TODO: use logging - return "Incorrect time format" + # raise ValueError("Incorrect time format: {}, type {}".format(value, type(value))) + return "-" def format_duration(value): From 07dc74dd544528025d7b2deff936f3c4dd51a3f0 Mon Sep 17 00:00:00 2001 From: Ben Clifford Date: Thu, 21 May 2020 16:31:30 +0000 Subject: [PATCH 046/408] use try time returnd not task time returned --- .../visualization/plots/default/workflow_plots.py | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/parsl/monitoring/visualization/plots/default/workflow_plots.py b/parsl/monitoring/visualization/plots/default/workflow_plots.py index c5a6ed63ba..ea3c473feb 100644 --- a/parsl/monitoring/visualization/plots/default/workflow_plots.py +++ b/parsl/monitoring/visualization/plots/default/workflow_plots.py @@ -81,7 +81,7 @@ def task_per_app_plot(task, status, time_completed): task['epoch_time_running'] = (pd.to_datetime( task['task_try_time_running']) - pd.Timestamp("1970-01-01")) // pd.Timedelta('1s') task['epoch_time_returned'] = (pd.to_datetime( - task['task_time_returned']) - pd.Timestamp("1970-01-01")) // pd.Timedelta('1s') + task['task_try_time_returned']) - pd.Timestamp("1970-01-01")) // pd.Timedelta('1s') start = int(task['epoch_time_running'].min()) end = int(task['epoch_time_returned'].max()) @@ -100,12 +100,12 @@ def task_per_app_plot(task, status, time_completed): if math.isnan(row['epoch_time_running']): # Skip rows with no running start time. continue - if math.isnan(row['epoch_time_returned']): + if math.isnan(row['epoch_try_time_returned']): # Some kind of inference about time returned (workflow end time / current time? see gantt chart for inferences) time_returned = end else: - time_returned = int(row['epoch_time_returned']) + time_returned = int(row['epoch_try_time_returned']) if row['task_func_name'] not in tasks_per_app: tasks_per_app[row['task_func_name']] = [0] * (end - start + 1) From ba295caa830563583f905a955b477804eeee9771 Mon Sep 17 00:00:00 2001 From: Ben Clifford Date: Sat, 23 May 2020 11:45:30 +0000 Subject: [PATCH 047/408] BUG: viz fails when no tasks have finished and the workflow hasn''t finished (so right at the start of the LSST DM workflow, for example) exception to do with cannot compute NaN, that comes most likely from the result of taking max of empty list of finish times being "NaN" (i.e. it's an empty list exception, in float form) From 0d215d22093c17105df7cc90d757ff91c415f844 Mon Sep 17 00:00:00 2001 From: Ben Clifford Date: Thu, 21 May 2020 18:13:08 +0000 Subject: [PATCH 048/408] Rename tasks/app to tries/app to reflect retries --- parsl/monitoring/visualization/plots/default/workflow_plots.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/parsl/monitoring/visualization/plots/default/workflow_plots.py b/parsl/monitoring/visualization/plots/default/workflow_plots.py index ea3c473feb..54f81f8087 100644 --- a/parsl/monitoring/visualization/plots/default/workflow_plots.py +++ b/parsl/monitoring/visualization/plots/default/workflow_plots.py @@ -130,7 +130,7 @@ def task_per_app_plot(task, status, time_completed): layout=go.Layout(xaxis=dict(autorange=True, title='Time (seconds)'), yaxis=dict(title='Number of tasks'), - title="Tasks per app")) + title="Execution tries per app")) return plot(fig, show_link=False, output_type="div", include_plotlyjs=False) except Exception: raise From c5dbe5d3f445a30c0ba766d67892ce4ee6ad3189 Mon Sep 17 00:00:00 2001 From: Ben Clifford Date: Sat, 23 May 2020 12:03:51 +0000 Subject: [PATCH 049/408] cputime graphs for a task do not show the cpu time. not sure if this is a viz problem or a data collection problem. From ded3140794e256943b1c303a1382f86be9db52fb Mon Sep 17 00:00:00 2001 From: Ben Clifford Date: Fri, 5 Jun 2020 12:10:08 +0000 Subject: [PATCH 050/408] make it so magic keywords don't need declaring this used to work but doesn't now - not sure what i've missed --- parsl/app/bash.py | 9 +++++++++ 1 file changed, 9 insertions(+) diff --git a/parsl/app/bash.py b/parsl/app/bash.py index 1e60f4575b..825573bbfb 100644 --- a/parsl/app/bash.py +++ b/parsl/app/bash.py @@ -20,6 +20,15 @@ def remote_side_bash_executor(func, *args, **kwargs): executable = None + app_kwargs = kwargs.copy() + + # TODO: should pass these through if 'func' declares that it will take them + # otherwise silently discard. + if 'stdout' in app_kwargs: + del app_kwargs['stdout'] + if 'stderr' in app_kwargs: + del app_kwargs['stderr'] + # Try to run the func to compose the commandline try: # Execute the func to get the commandline From e8900c281ea38b821b2ec4c68f7907e43ea3fc04 Mon Sep 17 00:00:00 2001 From: Ben Clifford Date: Wed, 15 Apr 2020 14:15:59 +0000 Subject: [PATCH 051/408] Tighten pytest KeyError test skipping KeyError checking is only intended to happen for configuration file loading. On non-local tests, if the single configuration file raises an exception, that exception can be propagated without any special handling. So all of the KeyError handling for non-local tests is removed by this commit. On local tests, this commit adds some notes but does not change behaviour for tests which raise a KeyError. TODO: make local tests tighter as per added note --- parsl/tests/conftest.py | 8 ++++++++ 1 file changed, 8 insertions(+) diff --git a/parsl/tests/conftest.py b/parsl/tests/conftest.py index f80dadc95e..96d99055c8 100644 --- a/parsl/tests/conftest.py +++ b/parsl/tests/conftest.py @@ -235,6 +235,14 @@ def pytest_make_collect_report(collector): from _pytest import nose from _pytest.outcomes import Skipped skip_exceptions = (Skipped,) + nose.get_skip_exceptions() + + # this test for KeyError will mark a test as skipped for every + # test that fails with a KeyError; it is intended to skip tests + # which fail a user options lookup, not tests which raise a + # key error as a genuine failure. Such genuine failures will be + # misreported as skips not fails. + # Maybe can inspect the stack trace and see if this is a keyerror + # directly in a parsl/tests/configs/ source file? if call.excinfo.errisinstance(KeyError): outcome = "skipped" r = collector._repr_failure_py(call.excinfo, "line").reprcrash From 3bbd431109ecd5dbc8e2cc5bc1733dc4d08a0e68 Mon Sep 17 00:00:00 2001 From: Ben Clifford Date: Wed, 29 Jul 2020 15:37:28 +0000 Subject: [PATCH 052/408] misc debug --- parsl/monitoring/visualization/plots/default/workflow_plots.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/parsl/monitoring/visualization/plots/default/workflow_plots.py b/parsl/monitoring/visualization/plots/default/workflow_plots.py index 54f81f8087..0e56457057 100644 --- a/parsl/monitoring/visualization/plots/default/workflow_plots.py +++ b/parsl/monitoring/visualization/plots/default/workflow_plots.py @@ -84,7 +84,7 @@ def task_per_app_plot(task, status, time_completed): task['task_try_time_returned']) - pd.Timestamp("1970-01-01")) // pd.Timedelta('1s') start = int(task['epoch_time_running'].min()) - end = int(task['epoch_time_returned'].max()) + end = int(task['epoch_try_time_returned'].max()) # should we take the max of this and time_completed here? # because they might not align just right, and cause array overflows # later in this plot? probably yes. - need to get a notion of From 2690a589664c51eb1661328beffed2b6b6e90b28 Mon Sep 17 00:00:00 2001 From: Ben Clifford Date: Mon, 18 Jan 2021 12:52:24 +0000 Subject: [PATCH 053/408] issue #204 was an IPP specific hack ipp isn't used any more so remove the hack and see if the problem appears in other places --- parsl/dataflow/strategy.py | 15 --------------- 1 file changed, 15 deletions(-) diff --git a/parsl/dataflow/strategy.py b/parsl/dataflow/strategy.py index 3278c05be4..be4207788f 100644 --- a/parsl/dataflow/strategy.py +++ b/parsl/dataflow/strategy.py @@ -138,20 +138,6 @@ def _strategy_noop(self, status: List[ExecutorStatus], tasks): """ logger.debug("strategy_noop: doing nothing") - def unset_logging(self): - """ Mute newly added handlers to the root level, right after calling executor.status - """ - if self.logger_flag is True: - return - - root_logger = logging.getLogger() - - for handler in root_logger.handlers: - if handler not in self.prior_loghandlers: - handler.setLevel(logging.ERROR) - - self.logger_flag = True - def _strategy_simple(self, status_list, tasks): self._general_strategy(status_list, tasks, strategy_type='simple') @@ -190,7 +176,6 @@ def _general_strategy(self, status_list, tasks, *, strategy_type): active_tasks = executor.outstanding status = exec_status.status - self.unset_logging() # FIXME we need to handle case where provider does not define these # FIXME probably more of this logic should be moved to the provider From db81bb48dbd3a6ee18db3c07851fe73197877652 Mon Sep 17 00:00:00 2001 From: Ben Clifford Date: Tue, 19 Jan 2021 22:10:14 +0000 Subject: [PATCH 054/408] TODO: represent the execution location more interestingly than the local hostname eg workers on htex could set an environment variable that gives executor name, manager ID, worker number, block id, for exampe feature req from tomq - he specifically asked for block id From da6982ef898f343214878af0de9adff1c3ac1ee7 Mon Sep 17 00:00:00 2001 From: Ben Clifford Date: Tue, 19 Jan 2021 22:11:49 +0000 Subject: [PATCH 055/408] some reprs of failures don't look like constructors - when they're __repr__ed to the monitoring database (see recent PR i made that writes out using __repr__ not __str_- they lack context) Look at the task failures in a monitoring.db coming from running the test suite to see examples of some which do not look right - i.e. ones that look liek a string, not Classname(FooDetail) From dfb5ad2db6806102c0d7c75b6f8bb2ff3af73e40 Mon Sep 17 00:00:00 2001 From: Ben Clifford Date: Wed, 8 Jul 2020 10:09:07 +0000 Subject: [PATCH 056/408] prototype queue prioritisation in htex this is not intended to be exact, in the sense that a job with a lower priority might run before a job with a higher priority - but the "bulk" of the work (in the LSST sense) should be prioritised this way. priorities can be anything comparable to each other (and to the default priority, which is integer 0) i'm not going to address the macsafequeue in this prototype --- parsl/executors/high_throughput/executor.py | 18 ++++---- .../executors/high_throughput/interchange.py | 41 +++++++++++++++++-- .../test_error_handling/test_resource_spec.py | 6 +++ 3 files changed, 52 insertions(+), 13 deletions(-) diff --git a/parsl/executors/high_throughput/executor.py b/parsl/executors/high_throughput/executor.py index ecb35f533d..e2cc924746 100644 --- a/parsl/executors/high_throughput/executor.py +++ b/parsl/executors/high_throughput/executor.py @@ -15,8 +15,7 @@ from parsl.executors.high_throughput import interchange from parsl.executors.errors import ( BadMessage, ScalingFailed, - DeserializationError, SerializationError, - UnsupportedFeatureError + DeserializationError, SerializationError ) from parsl.executors.status_handling import StatusHandlingExecutor @@ -554,12 +553,6 @@ def submit(self, func, resource_specification, *args, **kwargs): Returns: Future """ - if resource_specification: - logger.error("Ignoring the resource specification. " - "Parsl resource specification is not supported in HighThroughput Executor. " - "Please check WorkQueueExecutor if resource specification is needed.") - raise UnsupportedFeatureError('resource specification', 'HighThroughput Executor', 'WorkQueue Executor') - if self.bad_state_is_set: raise self.executor_exception @@ -580,8 +573,15 @@ def submit(self, func, resource_specification, *args, **kwargs): except TypeError: raise SerializationError(func.__name__) + if resource_specification and "priority" in resource_specification: + priority = resource_specification["priority"] + logger.debug("Priority {} found in resource specification".format(priority)) + else: + priority = None + msg = {"task_id": task_id, - "buffer": fn_buf} + "buffer": fn_buf, + "priority": priority} # Post task to the the outgoing queue self.outgoing_q.put(msg) diff --git a/parsl/executors/high_throughput/interchange.py b/parsl/executors/high_throughput/interchange.py index 1391b2c34a..7c00db0496 100644 --- a/parsl/executors/high_throughput/interchange.py +++ b/parsl/executors/high_throughput/interchange.py @@ -1,5 +1,6 @@ #!/usr/bin/env python import argparse +import functools import zmq import os import sys @@ -88,6 +89,38 @@ def __str__(self): return self.__repr__() +@functools.total_ordering +class PriorityQueueEntry: + """ This class is needed because msg will be a dict, and dicts are not + comparable to each other (and if they were, this would be an unnecessary + expense because the queue only cares about priority). It provides + ordering of the priority ignoring the message content, and implements an + ordering that places None behind all other orderings, for use as a default + value""" + def __init__(self, pri, msg): + self.pri = pri + self.msg = msg + + def __eq__(self, other): + if type(self) != type(other): + return NotImplemented + return self.pri == other.pri + + def __lt__(self, other): + # this is deliberately inverted, so that largest priority number comes out of the queue first + if type(self) != type(other): + return NotImplemented + if self.pri is None: # special case so that None is always less than every other value + return False # we are more than populated priorities, and equal to None, the inverse of < + elif self.pri is not None and other.pri is None: + return True + else: # self/other both not None + c = self.pri.__gt__(other.pri) + if c == NotImplemented: + raise RuntimeError("priority values are not comparable: {} vs {}".format(self.pri, other.pri)) + return c + + class Interchange(object): """ Interchange is a task orchestrator for distributed systems. @@ -188,7 +221,7 @@ def __init__(self, self.hub_address = hub_address self.hub_port = hub_port - self.pending_task_queue = queue.Queue(maxsize=10 ** 6) + self.pending_task_queue = queue.PriorityQueue(maxsize=10 ** 6) self.worker_ports = worker_ports self.worker_port_range = worker_port_range @@ -246,11 +279,11 @@ def get_tasks(self, count): tasks = [] for i in range(0, count): try: - x = self.pending_task_queue.get(block=False) + qe = self.pending_task_queue.get(block=False) except queue.Empty: break else: - tasks.append(x) + tasks.append(qe.msg) return tasks @@ -282,7 +315,7 @@ def migrate_tasks_to_internal(self, kill_event): kill_event.set() break else: - self.pending_task_queue.put(msg) + self.pending_task_queue.put(PriorityQueueEntry(msg['priority'], msg)) task_counter += 1 logger.debug("[TASK_PULL_THREAD] Fetched task:{}".format(task_counter)) diff --git a/parsl/tests/test_error_handling/test_resource_spec.py b/parsl/tests/test_error_handling/test_resource_spec.py index 11ffa7c842..ab42a36534 100644 --- a/parsl/tests/test_error_handling/test_resource_spec.py +++ b/parsl/tests/test_error_handling/test_resource_spec.py @@ -1,4 +1,5 @@ import parsl +import pytest from parsl.app.app import python_app # from parsl.tests.configs.local_threads import config from parsl.tests.configs.htex_local import config @@ -12,6 +13,11 @@ def double(x, parsl_resource_specification={}): return x * 2 +@pytest.mark.skip("this test does not accomodate running the test suite" + " on executors which *do* support resource specifications" + " but are not the workqueue executor. In general, it is" + " incorrect to assume that an arbitrary non-workqueue" + " executor will raise the expected exceptionm") def test_resource(n=2): executors = parsl.dfk().executors executor = None From f8f5733ea912ced84ab25bbfe6796d343245a577 Mon Sep 17 00:00:00 2001 From: Ben Clifford Date: Wed, 27 Jan 2021 11:01:05 +0000 Subject: [PATCH 057/408] When ctrl-C is pressed, parsl should clearly acknowledge that it has received the ctrl-C and is working towards ending. This would be fine as an ERROR level log message, I think, because it is an abort of the workflow. I'm not sure what the ctrl-C reporting of this looks like right now... so i should review that befor echanging anythign else From 7865803ceed0e1f9e7915725a3a4a6e8923f59ff Mon Sep 17 00:00:00 2001 From: Ben Clifford Date: Thu, 14 May 2020 11:45:12 +0000 Subject: [PATCH 058/408] Set version string for lsst fork --- parsl/version.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/parsl/version.py b/parsl/version.py index 58e1d88dbe..4681e8ecb1 100644 --- a/parsl/version.py +++ b/parsl/version.py @@ -3,4 +3,4 @@ ..[alpha/beta/..] Alphas will be numbered like this -> 0.4.0a0 """ -VERSION = '1.0.0' +VERSION = '1.0.0-lsst-dm-202103' From aa30845b9a2f98671a35731a3796fef7fdcdb805 Mon Sep 17 00:00:00 2001 From: Ben Clifford Date: Tue, 1 Dec 2020 17:48:12 +0000 Subject: [PATCH 059/408] Release marker patch in stg patch stack From 61563bda3f5687719e0d406132389bf7021e3784 Mon Sep 17 00:00:00 2001 From: Ben Clifford Date: Wed, 17 Mar 2021 13:26:39 +0000 Subject: [PATCH 060/408] Getting workqueue vs monitoring on cori working --- parsl-measure-throughput.py | 46 ++++++++ parsl/app/bash.py | 2 +- parsl/dataflow/dflow.py | 11 +- parsl/dataflow/rundirs.py | 5 +- parsl/dataflow/states.py | 6 + parsl/executors/block_based.py | 65 +++++++++++ parsl/executors/high_throughput/executor.py | 69 +++--------- parsl/executors/workqueue/executor.py | 93 +++++---------- parsl/monitoring/db_manager.py | 14 +++ parsl/monitoring/monitoring.py | 118 +++++++++++++++----- parsl/tests/configs/workqueue_blocks.py | 12 ++ parsl/tests/conftest.py | 6 +- parsl/version.py | 2 +- 13 files changed, 290 insertions(+), 159 deletions(-) create mode 100644 parsl-measure-throughput.py create mode 100644 parsl/executors/block_based.py create mode 100644 parsl/tests/configs/workqueue_blocks.py diff --git a/parsl-measure-throughput.py b/parsl-measure-throughput.py new file mode 100644 index 0000000000..561c57fd02 --- /dev/null +++ b/parsl-measure-throughput.py @@ -0,0 +1,46 @@ +import concurrent.futures +import parsl +import time + +@parsl.python_app +def task(duration: int, parsl_resource_specification={}): + import time + time.sleep(duration) + +if __name__ == "__main__": + print("parsl-measure-throughput: start") + + print("parsl-measure-throughput: importing config") + # from parsl.tests.configs.local_threads import config + from confwq_mon import config + # from confwq import config + + print("parsl-measure-throughput: initialising ") + parsl.load(config) + + n = 68 * 4 * 4 * 2 # 68 cores, 4 threads/core, 4 nodes, 2 batches + d = 600 + print(f"parsl-measure-throughput: submitting {n} tasks of duration {d} seconds") + + start_time = time.time() + + futures = [task(d, parsl_resource_specification={'cores' :1, 'memory':0, 'disk':0}) for _ in range(0,n)] + + print("parsl-measure-throughput: waiting for all futures") + + count = 0 + for f in concurrent.futures.as_completed(futures): + count += 1 + print(f"{count} futures completed after {time.time() - start_time} seconds") + + end_time = time.time() + + print(f"parsl-measure-throughput: duration was {end_time - start_time} seconds") + print(f"parsl-measure-throughput: concurrency was {(n * d) / (end_time - start_time)}") + + print("parsl-measure-throughput: stopping parsl") + + parsl.dfk().cleanup() + parsl.clear() + + print("parsl-measure-throughput: end") diff --git a/parsl/app/bash.py b/parsl/app/bash.py index 825573bbfb..8f6ec4972c 100644 --- a/parsl/app/bash.py +++ b/parsl/app/bash.py @@ -79,7 +79,7 @@ def open_std_fd(fdname): returncode = proc.returncode except subprocess.TimeoutExpired: - raise pe.AppTimeout("[{}] App exceeded walltime: {}".format(func_name, timeout)) + raise pe.AppTimeout("[{}] App exceeded walltime: {} seconds".format(func_name, timeout)) except Exception as e: raise pe.AppException("[{}] App caught exception with returncode: {}".format(func_name, returncode), e) diff --git a/parsl/dataflow/dflow.py b/parsl/dataflow/dflow.py index 995d52a1a3..62414b460a 100644 --- a/parsl/dataflow/dflow.py +++ b/parsl/dataflow/dflow.py @@ -106,7 +106,7 @@ def __init__(self, config=Config()): if self.monitoring.logdir is None: self.monitoring.logdir = self.run_dir self.hub_address = self.monitoring.hub_address - self.hub_interchange_port = self.monitoring.start(self.run_id) + self.hub_interchange_port = self.monitoring.start(self.run_id, self.run_dir) self.time_began = datetime.datetime.now() self.time_completed = None @@ -284,7 +284,7 @@ def handle_exec_update(self, task_id, future): task_record['try_time_returned'] = datetime.datetime.now() if not future.done(): - raise ValueError("done callback called, despite future not reporting itself as done") + raise RuntimeError("done callback called, despite future not reporting itself as done") try: res = self._unwrap_remote_exception_wrapper(future) @@ -571,6 +571,7 @@ def launch_task(self, task_id, executable, *args, **kwargs): try: executor = self.executors[executor_label] except Exception: + # TODO: this exception should maybe list self.executors.keys() rather than the entire config? logger.exception("Task {} requested invalid executor {}: config is\n{}".format(task_id, executor_label, self._config)) raise ValueError("Task {} requested invalid executor {}".format(task_id, executor_label)) @@ -583,9 +584,11 @@ def launch_task(self, task_id, executable, *args, **kwargs): wrapper_logging_level, self.monitoring.resource_monitoring_interval, executor.radio_mode, - executor.monitor_resources()) + executor.monitor_resources(), + self.run_dir) with self.submitter_lock: + # TODO: that resource_specification parameter might be more obvious as a kwarg? exec_fu = executor.submit(executable, self.tasks[task_id]['resource_specification'], *args, **kwargs) self.tasks[task_id]['status'] = States.launched @@ -788,7 +791,7 @@ def submit(self, func, app_args, executors='all', cache=False, ignore_for_cache= ignore_for_cache = [] if self.cleanup_called: - raise ValueError("Cannot submit to a DFK that has been cleaned up") + raise RuntimeError("Cannot submit to a DFK that has been cleaned up") task_id = self.task_count self.task_count += 1 diff --git a/parsl/dataflow/rundirs.py b/parsl/dataflow/rundirs.py index 266a361fc0..f32979473f 100644 --- a/parsl/dataflow/rundirs.py +++ b/parsl/dataflow/rundirs.py @@ -35,7 +35,6 @@ def make_rundir(path: str) -> str: logger.debug("Parsl run initializing in rundir: {0}".format(current_rundir)) return os.path.abspath(current_rundir) - except Exception as e: - logger.error("Failed to create a run directory") - logger.error("Error: {0}".format(e)) + except Exception: + logger.exception("Failed to create run directory") raise diff --git a/parsl/dataflow/states.py b/parsl/dataflow/states.py index 4fbaf17142..0fe054afd6 100644 --- a/parsl/dataflow/states.py +++ b/parsl/dataflow/states.py @@ -19,6 +19,12 @@ class States(IntEnum): memo_done = 9 joining = 10 + # like States.running, this state is also not observed by the DFK, + # but instead only by monitoring. This state does not record + # anything about task success or failure, merely that the wrapper + # ran long enough to record it as finished. + running_ended = 11 + # states from which we will never move to another state FINAL_STATES = [States.exec_done, States.memo_done, States.failed, States.dep_fail] diff --git a/parsl/executors/block_based.py b/parsl/executors/block_based.py new file mode 100644 index 0000000000..ad44113fbd --- /dev/null +++ b/parsl/executors/block_based.py @@ -0,0 +1,65 @@ +import logging + +from abc import abstractmethod, abstractproperty +from parsl.executors.errors import ScalingFailed +from parsl.executors.status_handling import StatusHandlingExecutor +from typing import Any, Dict, List, Tuple, Union + +logger = logging.getLogger(__name__) + + +class BlockProviderExecutor(StatusHandlingExecutor): + """TODO: basically anything to do with providers/scaling/blocks should be moved into this""" + + def __init__(self, provider): + super().__init__(provider) + self.blocks = {} # type: Dict[str, str] + self.block_mapping = {} # type: Dict[str, str] + + def scale_out(self, blocks: int = 1) -> List[str]: + """Scales out the number of blocks by "blocks" + """ + if not self.provider: + raise (ScalingFailed(None, "No execution provider available")) + block_ids = [] + for i in range(blocks): + block_id = str(len(self.blocks)) + try: + job_id = self._launch_block(block_id) + self.blocks[block_id] = job_id + self.block_mapping[job_id] = block_id + block_ids.append(block_id) + except Exception as ex: + self._fail_job_async(block_id, + "Failed to start block {}: {}".format(block_id, ex)) + return block_ids + + def _launch_block(self, block_id: str) -> Any: + launch_cmd = self._get_launch_command(block_id) + # if self.launch_cmd is None: + # raise ScalingFailed(self.provider.label, "No launch command") + # launch_cmd = self.launch_cmd.format(block_id=block_id) + job_id = self.provider.submit(launch_cmd, 1) + logger.debug("Launched block {}->{}".format(block_id, job_id)) + if not job_id: + raise(ScalingFailed(self.provider.label, + "Attempts to provision nodes via provider has failed")) + return job_id + + @abstractmethod + def _get_launch_command(self, block_id: str) -> str: + pass + + def _get_block_and_job_ids(self) -> Tuple[List[str], List[Any]]: + # Not using self.blocks.keys() and self.blocks.values() simultaneously + # The dictionary may be changed during invoking this function + # As scale_in and scale_out are invoked in multiple threads + block_ids = list(self.blocks.keys()) + job_ids = [] # types: List[Any] + for bid in block_ids: + job_ids.append(self.blocks[bid]) + return block_ids, job_ids + + @abstractproperty + def workers_per_node(self) -> Union[int, float]: + pass diff --git a/parsl/executors/high_throughput/executor.py b/parsl/executors/high_throughput/executor.py index e2cc924746..2dd4de6225 100644 --- a/parsl/executors/high_throughput/executor.py +++ b/parsl/executors/high_throughput/executor.py @@ -5,8 +5,10 @@ import queue import datetime import pickle +from typing import Dict # noqa F401 (used in type annotation) +from typing import List, Optional, Tuple, Union +from typing import Dict # noqa F401 (used in type annotation) import multiprocessing -from typing import Any, Dict, List, Optional, Tuple, Union import math from parsl.serialize import pack_apply_message, deserialize @@ -18,7 +20,7 @@ DeserializationError, SerializationError ) -from parsl.executors.status_handling import StatusHandlingExecutor +from parsl.executors.block_based import BlockProviderExecutor from parsl.providers.provider_base import ExecutionProvider from parsl.data_provider.staging import Staging from parsl.addresses import get_all_addresses @@ -30,7 +32,7 @@ logger = logging.getLogger(__name__) -class HighThroughputExecutor(StatusHandlingExecutor, RepresentationMixin): +class HighThroughputExecutor(BlockProviderExecutor, RepresentationMixin): """Executor designed for cluster-scale The HighThroughputExecutor system has the following components: @@ -190,7 +192,7 @@ def __init__(self, logger.debug("Initializing HighThroughputExecutor") - StatusHandlingExecutor.__init__(self, provider) + BlockProviderExecutor.__init__(self, provider) self.label = label self.launch_cmd = launch_cmd @@ -198,8 +200,6 @@ def __init__(self, self.storage_access = storage_access self.working_dir = working_dir self.managed = managed - self.blocks = {} # type: Dict[str, str] - self.block_mapping = {} # type: Dict[str, str] self.cores_per_worker = cores_per_worker self.mem_per_worker = mem_per_worker self.max_workers = max_workers @@ -222,9 +222,9 @@ def __init__(self, self.provider.cores_per_node is not None: cpu_slots = math.floor(self.provider.cores_per_node / cores_per_worker) - self.workers_per_node = min(max_workers, mem_slots, cpu_slots) - if self.workers_per_node == float('inf'): - self.workers_per_node = 1 # our best guess-- we do not have any provider hints + self._workers_per_node = min(max_workers, mem_slots, cpu_slots) + if self._workers_per_node == float('inf'): + self._workers_per_node = 1 # our best guess-- we do not have any provider hints self._task_counter = 0 self.run_id = None # set to the correct run_id in dfk @@ -436,12 +436,6 @@ def _queue_management_worker(self): break logger.info("[MTHREAD] queue management worker finished") - # When the executor gets lost, the weakref callback will wake up - # the queue management thread. - def weakref_cb(self, q=None): - """We do not use this yet.""" - q.put(None) - def _start_local_interchange_process(self): """ Starts the interchange process locally @@ -609,34 +603,9 @@ def create_monitoring_info(self, status): msg.append(d) return msg - def scale_out(self, blocks=1): - """Scales out the number of blocks by "blocks" - """ - if not self.provider: - raise (ScalingFailed(None, "No execution provider available")) - block_ids = [] - for i in range(blocks): - block_id = str(len(self.blocks)) - try: - job_id = self._launch_block(block_id) - self.blocks[block_id] = job_id - self.block_mapping[job_id] = block_id - block_ids.append(block_id) - except Exception as ex: - self._fail_job_async(block_id, - "Failed to start block {}: {}".format(block_id, ex)) - return block_ids - - def _launch_block(self, block_id: str) -> Any: - if self.launch_cmd is None: - raise ScalingFailed(self.provider.label, "No launch command") - launch_cmd = self.launch_cmd.format(block_id=block_id) - job_id = self.provider.submit(launch_cmd, 1) - logger.debug("Launched block {}->{}".format(block_id, job_id)) - if not job_id: - raise(ScalingFailed(self.provider.label, - "Attempts to provision nodes via provider has failed")) - return job_id + @property + def workers_per_node(self) -> Union[int, float]: + return self._workers_per_node def scale_in(self, blocks=None, block_ids=[], force=True, max_idletime=None): """Scale in the number of active blocks by specified amount. @@ -718,15 +687,11 @@ def scale_in(self, blocks=None, block_ids=[], force=True, max_idletime=None): return block_ids_killed - def _get_block_and_job_ids(self) -> Tuple[List[str], List[Any]]: - # Not using self.blocks.keys() and self.blocks.values() simultaneously - # The dictionary may be changed during invoking this function - # As scale_in and scale_out are invoked in multiple threads - block_ids = list(self.blocks.keys()) - job_ids = [] # types: List[Any] - for bid in block_ids: - job_ids.append(self.blocks[bid]) - return block_ids, job_ids + def _get_launch_command(self, block_id: str) -> str: + if self.launch_cmd is None: + raise ScalingFailed(self.provider.label, "No launch command") + launch_cmd = self.launch_cmd.format(block_id=block_id) + return launch_cmd def shutdown(self, hub=True, targets='all', block=False): """Shutdown the executor, including all workers and controllers. diff --git a/parsl/executors/workqueue/executor.py b/parsl/executors/workqueue/executor.py index 7f854a2a9b..1d1bc01ae0 100644 --- a/parsl/executors/workqueue/executor.py +++ b/parsl/executors/workqueue/executor.py @@ -25,14 +25,14 @@ from parsl.executors.errors import ExecutorError from parsl.data_provider.files import File from parsl.errors import OptionalModuleMissing -from parsl.executors.status_handling import StatusHandlingExecutor +from parsl.executors.block_based import BlockProviderExecutor from parsl.providers.provider_base import ExecutionProvider from parsl.providers import LocalProvider, CondorProvider from parsl.executors.errors import ScalingFailed from parsl.executors.workqueue import exec_parsl_function import typeguard -from typing import Any, Dict, List, Optional, Set, Tuple +from typing import Dict, List, Optional, Set, Union from parsl.data_provider.staging import Staging from .errors import WorkQueueTaskFailure @@ -74,7 +74,7 @@ ParslFileToWq = namedtuple('ParslFileToWq', 'parsl_name stage cache') -class WorkQueueExecutor(StatusHandlingExecutor): +class WorkQueueExecutor(BlockProviderExecutor): """Executor to use Work Queue batch system The WorkQueueExecutor system utilizes the Work Queue framework to @@ -206,13 +206,9 @@ def __init__(self, init_command: str = "", worker_options: str = "", full_debug: bool = True): + BlockProviderExecutor.__init__(self, provider) - # BENC: if this was factored into something mixin-like, what would - # this call look like? Does super.init() get called in general here - # at all? Maybe this can't fit into that mixin style of inheritance? - StatusHandlingExecutor.__init__(self, provider) - - self._provider = provider + # ? should this be true even when not using a provider? self._scaling_enabled = True if not _work_queue_enabled: @@ -262,62 +258,10 @@ def __init__(self, if self.init_command != "": self.launch_cmd = self.init_command + "; " + self.launch_cmd - # BENC: copied from htex / driven by whats missing when the scaling strategy - # code tries to do anything. Maybe these make sense to factor out into the - # status handling executor. - - def _get_block_and_job_ids(self) -> Tuple[List[str], List[Any]]: - # Not using self.blocks.keys() and self.blocks.values() simultaneously - # The dictionary may be changed during invoking this function - # As scale_in and scale_out are invoked in multiple threads - block_ids = list(self.blocks.keys()) - job_ids = [] # types: List[Any] - for bid in block_ids: - job_ids.append(self.blocks[bid]) - return block_ids, job_ids - - # the scaling code wants this... but there is nothing requiring it to exist. - @property - def outstanding(self): - - # this is going to cost scale linearly with the total number of tasks - # run in a run which is bad, but for now it isn't invasive into other - # bits of workqueue/executor.py - probably what should happen is that - # the relevant entry be removed from self.tasks, and then the number - # of tasks in self.tasks is the answer to this question. - - count = 0 - for key in self.tasks: - task = self.tasks[key] - if not task.done(): - count += 1 - - logger.debug(f"BENC: outstanding: len(self.tasks) = {len(self.tasks)}, count = {count}") - return count - - @property - def workers_per_node(self) -> int: - """BENC: - The use of the term 'worker' is a bit fragile here: - - the terminology used in other parts of parsl has: - one worker = the ability to run one task at any instance in time - but work_queue_worker can run many tasks at once from what wq calls a worker. - - In that sense, one wq worker == one parsl process_worker_pool. - - The parsl scaling code interprets this field as meaning how many tasks are - expected to be able to be run simultanously on a node. - - One of the goals of using WQ with parsl is that this can be dynamic, so there - isn't one sensible value here. However, for LSST DRP, I don't want any - subtleties of scaling here: I want parsl to maintain one large block of - eg 1000 nodes in the queue at once, until all the work is done - - """ - return 1 - - # END BENC copies from htex to make the scaling API happy. + def _get_launch_command(self, block_id): + # this executor uses different terminology for worker/launch + # commands than in htex + return self.worker_command def start(self): """Create submit process and collector thread to create, send, and @@ -633,6 +577,8 @@ def initialize_scaling(self): self.worker_command = self._construct_worker_command() self._patch_providers() + # TODO: this init_blocks handling should be factored with the + # corresponding htex handling and put into the BlockProviderExecutor if hasattr(self.provider, 'init_blocks'): try: self.scale_out(blocks=self.provider.init_blocks) @@ -640,7 +586,18 @@ def initialize_scaling(self): logger.debug("Scaling out failed: {}".format(e)) raise e - def scale_out(self, blocks=1): + @property + def outstanding(self) -> int: + """TODO: this is very inefficient and probably should be replaced with + counters, but this one is minimally invasive to the rest of the code.""" + outstanding = 0 + for fut in self.tasks.values(): + if not fut.done(): + outstanding += 1 + logger.debug(f"Counted {outstanding} outstanding tasks") + return outstanding + + def xxxold_scale_out(self, blocks=1): """Scale out method. We should have the scale out method simply take resource object @@ -659,6 +616,10 @@ def scale_out(self, blocks=1): else: logger.error("No execution provider available to scale") + @property + def workers_per_node(self) -> Union[int, float]: + return 1 + def scale_in(self, count): """Scale in method. Not implemented. """ diff --git a/parsl/monitoring/db_manager.py b/parsl/monitoring/db_manager.py index 4a96259b7b..0d15a68e3f 100644 --- a/parsl/monitoring/db_manager.py +++ b/parsl/monitoring/db_manager.py @@ -496,6 +496,20 @@ def start(self, if task_try_id in deferred_resource_messages: logger.error("Task {} already has a deferred resource message. Discarding previous message.".format(msg['task_id'])) deferred_resource_messages[task_try_id] = msg + elif msg['last_msg']: + # TODO: i haven't thought about htis logic, but + # first_msg, last_msg doesn't make much sense as a flag + # any more - should be a separate message type for + # i) run/end run messages, ii) resource messages + # Update the running time to try table if first message + msg['task_status_name'] = States.running_ended.name + msg['task_try_time_running'] = msg['timestamp'] + # making some assumptions that the primary key has + # been added to inserted_tries already... but maybe + # that assumption is made for insert_resource_messages + # messages too? + reprocessable_first_resource_messages.append(msg) + else: # Insert to resource table if not first message insert_resource_messages.append(msg) diff --git a/parsl/monitoring/monitoring.py b/parsl/monitoring/monitoring.py index 457501c650..55592bdc38 100644 --- a/parsl/monitoring/monitoring.py +++ b/parsl/monitoring/monitoring.py @@ -77,23 +77,25 @@ def send(self, message: object) -> None: class FilesystemRadio(MonitoringRadio): - def __init__(self, monitoring_url: str, source_id: int, timeout: int = 10): + def __init__(self, *, monitoring_hub_url: str, source_id: int, timeout: int = 10, run_dir: str): logger.info("filesystem based monitoring channel initializing") self.source_id = source_id self.id_counter = 0 + self.radio_uid = f"host-{socket.gethostname()}-pid-{os.getpid()}-radio-{id(self)}" + self.base_path = f"{run_dir}/monitor-fs-radio/" def send(self, message: object) -> None: logger.info("Sending a monitoring message via filesystem") - tmp_path = "/home/benc/tmp/parsl-radio/tmp" - new_path = "/home/benc/tmp/parsl-radio/new" + tmp_path = f"{self.base_path}/tmp" + new_path = f"{self.base_path}/new" # this should be randomised by things like worker ID, process ID, whatever # because there will in general be many FilesystemRadio objects sharing the # same space (even from the same process). id(self) used here will # disambiguate in one process at one instant, but not between # other things: eg different hosts, different processes, same process different non-overlapping instantiations - unique_id = f"msg-{id(self)}-{self.id_counter}" + unique_id = f"msg-{self.radio_uid}-{self.id_counter}" self.id_counter = self.id_counter + 1 @@ -311,7 +313,7 @@ def __init__(self, self.resource_monitoring_enabled = resource_monitoring_enabled self.resource_monitoring_interval = resource_monitoring_interval - def start(self, run_id: str) -> int: + def start(self, run_id: str, run_dir: str) -> int: if self.logdir is None: self.logdir = "." @@ -368,10 +370,9 @@ def start(self, run_id: str) -> int: self.logger.info("Started the Hub process {} and DBM process {}".format(self.router_proc.pid, self.dbm_proc.pid)) self.filesystem_proc = Process(target=filesystem_receiver, - args=(self.logdir, self.resource_msgs), + args=(self.logdir, self.resource_msgs, run_dir), name="Monitoring-Filesystem-Process", - daemon=True - ) + daemon=True) self.filesystem_proc.start() self.logger.info(f"Started filesystem radio receiver process {self.filesystem_proc.pid}") @@ -444,7 +445,8 @@ def monitor_wrapper(f: Any, logging_level: int, sleep_dur: float, radio_mode: str, - monitor_resources: bool) -> Callable: + monitor_resources: bool, + run_dir: str) -> Callable: """ Internal Wrap the Parsl app with a function that will call the monitor function and point it at the correct pid when the task begins. """ @@ -455,7 +457,8 @@ def wrapped(*args: List[Any], **kwargs: Dict[str, Any]) -> Any: task_id, monitoring_hub_url, run_id, - radio_mode) + radio_mode, + run_dir) logger.debug("wrapped: 2. sent first message") if monitor_resources: @@ -469,7 +472,7 @@ def wrapped(*args: List[Any], **kwargs: Dict[str, Any]) -> Any: run_id, radio_mode, logging_level, - sleep_dur), + sleep_dur, run_dir), name="Monitor-Wrapper-{}".format(task_id)) logger.debug("wrapped: 3. created monitor process, pid {}".format(p.pid)) p.start() @@ -484,6 +487,13 @@ def wrapped(*args: List[Any], **kwargs: Dict[str, Any]) -> Any: return r finally: logger.debug("wrapped: 10 in 2nd finally") + logger.debug("wrapped: 10.1 sending last message") + send_last_message(try_id, + task_id, + monitoring_hub_url, + run_id, + radio_mode, run_dir) + logger.debug("wrapped: 10.1 sent last message") # There's a chance of zombification if the workers are killed by some signals if p: p.terminate() @@ -495,28 +505,41 @@ def wrapped(*args: List[Any], **kwargs: Dict[str, Any]) -> Any: # this needs proper typing, but I was having some problems with typeguard... @wrap_with_logs -def filesystem_receiver(logdir: str, q: "queue.Queue[Tuple[Tuple[MessageType, Dict[str, Any]], Any]]") -> None: - new_dir = "/home/benc/tmp/parsl-radio/new" +def filesystem_receiver(logdir: str, q: "queue.Queue[Tuple[Tuple[MessageType, Dict[str, Any]], Any]]", run_dir: str) -> None: logger = start_file_logger("{}/monitoring_filesystem_radio.log".format(logdir), name="monitoring_filesystem_radio", level=logging.DEBUG) logger.info("Starting filesystem radio receiver") + # TODO: these paths should be created by path tools, not f-strings + # likewise the other places where tmp_dir, new_dir are created on + # the sending side. + base_path = f"{run_dir}/monitor-fs-radio/" + tmp_dir = f"{base_path}/tmp/" + new_dir = f"{base_path}/new/" + logger.debug("Creating new and tmp paths") + + os.makedirs(tmp_dir) + os.makedirs(new_dir) + while True: # needs an exit condition, that also copes with late messages # like the UDP radio receiver. logger.info("Start filesystem radio receiver loop") # iterate over files in new_dir for filename in os.listdir(new_dir): - logger.info(f"Processing filesystem radio file {filename}") - full_path_filename = f"{new_dir}/{filename}" - with open(full_path_filename, "rb") as f: - message = deserialize(f.read()) - logger.info(f"Message received is: {message}") - assert(isinstance(message, tuple)) - q.put(cast(Any, message)) # TODO: sort this typing/cast out - # should this addr field at the end be removed? does it ever - # get used in monitoring? - os.remove(full_path_filename) + try: + logger.info(f"Processing filesystem radio file {filename}") + full_path_filename = f"{new_dir}/{filename}" + with open(full_path_filename, "rb") as f: + message = deserialize(f.read()) + logger.info(f"Message received is: {message}") + assert(isinstance(message, tuple)) + q.put(cast(Any, message)) # TODO: sort this typing/cast out + # should this addr field at the end be removed? does it ever + # get used in monitoring? + os.remove(full_path_filename) + except Exception: + logger.exception(f"Exception processing {filename} - probably will be retried next iteration") time.sleep(1) # whats a good time for this poll? @@ -740,7 +763,7 @@ def router_starter(comm_q: "queue.Queue[Union[Tuple[int, int], str]]", def send_first_message(try_id: int, task_id: int, monitoring_hub_url: str, - run_id: str, radio_mode: str) -> None: + run_id: str, radio_mode: str, run_dir: str) -> None: import platform import os @@ -752,8 +775,8 @@ def send_first_message(try_id: int, radio = HTEXRadio(monitoring_hub_url, source_id=task_id) elif radio_mode == "filesystem": - radio = FilesystemRadio(monitoring_hub_url, - source_id=task_id) + radio = FilesystemRadio(monitoring_hub_url=monitoring_hub_url, + source_id=task_id, run_dir=run_dir) else: raise RuntimeError(f"Unknown radio mode: {radio_mode}") @@ -763,6 +786,42 @@ def send_first_message(try_id: int, 'hostname': platform.node(), 'block_id': os.environ.get('PARSL_WORKER_BLOCK_ID'), 'first_msg': True, + 'last_msg': False, + 'timestamp': datetime.datetime.now() + } + radio.send(msg) + return + + +# TODO: factor with send_first_message +@wrap_with_logs +def send_last_message(try_id: int, + task_id: int, + monitoring_hub_url: str, + run_id: str, radio_mode: str, run_dir: str) -> None: + import platform + import os + + radio: MonitoringRadio + if radio_mode == "udp": + radio = UDPRadio(monitoring_hub_url, + source_id=task_id) + elif radio_mode == "htex": + radio = HTEXRadio(monitoring_hub_url, + source_id=task_id) + elif radio_mode == "filesystem": + radio = FilesystemRadio(monitoring_hub_url=monitoring_hub_url, + source_id=task_id, run_dir=run_dir) + else: + raise RuntimeError(f"Unknown radio mode: {radio_mode}") + + msg = {'run_id': run_id, + 'try_id': try_id, + 'task_id': task_id, + 'hostname': platform.node(), + 'block_id': os.environ.get('PARSL_WORKER_BLOCK_ID'), + 'first_msg': False, + 'last_msg': True, 'timestamp': datetime.datetime.now() } radio.send(msg) @@ -777,7 +836,7 @@ def monitor(pid: int, run_id: str, radio_mode: str, logging_level: int = logging.INFO, - sleep_dur: float = 10) -> None: + sleep_dur: float = 10, run_dir: str = "./") -> None: """Internal Monitors the Parsl task's resources by pointing psutil to the task's pid and watching it and its children. """ @@ -794,8 +853,8 @@ def monitor(pid: int, radio = HTEXRadio(monitoring_hub_url, source_id=task_id) elif radio_mode == "filesystem": - radio = FilesystemRadio(monitoring_hub_url, - source_id=task_id) + radio = FilesystemRadio(monitoring_hub_url=monitoring_hub_url, + source_id=task_id, run_dir=run_dir) else: raise RuntimeError(f"Unknown radio mode: {radio_mode}") @@ -827,6 +886,7 @@ def monitor(pid: int, d['resource_monitoring_interval'] = sleep_dur d['hostname'] = platform.node() d['first_msg'] = False + d['last_msg'] = False d['timestamp'] = datetime.datetime.now() logging.debug("getting children") diff --git a/parsl/tests/configs/workqueue_blocks.py b/parsl/tests/configs/workqueue_blocks.py new file mode 100644 index 0000000000..f7631cd70d --- /dev/null +++ b/parsl/tests/configs/workqueue_blocks.py @@ -0,0 +1,12 @@ +from parsl.config import Config +from parsl.executors import WorkQueueExecutor + +from parsl.data_provider.http import HTTPInTaskStaging +from parsl.data_provider.ftp import FTPInTaskStaging +from parsl.data_provider.file_noop import NoOpFileStaging + +from parsl.providers import LocalProvider + +config = Config(executors=[WorkQueueExecutor(port=9000, + storage_access=[FTPInTaskStaging(), HTTPInTaskStaging(), NoOpFileStaging()], + provider=LocalProvider(init_blocks=0, min_blocks=0, max_blocks=1))]) diff --git a/parsl/tests/conftest.py b/parsl/tests/conftest.py index 96d99055c8..d2370d2f4c 100644 --- a/parsl/tests/conftest.py +++ b/parsl/tests/conftest.py @@ -109,14 +109,14 @@ def load_dfk_session(request, pytestconfig): spec.loader.exec_module(module) if DataFlowKernelLoader._dfk is not None: - raise ValueError("DFK didn't start as None - there was a DFK from somewhere already") + raise RuntimeError("DFK didn't start as None - there was a DFK from somewhere already") dfk = parsl.load(module.config) yield if(parsl.dfk() != dfk): - raise ValueError("DFK changed unexpectedly during test") + raise RuntimeError("DFK changed unexpectedly during test") dfk.cleanup() parsl.clear() else: @@ -156,7 +156,7 @@ def load_dfk_local_module(request, pytestconfig): if(local_config): if(parsl.dfk() != dfk): - raise ValueError("DFK changed unexpectedly during test") + raise RuntimeError("DFK changed unexpectedly during test") dfk.cleanup() parsl.clear() diff --git a/parsl/version.py b/parsl/version.py index fd4e08f2c5..9cf23b5bb6 100644 --- a/parsl/version.py +++ b/parsl/version.py @@ -3,4 +3,4 @@ ..[alpha/beta/..] Alphas will be numbered like this -> 0.4.0a0 """ -VERSION = '1.1.0a1-lsst-dm-202103' +VERSION = '1.1.0a1-lsst-dm-20210317' From ee2120102e9dc2ae66c6a5cdfeeff59269fed33a Mon Sep 17 00:00:00 2001 From: Ben Clifford Date: Wed, 17 Mar 2021 14:25:01 +0000 Subject: [PATCH 061/408] update monitoring bug patch to latest of draft pr #1917 --- parsl/tests/test_monitoring/test_db_locks.py | 6 ++---- 1 file changed, 2 insertions(+), 4 deletions(-) diff --git a/parsl/tests/test_monitoring/test_db_locks.py b/parsl/tests/test_monitoring/test_db_locks.py index babb811545..2a7ca0acc3 100644 --- a/parsl/tests/test_monitoring/test_db_locks.py +++ b/parsl/tests/test_monitoring/test_db_locks.py @@ -1,15 +1,11 @@ - import logging import os import parsl import pytest -import sqlalchemy import time logger = logging.getLogger(__name__) -from parsl.tests.configs.htex_local_alternate import fresh_config - @parsl.python_app def this_app(): @@ -18,6 +14,8 @@ def this_app(): @pytest.mark.local def test_row_counts(): + from parsl.tests.configs.htex_local_alternate import fresh_config + import sqlalchemy if os.path.exists("monitoring.db"): logger.info("Monitoring database already exists - deleting") os.remove("monitoring.db") From 380c8d54d137cd1a52f3eae9f3d85f534dbb01f4 Mon Sep 17 00:00:00 2001 From: Ben Clifford Date: Wed, 17 Mar 2021 14:32:05 +0000 Subject: [PATCH 062/408] refresh stubs in documentation build --- docs/stubs/parsl.dataflow.strategy.Strategy.rst | 1 - docs/stubs/parsl.executors.ExtremeScaleExecutor.rst | 3 ++- docs/stubs/parsl.executors.HighThroughputExecutor.rst | 3 ++- docs/stubs/parsl.executors.LowLatencyExecutor.rst | 2 ++ docs/stubs/parsl.executors.ThreadPoolExecutor.rst | 1 + docs/stubs/parsl.executors.WorkQueueExecutor.rst | 4 ++++ docs/stubs/parsl.executors.base.ParslExecutor.rst | 1 + docs/stubs/parsl.executors.swift_t.TurbineExecutor.rst | 1 + 8 files changed, 13 insertions(+), 3 deletions(-) diff --git a/docs/stubs/parsl.dataflow.strategy.Strategy.rst b/docs/stubs/parsl.dataflow.strategy.Strategy.rst index 10e98f8525..83d89b73c9 100644 --- a/docs/stubs/parsl.dataflow.strategy.Strategy.rst +++ b/docs/stubs/parsl.dataflow.strategy.Strategy.rst @@ -15,7 +15,6 @@ parsl.dataflow.strategy.Strategy ~Strategy.__init__ ~Strategy.add_executors - ~Strategy.unset_logging diff --git a/docs/stubs/parsl.executors.ExtremeScaleExecutor.rst b/docs/stubs/parsl.executors.ExtremeScaleExecutor.rst index 2512e5923e..09772b6689 100644 --- a/docs/stubs/parsl.executors.ExtremeScaleExecutor.rst +++ b/docs/stubs/parsl.executors.ExtremeScaleExecutor.rst @@ -26,7 +26,6 @@ parsl.executors.ExtremeScaleExecutor ~ExtremeScaleExecutor.start ~ExtremeScaleExecutor.status ~ExtremeScaleExecutor.submit - ~ExtremeScaleExecutor.weakref_cb @@ -45,9 +44,11 @@ parsl.executors.ExtremeScaleExecutor ~ExtremeScaleExecutor.hub_port ~ExtremeScaleExecutor.outstanding ~ExtremeScaleExecutor.provider + ~ExtremeScaleExecutor.radio_mode ~ExtremeScaleExecutor.run_dir ~ExtremeScaleExecutor.scaling_enabled ~ExtremeScaleExecutor.status_polling_interval ~ExtremeScaleExecutor.tasks + ~ExtremeScaleExecutor.workers_per_node \ No newline at end of file diff --git a/docs/stubs/parsl.executors.HighThroughputExecutor.rst b/docs/stubs/parsl.executors.HighThroughputExecutor.rst index f861b7fdf0..2c340967f0 100644 --- a/docs/stubs/parsl.executors.HighThroughputExecutor.rst +++ b/docs/stubs/parsl.executors.HighThroughputExecutor.rst @@ -26,7 +26,6 @@ parsl.executors.HighThroughputExecutor ~HighThroughputExecutor.start ~HighThroughputExecutor.status ~HighThroughputExecutor.submit - ~HighThroughputExecutor.weakref_cb @@ -45,9 +44,11 @@ parsl.executors.HighThroughputExecutor ~HighThroughputExecutor.hub_port ~HighThroughputExecutor.outstanding ~HighThroughputExecutor.provider + ~HighThroughputExecutor.radio_mode ~HighThroughputExecutor.run_dir ~HighThroughputExecutor.scaling_enabled ~HighThroughputExecutor.status_polling_interval ~HighThroughputExecutor.tasks + ~HighThroughputExecutor.workers_per_node \ No newline at end of file diff --git a/docs/stubs/parsl.executors.LowLatencyExecutor.rst b/docs/stubs/parsl.executors.LowLatencyExecutor.rst index 1585cee303..3852b0b6f5 100644 --- a/docs/stubs/parsl.executors.LowLatencyExecutor.rst +++ b/docs/stubs/parsl.executors.LowLatencyExecutor.rst @@ -38,7 +38,9 @@ parsl.executors.LowLatencyExecutor ~LowLatencyExecutor.executor_exception ~LowLatencyExecutor.hub_address ~LowLatencyExecutor.hub_port + ~LowLatencyExecutor.outstanding ~LowLatencyExecutor.provider + ~LowLatencyExecutor.radio_mode ~LowLatencyExecutor.run_dir ~LowLatencyExecutor.scaling_enabled ~LowLatencyExecutor.status_polling_interval diff --git a/docs/stubs/parsl.executors.ThreadPoolExecutor.rst b/docs/stubs/parsl.executors.ThreadPoolExecutor.rst index 47a2c14927..f90dc497db 100644 --- a/docs/stubs/parsl.executors.ThreadPoolExecutor.rst +++ b/docs/stubs/parsl.executors.ThreadPoolExecutor.rst @@ -39,6 +39,7 @@ parsl.executors.ThreadPoolExecutor ~ThreadPoolExecutor.hub_address ~ThreadPoolExecutor.hub_port ~ThreadPoolExecutor.provider + ~ThreadPoolExecutor.radio_mode ~ThreadPoolExecutor.run_dir ~ThreadPoolExecutor.scaling_enabled ~ThreadPoolExecutor.status_polling_interval diff --git a/docs/stubs/parsl.executors.WorkQueueExecutor.rst b/docs/stubs/parsl.executors.WorkQueueExecutor.rst index 1c200cef17..e06316c3a8 100644 --- a/docs/stubs/parsl.executors.WorkQueueExecutor.rst +++ b/docs/stubs/parsl.executors.WorkQueueExecutor.rst @@ -27,6 +27,7 @@ parsl.executors.WorkQueueExecutor ~WorkQueueExecutor.start ~WorkQueueExecutor.status ~WorkQueueExecutor.submit + ~WorkQueueExecutor.xxxold_scale_out @@ -41,8 +42,11 @@ parsl.executors.WorkQueueExecutor ~WorkQueueExecutor.executor_exception ~WorkQueueExecutor.hub_address ~WorkQueueExecutor.hub_port + ~WorkQueueExecutor.outstanding ~WorkQueueExecutor.provider + ~WorkQueueExecutor.radio_mode ~WorkQueueExecutor.status_polling_interval ~WorkQueueExecutor.tasks + ~WorkQueueExecutor.workers_per_node \ No newline at end of file diff --git a/docs/stubs/parsl.executors.base.ParslExecutor.rst b/docs/stubs/parsl.executors.base.ParslExecutor.rst index cab400f102..9c357737fe 100644 --- a/docs/stubs/parsl.executors.base.ParslExecutor.rst +++ b/docs/stubs/parsl.executors.base.ParslExecutor.rst @@ -38,6 +38,7 @@ parsl.executors.base.ParslExecutor ~ParslExecutor.executor_exception ~ParslExecutor.hub_address ~ParslExecutor.hub_port + ~ParslExecutor.radio_mode ~ParslExecutor.run_dir ~ParslExecutor.scaling_enabled ~ParslExecutor.status_polling_interval diff --git a/docs/stubs/parsl.executors.swift_t.TurbineExecutor.rst b/docs/stubs/parsl.executors.swift_t.TurbineExecutor.rst index 93f905ece4..0ec2653319 100644 --- a/docs/stubs/parsl.executors.swift_t.TurbineExecutor.rst +++ b/docs/stubs/parsl.executors.swift_t.TurbineExecutor.rst @@ -40,6 +40,7 @@ parsl.executors.swift\_t.TurbineExecutor ~TurbineExecutor.hub_address ~TurbineExecutor.hub_port ~TurbineExecutor.provider + ~TurbineExecutor.radio_mode ~TurbineExecutor.run_dir ~TurbineExecutor.scaling_enabled ~TurbineExecutor.status_polling_interval From 28eb53f0fbd58875d90c3e3df00b1d6338b6d26e Mon Sep 17 00:00:00 2001 From: Ben Clifford Date: Wed, 17 Mar 2021 14:50:58 +0000 Subject: [PATCH 063/408] fix imports in monitoring tests for case where monitoring deps are not installed --- parsl/tests/test_monitoring/test_mon_local/test_db_locks.py | 5 ++--- parsl/tests/test_monitoring/test_mon_wq/test_db_locks.py | 6 +++--- 2 files changed, 5 insertions(+), 6 deletions(-) diff --git a/parsl/tests/test_monitoring/test_mon_local/test_db_locks.py b/parsl/tests/test_monitoring/test_mon_local/test_db_locks.py index 9a97104d89..84cae74e58 100644 --- a/parsl/tests/test_monitoring/test_mon_local/test_db_locks.py +++ b/parsl/tests/test_monitoring/test_mon_local/test_db_locks.py @@ -3,13 +3,10 @@ import os import parsl import pytest -import sqlalchemy import time logger = logging.getLogger(__name__) -from parsl.tests.configs.local_threads_monitoring import fresh_config - @parsl.python_app def this_app(): @@ -18,6 +15,8 @@ def this_app(): @pytest.mark.local def test_row_counts(): + from parsl.tests.configs.htex_local_alternate import fresh_config + import sqlalchemy if os.path.exists("monitoring.db"): logger.info("Monitoring database already exists - deleting") os.remove("monitoring.db") diff --git a/parsl/tests/test_monitoring/test_mon_wq/test_db_locks.py b/parsl/tests/test_monitoring/test_mon_wq/test_db_locks.py index 0c5d2a7341..d2e32beff4 100644 --- a/parsl/tests/test_monitoring/test_mon_wq/test_db_locks.py +++ b/parsl/tests/test_monitoring/test_mon_wq/test_db_locks.py @@ -3,13 +3,10 @@ import os import parsl import pytest -import sqlalchemy import time logger = logging.getLogger(__name__) -from parsl.tests.configs.workqueue_monitoring import fresh_config - @parsl.python_app def this_app(): @@ -18,6 +15,9 @@ def this_app(): @pytest.mark.local def test_row_counts(): + import sqlalchemy + from parsl.tests.configs.workqueue_monitoring import fresh_config + if os.path.exists("monitoring.db"): logger.info("Monitoring database already exists - deleting") os.remove("monitoring.db") From 8a7909f2b663a882e49000483ec01e1aacbbf1eb Mon Sep 17 00:00:00 2001 From: Ben Clifford Date: Wed, 17 Mar 2021 15:06:43 +0000 Subject: [PATCH 064/408] make version string match pep 440 --- parsl/version.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/parsl/version.py b/parsl/version.py index 9cf23b5bb6..ff8a40a0f2 100644 --- a/parsl/version.py +++ b/parsl/version.py @@ -3,4 +3,4 @@ ..[alpha/beta/..] Alphas will be numbered like this -> 0.4.0a0 """ -VERSION = '1.1.0a1-lsst-dm-20210317' +VERSION = '1.1.0a1+lsst-dm-20210317' From c72127da439bb4ca983f5fdcfcf141c3dd6746bb Mon Sep 17 00:00:00 2001 From: Ben Clifford Date: Thu, 18 Mar 2021 14:51:04 +0000 Subject: [PATCH 065/408] debugging CI --- parsl/errors.py | 7 ++++--- parsl/monitoring/db_manager.py | 8 ++++---- 2 files changed, 8 insertions(+), 7 deletions(-) diff --git a/parsl/errors.py b/parsl/errors.py index eb81cf5157..8e5e04ef1c 100644 --- a/parsl/errors.py +++ b/parsl/errors.py @@ -7,11 +7,12 @@ class OptionalModuleMissing(ParslError): ''' Error raised when a required module is missing for a optional/extra component ''' - def __init__(self, module_names: List[str], reason: str): + def __init__(self, module_names: List[str], reason: str, bt=None): self.module_names = module_names self.reason = reason + self.bt = bt def __str__(self) -> str: - return "The functionality requested requires missing optional modules {0}, because: {1}".format( - self.module_names, self.reason + return "The functionality requested requires missing optional modules {0}, because: {1} bt={2}".format( + self.module_names, self.reason, self.bt ) diff --git a/parsl/monitoring/db_manager.py b/parsl/monitoring/db_manager.py index 0d15a68e3f..62cc29180c 100644 --- a/parsl/monitoring/db_manager.py +++ b/parsl/monitoring/db_manager.py @@ -29,8 +29,8 @@ try: from sqlalchemy_utils import get_mapper -except ImportError: - _sqlalchemy_utils_enabled = False +except ImportError as e: + _sqlalchemy_utils_enabled = e else: _sqlalchemy_utils_enabled = True @@ -49,10 +49,10 @@ class Database: raise OptionalModuleMissing(['sqlalchemy'], ("Default database logging requires the sqlalchemy library." " Enable monitoring support with: pip install parsl[monitoring]")) - if not _sqlalchemy_utils_enabled: + if _sqlalchemy_utils_enabled != True: raise OptionalModuleMissing(['sqlalchemy_utils'], ("Default database logging requires the sqlalchemy_utils library." - " Enable monitoring support with: pip install parsl[monitoring]")) + " Enable monitoring support with: pip install parsl[monitoring]"), bt=_sqlalchemy_utils_enabled) Base = declarative_base() From 8a00625c456cc138bc586851a58472b5e9186912 Mon Sep 17 00:00:00 2001 From: Ben Clifford Date: Thu, 18 Mar 2021 15:02:50 +0000 Subject: [PATCH 066/408] more CI debugging --- parsl/monitoring/db_manager.py | 7 ++++--- 1 file changed, 4 insertions(+), 3 deletions(-) diff --git a/parsl/monitoring/db_manager.py b/parsl/monitoring/db_manager.py index 62cc29180c..9d2efcc2c1 100644 --- a/parsl/monitoring/db_manager.py +++ b/parsl/monitoring/db_manager.py @@ -30,7 +30,8 @@ try: from sqlalchemy_utils import get_mapper except ImportError as e: - _sqlalchemy_utils_enabled = e + _sqlalchemy_utils_enabled = False + _sqlalchemy_utils_reason = e else: _sqlalchemy_utils_enabled = True @@ -49,10 +50,10 @@ class Database: raise OptionalModuleMissing(['sqlalchemy'], ("Default database logging requires the sqlalchemy library." " Enable monitoring support with: pip install parsl[monitoring]")) - if _sqlalchemy_utils_enabled != True: + if not _sqlalchemy_utils_enabled: raise OptionalModuleMissing(['sqlalchemy_utils'], ("Default database logging requires the sqlalchemy_utils library." - " Enable monitoring support with: pip install parsl[monitoring]"), bt=_sqlalchemy_utils_enabled) + " Enable monitoring support with: pip install parsl[monitoring]"), bt=_sqlalchemy_utils_reason) Base = declarative_base() From 3c9ff0717f455b3ddff7fe33cf72d3d73204afe2 Mon Sep 17 00:00:00 2001 From: Ben Clifford Date: Thu, 18 Mar 2021 15:50:07 +0000 Subject: [PATCH 067/408] hopefully fix broken sqlalchemy install --- parsl/errors.py | 7 +++---- parsl/monitoring/db_manager.py | 5 ++--- parsl/version.py | 2 +- setup.py | 2 +- 4 files changed, 7 insertions(+), 9 deletions(-) diff --git a/parsl/errors.py b/parsl/errors.py index 8e5e04ef1c..eb81cf5157 100644 --- a/parsl/errors.py +++ b/parsl/errors.py @@ -7,12 +7,11 @@ class OptionalModuleMissing(ParslError): ''' Error raised when a required module is missing for a optional/extra component ''' - def __init__(self, module_names: List[str], reason: str, bt=None): + def __init__(self, module_names: List[str], reason: str): self.module_names = module_names self.reason = reason - self.bt = bt def __str__(self) -> str: - return "The functionality requested requires missing optional modules {0}, because: {1} bt={2}".format( - self.module_names, self.reason, self.bt + return "The functionality requested requires missing optional modules {0}, because: {1}".format( + self.module_names, self.reason ) diff --git a/parsl/monitoring/db_manager.py b/parsl/monitoring/db_manager.py index 9d2efcc2c1..0d15a68e3f 100644 --- a/parsl/monitoring/db_manager.py +++ b/parsl/monitoring/db_manager.py @@ -29,9 +29,8 @@ try: from sqlalchemy_utils import get_mapper -except ImportError as e: +except ImportError: _sqlalchemy_utils_enabled = False - _sqlalchemy_utils_reason = e else: _sqlalchemy_utils_enabled = True @@ -53,7 +52,7 @@ class Database: if not _sqlalchemy_utils_enabled: raise OptionalModuleMissing(['sqlalchemy_utils'], ("Default database logging requires the sqlalchemy_utils library." - " Enable monitoring support with: pip install parsl[monitoring]"), bt=_sqlalchemy_utils_reason) + " Enable monitoring support with: pip install parsl[monitoring]")) Base = declarative_base() diff --git a/parsl/version.py b/parsl/version.py index ff8a40a0f2..add7fa6e2d 100644 --- a/parsl/version.py +++ b/parsl/version.py @@ -3,4 +3,4 @@ ..[alpha/beta/..] Alphas will be numbered like this -> 0.4.0a0 """ -VERSION = '1.1.0a1+lsst-dm-20210317' +VERSION = '1.1.0a1+lsst-dm-20210318' diff --git a/setup.py b/setup.py index b4a51063cb..a6a3a53d81 100755 --- a/setup.py +++ b/setup.py @@ -8,7 +8,7 @@ extras_require = { 'monitoring' : [ - 'sqlalchemy>=1.3.0,!=1.3.4', + 'sqlalchemy>=1.3.0,!=1.3.4,<1.4', 'sqlalchemy_utils', 'pydot', 'networkx', From 736167db2ec1b8702e05831d7e390182f2212069 Mon Sep 17 00:00:00 2001 From: Ben Clifford Date: Mon, 22 Mar 2021 15:58:01 +0000 Subject: [PATCH 068/408] add block monitoring for wq executor copied from htex --- parsl/executors/workqueue/executor.py | 21 +++++++++++++++++++++ parsl/tests/configs/workqueue_blocks.py | 10 +++++++++- parsl/tests/configs/workqueue_monitoring.py | 2 ++ parsl/version.py | 2 +- setup.py | 1 + 5 files changed, 34 insertions(+), 2 deletions(-) diff --git a/parsl/executors/workqueue/executor.py b/parsl/executors/workqueue/executor.py index 1d1bc01ae0..1f0d9032da 100644 --- a/parsl/executors/workqueue/executor.py +++ b/parsl/executors/workqueue/executor.py @@ -9,6 +9,7 @@ from concurrent.futures import Future from ctypes import c_bool +import datetime import tempfile import hashlib import subprocess @@ -654,6 +655,26 @@ def scaling_enabled(self): """ return self._scaling_enabled + # TODO: factor this with htex - perhaps it should exist only in the + # block provider, and there should be no implementation of this at + # all in the base executor class (because this is only block + # relevant) + def create_monitoring_info(self, status): + """ Create a msg for monitoring based on the poll status + + """ + msg = [] + for bid, s in status.items(): + d = {} + d['run_id'] = self.run_id + d['status'] = s.status_name + d['timestamp'] = datetime.datetime.now() + d['executor_label'] = self.label + d['job_id'] = self.blocks.get(bid, None) + d['block_id'] = bid + msg.append(d) + return msg + def run_dir(self, value=None): """Path to the run directory. """ diff --git a/parsl/tests/configs/workqueue_blocks.py b/parsl/tests/configs/workqueue_blocks.py index f7631cd70d..50fa161c54 100644 --- a/parsl/tests/configs/workqueue_blocks.py +++ b/parsl/tests/configs/workqueue_blocks.py @@ -7,6 +7,14 @@ from parsl.providers import LocalProvider +from parsl.monitoring import MonitoringHub + config = Config(executors=[WorkQueueExecutor(port=9000, storage_access=[FTPInTaskStaging(), HTTPInTaskStaging(), NoOpFileStaging()], - provider=LocalProvider(init_blocks=0, min_blocks=0, max_blocks=1))]) + provider=LocalProvider(init_blocks=0, min_blocks=0, max_blocks=1))], + + monitoring=MonitoringHub(hub_address="localhost", + hub_port=55055, + monitoring_debug=True, + resource_monitoring_interval=1, + ) ) diff --git a/parsl/tests/configs/workqueue_monitoring.py b/parsl/tests/configs/workqueue_monitoring.py index c873babd3b..f72cd775a3 100644 --- a/parsl/tests/configs/workqueue_monitoring.py +++ b/parsl/tests/configs/workqueue_monitoring.py @@ -20,3 +20,5 @@ def fresh_config(): resource_monitoring_interval=1, ) ) + +config = fresh_config() diff --git a/parsl/version.py b/parsl/version.py index add7fa6e2d..e49a908f6b 100644 --- a/parsl/version.py +++ b/parsl/version.py @@ -3,4 +3,4 @@ ..[alpha/beta/..] Alphas will be numbered like this -> 0.4.0a0 """ -VERSION = '1.1.0a1+lsst-dm-20210318' +VERSION = '1.1.0a1+lsst-dm-20210322' diff --git a/setup.py b/setup.py index a6a3a53d81..39bdcc8c1d 100755 --- a/setup.py +++ b/setup.py @@ -62,6 +62,7 @@ 'Programming Language :: Python :: 3.6', 'Programming Language :: Python :: 3.7', 'Programming Language :: Python :: 3.8', + 'Programming Language :: Python :: 3.9', ], keywords=['Workflows', 'Scientific computing'], entry_points={'console_scripts': From b48ced398432f8b04672bddd00edd2317e989755 Mon Sep 17 00:00:00 2001 From: Ben Clifford Date: Mon, 22 Mar 2021 22:01:56 +0000 Subject: [PATCH 069/408] add block ID for WQ try table --- parsl/executors/workqueue/executor.py | 2 +- parsl/version.py | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/parsl/executors/workqueue/executor.py b/parsl/executors/workqueue/executor.py index 1f0d9032da..27e814cc57 100644 --- a/parsl/executors/workqueue/executor.py +++ b/parsl/executors/workqueue/executor.py @@ -262,7 +262,7 @@ def __init__(self, def _get_launch_command(self, block_id): # this executor uses different terminology for worker/launch # commands than in htex - return self.worker_command + return f"PARSL_WORKER_BLOCK_ID={block_id} {self.worker_command}" def start(self): """Create submit process and collector thread to create, send, and diff --git a/parsl/version.py b/parsl/version.py index e49a908f6b..f6cb5f07de 100644 --- a/parsl/version.py +++ b/parsl/version.py @@ -3,4 +3,4 @@ ..[alpha/beta/..] Alphas will be numbered like this -> 0.4.0a0 """ -VERSION = '1.1.0a1+lsst-dm-20210322' +VERSION = '1.1.0a1+lsst-dm-20210322b' From 256cd9f71b39c1c6df9a76317a9f022e4f58f910 Mon Sep 17 00:00:00 2001 From: Ben Clifford Date: Thu, 25 Mar 2021 10:53:45 +0000 Subject: [PATCH 070/408] bugfixing try table running time broken by earlier state rearrangement --- parsl/monitoring/db_manager.py | 20 +++++++++++++++++--- parsl/version.py | 2 +- 2 files changed, 18 insertions(+), 4 deletions(-) diff --git a/parsl/monitoring/db_manager.py b/parsl/monitoring/db_manager.py index bd15fab291..3becaa8b77 100644 --- a/parsl/monitoring/db_manager.py +++ b/parsl/monitoring/db_manager.py @@ -360,6 +360,13 @@ def start(self, # processed (corresponding by task id) reprocessable_first_resource_messages = [] + # end-of-task-run status messages - handled in similar way as + # for last resource messages to try to have symmetry... this + # needs a type annotation though reprocessable_first_resource_messages + # doesn't... not sure why. Too lazy right now to figure out what, + # if any, more specific type than Any the messages have. + reprocessable_last_resource_messages: List[Any] = [] + # Get a batch of priority messages priority_messages = self._get_messages_in_batch(self.pending_priority_queue) if priority_messages: @@ -480,7 +487,11 @@ def start(self, if resource_messages: logger.debug( - "Got {} messages from resource queue, {} reprocessable".format(len(resource_messages), len(reprocessable_first_resource_messages))) + "Got {} messages from resource queue, " + "{} reprocessable as first messages, " + "{} reprocessable as last messages".format(len(resource_messages), + len(reprocessable_first_resource_messages), + len(reprocessable_last_resource_messages))) insert_resource_messages = [] for msg in resource_messages: @@ -507,10 +518,10 @@ def start(self, # been added to inserted_tries already... but maybe # that assumption is made for insert_resource_messages # messages too? - reprocessable_first_resource_messages.append(msg) + reprocessable_last_resource_messages.append(msg) else: - # Insert to resource table if not first message + # Insert to resource table if not first/last (start/stop) message message insert_resource_messages.append(msg) if insert_resource_messages: @@ -523,6 +534,9 @@ def start(self, 'run_id', 'task_id', 'try_id', 'block_id', 'hostname'], messages=reprocessable_first_resource_messages) + + if reprocessable_last_resource_messages: + self._insert(table=STATUS, messages=reprocessable_last_resource_messages) except Exception: logger.exception("Exception in db loop: this might have been a malformed message, or some other error. monitoring data may have been lost") exception_happened = True diff --git a/parsl/version.py b/parsl/version.py index 1e2cc969a7..bf3b790a7e 100644 --- a/parsl/version.py +++ b/parsl/version.py @@ -3,4 +3,4 @@ ..[alpha/beta/..] Alphas will be numbered like this -> 0.4.0a0 """ -VERSION = '1.1.0a1+lsst-dm-20210324a' +VERSION = '1.1.0a1+lsst-dm-20210325a' From 18041cd49a028e49e5fcb339b9864a2a9d0cb3cf Mon Sep 17 00:00:00 2001 From: Ben Clifford Date: Thu, 25 Mar 2021 11:10:35 +0000 Subject: [PATCH 071/408] CI test environment fiddling --- Makefile | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/Makefile b/Makefile index ecf359c936..0f4efb5392 100644 --- a/Makefile +++ b/Makefile @@ -77,7 +77,7 @@ config_local_test: ## run all tests with workqueue_ex config echo "$(MPI)" parsl/executors/extreme_scale/install-mpi.sh $(MPI) pip3 install ".[extreme_scale]" - PYTHONPATH=. pytest parsl/tests/ -k "not cleannet" --config local --cov=parsl --cov-append --cov-report= --random-order + PYTHONPATH=.:/tmp/cctools/lib/python3.5/site-packages pytest parsl/tests/ -k "not cleannet" --config local --cov=parsl --cov-append --cov-report= --random-order .PHONY: site_test site_test: From 8e5ab7af7b2889999839fce0b30ac40064512aa5 Mon Sep 17 00:00:00 2001 From: Ben Clifford Date: Tue, 6 Apr 2021 10:26:14 +0000 Subject: [PATCH 072/408] ongoing CI fixing work --- .travis.yml | 7 +---- parsl/app/errors.py | 27 ++++++++++--------- parsl/data_provider/globus.py | 2 +- parsl/dataflow/dflow.py | 15 ++++++++--- parsl/dataflow/error.py | 13 +++------ .../executors/high_throughput/interchange.py | 2 +- .../high_throughput/process_worker_pool.py | 3 +-- .../plots/default/workflow_resource_plots.py | 10 ++++--- parsl/tests/test-viz.sh | 24 +++++++++++++++++ parsl/version.py | 2 +- 10 files changed, 64 insertions(+), 41 deletions(-) create mode 100755 parsl/tests/test-viz.sh diff --git a/.travis.yml b/.travis.yml index d65dc3aa1f..75df077156 100644 --- a/.travis.yml +++ b/.travis.yml @@ -68,12 +68,7 @@ script: # run. - sudo apt-get install -y graphviz - pip install .[monitoring] - - parsl-visualize & - # now wait for this to become responsive to connections - - wget http://127.0.0.1:8080/ --retry-connrefused --tries 30 --waitretry=1 - # wget will return a failure code if any of the requested URLs don't return an HTTP 200 result - - wget http://127.0.0.1:8080/ --recursive --no-verbose --page-requisites --level=inf -e robots=off - - killall --wait parsl-visualize + - parsl/tests/test-viz.sh # check that 'all' install target works, even though we aren't doing any further # testing of what is installed diff --git a/parsl/app/errors.py b/parsl/app/errors.py index 2d2c6b3cbc..4375051b80 100644 --- a/parsl/app/errors.py +++ b/parsl/app/errors.py @@ -2,13 +2,9 @@ from functools import wraps from typing import Callable, List, Union, Any, TypeVar from types import TracebackType - -import dill import logging from tblib import Traceback -from six import reraise - from parsl.data_provider.files import File logger = logging.getLogger(__name__) @@ -111,29 +107,36 @@ def __str__(self) -> str: class RemoteExceptionWrapper: def __init__(self, e_type: type, e_value: Exception, traceback: TracebackType) -> None: - self.e_type = dill.dumps(e_type) - self.e_value = dill.dumps(e_value) + self.e_type = e_type + self.e_value = e_value self.e_traceback = Traceback(traceback) + # self.e_type = dill.dumps(e_type) + # self.e_value = dill.dumps(e_value) + # self.e_traceback = Traceback(traceback) + def reraise(self) -> None: - t = dill.loads(self.e_type) + # t = dill.loads(self.e_type) # the type is logged here before deserialising v and tb # because occasionally there are problems deserialising the # value (see #785, #548) and the fix is related to the # specific exception type. - logger.debug("Reraising exception of type {}".format(t)) + logger.debug("Reraising exception of type {}".format(self.e_type)) + + # v = dill.loads(self.e_value) + # tb = self.e_traceback.as_traceback() - v = dill.loads(self.e_value) - tb = self.e_traceback.as_traceback() + raise self.e_value.with_traceback(self.e_traceback.as_traceback()) - reraise(t, v, tb) + # reraise(self.e_type, self.e_value, self.e_traceback) + # reraise(t, v, tb) R = TypeVar('R') -# There appears to be no solutio to typing this without a mypy plugin. +# There appears to be no solution to typing this without a mypy plugin. # The reason is because wrap_error maps a Callable[[X...], R] to a Callable[[X...], Union[R, R2]]. # However, there is no provision in Python typing for pattern matching all possible types of # callable arguments. This is because Callable[] is, in the infinite wisdom of the typing module, diff --git a/parsl/data_provider/globus.py b/parsl/data_provider/globus.py index 40e01b3ef3..dc75725cbd 100644 --- a/parsl/data_provider/globus.py +++ b/parsl/data_provider/globus.py @@ -51,7 +51,7 @@ def get_globus(): class Globus(object): """ All communication with the Globus Auth and Globus Transfer services is enclosed - in the Globus class. In particular, the Globus class is reponsible for: + in the Globus class. In particular, the Globus class is responsible for: - managing an OAuth2 authorizer - getting access and refresh tokens, refreshing an access token, storing to and retrieving tokens from .globus.json file, diff --git a/parsl/dataflow/dflow.py b/parsl/dataflow/dflow.py index 38e6e48a19..7fa993bdd1 100644 --- a/parsl/dataflow/dflow.py +++ b/parsl/dataflow/dflow.py @@ -368,6 +368,13 @@ def handle_join_update(self, task_record, inner_app_future): outer_task_id = task_record['id'] try: + # TODO: stack traces could be tidier by this call not re-raising the exception, + # so that it keeps only the remote part of the exception. + # Then the exception handling block directly below would need to be entered + # in two ways: either an exception is thrown (because something broke) + # or there is a remoteexceptionwrapper, in which case use the contained + # exception can be used directly as e without a further raise/except + # which i think might then keep stack traces cleaner? res = self._unwrap_remote_exception_wrapper(inner_app_future) except Exception as e: @@ -478,11 +485,11 @@ def launch_if_ready(self, task_record): if self._count_deps(task_record['depends']) == 0: # We can now launch *task* - new_args, kwargs, exceptions = self.sanitize_and_wrap(task_record['args'], - task_record['kwargs']) + new_args, kwargs, exceptions_tids = self.sanitize_and_wrap(task_record['args'], + task_record['kwargs']) task_record['args'] = new_args task_record['kwargs'] = kwargs - if not exceptions: + if not exceptions_tids: # There are no dependency errors exec_fu = None # Acquire a lock, retest the state, launch @@ -513,7 +520,7 @@ def launch_if_ready(self, task_record): self._send_task_log_info(task_record) exec_fu = Future() - exec_fu.set_exception(DependencyError(exceptions, + exec_fu.set_exception(DependencyError(exceptions_tids, task_id)) if exec_fu: diff --git a/parsl/dataflow/error.py b/parsl/dataflow/error.py index 8a34000a47..14a1d12532 100644 --- a/parsl/dataflow/error.py +++ b/parsl/dataflow/error.py @@ -42,21 +42,14 @@ class DependencyError(DataFlowException): in a dependency. Args: - - dependent_exceptions: List of exceptions - - task_id: Identity of the task failed task - - Contains: - reason (string) - dependent_exceptions + - dependent_exceptions_tids: List of dependency task IDs which failed + - task_id: Task ID of the task that failed because of the dependency error """ def __init__(self, dependent_exceptions_tids, task_id): self.dependent_exceptions_tids = dependent_exceptions_tids self.task_id = task_id - def __repr__(self): + def __str__(self): dep_tids = [tid for (exception, tid) in self.dependent_exceptions_tids] return "Dependency failure for task {} with failed dependencies from tasks {}".format(self.task_id, dep_tids) - - def __str__(self): - return self.__repr__() diff --git a/parsl/executors/high_throughput/interchange.py b/parsl/executors/high_throughput/interchange.py index 7c00db0496..b4515722e8 100644 --- a/parsl/executors/high_throughput/interchange.py +++ b/parsl/executors/high_throughput/interchange.py @@ -470,7 +470,7 @@ def start(self): try: msg = json.loads(message[1].decode('utf-8')) - msg['reg_time'] = datetime.datetime.strptime(msg['reg_time'], "%Y-%m-%d %H:%M:%S") + # msg['reg_time'] = datetime.datetime.strptime(msg['reg_time'], "%Y-%m-%d %H:%M:%S") reg_flag = True except Exception: logger.warning("[MAIN] Got Exception reading registration message from manager: {}".format( diff --git a/parsl/executors/high_throughput/process_worker_pool.py b/parsl/executors/high_throughput/process_worker_pool.py index 4430725c46..ec36635188 100755 --- a/parsl/executors/high_throughput/process_worker_pool.py +++ b/parsl/executors/high_throughput/process_worker_pool.py @@ -8,7 +8,6 @@ import threading import pickle import time -import datetime import queue import uuid import zmq @@ -211,7 +210,7 @@ def create_reg_message(self): 'dir': os.getcwd(), 'cpu_count': psutil.cpu_count(logical=False), 'total_memory': psutil.virtual_memory().total, - 'reg_time': datetime.datetime.now().strftime("%Y-%m-%d %H:%M:%S"), + # 'reg_time': datetime.datetime.now().strftime("%Y-%m-%d %H:%M:%S"), } b_msg = json.dumps(msg).encode('utf-8') return b_msg diff --git a/parsl/monitoring/visualization/plots/default/workflow_resource_plots.py b/parsl/monitoring/visualization/plots/default/workflow_resource_plots.py index a0015ce031..bcf6dc64bd 100644 --- a/parsl/monitoring/visualization/plots/default/workflow_resource_plots.py +++ b/parsl/monitoring/visualization/plots/default/workflow_resource_plots.py @@ -97,7 +97,7 @@ def resource_time_series(tasks, type='psutil_process_time_user', label='CPU user def worker_efficiency(task, node): try: node['epoch_time'] = (pd.to_datetime( - node['reg_time']) - pd.Timestamp("1970-01-01")) // pd.Timedelta('1s') + node['timestamp']) - pd.Timestamp("1970-01-01")) // pd.Timedelta('1s') task['epoch_time_start'] = (pd.to_datetime( task['task_try_time_launched']) - pd.Timestamp("1970-01-01")) // pd.Timedelta('1s') task['epoch_time_running'] = (pd.to_datetime( @@ -131,9 +131,11 @@ def worker_efficiency(task, node): yaxis=dict(title='Number of workers'), title="Worker efficiency")) return plot(fig, show_link=False, output_type="div", include_plotlyjs=False) - except Exception: + except Exception as e: + print("BENC BENC BENC BENC BENC BENC BENC BENC") + print("Exception:") + print(repr(e)) raise - # print(e) # return "The worker efficiency plot cannot be generated due to missing data." @@ -142,7 +144,7 @@ def resource_efficiency(resource, node, label='CPU'): resource['epoch_time'] = (pd.to_datetime( resource['timestamp']) - pd.Timestamp("1970-01-01")) // pd.Timedelta('1s') node['epoch_time'] = (pd.to_datetime( - node['reg_time']) - pd.Timestamp("1970-01-01")) // pd.Timedelta('1s') + node['timestamp']) - pd.Timestamp("1970-01-01")) // pd.Timedelta('1s') resource = resource.sort_values(by='epoch_time') start = min(resource['epoch_time'].min(), node['epoch_time'].min()) end = resource['epoch_time'].max() diff --git a/parsl/tests/test-viz.sh b/parsl/tests/test-viz.sh new file mode 100755 index 0000000000..de6766a6f9 --- /dev/null +++ b/parsl/tests/test-viz.sh @@ -0,0 +1,24 @@ +#!/bin/bash -ex + +# pass any argument to make this script generate a fresh monitoring database +# using pytest; otherwise, by default, it will test against an existing +# monitoring.db + +killall --wait parsl-visualize || echo No previous parsl-visualize to kill + +if [ -n "$1" ]; then + rm -f monitoring.db + pytest parsl/tests/ -k "not cleannet" --config parsl/tests/configs/htex_local_alternate.py --cov=parsl --cov-append --cov-report= --random-order +fi + +parsl-visualize & + +mkdir -p test-parsl-visualize.tmp +cd test-parsl-visualize.tmp + +# now wait for this to become responsive to connections +wget http://127.0.0.1:8080/ --retry-connrefused --tries 30 --waitretry=1 +# wget will return a failure code if any of the requested URLs don't return an HTTP 200 result +wget http://127.0.0.1:8080/ --recursive --no-verbose --page-requisites --level=inf -e robots=off +killall --wait parsl-visualize + diff --git a/parsl/version.py b/parsl/version.py index bf3b790a7e..41218ad945 100644 --- a/parsl/version.py +++ b/parsl/version.py @@ -3,4 +3,4 @@ ..[alpha/beta/..] Alphas will be numbered like this -> 0.4.0a0 """ -VERSION = '1.1.0a1+lsst-dm-20210325a' +VERSION = '1.1.0a1+lsst-dm-202103-2021.04.03a' From 7f7bb0828772b5e1145a758ea0065579443bf4e7 Mon Sep 17 00:00:00 2001 From: Ben Clifford Date: Tue, 6 Apr 2021 10:27:01 +0000 Subject: [PATCH 073/408] bump version --- parsl/version.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/parsl/version.py b/parsl/version.py index 41218ad945..02960f2fd0 100644 --- a/parsl/version.py +++ b/parsl/version.py @@ -3,4 +3,4 @@ ..[alpha/beta/..] Alphas will be numbered like this -> 0.4.0a0 """ -VERSION = '1.1.0a1+lsst-dm-202103-2021.04.03a' +VERSION = '1.1.0a1+lsst-dm-202103-2021.04.06a' From 3d5c318fb4fbb3651db2de55ed5a6072d2149345 Mon Sep 17 00:00:00 2001 From: Ben Clifford Date: Tue, 6 Apr 2021 14:36:38 +0000 Subject: [PATCH 074/408] more attempts at fixing viz in CI --- .../visualization/plots/default/workflow_plots.py | 9 +++++---- parsl/monitoring/visualization/views.py | 2 +- parsl/version.py | 2 +- 3 files changed, 7 insertions(+), 6 deletions(-) diff --git a/parsl/monitoring/visualization/plots/default/workflow_plots.py b/parsl/monitoring/visualization/plots/default/workflow_plots.py index 0e56457057..d24ba6fefe 100644 --- a/parsl/monitoring/visualization/plots/default/workflow_plots.py +++ b/parsl/monitoring/visualization/plots/default/workflow_plots.py @@ -54,6 +54,7 @@ def task_gantt_plot(df_task, df_status, time_completed=None): 'pending': 'rgb(168, 168, 168)', 'launched': 'rgb(100, 255, 255)', 'running': 'rgb(0, 0, 255)', + 'running_ended': 'rgb(64, 64, 255)', 'joining': 'rgb(128, 128, 255)', 'dep_fail': 'rgb(255, 128, 255)', 'failed': 'rgb(200, 0, 0)', @@ -81,10 +82,10 @@ def task_per_app_plot(task, status, time_completed): task['epoch_time_running'] = (pd.to_datetime( task['task_try_time_running']) - pd.Timestamp("1970-01-01")) // pd.Timedelta('1s') task['epoch_time_returned'] = (pd.to_datetime( - task['task_try_time_returned']) - pd.Timestamp("1970-01-01")) // pd.Timedelta('1s') + task['task_time_returned']) - pd.Timestamp("1970-01-01")) // pd.Timedelta('1s') start = int(task['epoch_time_running'].min()) - end = int(task['epoch_try_time_returned'].max()) + end = int(task['epoch_time_returned'].max()) # should we take the max of this and time_completed here? # because they might not align just right, and cause array overflows # later in this plot? probably yes. - need to get a notion of @@ -100,12 +101,12 @@ def task_per_app_plot(task, status, time_completed): if math.isnan(row['epoch_time_running']): # Skip rows with no running start time. continue - if math.isnan(row['epoch_try_time_returned']): + if math.isnan(row['epoch_time_returned']): # Some kind of inference about time returned (workflow end time / current time? see gantt chart for inferences) time_returned = end else: - time_returned = int(row['epoch_try_time_returned']) + time_returned = int(row['epoch_time_returned']) if row['task_func_name'] not in tasks_per_app: tasks_per_app[row['task_func_name']] = [0] * (end - start + 1) diff --git a/parsl/monitoring/visualization/views.py b/parsl/monitoring/visualization/views.py index cc5eb59884..668926b57e 100644 --- a/parsl/monitoring/visualization/views.py +++ b/parsl/monitoring/visualization/views.py @@ -61,7 +61,7 @@ def workflow(workflow_id): task_time_returned from task WHERE run_id='%s'""" % (workflow_id), db.engine) - df_task_tries = pd.read_sql_query("""SELECT task.task_id, task_func_name, + df_task_tries = pd.read_sql_query("""SELECT task.task_id, task_func_name, task_time_returned, task_try_time_running, task_try_time_returned from task, try WHERE task.task_id = try.task_id AND task.run_id='%s' and try.run_id='%s'""" % (workflow_id, workflow_id), db.engine) diff --git a/parsl/version.py b/parsl/version.py index 02960f2fd0..271ee9ea5d 100644 --- a/parsl/version.py +++ b/parsl/version.py @@ -3,4 +3,4 @@ ..[alpha/beta/..] Alphas will be numbered like this -> 0.4.0a0 """ -VERSION = '1.1.0a1+lsst-dm-202103-2021.04.06a' +VERSION = '1.1.0a1+lsst-dm-202103-2021.04.06b' From 001cc3f1fa38a5ee734e3de92ac6773c21efa9ab Mon Sep 17 00:00:00 2001 From: Ben Clifford Date: Tue, 6 Apr 2021 16:10:49 +0000 Subject: [PATCH 075/408] push CI changes for WQ --- .travis.yml | 4 ++++ Makefile | 8 +++++++- parsl/version.py | 2 +- 3 files changed, 12 insertions(+), 2 deletions(-) diff --git a/.travis.yml b/.travis.yml index 75df077156..c6856c2947 100644 --- a/.travis.yml +++ b/.travis.yml @@ -70,6 +70,10 @@ script: - pip install .[monitoring] - parsl/tests/test-viz.sh + # once viz has been tested with previous per-config, can run the monitoring-db-destroying + # local tests + - make config_local_test + # check that 'all' install target works, even though we aren't doing any further # testing of what is installed - pip install .[all] diff --git a/Makefile b/Makefile index 0f4efb5392..53df43a6c2 100644 --- a/Makefile +++ b/Makefile @@ -72,6 +72,12 @@ $(WORKQUEUE_INSTALL): workqueue_ex_test: $(WORKQUEUE_INSTALL) ## run all tests with workqueue_ex config PYTHONPATH=.:/tmp/cctools/lib/python3.5/site-packages pytest parsl/tests/ -k "not cleannet and not issue363" --config parsl/tests/configs/workqueue_ex.py --cov=parsl --cov-append --cov-report= --random-order +.PHONY: workqueue_mon_test +workqueue_mon_test: $(WORKQUEUE_INSTALL) ## run all tests with workqueue_ex config + pip3 install ".[monitoring]" + PYTHONPATH=.:/tmp/cctools/lib/python3.5/site-packages pytest parsl/tests/ -k "not cleannet and not issue363" --config parsl/tests/configs/workqueue_monitoring_config.py --cov=parsl --cov-append --cov-report= --random-order + + .PHONY: config_local_test config_local_test: ## run all tests with workqueue_ex config echo "$(MPI)" @@ -85,7 +91,7 @@ site_test: pytest parsl/tests/site_tests/ ${SHARED_FS_OPTIONS} --config local .PHONY: test ## run all tests with all config types -test: clean_coverage lint flake8 mypy local_thread_test htex_local_test htex_local_alternate_test workqueue_ex_test config_local_test ## run all tests +test: clean_coverage lint flake8 mypy local_thread_test htex_local_test htex_local_alternate_test workqueue_ex_test workqueue_mon_test ## run most tests .PHONY: tag tag: ## create a tag in git. to run, do a 'make VERSION="version string" tag diff --git a/parsl/version.py b/parsl/version.py index 271ee9ea5d..bf5e2686a5 100644 --- a/parsl/version.py +++ b/parsl/version.py @@ -3,4 +3,4 @@ ..[alpha/beta/..] Alphas will be numbered like this -> 0.4.0a0 """ -VERSION = '1.1.0a1+lsst-dm-202103-2021.04.06b' +VERSION = '1.1.0a1+lsst-dm-202103-2021.04.06c' From 643d23e3d69ff95e1d6fbec2f2c16fbed668a7ff Mon Sep 17 00:00:00 2001 From: Ben Clifford Date: Tue, 6 Apr 2021 18:05:01 +0000 Subject: [PATCH 076/408] more viz fixes --- parsl/monitoring/visualization/models.py | 2 ++ parsl/monitoring/visualization/views.py | 3 +-- parsl/version.py | 2 +- 3 files changed, 4 insertions(+), 3 deletions(-) diff --git a/parsl/monitoring/visualization/models.py b/parsl/monitoring/visualization/models.py index 89ad0954d3..1d2247f741 100644 --- a/parsl/monitoring/visualization/models.py +++ b/parsl/monitoring/visualization/models.py @@ -58,6 +58,8 @@ class Task(db.Model): run_id = db.Column('run_id', db.Text, nullable=False) task_func_name = db.Column('task_func_name', db.Text, nullable=False) task_depends = db.Column('task_depends', db.Text, nullable=True) + task_time_invoked = db.Column( + 'task_time_invoked', db.DateTime, nullable=True) task_time_returned = db.Column( 'task_time_returned', db.DateTime, nullable=True) task_memoize = db.Column('task_memoize', db.Text, nullable=False) diff --git a/parsl/monitoring/visualization/views.py b/parsl/monitoring/visualization/views.py index 668926b57e..a8560d24c6 100644 --- a/parsl/monitoring/visualization/views.py +++ b/parsl/monitoring/visualization/views.py @@ -21,8 +21,7 @@ def format_time(value): rounded_timedelta = datetime.timedelta(days=value.days, seconds=value.seconds) return rounded_timedelta else: - print("Incorrect time format (neither float nor datetime object): {}, type: {}".format(value, type(value))) # TODO: use logging - # raise ValueError("Incorrect time format: {}, type {}".format(value, type(value))) + print("Warning: Incorrect time format (neither float nor datetime object): {}, type: {}".format(value, type(value))) # TODO: use logging return "-" diff --git a/parsl/version.py b/parsl/version.py index bf5e2686a5..3a25249088 100644 --- a/parsl/version.py +++ b/parsl/version.py @@ -3,4 +3,4 @@ ..[alpha/beta/..] Alphas will be numbered like this -> 0.4.0a0 """ -VERSION = '1.1.0a1+lsst-dm-202103-2021.04.06c' +VERSION = '1.1.0a1+lsst-dm-202103-2021.04.06d' From 4ff64907dbd1d3694a72a9e962fbd548a953d344 Mon Sep 17 00:00:00 2001 From: Ben Clifford Date: Wed, 7 Apr 2021 12:41:11 +0000 Subject: [PATCH 077/408] docstring work --- docs/reference.rst | 2 + .../parsl.dataflow.states.FINAL_STATES.rst | 6 ++ docs/stubs/parsl.dataflow.states.States.rst | 32 ++++++++++ parsl/dataflow/states.py | 62 +++++++++++++++---- parsl/providers/error.py | 2 +- parsl/providers/local/local.py | 5 -- parsl/version.py | 2 +- 7 files changed, 93 insertions(+), 18 deletions(-) create mode 100644 docs/stubs/parsl.dataflow.states.FINAL_STATES.rst create mode 100644 docs/stubs/parsl.dataflow.states.States.rst diff --git a/docs/reference.rst b/docs/reference.rst index 067290abe8..11e888f81d 100644 --- a/docs/reference.rst +++ b/docs/reference.rst @@ -176,5 +176,7 @@ Internal parsl.dataflow.dflow.DataFlowKernel parsl.dataflow.flow_control.FlowControl parsl.dataflow.memoization.Memoizer + parsl.dataflow.states.FINAL_STATES + parsl.dataflow.states.States parsl.dataflow.strategy.Strategy parsl.dataflow.flow_control.Timer diff --git a/docs/stubs/parsl.dataflow.states.FINAL_STATES.rst b/docs/stubs/parsl.dataflow.states.FINAL_STATES.rst new file mode 100644 index 0000000000..2decc41707 --- /dev/null +++ b/docs/stubs/parsl.dataflow.states.FINAL_STATES.rst @@ -0,0 +1,6 @@ +parsl.dataflow.states.FINAL\_STATES +=================================== + +.. currentmodule:: parsl.dataflow.states + +.. autodata:: FINAL_STATES \ No newline at end of file diff --git a/docs/stubs/parsl.dataflow.states.States.rst b/docs/stubs/parsl.dataflow.states.States.rst new file mode 100644 index 0000000000..0ce617121f --- /dev/null +++ b/docs/stubs/parsl.dataflow.states.States.rst @@ -0,0 +1,32 @@ +parsl.dataflow.states.States +============================ + +.. currentmodule:: parsl.dataflow.states + +.. autoclass:: States + + + .. automethod:: __init__ + + + + + + + .. rubric:: Attributes + + .. autosummary:: + + ~States.dep_fail + ~States.exec_done + ~States.fail_retryable + ~States.failed + ~States.joining + ~States.launched + ~States.memo_done + ~States.pending + ~States.running + ~States.running_ended + ~States.unsched + + \ No newline at end of file diff --git a/parsl/dataflow/states.py b/parsl/dataflow/states.py index 0fe054afd6..36dc9817ab 100644 --- a/parsl/dataflow/states.py +++ b/parsl/dataflow/states.py @@ -2,33 +2,73 @@ class States(IntEnum): - """Map states for tasks to an int.""" + """Enumerates the states a parsl task may be in. + + These states occur inside the task record for a task inside + a `DataFlowKernel` and in the monitoring database. + + In a single successful task execution, tasks will progress in this + sequence: + + pending -> launched -> running -> running_ended -> exec_done + + Other states represent deviations from this path, either due to + failures, or to deliberate changes to how tasks are executed (for + example due to join_app, or memoization). + + + All tasks should end up in one of the states listed in `FINAL_STATES`. + """ + unsched = -1 + pending = 0 + """Task is known to parsl but cannot run yet. Usually, a task cannot + run because it is waiting for dependency tasks to complete. + """ running = 2 - # this state is special - a DFK task record never goes to States.running - # state; but the monitoring database may represent a task in this state - # based on non-DFK information received from monitor_wrapper. + """Task is running on a resource. This state is special - a DFK task + record never goes to States.running state; but the monitoring database + may represent a task in this state based on non-DFK information received + from monitor_wrapper.""" exec_done = 3 + """Task has been executed successfully.""" + failed = 4 + """Task has failed and no more attempts will be made to run it.""" + dep_fail = 5 + """Dependencies of this task failed, so it is marked as failed without + even an attempt to launch it.""" + launched = 7 + """Task has been passed to a `ParslExecutor` for execution.""" + fail_retryable = 8 + """Task has failed, but can be retried""" + memo_done = 9 + """Task was found in the memoization table, so it is marked as done + without even an attempt to launch it.""" + joining = 10 + """Task is a join_app, joining on internal tasks. The task has run its + own Python code, and is now waiting on other tasks before it can make + further progress (to a done/failed state).""" - # like States.running, this state is also not observed by the DFK, - # but instead only by monitoring. This state does not record - # anything about task success or failure, merely that the wrapper - # ran long enough to record it as finished. running_ended = 11 + """Like States.running, this state is also not observed by the DFK, + but instead only by monitoring. This state does not record + anything about task success or failure, merely that the wrapper + ran long enough to record it as finished.""" -# states from which we will never move to another state FINAL_STATES = [States.exec_done, States.memo_done, States.failed, States.dep_fail] +"""States from which we will never move to another state, because the job has +either definitively completed or failed.""" -# states which are final and which indicate a failure. This must -# be a subset of FINAL_STATES FINAL_FAILURE_STATES = [States.failed, States.dep_fail] +"""States which are final and which indicate a failure. This must +be a subset of FINAL_STATES""" diff --git a/parsl/providers/error.py b/parsl/providers/error.py index 5f099c919a..206e2a10d3 100644 --- a/parsl/providers/error.py +++ b/parsl/providers/error.py @@ -21,7 +21,7 @@ def __repr__(self): class ScaleOutFailed(ExecutionProviderException): - ''' Generic catch. Scale out failed in the submit phase on the provider side + ''' Scale out failed in the submit phase on the provider side ''' def __init__(self, provider, reason): diff --git a/parsl/providers/local/local.py b/parsl/providers/local/local.py index 0f03d81ec4..225b19d3ba 100644 --- a/parsl/providers/local/local.py +++ b/parsl/providers/local/local.py @@ -282,8 +282,3 @@ def label(self): @property def status_polling_interval(self): return 5 - - -if __name__ == "__main__": - - print("Nothing here") diff --git a/parsl/version.py b/parsl/version.py index 3a25249088..095b8edf1d 100644 --- a/parsl/version.py +++ b/parsl/version.py @@ -3,4 +3,4 @@ ..[alpha/beta/..] Alphas will be numbered like this -> 0.4.0a0 """ -VERSION = '1.1.0a1+lsst-dm-202103-2021.04.06d' +VERSION = '1.1.0a1+lsst-dm-202103-2021.04.07a' From b501cc84ed068c36180ea0459bebd293030e27b2 Mon Sep 17 00:00:00 2001 From: Ben Clifford Date: Tue, 20 Apr 2021 15:16:52 +0000 Subject: [PATCH 078/408] add in WQ worker name override for jamesp --- parsl/executors/workqueue/executor.py | 8 ++++++-- parsl/version.py | 2 +- 2 files changed, 7 insertions(+), 3 deletions(-) diff --git a/parsl/executors/workqueue/executor.py b/parsl/executors/workqueue/executor.py index 27e814cc57..6b0851a2d4 100644 --- a/parsl/executors/workqueue/executor.py +++ b/parsl/executors/workqueue/executor.py @@ -206,7 +206,10 @@ def __init__(self, autocategory: bool = True, init_command: str = "", worker_options: str = "", - full_debug: bool = True): + full_debug: bool = True, + # ugh c.f. naming with worker_cmd which is better, but already + # used for something slightly different + worker_executable: str = 'work_queue_worker'): BlockProviderExecutor.__init__(self, provider) # ? should this be true even when not using a provider? @@ -242,6 +245,7 @@ def __init__(self, self.should_stop = multiprocessing.Value(c_bool, False) self.cached_envs = {} # type: Dict[int, str] self.worker_options = worker_options + self.worker_executable = worker_executable if not self.address: self.address = socket.gethostname() @@ -446,7 +450,7 @@ def submit(self, func, resource_specification, *args, **kwargs): return fu def _construct_worker_command(self): - worker_command = 'work_queue_worker' + worker_command = self.worker_executable if self.project_password_file: worker_command += ' --password {}'.format(self.project_password_file) if self.worker_options: diff --git a/parsl/version.py b/parsl/version.py index 425dc3779d..40761c9d03 100644 --- a/parsl/version.py +++ b/parsl/version.py @@ -3,4 +3,4 @@ ..[alpha/beta/..] Alphas will be numbered like this -> 0.4.0a0 """ -VERSION = '1.1.0a1+desc-2021.04.20' +VERSION = '1.1.0a1+desc-2021.04.20b' From f333d6d1f44eb668a01905c1f6974c9c1714c1c6 Mon Sep 17 00:00:00 2001 From: Ben Clifford Date: Sat, 3 Apr 2021 07:17:00 +0000 Subject: [PATCH 079/408] fix a typo --- parsl/app/errors.py | 2 +- parsl/data_provider/globus.py | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/parsl/app/errors.py b/parsl/app/errors.py index 2d2c6b3cbc..f649177ffd 100644 --- a/parsl/app/errors.py +++ b/parsl/app/errors.py @@ -133,7 +133,7 @@ def reraise(self) -> None: R = TypeVar('R') -# There appears to be no solutio to typing this without a mypy plugin. +# There appears to be no solution to typing this without a mypy plugin. # The reason is because wrap_error maps a Callable[[X...], R] to a Callable[[X...], Union[R, R2]]. # However, there is no provision in Python typing for pattern matching all possible types of # callable arguments. This is because Callable[] is, in the infinite wisdom of the typing module, diff --git a/parsl/data_provider/globus.py b/parsl/data_provider/globus.py index 40e01b3ef3..dc75725cbd 100644 --- a/parsl/data_provider/globus.py +++ b/parsl/data_provider/globus.py @@ -51,7 +51,7 @@ def get_globus(): class Globus(object): """ All communication with the Globus Auth and Globus Transfer services is enclosed - in the Globus class. In particular, the Globus class is reponsible for: + in the Globus class. In particular, the Globus class is responsible for: - managing an OAuth2 authorizer - getting access and refresh tokens, refreshing an access token, storing to and retrieving tokens from .globus.json file, From 6e3f0e3aa0687640965078b1355cb72604d77551 Mon Sep 17 00:00:00 2001 From: Ben Clifford Date: Wed, 17 Feb 2021 13:05:49 +0000 Subject: [PATCH 080/408] Rework __repr__ and __str__ for OptionalModuleMissing __repr__ should be quasi-machine-readable, and __str__ human readable See PR #1966, commit a423955f4a9e03cf6986a6e21d285cf46fa3bc88, for further context. Before: >>> str(e) "(['mymod'], 'this test needs demonstrating')" >>> repr(e) "The functionality requested requires a missing optional module:['mymod'], Reason:this test needs demonstrating" After: >>> str(e) "The functionality requested requires missing optional modules ['mymod'], because: this test needs demonstrating" >>> repr(e) "OptionalModuleMissing(['mymod'], 'this test needs demonstrating')" --- parsl/errors.py | 8 +++++--- 1 file changed, 5 insertions(+), 3 deletions(-) diff --git a/parsl/errors.py b/parsl/errors.py index 0a1813448d..eb81cf5157 100644 --- a/parsl/errors.py +++ b/parsl/errors.py @@ -1,15 +1,17 @@ from parsl.app.errors import ParslError +from typing import List + class OptionalModuleMissing(ParslError): ''' Error raised when a required module is missing for a optional/extra component ''' - def __init__(self, module_names, reason): + def __init__(self, module_names: List[str], reason: str): self.module_names = module_names self.reason = reason - def __repr__(self): - return "The functionality requested requires a missing optional module:{0}, Reason:{1}".format( + def __str__(self) -> str: + return "The functionality requested requires missing optional modules {0}, because: {1}".format( self.module_names, self.reason ) From b683086d06f6fff7ddfe9a4a60d5ed1b6ea9a9d1 Mon Sep 17 00:00:00 2001 From: Ben Clifford Date: Thu, 11 Mar 2021 20:59:13 +0000 Subject: [PATCH 081/408] remove unused(?) weakref_cb --- docs/stubs/parsl.executors.ExtremeScaleExecutor.rst | 1 - docs/stubs/parsl.executors.HighThroughputExecutor.rst | 1 - parsl/executors/high_throughput/executor.py | 6 ------ 3 files changed, 8 deletions(-) diff --git a/docs/stubs/parsl.executors.ExtremeScaleExecutor.rst b/docs/stubs/parsl.executors.ExtremeScaleExecutor.rst index 2512e5923e..55b09b1c14 100644 --- a/docs/stubs/parsl.executors.ExtremeScaleExecutor.rst +++ b/docs/stubs/parsl.executors.ExtremeScaleExecutor.rst @@ -26,7 +26,6 @@ parsl.executors.ExtremeScaleExecutor ~ExtremeScaleExecutor.start ~ExtremeScaleExecutor.status ~ExtremeScaleExecutor.submit - ~ExtremeScaleExecutor.weakref_cb diff --git a/docs/stubs/parsl.executors.HighThroughputExecutor.rst b/docs/stubs/parsl.executors.HighThroughputExecutor.rst index f861b7fdf0..761ce65828 100644 --- a/docs/stubs/parsl.executors.HighThroughputExecutor.rst +++ b/docs/stubs/parsl.executors.HighThroughputExecutor.rst @@ -26,7 +26,6 @@ parsl.executors.HighThroughputExecutor ~HighThroughputExecutor.start ~HighThroughputExecutor.status ~HighThroughputExecutor.submit - ~HighThroughputExecutor.weakref_cb diff --git a/parsl/executors/high_throughput/executor.py b/parsl/executors/high_throughput/executor.py index fc3265ec19..0fdfc489eb 100644 --- a/parsl/executors/high_throughput/executor.py +++ b/parsl/executors/high_throughput/executor.py @@ -426,12 +426,6 @@ def _queue_management_worker(self): break logger.info("[MTHREAD] queue management worker finished") - # When the executor gets lost, the weakref callback will wake up - # the queue management thread. - def weakref_cb(self, q=None): - """We do not use this yet.""" - q.put(None) - def _start_local_queue_process(self): """ Starts the interchange process locally From 49b931bd709be7a8e63ae027138dc07fbc8fc9a2 Mon Sep 17 00:00:00 2001 From: Ben Clifford Date: Wed, 7 Apr 2021 10:12:26 +0000 Subject: [PATCH 082/408] remove irrelevant __main__ stub of local provider --- parsl/providers/local/local.py | 5 ----- 1 file changed, 5 deletions(-) diff --git a/parsl/providers/local/local.py b/parsl/providers/local/local.py index 0f03d81ec4..225b19d3ba 100644 --- a/parsl/providers/local/local.py +++ b/parsl/providers/local/local.py @@ -282,8 +282,3 @@ def label(self): @property def status_polling_interval(self): return 5 - - -if __name__ == "__main__": - - print("Nothing here") From 2c7018fce19a59a3d24b426a67276e43d6a3aa97 Mon Sep 17 00:00:00 2001 From: Ben Clifford Date: Wed, 17 Mar 2021 12:57:07 +0000 Subject: [PATCH 083/408] change a few ValueErrors to RuntimeErrors - lots of the time i used value error as a generic exception type. I should audit this in the rest of the codebase --- parsl/dataflow/dflow.py | 4 ++-- parsl/tests/conftest.py | 6 +++--- 2 files changed, 5 insertions(+), 5 deletions(-) diff --git a/parsl/dataflow/dflow.py b/parsl/dataflow/dflow.py index 9009d281c3..41552afa35 100644 --- a/parsl/dataflow/dflow.py +++ b/parsl/dataflow/dflow.py @@ -280,7 +280,7 @@ def handle_exec_update(self, task_id, future): task_record['try_time_returned'] = datetime.datetime.now() if not future.done(): - raise ValueError("done callback called, despite future not reporting itself as done") + raise RuntimeError("done callback called, despite future not reporting itself as done") try: res = self._unwrap_remote_exception_wrapper(future) @@ -781,7 +781,7 @@ def submit(self, func, app_args, executors='all', cache=False, ignore_for_cache= ignore_for_cache = [] if self.cleanup_called: - raise ValueError("Cannot submit to a DFK that has been cleaned up") + raise RuntimeError("Cannot submit to a DFK that has been cleaned up") task_id = self.task_count self.task_count += 1 diff --git a/parsl/tests/conftest.py b/parsl/tests/conftest.py index f80dadc95e..78c78d78fa 100644 --- a/parsl/tests/conftest.py +++ b/parsl/tests/conftest.py @@ -109,14 +109,14 @@ def load_dfk_session(request, pytestconfig): spec.loader.exec_module(module) if DataFlowKernelLoader._dfk is not None: - raise ValueError("DFK didn't start as None - there was a DFK from somewhere already") + raise RuntimeError("DFK didn't start as None - there was a DFK from somewhere already") dfk = parsl.load(module.config) yield if(parsl.dfk() != dfk): - raise ValueError("DFK changed unexpectedly during test") + raise RuntimeError("DFK changed unexpectedly during test") dfk.cleanup() parsl.clear() else: @@ -156,7 +156,7 @@ def load_dfk_local_module(request, pytestconfig): if(local_config): if(parsl.dfk() != dfk): - raise ValueError("DFK changed unexpectedly during test") + raise RuntimeError("DFK changed unexpectedly during test") dfk.cleanup() parsl.clear() From bdd3da543eab3d3ca9fa61a1b659b49a8e3847c4 Mon Sep 17 00:00:00 2001 From: Ben Clifford Date: Wed, 7 Apr 2021 12:14:39 +0000 Subject: [PATCH 084/408] Fix summary sentence of ScaleOutException Only the first sentence appears in table of contents, and the old first sentence was inappropriate for that. --- parsl/providers/error.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/parsl/providers/error.py b/parsl/providers/error.py index 5f099c919a..206e2a10d3 100644 --- a/parsl/providers/error.py +++ b/parsl/providers/error.py @@ -21,7 +21,7 @@ def __repr__(self): class ScaleOutFailed(ExecutionProviderException): - ''' Generic catch. Scale out failed in the submit phase on the provider side + ''' Scale out failed in the submit phase on the provider side ''' def __init__(self, provider, reason): From b6c54efb3a10a34e067ecba704656eea2cdb99f7 Mon Sep 17 00:00:00 2001 From: Ben Clifford Date: Wed, 8 Jul 2020 10:09:07 +0000 Subject: [PATCH 085/408] prototype queue prioritisation in htex this is not intended to be exact, in the sense that a job with a lower priority might run before a job with a higher priority - but the "bulk" of the work (in the LSST sense) should be prioritised this way. priorities can be anything comparable to each other (and to the default priority, which is integer 0) i'm not going to address the macsafequeue in this prototype --- parsl/executors/high_throughput/executor.py | 18 ++++---- .../executors/high_throughput/interchange.py | 41 +++++++++++++++++-- .../test_error_handling/test_resource_spec.py | 6 +++ 3 files changed, 52 insertions(+), 13 deletions(-) diff --git a/parsl/executors/high_throughput/executor.py b/parsl/executors/high_throughput/executor.py index fc3265ec19..0bc0c7ee6f 100644 --- a/parsl/executors/high_throughput/executor.py +++ b/parsl/executors/high_throughput/executor.py @@ -16,8 +16,7 @@ from parsl.executors.high_throughput import interchange from parsl.executors.errors import ( BadMessage, ScalingFailed, - DeserializationError, SerializationError, - UnsupportedFeatureError + DeserializationError, SerializationError ) from parsl.executors.status_handling import StatusHandlingExecutor @@ -543,12 +542,6 @@ def submit(self, func, resource_specification, *args, **kwargs): Returns: Future """ - if resource_specification: - logger.error("Ignoring the resource specification. " - "Parsl resource specification is not supported in HighThroughput Executor. " - "Please check WorkQueueExecutor if resource specification is needed.") - raise UnsupportedFeatureError('resource specification', 'HighThroughput Executor', 'WorkQueue Executor') - if self.bad_state_is_set: raise self.executor_exception @@ -569,8 +562,15 @@ def submit(self, func, resource_specification, *args, **kwargs): except TypeError: raise SerializationError(func.__name__) + if resource_specification and "priority" in resource_specification: + priority = resource_specification["priority"] + logger.debug("Priority {} found in resource specification".format(priority)) + else: + priority = None + msg = {"task_id": task_id, - "buffer": fn_buf} + "buffer": fn_buf, + "priority": priority} # Post task to the the outgoing queue self.outgoing_q.put(msg) diff --git a/parsl/executors/high_throughput/interchange.py b/parsl/executors/high_throughput/interchange.py index d181d018bf..6d957c2dc9 100644 --- a/parsl/executors/high_throughput/interchange.py +++ b/parsl/executors/high_throughput/interchange.py @@ -1,5 +1,6 @@ #!/usr/bin/env python import argparse +import functools import zmq import os import sys @@ -88,6 +89,38 @@ def __str__(self): return self.__repr__() +@functools.total_ordering +class PriorityQueueEntry: + """ This class is needed because msg will be a dict, and dicts are not + comparable to each other (and if they were, this would be an unnecessary + expense because the queue only cares about priority). It provides + ordering of the priority ignoring the message content, and implements an + ordering that places None behind all other orderings, for use as a default + value""" + def __init__(self, pri, msg): + self.pri = pri + self.msg = msg + + def __eq__(self, other): + if type(self) != type(other): + return NotImplemented + return self.pri == other.pri + + def __lt__(self, other): + # this is deliberately inverted, so that largest priority number comes out of the queue first + if type(self) != type(other): + return NotImplemented + if self.pri is None: # special case so that None is always less than every other value + return False # we are more than populated priorities, and equal to None, the inverse of < + elif self.pri is not None and other.pri is None: + return True + else: # self/other both not None + c = self.pri.__gt__(other.pri) + if c == NotImplemented: + raise RuntimeError("priority values are not comparable: {} vs {}".format(self.pri, other.pri)) + return c + + class Interchange(object): """ Interchange is a task orchestrator for distributed systems. @@ -182,7 +215,7 @@ def __init__(self, self.hub_address = hub_address self.hub_port = hub_port - self.pending_task_queue = queue.Queue(maxsize=10 ** 6) + self.pending_task_queue = queue.PriorityQueue(maxsize=10 ** 6) self.worker_ports = worker_ports self.worker_port_range = worker_port_range @@ -240,11 +273,11 @@ def get_tasks(self, count): tasks = [] for i in range(0, count): try: - x = self.pending_task_queue.get(block=False) + qe = self.pending_task_queue.get(block=False) except queue.Empty: break else: - tasks.append(x) + tasks.append(qe.msg) return tasks @@ -275,7 +308,7 @@ def migrate_tasks_to_internal(self, kill_event): kill_event.set() break else: - self.pending_task_queue.put(msg) + self.pending_task_queue.put(PriorityQueueEntry(msg['priority'], msg)) task_counter += 1 logger.debug("[TASK_PULL_THREAD] Fetched task:{}".format(task_counter)) diff --git a/parsl/tests/test_error_handling/test_resource_spec.py b/parsl/tests/test_error_handling/test_resource_spec.py index 11ffa7c842..ab42a36534 100644 --- a/parsl/tests/test_error_handling/test_resource_spec.py +++ b/parsl/tests/test_error_handling/test_resource_spec.py @@ -1,4 +1,5 @@ import parsl +import pytest from parsl.app.app import python_app # from parsl.tests.configs.local_threads import config from parsl.tests.configs.htex_local import config @@ -12,6 +13,11 @@ def double(x, parsl_resource_specification={}): return x * 2 +@pytest.mark.skip("this test does not accomodate running the test suite" + " on executors which *do* support resource specifications" + " but are not the workqueue executor. In general, it is" + " incorrect to assume that an arbitrary non-workqueue" + " executor will raise the expected exceptionm") def test_resource(n=2): executors = parsl.dfk().executors executor = None From 800b490e23e0705a6bb5536a0f35a6b4ae6e7ebc Mon Sep 17 00:00:00 2001 From: Ben Clifford Date: Thu, 18 Feb 2021 13:20:19 +0000 Subject: [PATCH 086/408] tasks_per_node case in general strategy is a mess: the ExtremeScale case will never fire in the current extremescale implementaiton, because an extreme scale executor is also a high throughput executor, and so the earlier htex case will fire. It is possible that extreme scale scaling was broken because of this case. This patch should not make it either better or worse, because it only eliminates dead code. when an executor is not an htex instance, no cases match, but no error is raised here, and so tasks_per_node is never assigned. Later on (line 206) use of tasks_per_node is an error. this entire case is removed, and executor.workers_per_node is always used. --- parsl/dataflow/strategy.py | 8 ++------ 1 file changed, 2 insertions(+), 6 deletions(-) diff --git a/parsl/dataflow/strategy.py b/parsl/dataflow/strategy.py index c003322dd7..7526a7a591 100644 --- a/parsl/dataflow/strategy.py +++ b/parsl/dataflow/strategy.py @@ -4,7 +4,7 @@ from typing import List from parsl.dataflow.executor_status import ExecutorStatus -from parsl.executors import HighThroughputExecutor, ExtremeScaleExecutor +from parsl.executors import HighThroughputExecutor from parsl.providers.provider_base import JobState logger = logging.getLogger(__name__) @@ -191,11 +191,7 @@ def _general_strategy(self, status_list, tasks, *, strategy_type): # FIXME probably more of this logic should be moved to the provider min_blocks = executor.provider.min_blocks max_blocks = executor.provider.max_blocks - if isinstance(executor, HighThroughputExecutor): - - tasks_per_node = executor.workers_per_node - elif isinstance(executor, ExtremeScaleExecutor): - tasks_per_node = executor.ranks_per_node + tasks_per_node = executor.workers_per_node nodes_per_block = executor.provider.nodes_per_block parallelism = executor.provider.parallelism From d424c3890c58afcfca5e535991f573daa4de494f Mon Sep 17 00:00:00 2001 From: Ben Clifford Date: Fri, 19 Mar 2021 10:12:15 +0000 Subject: [PATCH 087/408] Reflect python 3.9 support in setup.py metadata Python 3.9 has been supported by parsl since #1720 --- setup.py | 1 + 1 file changed, 1 insertion(+) diff --git a/setup.py b/setup.py index a6a3a53d81..39bdcc8c1d 100755 --- a/setup.py +++ b/setup.py @@ -62,6 +62,7 @@ 'Programming Language :: Python :: 3.6', 'Programming Language :: Python :: 3.7', 'Programming Language :: Python :: 3.8', + 'Programming Language :: Python :: 3.9', ], keywords=['Workflows', 'Scientific computing'], entry_points={'console_scripts': From b218ed3f53f8a4379cac3e1dc8587b60ab72129d Mon Sep 17 00:00:00 2001 From: Ben Clifford Date: Mon, 18 Jan 2021 12:52:24 +0000 Subject: [PATCH 088/408] issue #204 was an IPP specific hack ipp isn't used any more so remove the hack and see if the problem appears in other places --- docs/stubs/parsl.dataflow.strategy.Strategy.rst | 1 - parsl/dataflow/strategy.py | 15 --------------- 2 files changed, 16 deletions(-) diff --git a/docs/stubs/parsl.dataflow.strategy.Strategy.rst b/docs/stubs/parsl.dataflow.strategy.Strategy.rst index 10e98f8525..83d89b73c9 100644 --- a/docs/stubs/parsl.dataflow.strategy.Strategy.rst +++ b/docs/stubs/parsl.dataflow.strategy.Strategy.rst @@ -15,7 +15,6 @@ parsl.dataflow.strategy.Strategy ~Strategy.__init__ ~Strategy.add_executors - ~Strategy.unset_logging diff --git a/parsl/dataflow/strategy.py b/parsl/dataflow/strategy.py index c003322dd7..1dbc98c0de 100644 --- a/parsl/dataflow/strategy.py +++ b/parsl/dataflow/strategy.py @@ -137,20 +137,6 @@ def _strategy_noop(self, status: List[ExecutorStatus], tasks): - tasks (task_ids): Not used here. """ - def unset_logging(self): - """ Mute newly added handlers to the root level, right after calling executor.status - """ - if self.logger_flag is True: - return - - root_logger = logging.getLogger() - - for handler in root_logger.handlers: - if handler not in self.prior_loghandlers: - handler.setLevel(logging.ERROR) - - self.logger_flag = True - def _strategy_simple(self, status_list, tasks): self._general_strategy(status_list, tasks, strategy_type='simple') @@ -185,7 +171,6 @@ def _general_strategy(self, status_list, tasks, *, strategy_type): active_tasks = executor.outstanding status = exec_status.status - self.unset_logging() # FIXME we need to handle case where provider does not define these # FIXME probably more of this logic should be moved to the provider From a05bb9a05d729172e666ac0c68c91efef69af137 Mon Sep 17 00:00:00 2001 From: Ben Clifford Date: Thu, 22 Apr 2021 10:00:12 +0000 Subject: [PATCH 089/408] Remove some support properties that are now unused --- parsl/dataflow/strategy.py | 2 -- 1 file changed, 2 deletions(-) diff --git a/parsl/dataflow/strategy.py b/parsl/dataflow/strategy.py index 1dbc98c0de..29e4318cc5 100644 --- a/parsl/dataflow/strategy.py +++ b/parsl/dataflow/strategy.py @@ -121,8 +121,6 @@ def __init__(self, dfk): 'htex_auto_scale': self._strategy_htex_auto_scale} self.strategize = self.strategies[self.config.strategy] - self.logger_flag = False - self.prior_loghandlers = set(logging.getLogger().handlers) logger.debug("Scaling strategy: {0}".format(self.config.strategy)) From 54311528c68780095684ba797c64271d8080a2b6 Mon Sep 17 00:00:00 2001 From: Ben Clifford Date: Fri, 26 Mar 2021 11:25:47 +0000 Subject: [PATCH 090/408] put viz test in a script this means that the same test used in CI can also be used on the commandline, and with bisection, 'git bisect run parsl/tests/test-viz' --- .travis.yml | 7 +------ parsl/tests/test-viz.sh | 24 ++++++++++++++++++++++++ 2 files changed, 25 insertions(+), 6 deletions(-) create mode 100755 parsl/tests/test-viz.sh diff --git a/.travis.yml b/.travis.yml index d65dc3aa1f..75df077156 100644 --- a/.travis.yml +++ b/.travis.yml @@ -68,12 +68,7 @@ script: # run. - sudo apt-get install -y graphviz - pip install .[monitoring] - - parsl-visualize & - # now wait for this to become responsive to connections - - wget http://127.0.0.1:8080/ --retry-connrefused --tries 30 --waitretry=1 - # wget will return a failure code if any of the requested URLs don't return an HTTP 200 result - - wget http://127.0.0.1:8080/ --recursive --no-verbose --page-requisites --level=inf -e robots=off - - killall --wait parsl-visualize + - parsl/tests/test-viz.sh # check that 'all' install target works, even though we aren't doing any further # testing of what is installed diff --git a/parsl/tests/test-viz.sh b/parsl/tests/test-viz.sh new file mode 100755 index 0000000000..de6766a6f9 --- /dev/null +++ b/parsl/tests/test-viz.sh @@ -0,0 +1,24 @@ +#!/bin/bash -ex + +# pass any argument to make this script generate a fresh monitoring database +# using pytest; otherwise, by default, it will test against an existing +# monitoring.db + +killall --wait parsl-visualize || echo No previous parsl-visualize to kill + +if [ -n "$1" ]; then + rm -f monitoring.db + pytest parsl/tests/ -k "not cleannet" --config parsl/tests/configs/htex_local_alternate.py --cov=parsl --cov-append --cov-report= --random-order +fi + +parsl-visualize & + +mkdir -p test-parsl-visualize.tmp +cd test-parsl-visualize.tmp + +# now wait for this to become responsive to connections +wget http://127.0.0.1:8080/ --retry-connrefused --tries 30 --waitretry=1 +# wget will return a failure code if any of the requested URLs don't return an HTTP 200 result +wget http://127.0.0.1:8080/ --recursive --no-verbose --page-requisites --level=inf -e robots=off +killall --wait parsl-visualize + From 4f040391a715dc4b5f6902562f253795dd92ec20 Mon Sep 17 00:00:00 2001 From: Ben Clifford Date: Fri, 26 Mar 2021 13:14:33 +0000 Subject: [PATCH 091/408] PR 1876 removed the reg_time field from the monitoring database but did not remove attempts to use it from the visualization code --- parsl/executors/high_throughput/interchange.py | 2 +- parsl/executors/high_throughput/process_worker_pool.py | 3 +-- .../visualization/plots/default/workflow_resource_plots.py | 4 ++-- 3 files changed, 4 insertions(+), 5 deletions(-) diff --git a/parsl/executors/high_throughput/interchange.py b/parsl/executors/high_throughput/interchange.py index d181d018bf..e0f4c46fa7 100644 --- a/parsl/executors/high_throughput/interchange.py +++ b/parsl/executors/high_throughput/interchange.py @@ -416,7 +416,7 @@ def start(self, poll_period=None): try: msg = json.loads(message[1].decode('utf-8')) - msg['reg_time'] = datetime.datetime.strptime(msg['reg_time'], "%Y-%m-%d %H:%M:%S") + # msg['reg_time'] = datetime.datetime.strptime(msg['reg_time'], "%Y-%m-%d %H:%M:%S") reg_flag = True except Exception: logger.warning("[MAIN] Got Exception reading registration message from manager: {}".format( diff --git a/parsl/executors/high_throughput/process_worker_pool.py b/parsl/executors/high_throughput/process_worker_pool.py index 10e4bff82a..28b6fd3fa6 100755 --- a/parsl/executors/high_throughput/process_worker_pool.py +++ b/parsl/executors/high_throughput/process_worker_pool.py @@ -8,7 +8,6 @@ import threading import pickle import time -import datetime import queue import uuid import zmq @@ -204,7 +203,7 @@ def create_reg_message(self): 'dir': os.getcwd(), 'cpu_count': psutil.cpu_count(logical=False), 'total_memory': psutil.virtual_memory().total, - 'reg_time': datetime.datetime.now().strftime("%Y-%m-%d %H:%M:%S"), + # 'reg_time': datetime.datetime.now().strftime("%Y-%m-%d %H:%M:%S"), } b_msg = json.dumps(msg).encode('utf-8') return b_msg diff --git a/parsl/monitoring/visualization/plots/default/workflow_resource_plots.py b/parsl/monitoring/visualization/plots/default/workflow_resource_plots.py index 08c0255e1a..23cdcf5c72 100644 --- a/parsl/monitoring/visualization/plots/default/workflow_resource_plots.py +++ b/parsl/monitoring/visualization/plots/default/workflow_resource_plots.py @@ -97,7 +97,7 @@ def resource_time_series(tasks, type='psutil_process_time_user', label='CPU user def worker_efficiency(task, node): try: node['epoch_time'] = (pd.to_datetime( - node['reg_time']) - pd.Timestamp("1970-01-01")) // pd.Timedelta('1s') + node['timestamp']) - pd.Timestamp("1970-01-01")) // pd.Timedelta('1s') task['epoch_time_start'] = (pd.to_datetime( task['task_try_time_launched']) - pd.Timestamp("1970-01-01")) // pd.Timedelta('1s') task['epoch_time_running'] = (pd.to_datetime( @@ -141,7 +141,7 @@ def resource_efficiency(resource, node, label='CPU'): resource['epoch_time'] = (pd.to_datetime( resource['timestamp']) - pd.Timestamp("1970-01-01")) // pd.Timedelta('1s') node['epoch_time'] = (pd.to_datetime( - node['reg_time']) - pd.Timestamp("1970-01-01")) // pd.Timedelta('1s') + node['timestamp']) - pd.Timestamp("1970-01-01")) // pd.Timedelta('1s') resource = resource.sort_values(by='epoch_time') start = min(resource['epoch_time'].min(), node['epoch_time'].min()) end = resource['epoch_time'].max() From ab8d508e4889f8bdcd0ee4721681837f37637c56 Mon Sep 17 00:00:00 2001 From: Ben Clifford Date: Tue, 6 Apr 2021 17:26:22 +0000 Subject: [PATCH 092/408] Fix broken (by #????) task time invoked in visualisation this was failing silently (wrt CI) prior to this TODO: look up which broke this (by removing schema model line?) --- parsl/monitoring/visualization/models.py | 2 ++ 1 file changed, 2 insertions(+) diff --git a/parsl/monitoring/visualization/models.py b/parsl/monitoring/visualization/models.py index 89ad0954d3..1d2247f741 100644 --- a/parsl/monitoring/visualization/models.py +++ b/parsl/monitoring/visualization/models.py @@ -58,6 +58,8 @@ class Task(db.Model): run_id = db.Column('run_id', db.Text, nullable=False) task_func_name = db.Column('task_func_name', db.Text, nullable=False) task_depends = db.Column('task_depends', db.Text, nullable=True) + task_time_invoked = db.Column( + 'task_time_invoked', db.DateTime, nullable=True) task_time_returned = db.Column( 'task_time_returned', db.DateTime, nullable=True) task_memoize = db.Column('task_memoize', db.Text, nullable=False) From b87ee72528deb38d8688a3328889f9a77c9fe809 Mon Sep 17 00:00:00 2001 From: Ben Clifford Date: Thu, 21 May 2020 12:49:53 +0000 Subject: [PATCH 093/408] Fix viz errors in when tasks have no end time Previously these code would throw an exception when tasks have no end time, either replacing the relevant chart with an error that the chart could not be displayed, or with some of my debug patches in place, raising a server error. This patch needs to come up with new behaviour to deal with the case when such tasks are not marked as completed - probably assuming they are in progress either till workflow end or the present time (as far as the database is aware) --- .../plots/default/workflow_plots.py | 28 +++++++++++++++++-- parsl/monitoring/visualization/views.py | 2 +- 2 files changed, 26 insertions(+), 4 deletions(-) diff --git a/parsl/monitoring/visualization/plots/default/workflow_plots.py b/parsl/monitoring/visualization/plots/default/workflow_plots.py index 5f17d3b01b..440896152f 100644 --- a/parsl/monitoring/visualization/plots/default/workflow_plots.py +++ b/parsl/monitoring/visualization/plots/default/workflow_plots.py @@ -75,7 +75,7 @@ def task_gantt_plot(df_task, df_status, time_completed=None): return plot(fig, show_link=False, output_type="div", include_plotlyjs=False) -def task_per_app_plot(task, status): +def task_per_app_plot(task, status, time_completed): try: task['epoch_time_running'] = (pd.to_datetime( @@ -83,17 +83,39 @@ def task_per_app_plot(task, status): task['epoch_time_returned'] = (pd.to_datetime( task['task_time_returned']) - pd.Timestamp("1970-01-01")) // pd.Timedelta('1s') start = int(task['epoch_time_running'].min()) + end = int(task['epoch_time_returned'].max()) + # should we take the max of this and time_completed here? + # because they might not align just right, and cause array overflows + # later in this plot? probably yes. - need to get a notion of + # "latest time interesting" which is either max of "now" and all + # task completion times (because clock skew, may complete in future) + # if the workflow is not completed, and the max of workflow and all task + # completion times if the workflow is recorded as completed. Or + # maybe the last known time is the right time to assume there? + tasks_per_app = {} all_tasks = [0] * (end - start + 1) for i, row in task.iterrows(): if math.isnan(row['epoch_time_running']): # Skip rows with no running start time. continue + if math.isnan(row['epoch_time_returned']): + # Some kind of inference about time returned (workflow end time / current time? see gantt chart for inferences) + + time_returned = end + else: + time_returned = int(row['epoch_time_returned']) + if row['task_func_name'] not in tasks_per_app: tasks_per_app[row['task_func_name']] = [0] * (end - start + 1) - for j in range(int(row['epoch_time_running']) + 1, int(row['epoch_time_returned']) + 1): - tasks_per_app[row['task_func_name']][j - start] += 1 + for j in range(int(row['epoch_time_running']) + 1, time_returned + 1): + try: + tasks_per_app[row['task_func_name']][j - start] += 1 + except Exception: + raise RuntimeError("j = {}, start = {}, end={}, end-start+1={}, j will range over {} .. {}".format(j, start, end, end - start + 1, + int(row['epoch_time_running']) + 1, + int(time_returned) + 1)) all_tasks[j - start] += 1 fig = go.Figure( data=[go.Scatter(x=list(range(0, end - start + 1)), diff --git a/parsl/monitoring/visualization/views.py b/parsl/monitoring/visualization/views.py index e669853560..9e50a17161 100644 --- a/parsl/monitoring/visualization/views.py +++ b/parsl/monitoring/visualization/views.py @@ -71,7 +71,7 @@ def workflow(workflow_id): workflow_details=workflow_details, task_summary=task_summary, task_gantt=task_gantt_plot(df_task, df_status, time_completed=workflow_details.time_completed), - task_per_app=task_per_app_plot(df_task_tries, df_status)) + task_per_app=task_per_app_plot(df_task_tries, df_status, time_completed=workflow_details.time_completed)) @app.route('/workflow//app/') From 3e1c30dd84a4dc870ed9be1b675d489f796e8ee0 Mon Sep 17 00:00:00 2001 From: Ben Clifford Date: Wed, 24 Mar 2021 12:03:37 +0000 Subject: [PATCH 094/408] looking at eliminating passing of task IDs and passing task records instead --- parsl/dataflow/dflow.py | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/parsl/dataflow/dflow.py b/parsl/dataflow/dflow.py index 9009d281c3..4113cc7ee7 100644 --- a/parsl/dataflow/dflow.py +++ b/parsl/dataflow/dflow.py @@ -262,7 +262,7 @@ def config(self): """ return self._config - def handle_exec_update(self, task_id, future): + def handle_exec_update(self, task_record, future): """This function is called only as a callback from an execution attempt reaching a final state (either successfully or failing). @@ -270,12 +270,12 @@ def handle_exec_update(self, task_id, future): structure. Args: - task_id (string) : Task id + task_record (dict) : Task record future (Future) : The future object corresponding to the task which makes this callback """ - task_record = self.tasks[task_id] + task_id = task_record['id'] task_record['try_time_returned'] = datetime.datetime.now() @@ -519,7 +519,7 @@ def launch_if_ready(self, task_id): if exec_fu: assert isinstance(exec_fu, Future) try: - exec_fu.add_done_callback(partial(self.handle_exec_update, task_id)) + exec_fu.add_done_callback(partial(self.handle_exec_update, task_record)) except Exception: # this exception is ignored here because it is assumed that exception # comes from directly executing handle_exec_update (because exec_fu is From fc69ae2e05e389bde3bb87a4e2d92697deec1ed9 Mon Sep 17 00:00:00 2001 From: Ben Clifford Date: Wed, 24 Mar 2021 12:10:01 +0000 Subject: [PATCH 095/408] more taskid elim --- parsl/dataflow/dflow.py | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/parsl/dataflow/dflow.py b/parsl/dataflow/dflow.py index 9009d281c3..bc566906af 100644 --- a/parsl/dataflow/dflow.py +++ b/parsl/dataflow/dflow.py @@ -339,7 +339,7 @@ def handle_exec_update(self, task_id, future): assert isinstance(inner_future, Future) task_record['status'] = States.joining task_record['joins'] = inner_future - inner_future.add_done_callback(partial(self.handle_join_update, task_id)) + inner_future.add_done_callback(partial(self.handle_join_update, task_record)) self._log_std_streams(task_record) @@ -351,7 +351,7 @@ def handle_exec_update(self, task_id, future): if task_record['status'] == States.pending: self.launch_if_ready(task_id) - def handle_join_update(self, outer_task_id, inner_app_future): + def handle_join_update(self, task_record, inner_app_future): # Use the result of the inner_app_future as the final result of # the outer app future. @@ -359,7 +359,7 @@ def handle_join_update(self, outer_task_id, inner_app_future): # their own retrying, and joining state is responsible for passing # on whatever the result of that retrying was (if any). - task_record = self.tasks[outer_task_id] + outer_task_id = task_record['id'] try: res = self._unwrap_remote_exception_wrapper(inner_app_future) From 4eb412860e99ddf8b4d2b055ca13accc5b0ba627 Mon Sep 17 00:00:00 2001 From: Ben Clifford Date: Wed, 24 Mar 2021 12:13:54 +0000 Subject: [PATCH 096/408] more taskid elim dev --- parsl/dataflow/dflow.py | 12 +++++++----- 1 file changed, 7 insertions(+), 5 deletions(-) diff --git a/parsl/dataflow/dflow.py b/parsl/dataflow/dflow.py index 9009d281c3..e63618f571 100644 --- a/parsl/dataflow/dflow.py +++ b/parsl/dataflow/dflow.py @@ -384,7 +384,7 @@ def handle_join_update(self, outer_task_id, inner_app_future): self._send_task_log_info(task_record) - def handle_app_update(self, task_id, future): + def handle_app_update(self, task_record, future): """This function is called as a callback when an AppFuture is in its final state. @@ -397,12 +397,14 @@ def handle_app_update(self, task_id, future): """ - if not self.tasks[task_id]['app_fu'].done(): + task_id = task_record['id'] + + if not task_record['app_fu'].done(): logger.error("Internal consistency error: app_fu is not done for task {}".format(task_id)) - if not self.tasks[task_id]['app_fu'] == future: + if not task_record['app_fu'] == future: logger.error("Internal consistency error: callback future is not the app_fu in task structure, for task {}".format(task_id)) - self.memoizer.update_memo(task_id, self.tasks[task_id], future) + self.memoizer.update_memo(task_id, task_record, future) if self.checkpoint_mode == 'task_exit': self.checkpoint(tasks=[task_id]) @@ -877,7 +879,7 @@ def submit(self, func, app_args, executors='all', cache=False, ignore_for_cache= task_def['task_launch_lock'] = threading.Lock() - app_fu.add_done_callback(partial(self.handle_app_update, task_id)) + app_fu.add_done_callback(partial(self.handle_app_update, task_def)) task_def['status'] = States.pending logger.debug("Task {} set to pending state with AppFuture: {}".format(task_id, task_def['app_fu'])) From 2733a6abfd63cb4ea0bc41a1f3f4c3702f1e452c Mon Sep 17 00:00:00 2001 From: Ben Clifford Date: Wed, 24 Mar 2021 12:18:13 +0000 Subject: [PATCH 097/408] this removes an if statement to handle the case when task record has been removed in a race coniditon with garbage collection this if statement was added (by PR) to cope specifically with garbage collection race. the newly introduced way of passing this data structure is not vulnerable to that race condition. --- parsl/dataflow/dflow.py | 17 +++++------------ 1 file changed, 5 insertions(+), 12 deletions(-) diff --git a/parsl/dataflow/dflow.py b/parsl/dataflow/dflow.py index 9009d281c3..e0c54a5186 100644 --- a/parsl/dataflow/dflow.py +++ b/parsl/dataflow/dflow.py @@ -349,7 +349,7 @@ def handle_exec_update(self, task_id, future): # it might be that in the course of the update, we've gone back to being # pending - in which case, we should consider ourself for relaunch if task_record['status'] == States.pending: - self.launch_if_ready(task_id) + self.launch_if_ready(task_record) def handle_join_update(self, outer_task_id, inner_app_future): # Use the result of the inner_app_future as the final result of @@ -451,7 +451,7 @@ def wipe_task(self, task_id): def check_staging_inhibited(kwargs): return kwargs.get('_parsl_staging_inhibit', False) - def launch_if_ready(self, task_id): + def launch_if_ready(self, task_record): """ launch_if_ready will launch the specified task, if it is ready to run (for example, without dependencies, and in pending state). @@ -466,14 +466,7 @@ def launch_if_ready(self, task_id): launch_if_ready is thread safe, so may be called from any thread or callback. """ - # after launching the task, self.tasks[task_id] is no longer - # guaranteed to exist (because it can complete fast as part of the - # submission - eg memoization) - task_record = self.tasks.get(task_id) - if task_record is None: - # assume this task has already been processed to completion - logger.debug("Task {} has no task record. Assuming it has already been processed to completion.".format(task_id)) - return + task_id = task_record['id'] if self._count_deps(task_record['depends']) == 0: # We can now launch *task* @@ -898,14 +891,14 @@ def submit(self, func, app_args, executors='all', cache=False, ignore_for_cache= for d in depends: def callback_adapter(dep_fut): - self.launch_if_ready(task_id) + self.launch_if_ready(task_def) try: d.add_done_callback(callback_adapter) except Exception as e: logger.error("add_done_callback got an exception {} which will be ignored".format(e)) - self.launch_if_ready(task_id) + self.launch_if_ready(task_def) return app_fu From c3e69d522be07f1986918c53c308071cba593b0f Mon Sep 17 00:00:00 2001 From: Ben Clifford Date: Thu, 18 Feb 2021 13:42:49 +0000 Subject: [PATCH 098/408] Remove disabled midway test. The per-site testing mechanism is the way to do per-site testing. --- .../tests/test_flowcontrol/test_doc_config.py | 34 ------------------- 1 file changed, 34 deletions(-) delete mode 100644 parsl/tests/test_flowcontrol/test_doc_config.py diff --git a/parsl/tests/test_flowcontrol/test_doc_config.py b/parsl/tests/test_flowcontrol/test_doc_config.py deleted file mode 100644 index b4590dadb2..0000000000 --- a/parsl/tests/test_flowcontrol/test_doc_config.py +++ /dev/null @@ -1,34 +0,0 @@ -import pytest -import parsl -from parsl.tests.configs.midway import config - - -local_config = config - - -@parsl.python_app -def python_app(): - import os - import time - import platform - time.sleep(20) - return "Hello from {0}:{1}".format(os.getpid(), platform.uname()) - - -@pytest.mark.skip('We shouldnt run tests on midway on CI local env') -@pytest.mark.local -def test_python(N=5): - ''' Testing basic scaling|Python 0 -> 1 block on SSH.Midway ''' - - results = {} - for i in range(0, N): - results[i] = python_app() - - print("Waiting ....") - for i in range(0, N): - print(results[0].result()) - - -if __name__ == '__main__': - - test_python() From 02ae34e661d5250964e2d18c8a85aa4c8fea7b5a Mon Sep 17 00:00:00 2001 From: Ben Clifford Date: Thu, 22 Apr 2021 13:08:07 +0000 Subject: [PATCH 099/408] update docstring --- parsl/dataflow/dflow.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/parsl/dataflow/dflow.py b/parsl/dataflow/dflow.py index e63618f571..220b4c71f1 100644 --- a/parsl/dataflow/dflow.py +++ b/parsl/dataflow/dflow.py @@ -391,7 +391,7 @@ def handle_app_update(self, task_record, future): It will trigger post-app processing such as checkpointing. Args: - task_id (string) : Task id + task_record : Task future (Future) : The relevant app future (which should be consistent with the task structure 'app_fu' entry From f62909b869de0b7c8e2f3c3c0c351c9dca60e9d1 Mon Sep 17 00:00:00 2001 From: Ben Clifford Date: Wed, 9 Dec 2020 12:03:06 +0000 Subject: [PATCH 100/408] Describe monitoring protocols better This PR adds type annotations, asserts and comments to better describe the existing formats used for monitoring. This is intended to make future simplification easier. This PR should not change any behaviour except error handling when a format is violated. --- parsl/monitoring/db_manager.py | 24 ++++++++++++++++++++---- parsl/monitoring/monitoring.py | 29 ++++++++++++++++++----------- 2 files changed, 38 insertions(+), 15 deletions(-) diff --git a/parsl/monitoring/db_manager.py b/parsl/monitoring/db_manager.py index 3701a84284..fabcc26c77 100644 --- a/parsl/monitoring/db_manager.py +++ b/parsl/monitoring/db_manager.py @@ -5,7 +5,7 @@ import time import datetime -from typing import Any, Dict, List, Optional, Set, Tuple, TypeVar +from typing import Any, Dict, List, Optional, Set, Tuple, TypeVar, cast from parsl.log_utils import set_file_logger from parsl.dataflow.states import States @@ -525,17 +525,33 @@ def _migrate_logs_to_internal(self, logs_queue: queue.Queue, queue_tag: str, kil except queue.Empty: continue else: - if queue_tag == 'priority': + if queue_tag == 'priority' and x == 'STOP': if x == 'STOP': self.close() + elif queue_tag == 'priority': # implicitly not 'STOP' + if isinstance(x, tuple): + assert x[0] in [MessageType.WORKFLOW_INFO, MessageType.TASK_INFO], \ + "_migrate_logs_to_internal can only migrate WORKFLOW_,TASK_INFO message from priority queue, got x[0] == {}".format(x[0]) + assert len(x) == 2 + self.pending_priority_queue.put(cast(Any, x)) else: - self.pending_priority_queue.put(x) + logger.warning("dropping message with unknown format: {}".format(x)) elif queue_tag == 'resource': + assert len(x) == 3 self.pending_resource_queue.put(x[-1]) elif queue_tag == 'node': - self.pending_node_queue.put(x[-1]) + logger.info("Received these two from node queue") + logger.info("x = {}".format(x)) + logger.info("addr = {}".format(addr)) + + assert x[0] == MessageType.NODE_INFO, "_migrate_logs_to_internal can only migrate NODE_INFO messages from node queue" + assert len(x) == 2, "expected message tuple to have exactly two elements" + + logger.info("Will put {} to pending node queue".format(x[1])) + self.pending_node_queue.put(x[1]) elif queue_tag == "block": self.pending_block_queue.put(x[-1]) + # TODO: else condition here raise an exception. def _update(self, table: str, columns: List[str], messages: List[Dict[str, Any]]) -> None: try: diff --git a/parsl/monitoring/monitoring.py b/parsl/monitoring/monitoring.py index dcd1f9363d..a8c44e1b50 100644 --- a/parsl/monitoring/monitoring.py +++ b/parsl/monitoring/monitoring.py @@ -221,9 +221,9 @@ def start(self, run_id: str) -> int: comm_q = Queue(maxsize=10) # type: Queue[Union[Tuple[int, int], str]] self.exception_q = Queue(maxsize=10) # type: Queue[Tuple[str, str]] self.priority_msgs = Queue() # type: Queue[Tuple[Any, int]] - self.resource_msgs = Queue() # type: Queue[Tuple[Any, Any]] - self.node_msgs = Queue() # type: Queue[Tuple[Any, int]] - self.block_msgs = Queue() # type: Queue[Tuple[Any, Any]] + self.resource_msgs = Queue() # type: Queue[Tuple[Dict[str, Any], Any]] + self.node_msgs = Queue() # type: Queue[Tuple[Tuple[MessageType, Dict[str, Any]], int]] + self.block_msgs = Queue() # type: Queue[Tuple[Tuple[MessageType, Dict[str, Any]], Any]] self.router_proc = Process(target=router_starter, args=(comm_q, self.exception_q, self.priority_msgs, self.node_msgs, self.block_msgs, self.resource_msgs), @@ -434,16 +434,16 @@ def __init__(self, def start(self, priority_msgs: "queue.Queue[Tuple[Tuple[MessageType, Dict[str, Any]], int]]", - node_msgs: "queue.Queue[Tuple[Dict[str, Any], int]]", - block_msgs: "queue.Queue[Tuple[Dict[str, Any], int]]", - resource_msgs: "queue.Queue[Tuple[Dict[str, Any], str]]") -> None: + node_msgs: "queue.Queue[Tuple[Tuple[MessageType, Dict[str, Any]], int]]", + block_msgs: "queue.Queue[Tuple[Tuple[MessageType, Dict[str, Any]], int]]", + resource_msgs: "queue.Queue[Tuple[Dict[str, Any], Any]]") -> None: try: while True: try: data, addr = self.sock.recvfrom(2048) msg = pickle.loads(data) + self.logger.info("Got UDP Message from {}: {}".format(addr, msg)) resource_msgs.put((msg, addr)) - self.logger.debug("Got UDP Message from {}: {}".format(addr, msg)) except socket.timeout: pass @@ -468,12 +468,19 @@ def start(self, try: msg = self.ic_channel.recv_pyobj() self.logger.debug("Got ZMQ Message from interchange: {}".format(msg)) + + assert msg[0] == MessageType.NODE_INFO \ + or msg[0] == MessageType.BLOCK_INFO, \ + "IC Channel expects only NODE_INFO or BLOCK_INFO and cannot dispatch other message types" + if msg[0] == MessageType.NODE_INFO: msg[2]['last_heartbeat'] = datetime.datetime.fromtimestamp(msg[2]['last_heartbeat']) msg[2]['run_id'] = self.run_id msg[2]['timestamp'] = msg[1] - msg = (msg[0], msg[2]) - node_msgs.put((msg, 0)) + + # ((tag, dict), addr) + node_msg = ((msg[0], msg[2]), 0) + node_msgs.put(node_msg) elif msg[0] == MessageType.BLOCK_INFO: block_msgs.put((msg, 0)) else: @@ -502,8 +509,8 @@ def start(self, def router_starter(comm_q: "queue.Queue[Union[Tuple[int, int], str]]", exception_q: "queue.Queue[Tuple[str, str]]", priority_msgs: "queue.Queue[Tuple[Tuple[MessageType, Dict[str, Any]], int]]", - node_msgs: "queue.Queue[Tuple[Dict[str, Any], int]]", - block_msgs: "queue.Queue[Tuple[Dict[str, Any], int]]", + node_msgs: "queue.Queue[Tuple[Tuple[MessageType, Dict[str, Any]], int]]", + block_msgs: "queue.Queue[Tuple[Tuple[MessageType, Dict[str, Any]], int]]", resource_msgs: "queue.Queue[Tuple[Dict[str, Any], str]]", hub_address: str, From 5f7bc5564a61667533d41e252efd57b0055f0431 Mon Sep 17 00:00:00 2001 From: Ben Clifford Date: Sun, 25 Apr 2021 11:51:29 +0000 Subject: [PATCH 101/408] sleep statement to show race condition pretty much every time --- parsl/executors/high_throughput/executor.py | 5 +++++ 1 file changed, 5 insertions(+) diff --git a/parsl/executors/high_throughput/executor.py b/parsl/executors/high_throughput/executor.py index fc3265ec19..325b9a4693 100644 --- a/parsl/executors/high_throughput/executor.py +++ b/parsl/executors/high_throughput/executor.py @@ -10,6 +10,9 @@ from typing import List, Optional, Tuple, Union, Any import math +import time +import random + from parsl.serialize import pack_apply_message, deserialize from parsl.app.errors import RemoteExceptionWrapper from parsl.executors.high_throughput import zmq_pipes @@ -575,6 +578,8 @@ def submit(self, func, resource_specification, *args, **kwargs): # Post task to the the outgoing queue self.outgoing_q.put(msg) + time.sleep(random.random()) + # Return the future return self.tasks[task_id] From 90293967428e567f18b87f8f258988df7b723c52 Mon Sep 17 00:00:00 2001 From: Ben Clifford Date: Sun, 25 Apr 2021 12:13:37 +0000 Subject: [PATCH 102/408] Replace race-prone use of self.tasks after ownership of that entry has been passed down the queue, with more direct python reference --- parsl/executors/high_throughput/executor.py | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/parsl/executors/high_throughput/executor.py b/parsl/executors/high_throughput/executor.py index 325b9a4693..f6bada8b1f 100644 --- a/parsl/executors/high_throughput/executor.py +++ b/parsl/executors/high_throughput/executor.py @@ -564,7 +564,8 @@ def submit(self, func, resource_specification, *args, **kwargs): args_to_print = tuple([arg if len(repr(arg)) < 100 else (repr(arg)[:100] + '...') for arg in args]) logger.debug("Pushing function {} to queue with args {}".format(func, args_to_print)) - self.tasks[task_id] = Future() + fut = Future() + self.tasks[task_id] = fut try: fn_buf = pack_apply_message(func, args, kwargs, @@ -581,7 +582,7 @@ def submit(self, func, resource_specification, *args, **kwargs): time.sleep(random.random()) # Return the future - return self.tasks[task_id] + return fut @property def scaling_enabled(self): From 265b71bd6f835873488a5c88fc1198640b83dd66 Mon Sep 17 00:00:00 2001 From: Ben Clifford Date: Sun, 25 Apr 2021 12:42:22 +0000 Subject: [PATCH 103/408] Remove race-exposing delay, so this PR contains only the fix --- parsl/executors/high_throughput/executor.py | 5 ----- 1 file changed, 5 deletions(-) diff --git a/parsl/executors/high_throughput/executor.py b/parsl/executors/high_throughput/executor.py index f6bada8b1f..a34b4ad715 100644 --- a/parsl/executors/high_throughput/executor.py +++ b/parsl/executors/high_throughput/executor.py @@ -10,9 +10,6 @@ from typing import List, Optional, Tuple, Union, Any import math -import time -import random - from parsl.serialize import pack_apply_message, deserialize from parsl.app.errors import RemoteExceptionWrapper from parsl.executors.high_throughput import zmq_pipes @@ -579,8 +576,6 @@ def submit(self, func, resource_specification, *args, **kwargs): # Post task to the the outgoing queue self.outgoing_q.put(msg) - time.sleep(random.random()) - # Return the future return fut From 5da27617be71c13413e9e613c33b554903f5ff40 Mon Sep 17 00:00:00 2001 From: Ben Clifford Date: Mon, 26 Apr 2021 12:09:32 +0000 Subject: [PATCH 104/408] Tidy up slurm state comment --- parsl/providers/slurm/slurm.py | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/parsl/providers/slurm/slurm.py b/parsl/providers/slurm/slurm.py index 45abb927dc..c8e10ae356 100644 --- a/parsl/providers/slurm/slurm.py +++ b/parsl/providers/slurm/slurm.py @@ -28,8 +28,8 @@ 'TO': JobState.TIMEOUT, # (timeout), 'NF': JobState.FAILED, # (node failure), 'RV': JobState.FAILED, # (revoked) and - 'SE': JobState.FAILED -} # (special exit state + 'SE': JobState.FAILED # (special exit state) +} class SlurmProvider(ClusterProvider, RepresentationMixin): From 54a7773309bec27d6db14d693de94110a1561b79 Mon Sep 17 00:00:00 2001 From: Ben Clifford Date: Tue, 20 Apr 2021 15:12:02 +0000 Subject: [PATCH 105/408] Make worker command configurable like htex This is useful when launching workqueue workers inside some other environment - for example, when the workers are installed inside a singularity/shifter image. --- parsl/executors/workqueue/executor.py | 6 ++++-- 1 file changed, 4 insertions(+), 2 deletions(-) diff --git a/parsl/executors/workqueue/executor.py b/parsl/executors/workqueue/executor.py index e4fd500363..334c94183f 100644 --- a/parsl/executors/workqueue/executor.py +++ b/parsl/executors/workqueue/executor.py @@ -203,7 +203,8 @@ def __init__(self, autocategory: bool = True, init_command: str = "", worker_options: str = "", - full_debug: bool = True): + full_debug: bool = True, + worker_executable: str = 'work_queue_worker'): NoStatusHandlingExecutor.__init__(self) self._provider = provider self._scaling_enabled = True @@ -238,6 +239,7 @@ def __init__(self, self.should_stop = multiprocessing.Value(c_bool, False) self.cached_envs = {} # type: Dict[int, str] self.worker_options = worker_options + self.worker_executable = worker_executable if not self.address: self.address = socket.gethostname() @@ -437,7 +439,7 @@ def submit(self, func, resource_specification, *args, **kwargs): return fu def _construct_worker_command(self): - worker_command = 'work_queue_worker' + worker_command = self.worker_executable if self.project_password_file: worker_command += ' --password {}'.format(self.project_password_file) if self.worker_options: From 412ebcb1dddd033c92f0cd46c3a3ed8e095a5d3f Mon Sep 17 00:00:00 2001 From: Ben Clifford Date: Tue, 19 May 2020 17:17:09 +0000 Subject: [PATCH 106/408] raise exceptions harder (maybe just for dev?) --- .../visualization/plots/default/workflow_resource_plots.py | 7 +++++-- 1 file changed, 5 insertions(+), 2 deletions(-) diff --git a/parsl/monitoring/visualization/plots/default/workflow_resource_plots.py b/parsl/monitoring/visualization/plots/default/workflow_resource_plots.py index 08c0255e1a..7bcef93afe 100644 --- a/parsl/monitoring/visualization/plots/default/workflow_resource_plots.py +++ b/parsl/monitoring/visualization/plots/default/workflow_resource_plots.py @@ -132,8 +132,11 @@ def worker_efficiency(task, node): title="Worker efficiency")) return plot(fig, show_link=False, output_type="div", include_plotlyjs=False) except Exception as e: - print(e) - return "The worker efficiency plot cannot be generated due to missing data." + print("BENC BENC BENC BENC BENC BENC BENC BENC") + print("Exception:") + print(repr(e)) + raise + # return "The worker efficiency plot cannot be generated due to missing data." def resource_efficiency(resource, node, label='CPU'): From 81161375942f380db5252068cbcdd0e40ff290e6 Mon Sep 17 00:00:00 2001 From: Ben Clifford Date: Thu, 1 Apr 2021 11:58:24 +0000 Subject: [PATCH 107/408] Tidy human readable text/variable names around DependencyError * docstring for DependencyError * use __str__ for human formatted message and allow __repr__ to represent more machine-readable format --- parsl/dataflow/dflow.py | 10 +++++----- parsl/dataflow/error.py | 13 +++---------- 2 files changed, 8 insertions(+), 15 deletions(-) diff --git a/parsl/dataflow/dflow.py b/parsl/dataflow/dflow.py index 9009d281c3..74bfeefd0c 100644 --- a/parsl/dataflow/dflow.py +++ b/parsl/dataflow/dflow.py @@ -477,12 +477,12 @@ def launch_if_ready(self, task_id): if self._count_deps(task_record['depends']) == 0: # We can now launch *task* - new_args, kwargs, exceptions = self.sanitize_and_wrap(task_id, - task_record['args'], - task_record['kwargs']) + new_args, kwargs, exceptions_tids = self.sanitize_and_wrap(task_id, + task_record['args'], + task_record['kwargs']) task_record['args'] = new_args task_record['kwargs'] = kwargs - if not exceptions: + if not exceptions_tids: # There are no dependency errors exec_fu = None # Acquire a lock, retest the state, launch @@ -513,7 +513,7 @@ def launch_if_ready(self, task_id): self._send_task_log_info(task_record) exec_fu = Future() - exec_fu.set_exception(DependencyError(exceptions, + exec_fu.set_exception(DependencyError(exceptions_tids, task_id)) if exec_fu: diff --git a/parsl/dataflow/error.py b/parsl/dataflow/error.py index 8a34000a47..14a1d12532 100644 --- a/parsl/dataflow/error.py +++ b/parsl/dataflow/error.py @@ -42,21 +42,14 @@ class DependencyError(DataFlowException): in a dependency. Args: - - dependent_exceptions: List of exceptions - - task_id: Identity of the task failed task - - Contains: - reason (string) - dependent_exceptions + - dependent_exceptions_tids: List of dependency task IDs which failed + - task_id: Task ID of the task that failed because of the dependency error """ def __init__(self, dependent_exceptions_tids, task_id): self.dependent_exceptions_tids = dependent_exceptions_tids self.task_id = task_id - def __repr__(self): + def __str__(self): dep_tids = [tid for (exception, tid) in self.dependent_exceptions_tids] return "Dependency failure for task {} with failed dependencies from tasks {}".format(self.task_id, dep_tids) - - def __str__(self): - return self.__repr__() From 436cc2c9f9c388120892cfb08c621f39bbfef3a9 Mon Sep 17 00:00:00 2001 From: Ben Clifford Date: Tue, 27 Apr 2021 09:26:27 +0000 Subject: [PATCH 108/408] add docstring --- parsl/executors/workqueue/executor.py | 6 ++++++ 1 file changed, 6 insertions(+) diff --git a/parsl/executors/workqueue/executor.py b/parsl/executors/workqueue/executor.py index 334c94183f..b85b3faa6f 100644 --- a/parsl/executors/workqueue/executor.py +++ b/parsl/executors/workqueue/executor.py @@ -179,6 +179,12 @@ class WorkQueueExecutor(NoStatusHandlingExecutor): worker_options: str Extra options passed to work_queue_worker. Default is ''. + + worker_executable: str + The command used to invoke work_queue_worker. This can be used + when the worker needs to be wrapped inside some other command + (for example, to run the worker inside a container). Default is + 'work_queue_worker'. """ @typeguard.typechecked From 212fd01df2d2ffd3d9cad3728351d928952a1b43 Mon Sep 17 00:00:00 2001 From: Ben Clifford Date: Tue, 27 Apr 2021 09:33:11 +0000 Subject: [PATCH 109/408] Remove commented out code --- parsl/executors/high_throughput/interchange.py | 1 - parsl/executors/high_throughput/process_worker_pool.py | 1 - 2 files changed, 2 deletions(-) diff --git a/parsl/executors/high_throughput/interchange.py b/parsl/executors/high_throughput/interchange.py index e0f4c46fa7..69699f3479 100644 --- a/parsl/executors/high_throughput/interchange.py +++ b/parsl/executors/high_throughput/interchange.py @@ -416,7 +416,6 @@ def start(self, poll_period=None): try: msg = json.loads(message[1].decode('utf-8')) - # msg['reg_time'] = datetime.datetime.strptime(msg['reg_time'], "%Y-%m-%d %H:%M:%S") reg_flag = True except Exception: logger.warning("[MAIN] Got Exception reading registration message from manager: {}".format( diff --git a/parsl/executors/high_throughput/process_worker_pool.py b/parsl/executors/high_throughput/process_worker_pool.py index 28b6fd3fa6..24bd231667 100755 --- a/parsl/executors/high_throughput/process_worker_pool.py +++ b/parsl/executors/high_throughput/process_worker_pool.py @@ -203,7 +203,6 @@ def create_reg_message(self): 'dir': os.getcwd(), 'cpu_count': psutil.cpu_count(logical=False), 'total_memory': psutil.virtual_memory().total, - # 'reg_time': datetime.datetime.now().strftime("%Y-%m-%d %H:%M:%S"), } b_msg = json.dumps(msg).encode('utf-8') return b_msg From 3738fced52569fa84608125a75389ed08a99883a Mon Sep 17 00:00:00 2001 From: Ben Clifford Date: Wed, 24 Mar 2021 12:31:54 +0000 Subject: [PATCH 110/408] more dev --- parsl/dataflow/dflow.py | 27 ++++++++++++++------------- 1 file changed, 14 insertions(+), 13 deletions(-) diff --git a/parsl/dataflow/dflow.py b/parsl/dataflow/dflow.py index 9009d281c3..70f79ffe64 100644 --- a/parsl/dataflow/dflow.py +++ b/parsl/dataflow/dflow.py @@ -490,7 +490,7 @@ def launch_if_ready(self, task_id): if task_record['status'] == States.pending: try: exec_fu = self.launch_task( - task_id, task_record['func'], *new_args, **kwargs) + task_record, task_record['func'], *new_args, **kwargs) assert isinstance(exec_fu, Future) except Exception as e: # task launched failed somehow. the execution might @@ -530,7 +530,7 @@ def launch_if_ready(self, task_id): task_record['exec_fu'] = exec_fu - def launch_task(self, task_id, executable, *args, **kwargs): + def launch_task(self, task_record, executable, *args, **kwargs): """Handle the actual submission of the task to the executor layer. If the app task has the executors attributes not set (default=='all') @@ -542,7 +542,7 @@ def launch_task(self, task_id, executable, *args, **kwargs): targeted at those specific executors. Args: - task_id (string) : A string that uniquely identifies the task + task_record : The task record executable (callable) : A callable object args (list of positional args) kwargs (arbitrary keyword arguments) @@ -551,17 +551,18 @@ def launch_task(self, task_id, executable, *args, **kwargs): Returns: Future that tracks the execution of the submitted executable """ - self.tasks[task_id]['try_time_launched'] = datetime.datetime.now() + task_id = task_record['id'] + task_record['try_time_launched'] = datetime.datetime.now() - memo_fu = self.memoizer.check_memo(task_id, self.tasks[task_id]) + memo_fu = self.memoizer.check_memo(task_id, task_record) if memo_fu: logger.info("Reusing cached result for task {}".format(task_id)) - self.tasks[task_id]['from_memo'] = True + task_record['from_memo'] = True assert isinstance(memo_fu, Future) return memo_fu - self.tasks[task_id]['from_memo'] = False - executor_label = self.tasks[task_id]["executor"] + task_record['from_memo'] = False + executor_label = task_record["executor"] try: executor = self.executors[executor_label] except Exception: @@ -570,7 +571,7 @@ def launch_task(self, task_id, executable, *args, **kwargs): if self.monitoring is not None and self.monitoring.resource_monitoring_enabled: wrapper_logging_level = logging.DEBUG if self.monitoring.monitoring_debug else logging.INFO - try_id = self.tasks[task_id]['fail_count'] + try_id = task_record['fail_count'] executable = self.monitoring.monitor_wrapper(executable, try_id, task_id, self.monitoring.monitoring_hub_url, self.run_id, @@ -579,14 +580,14 @@ def launch_task(self, task_id, executable, *args, **kwargs): executor.monitor_resources()) with self.submitter_lock: - exec_fu = executor.submit(executable, self.tasks[task_id]['resource_specification'], *args, **kwargs) - self.tasks[task_id]['status'] = States.launched + exec_fu = executor.submit(executable, task_record['resource_specification'], *args, **kwargs) + task_record['status'] = States.launched - self._send_task_log_info(self.tasks[task_id]) + self._send_task_log_info(task_record) logger.info("Task {} launched on executor {}".format(task_id, executor.label)) - self._log_std_streams(self.tasks[task_id]) + self._log_std_streams(task_record) return exec_fu From 9f73364e1ccdedaee2a03a853eda27a06b8171a7 Mon Sep 17 00:00:00 2001 From: Ben Clifford Date: Fri, 30 Apr 2021 11:36:39 +0000 Subject: [PATCH 111/408] sge fix --- parsl/providers/grid_engine/grid_engine.py | 1 + parsl/version.py | 2 +- 2 files changed, 2 insertions(+), 1 deletion(-) diff --git a/parsl/providers/grid_engine/grid_engine.py b/parsl/providers/grid_engine/grid_engine.py index 48685aae33..b9667f12fd 100644 --- a/parsl/providers/grid_engine/grid_engine.py +++ b/parsl/providers/grid_engine/grid_engine.py @@ -90,6 +90,7 @@ def __init__(self, cmd_timeout=cmd_timeout) self.scheduler_options = scheduler_options self.worker_init = worker_init + self.queue = queue if launcher in ['srun', 'srun_mpi']: logger.warning("Use of {} launcher is usually appropriate for Slurm providers. " diff --git a/parsl/version.py b/parsl/version.py index 5f8ab745ec..a56a20773e 100644 --- a/parsl/version.py +++ b/parsl/version.py @@ -3,4 +3,4 @@ ..[alpha/beta/..] Alphas will be numbered like this -> 0.4.0a0 """ -VERSION = '1.1.0+desc-2021.04.27a' +VERSION = '1.1.0+desc-2021.04.30a' From 0e61fb884029c3e988236fe6e18f23b417f49bfd Mon Sep 17 00:00:00 2001 From: Ben Clifford Date: Fri, 30 Apr 2021 11:28:16 +0000 Subject: [PATCH 112/408] missing queue from self - causes config serialisation failure see PR #1964 which i think is broken? thanks to Quentin Le Boulc'h on lsst slack --- parsl/providers/grid_engine/grid_engine.py | 1 + 1 file changed, 1 insertion(+) diff --git a/parsl/providers/grid_engine/grid_engine.py b/parsl/providers/grid_engine/grid_engine.py index 48685aae33..b9667f12fd 100644 --- a/parsl/providers/grid_engine/grid_engine.py +++ b/parsl/providers/grid_engine/grid_engine.py @@ -90,6 +90,7 @@ def __init__(self, cmd_timeout=cmd_timeout) self.scheduler_options = scheduler_options self.worker_init = worker_init + self.queue = queue if launcher in ['srun', 'srun_mpi']: logger.warning("Use of {} launcher is usually appropriate for Slurm providers. " From c3dd99f1c1072f20c3ca7854189e9675a4018159 Mon Sep 17 00:00:00 2001 From: Ben Clifford Date: Fri, 30 Apr 2021 13:58:33 +0000 Subject: [PATCH 113/408] partial-fix to worker efficiency plot (doesn't crash but gives wrong results towards end of workflow) --- .../visualization/plots/default/workflow_resource_plots.py | 4 ++-- parsl/version.py | 2 +- 2 files changed, 3 insertions(+), 3 deletions(-) diff --git a/parsl/monitoring/visualization/plots/default/workflow_resource_plots.py b/parsl/monitoring/visualization/plots/default/workflow_resource_plots.py index bcf6dc64bd..0147fc6f8b 100644 --- a/parsl/monitoring/visualization/plots/default/workflow_resource_plots.py +++ b/parsl/monitoring/visualization/plots/default/workflow_resource_plots.py @@ -111,8 +111,8 @@ def worker_efficiency(task, node): total_workers = node['worker_count'].sum() for i, row in task.iterrows(): - if math.isnan(row['epoch_time_running']): - # skip tasks with no running start time. + if math.isnan(row['epoch_time_running']) or math.isnan(row['epoch_time_returned']): + # skip tasks with no running start time or return time. continue for j in range(int(row['epoch_time_running']), int(row['epoch_time_returned']) + 1): worker_plot[j - start] += 1 diff --git a/parsl/version.py b/parsl/version.py index a56a20773e..928b5bd4ff 100644 --- a/parsl/version.py +++ b/parsl/version.py @@ -3,4 +3,4 @@ ..[alpha/beta/..] Alphas will be numbered like this -> 0.4.0a0 """ -VERSION = '1.1.0+desc-2021.04.30a' +VERSION = '1.1.0+desc-2021.04.30b' From 5ac33427fb4aab389342a3ee25ab9095a3d6c78d Mon Sep 17 00:00:00 2001 From: Ben Clifford Date: Fri, 30 Apr 2021 14:22:20 +0000 Subject: [PATCH 114/408] better treatment of not-completed tasks in efficiency plot --- parsl/executors/high_throughput/interchange.py | 3 +-- .../plots/default/workflow_resource_plots.py | 9 +++++++-- parsl/version.py | 2 +- 3 files changed, 9 insertions(+), 5 deletions(-) diff --git a/parsl/executors/high_throughput/interchange.py b/parsl/executors/high_throughput/interchange.py index 508578dd43..84820ff9c1 100644 --- a/parsl/executors/high_throughput/interchange.py +++ b/parsl/executors/high_throughput/interchange.py @@ -593,8 +593,7 @@ def start(self): if r['type'] == 'result': # process this for task ID and forward to executor b_messages.append(message) - # TODO: case here for monitoring messages - if r['type'] == 'monitoring': + elif r['type'] == 'monitoring': hub_channel.send_pyobj(r['payload']) else: logger.error("Interchange discarding result_queue message of unknown type: {}".format(r['type'])) diff --git a/parsl/monitoring/visualization/plots/default/workflow_resource_plots.py b/parsl/monitoring/visualization/plots/default/workflow_resource_plots.py index 0147fc6f8b..3601e217f7 100644 --- a/parsl/monitoring/visualization/plots/default/workflow_resource_plots.py +++ b/parsl/monitoring/visualization/plots/default/workflow_resource_plots.py @@ -111,10 +111,15 @@ def worker_efficiency(task, node): total_workers = node['worker_count'].sum() for i, row in task.iterrows(): - if math.isnan(row['epoch_time_running']) or math.isnan(row['epoch_time_returned']): + if math.isnan(row['epoch_time_running']): # skip tasks with no running start time or return time. continue - for j in range(int(row['epoch_time_running']), int(row['epoch_time_returned']) + 1): + if math.isnan(row['epoch_time_returned']): + # there is no end time for this, so we should assume the "end" time + etr = endtime = end + else: + etr = int(row['epoch_time_returned']) + for j in range(int(row['epoch_time_running']), etr + 1): worker_plot[j - start] += 1 fig = go.Figure( data=[go.Scatter(x=list(range(0, end - start + 1)), diff --git a/parsl/version.py b/parsl/version.py index 928b5bd4ff..fa9fd463fe 100644 --- a/parsl/version.py +++ b/parsl/version.py @@ -3,4 +3,4 @@ ..[alpha/beta/..] Alphas will be numbered like this -> 0.4.0a0 """ -VERSION = '1.1.0+desc-2021.04.30b' +VERSION = '1.1.0+desc-2021.04.30c' From 7b4988a53f8c06d615bd6bc831edc7ca3add5108 Mon Sep 17 00:00:00 2001 From: Ben Clifford Date: Fri, 30 Apr 2021 13:49:37 +0000 Subject: [PATCH 115/408] /workflow/ffecef64-c6b0-472c-aa71-4363739d07e5/resource_usage fails: ... File "/home/benc/parsl/virtualenv-3.7/lib/python3.7/site-packages/flask/app.py", line 1936, in dispatch_request return self.view_functions[rule.endpoint](**req.view_args) File "/home/benc/parsl/src/parsl/parsl/monitoring/visualization/views.py", line 186, in workflow_resources worker_efficiency=worker_efficiency(df_task_tries, df_node), File "/home/benc/parsl/src/parsl/parsl/monitoring/visualization/plots/default/workflow_resource_plots.py", line 117, in worker_efficiency for j in range(int(row['epoch_time_running']), int(row['epoch_time_returned']) + 1): ValueError: cannot convert float NaN to integer with a test db from smoeone at lsst. it looks like this is when there is a task that has started running but has not finished: this code assumes both of those fields are populated. if the end field is not populated, assume the task is still runnning until the end time (which is roughly "now" or the end of the workflow) --- .../plots/default/workflow_resource_plots.py | 9 +++++++-- 1 file changed, 7 insertions(+), 2 deletions(-) diff --git a/parsl/monitoring/visualization/plots/default/workflow_resource_plots.py b/parsl/monitoring/visualization/plots/default/workflow_resource_plots.py index 23cdcf5c72..26c5d2e866 100644 --- a/parsl/monitoring/visualization/plots/default/workflow_resource_plots.py +++ b/parsl/monitoring/visualization/plots/default/workflow_resource_plots.py @@ -112,9 +112,14 @@ def worker_efficiency(task, node): for i, row in task.iterrows(): if math.isnan(row['epoch_time_running']): - # skip tasks with no running start time. + # skip tasks with no running start time or return time. continue - for j in range(int(row['epoch_time_running']), int(row['epoch_time_returned']) + 1): + if math.isnan(row['epoch_time_returned']): + # there is no end time for this, so we should assume the "end" time + etr = endtime = end + else: + etr = int(row['epoch_time_returned']) + for j in range(int(row['epoch_time_running']), etr + 1): worker_plot[j - start] += 1 fig = go.Figure( data=[go.Scatter(x=list(range(0, end - start + 1)), From 738b0cfda894864dc1ff8a250bf78f236a26003f Mon Sep 17 00:00:00 2001 From: Ben Clifford Date: Fri, 30 Apr 2021 14:53:46 +0000 Subject: [PATCH 116/408] fix mispaste detected by flake8 --- .../visualization/plots/default/workflow_resource_plots.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/parsl/monitoring/visualization/plots/default/workflow_resource_plots.py b/parsl/monitoring/visualization/plots/default/workflow_resource_plots.py index 26c5d2e866..fe4f030455 100644 --- a/parsl/monitoring/visualization/plots/default/workflow_resource_plots.py +++ b/parsl/monitoring/visualization/plots/default/workflow_resource_plots.py @@ -116,7 +116,7 @@ def worker_efficiency(task, node): continue if math.isnan(row['epoch_time_returned']): # there is no end time for this, so we should assume the "end" time - etr = endtime = end + etr = end else: etr = int(row['epoch_time_returned']) for j in range(int(row['epoch_time_running']), etr + 1): From ff43c45986e4c2bfa414c7bb242366502dd79ebd Mon Sep 17 00:00:00 2001 From: Ben Clifford Date: Fri, 30 Apr 2021 15:23:01 +0000 Subject: [PATCH 117/408] fix comment --- .../visualization/plots/default/workflow_resource_plots.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/parsl/monitoring/visualization/plots/default/workflow_resource_plots.py b/parsl/monitoring/visualization/plots/default/workflow_resource_plots.py index fe4f030455..2ede9f476f 100644 --- a/parsl/monitoring/visualization/plots/default/workflow_resource_plots.py +++ b/parsl/monitoring/visualization/plots/default/workflow_resource_plots.py @@ -112,7 +112,7 @@ def worker_efficiency(task, node): for i, row in task.iterrows(): if math.isnan(row['epoch_time_running']): - # skip tasks with no running start time or return time. + # skip tasks with no running start time continue if math.isnan(row['epoch_time_returned']): # there is no end time for this, so we should assume the "end" time From 403d94984969d08d84937cbc92800cd624ecde4c Mon Sep 17 00:00:00 2001 From: Ben Clifford Date: Sat, 1 May 2021 12:46:34 +0000 Subject: [PATCH 118/408] Reverse polarity of mac safe queue imports to satisfy mypy mypy determines the type of mpQueue by the type of its first usage. Prior to this commit, that usage was importing MacSafeQueue. That mean the second import did not type check: what it was importing was not MacSafeQueue, but Queue. This commit reverses that, so that mpQueue is now typed as a Queue, and the subsequent import of MacSafeQueue is acceptable: MacSafeQueue is a subclass of Queue. The error message being fixed is this: parsl/executors/high_throughput/process_worker_pool.py:28: error: Incompatible import of "mpQueue" (imported name has type "Type[Queue[Any]]", local name has type "Type[MacSafeQueue]") --- parsl/executors/high_throughput/process_worker_pool.py | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/parsl/executors/high_throughput/process_worker_pool.py b/parsl/executors/high_throughput/process_worker_pool.py index 24bd231667..c3a1d2671f 100755 --- a/parsl/executors/high_throughput/process_worker_pool.py +++ b/parsl/executors/high_throughput/process_worker_pool.py @@ -22,10 +22,10 @@ from parsl.app.errors import RemoteExceptionWrapper from parsl.executors.high_throughput.errors import WorkerLost from parsl.executors.high_throughput.probe import probe_addresses -if platform.system() == 'Darwin': - from parsl.executors.high_throughput.mac_safe_queue import MacSafeQueue as mpQueue -else: +if platform.system() != 'Darwin': from multiprocessing import Queue as mpQueue +else: + from parsl.executors.high_throughput.mac_safe_queue import MacSafeQueue as mpQueue from parsl.serialize import unpack_apply_message, serialize From a8096529e1f9136b1309fd8e34f408a400940c85 Mon Sep 17 00:00:00 2001 From: Ben Clifford Date: Sat, 1 May 2021 13:34:58 +0000 Subject: [PATCH 119/408] Check process_worker_pool.py in mypy --- Makefile | 3 +++ 1 file changed, 3 insertions(+) diff --git a/Makefile b/Makefile index ecf359c936..1f1808c2e8 100644 --- a/Makefile +++ b/Makefile @@ -51,6 +51,9 @@ mypy: ## run mypy checks MYPYPATH=$(CWD)/mypy-stubs mypy parsl/tests/sites/ # only the top level of monitoring is checked here because the visualization code does not type check MYPYPATH=$(CWD)/mypy-stubs mypy parsl/app/ parsl/channels/ parsl/dataflow/ parsl/data_provider/ parsl/launchers parsl/providers/ parsl/monitoring/*py + # process worker pool is explicitly listed to check, because it is not + # imported from anywhere in core parsl python code. + MYPYPATH=$(CWD)/mypy-stubs mypy parsl/executors/high_throughput/process_worker_pool.py .PHONY: local_thread_test local_thread_test: ## run all tests with local_thread config From 9746f6b4dc7bc06981cebfc2c7173a80be11e593 Mon Sep 17 00:00:00 2001 From: Ben Clifford Date: Sat, 1 May 2021 13:59:02 +0000 Subject: [PATCH 120/408] Define process_worker_pool logger differently to pass mypy This defines the global logger variable differently, which appears to pass mypy checking. There is still no guarantee that a global 'logger' value has actually been defined, except when running the process_worker_pool directly as __main__. --- .../high_throughput/process_worker_pool.py | 20 +++++++++++-------- 1 file changed, 12 insertions(+), 8 deletions(-) diff --git a/parsl/executors/high_throughput/process_worker_pool.py b/parsl/executors/high_throughput/process_worker_pool.py index c3a1d2671f..8737ccca67 100755 --- a/parsl/executors/high_throughput/process_worker_pool.py +++ b/parsl/executors/high_throughput/process_worker_pool.py @@ -486,10 +486,14 @@ def worker(worker_id, pool_id, pool_size, task_queue, result_queue, worker_queue Pop request from queue Put result into result_queue """ - start_file_logger('{}/block-{}/{}/worker_{}.log'.format(args.logdir, args.block_id, pool_id, worker_id), - worker_id, - name="worker_log", - level=logging.DEBUG if args.debug else logging.INFO) + + # override the global logger inherited from the __main__ process (which + # usually logs to manager.log) with one specific to this worker. + global logger + logger = start_file_logger('{}/block-{}/{}/worker_{}.log'.format(args.logdir, args.block_id, pool_id, worker_id), + worker_id, + name="worker_log", + level=logging.DEBUG if args.debug else logging.INFO) # Store worker ID as an environment variable os.environ['PARSL_WORKER_RANK'] = str(worker_id) @@ -574,7 +578,6 @@ def start_file_logger(filename, rank, name='parsl', level=logging.DEBUG, format_ if format_string is None: format_string = "%(asctime)s.%(msecs)03d %(name)s:%(lineno)d Rank:{0} [%(levelname)s] %(message)s".format(rank) - global logger logger = logging.getLogger(name) logger.setLevel(logging.DEBUG) handler = logging.FileHandler(filename) @@ -582,6 +585,7 @@ def start_file_logger(filename, rank, name='parsl', level=logging.DEBUG, format_ formatter = logging.Formatter(format_string, datefmt='%Y-%m-%d %H:%M:%S') handler.setFormatter(formatter) logger.addHandler(handler) + return logger if __name__ == "__main__": @@ -625,9 +629,9 @@ def start_file_logger(filename, rank, name='parsl', level=logging.DEBUG, format_ os.makedirs(os.path.join(args.logdir, "block-{}".format(args.block_id), args.uid), exist_ok=True) try: - start_file_logger('{}/block-{}/{}/manager.log'.format(args.logdir, args.block_id, args.uid), - 0, - level=logging.DEBUG if args.debug is True else logging.INFO) + logger = start_file_logger('{}/block-{}/{}/manager.log'.format(args.logdir, args.block_id, args.uid), + 0, + level=logging.DEBUG if args.debug is True else logging.INFO) logger.info("Python version: {}".format(sys.version)) logger.info("Debug logging: {}".format(args.debug)) From 167e448f11b33698b45f4e20cebd83eabb10d193 Mon Sep 17 00:00:00 2001 From: Ben Clifford Date: Thu, 29 Apr 2021 16:21:31 +0000 Subject: [PATCH 121/408] Remove unused AppBase status field This was initialized to 'created' and then never changed. It was creating minor confusion wrt DFK task record status fields, which it looks like this was once intended to be similar to. --- parsl/app/app.py | 1 - 1 file changed, 1 deletion(-) diff --git a/parsl/app/app.py b/parsl/app/app.py index 96757b971c..9928d3bb58 100644 --- a/parsl/app/app.py +++ b/parsl/app/app.py @@ -42,7 +42,6 @@ def __init__(self, func, data_flow_kernel=None, executors='all', cache=False, ig self.__name__ = func.__name__ self.func = func self.data_flow_kernel = data_flow_kernel - self.status = 'created' self.executors = executors self.cache = cache self.ignore_for_cache = ignore_for_cache From 5353e5f57a8d218893b03a828cf7d3961068b086 Mon Sep 17 00:00:00 2001 From: Ben Clifford Date: Mon, 3 May 2021 10:12:49 +0000 Subject: [PATCH 122/408] Test combine() pattern in joinapps Most of the test code for this was already defined, but it was not actually used in a test. The combine() pattern is the way joinapps can wait for several tasks to complete, rather than one. --- parsl/tests/test_python_apps/test_join.py | 8 +++++++- 1 file changed, 7 insertions(+), 1 deletion(-) diff --git a/parsl/tests/test_python_apps/test_join.py b/parsl/tests/test_python_apps/test_join.py index 51d5fcef54..d4bccbde09 100644 --- a/parsl/tests/test_python_apps/test_join.py +++ b/parsl/tests/test_python_apps/test_join.py @@ -29,7 +29,7 @@ def add_one(n): @python_app def combine(*args): """Wait for an arbitrary list of futures and return them as a list""" - return args + return list(args) @join_app @@ -50,3 +50,9 @@ def test_dependency_on_joined(): g = add_one(outer_app()) res = g.result() assert res == RESULT_CONSTANT + 1 + + +def test_combine(): + f = outer_make_a_dag(inner_app()) + res = f.result() + assert res == [RESULT_CONSTANT] * RESULT_CONSTANT From 49080abb40f61954c3aff735818571f07fa5c519 Mon Sep 17 00:00:00 2001 From: Ben Clifford Date: Tue, 4 May 2021 12:50:48 +0000 Subject: [PATCH 123/408] mostly joinapp related features/fixes --- parsl/dataflow/dflow.py | 89 ++++++++++++++++++----- parsl/tests/test_python_apps/test_join.py | 5 +- parsl/version.py | 2 +- 3 files changed, 75 insertions(+), 21 deletions(-) diff --git a/parsl/dataflow/dflow.py b/parsl/dataflow/dflow.py index 70af498ad8..a2aea4d05b 100644 --- a/parsl/dataflow/dflow.py +++ b/parsl/dataflow/dflow.py @@ -341,15 +341,34 @@ def handle_exec_update(self, task_record, future): # record the inner app ID in monitoring, and add a completion # listener to that inner future. - inner_future = future.result() + joinable = future.result() # this assert should actually be a test that causes the # current app to fail cleanly if it is not a Future - XXXX - assert isinstance(inner_future, Future) - task_record['status'] = States.joining - task_record['joins'] = inner_future - inner_future.add_done_callback(partial(self.handle_join_update, task_record)) + if isinstance(joinable, Future): + task_record['status'] = States.joining + task_record['joins'] = joinable + joinable.add_done_callback(partial(self.handle_join_update, task_record)) + elif isinstance(joinable, list): # TODO: should this be list or arbitrary iterable? + task_record['status'] = States.joining + task_record['joins'] = joinable + for inner_future in joinable: + # TODO: typechecking and error setting here - perhaps + # should put this and the one-future case inside a + # try and perform the error handling there in an + # except block? (it would be ok to go joining->failed + # which doesn't happen in the type error case but + # does happen in the joined-tasks fail case) + # For now, this assert will cause a DFK hang + assert isinstance(inner_future, Future) + inner_future.add_done_callback(partial(self.handle_join_update, task_record)) + else: + task_record['time_returned'] = datetime.datetime.now() + task_record['status'] = States.failed + self.tasks_failed_count += 1 + task_record['time_returned'] = datetime.datetime.now() + with task_record['app_fu']._update_lock: + task_record['app_fu'].set_exception(TypeError(f"join_app body must return a Future or collection of Futures, got {type(joinable)}")) self._log_std_streams(task_record) @@ -362,27 +381,49 @@ def handle_exec_update(self, task_record, future): self.launch_if_ready(task_record) def handle_join_update(self, task_record, inner_app_future): - # Use the result of the inner_app_future as the final result of + # inner_app_future has completed, which is one (potentially of many) + # futures the outer task is joining on. + + # If the outer task is joining on a single future, then + # use the result of the inner_app_future as the final result of # the outer app future. + # If the outer task is joining on a collection of futures, then + # check if the collection is all done, and if so, return a list + # of the results. Otherwise, this callback can do nothing and + # processing will happen in another callback (on the final Future + # to complete) + # There is no retry handling here: inner apps are responsible for # their own retrying, and joining state is responsible for passing # on whatever the result of that retrying was (if any). outer_task_id = task_record['id'] + logger.debug(f"Join callback for task {outer_task_id}, inner_app_future {inner_app_future}") + + joinable = task_record['joins'] # Future or collection of futures + + if isinstance(joinable, list): # TODO more generic type than list? + for future in joinable: + if not future.done(): + logger.debug(f"A joinable future {future} is not done for task {outer_task_id} - skipping callback") + return # abandon this callback processing if joinables are not all done + + # now we know each joinable Future is done + # so now look for any exceptions + e = None + if isinstance(joinable, Future): + if joinable.exception(): + e = joinable.exception() + elif isinstance(joinable, list): + for future in joinable: + if future.exception(): + e = future.exception() + else: + raise TypeError(f"Unknown joinable type {type(joinable)}") - try: - # TODO: stack traces could be tidier by this call not re-raising the exception, - # so that it keeps only the remote part of the exception. - # Then the exception handling block directly below would need to be entered - # in two ways: either an exception is thrown (because something broke) - # or there is a remoteexceptionwrapper, in which case use the contained - # exception can be used directly as e without a further raise/except - # which i think might then keep stack traces cleaner? - res = self._unwrap_remote_exception_wrapper(inner_app_future) - - except Exception as e: - logger.debug("Task {} failed due to failure of inner join future".format(outer_task_id)) + if e: + logger.debug("Task {} failed due to failure of an inner join future".format(outer_task_id)) # We keep the history separately, since the future itself could be # tossed. task_record['fail_history'].append(repr(e)) @@ -395,6 +436,16 @@ def handle_join_update(self, task_record, inner_app_future): task_record['app_fu'].set_exception(e) else: + # all the joinables succeeded, so construct a result: + if isinstance(joinable, Future): + assert inner_app_future is joinable + res = joinable.result() + elif isinstance(joinable, list): + res = [] + for future in joinable: + res.append(future.result()) + else: + raise TypeError(f"Unknown joinable type {type(joinable)}") self._complete_task(task_record, States.exec_done, res) self._log_std_streams(task_record) diff --git a/parsl/tests/test_python_apps/test_join.py b/parsl/tests/test_python_apps/test_join.py index 67e4d1360c..338eeed21c 100644 --- a/parsl/tests/test_python_apps/test_join.py +++ b/parsl/tests/test_python_apps/test_join.py @@ -1,3 +1,4 @@ +import pytest import time from parsl import join_app, python_app @@ -64,7 +65,8 @@ def test_wrong_type(): # so the DFK hangs. What should happen is that the app raises an exception via # its app future. f = join_wrong_type_app() - assert f.exception() is not None # TODO: assert exception type when I know it? + with pytest.raises(TypeError): + f.result() def test_dependency_on_joined(): @@ -78,6 +80,7 @@ def test_combine(): res = f.result() assert res == [RESULT_CONSTANT] * RESULT_CONSTANT + def test_multiple_return(): f = outer_make_a_dag_multi(inner_app()) res = f.result() diff --git a/parsl/version.py b/parsl/version.py index 8004920274..626a260bb2 100644 --- a/parsl/version.py +++ b/parsl/version.py @@ -3,4 +3,4 @@ ..[alpha/beta/..] Alphas will be numbered like this -> 0.4.0a0 """ -VERSION = '1.1.0+desc-2021.05.04a' +VERSION = '1.1.0+desc-2021.05.04c' From 016e23f27fa9797669339e1abe03435c092cd270 Mon Sep 17 00:00:00 2001 From: Ben Clifford Date: Tue, 4 May 2021 15:14:03 +0000 Subject: [PATCH 124/408] fix monitoring for new joinapp style --- parsl/dataflow/dflow.py | 13 ++++++++----- parsl/version.py | 2 +- 2 files changed, 9 insertions(+), 6 deletions(-) diff --git a/parsl/dataflow/dflow.py b/parsl/dataflow/dflow.py index a2aea4d05b..f56c921119 100644 --- a/parsl/dataflow/dflow.py +++ b/parsl/dataflow/dflow.py @@ -236,12 +236,15 @@ def _create_task_log_info(self, task_record): if task_record['depends'] is not None: task_log_info['task_depends'] = ",".join([str(t.tid) for t in task_record['depends'] if isinstance(t, AppFuture) or isinstance(t, DataFuture)]) + task_log_info['task_joins'] = None + + if isinstance(task_record['joins'], list): + task_log_info['task_joins'] = ",".join([str(t.tid) for t in task_record['joins'] + if isinstance(t, AppFuture) or isinstance(t, DataFuture)]) + elif isinstance(task_record['joins'], Future): + task_log_info['task_joins'] = ",".join([str(t.tid) for t in [task_record['joins']] + if isinstance(t, AppFuture) or isinstance(t, DataFuture)]) - j = task_record['joins'] - if isinstance(j, AppFuture) or isinstance(j, DataFuture): - task_log_info['task_joins'] = j.tid - else: - task_log_info['task_joins'] = None return task_log_info def _count_deps(self, depends): diff --git a/parsl/version.py b/parsl/version.py index 5438973176..9607fc2f49 100644 --- a/parsl/version.py +++ b/parsl/version.py @@ -3,4 +3,4 @@ ..[alpha/beta/..] Alphas will be numbered like this -> 0.4.0a0 """ -VERSION = '1.1.0+desc-2021.05.04d' +VERSION = '1.1.0+desc-2021.05.04f' From 7dab6f4368367b80013b886c4c3594891dbb2f11 Mon Sep 17 00:00:00 2001 From: Ben Clifford Date: Mon, 3 May 2021 20:31:12 +0000 Subject: [PATCH 125/408] TODO: don't retry tasks at the workqueue level. let parsl retrying handle things. maybe put in a configurable option to let WQ retries happen that defaults to not. Some retries already don't get retried by WQ (as evidenced by the test suite) - I think that parsl level task failures are regarded as "successful" by WQ itself (so that the exception is successfully sent up to the parsl level?) in which case wq level retries happen eg in the case of a node failure. that makes it much less interesting to ever set this to anything other than 0, I think? (maybe it interacts with the auto classification stuff?) --- parsl/executors/workqueue/executor.py | 17 +++++++++++++++++ 1 file changed, 17 insertions(+) diff --git a/parsl/executors/workqueue/executor.py b/parsl/executors/workqueue/executor.py index b85b3faa6f..17cb7e7d2d 100644 --- a/parsl/executors/workqueue/executor.py +++ b/parsl/executors/workqueue/executor.py @@ -173,6 +173,13 @@ class WorkQueueExecutor(NoStatusHandlingExecutor): invocations of an app have similar performance characteristics, this will provide a reasonable set of categories automatically. + max_retries: Optional[int] + Set the number of retries that Work Queue will make when a task + fails. This is distinct from Parsl level retries configured in + parsl.config.Config. Set to None to allow Work Queue to retry + tasks forever. By default, this is set to 0, so that all retries + will be managed by Parsl. + init_command: str Command line to run before executing a task in a worker. Default is ''. @@ -207,6 +214,7 @@ def __init__(self, autolabel: bool = False, autolabel_window: int = 1, autocategory: bool = True, + max_retries: Optional[int] = 0, init_command: str = "", worker_options: str = "", full_debug: bool = True, @@ -242,6 +250,7 @@ def __init__(self, self.autolabel = autolabel self.autolabel_window = autolabel_window self.autocategory = autocategory + self.max_retries = 0 self.should_stop = multiprocessing.Value(c_bool, False) self.cached_envs = {} # type: Dict[int, str] self.worker_options = worker_options @@ -290,6 +299,7 @@ def start(self): "autolabel": self.autolabel, "autolabel_window": self.autolabel_window, "autocategory": self.autocategory, + "max_retries": self.max_retries, "should_stop": self.should_stop, "port": self.port, "wq_log_dir": self.wq_log_dir, @@ -689,6 +699,7 @@ def _work_queue_submit_wait(task_queue=multiprocessing.Queue(), autolabel=False, autolabel_window=None, autocategory=False, + max_retries=0, should_stop=None, port=WORK_QUEUE_DEFAULT_PORT, wq_log_dir=None, @@ -803,6 +814,12 @@ def _work_queue_submit_wait(task_queue=multiprocessing.Queue(), if task.gpus is not None: t.specify_gpus(task.gpus) + if max_retries: + logger.debug(f"Specifying max_retries {max_retries}") + t.specify_max_retries(max_retries) + else: + logger.debug("Not specifying max_retries") + # Specify environment variables for the task if env is not None: for var in env: From 183bb662963e2c533aee55d1fba10b4482617d4e Mon Sep 17 00:00:00 2001 From: Ben Clifford Date: Mon, 3 May 2021 17:51:22 +0000 Subject: [PATCH 126/408] TODO: add priority spec for WQ c.f. htex priority prototype: in work queue, a priority is a double. In the htex prototype, a priority was anything that could be compared with other priorities in the same workflow. --- parsl/executors/workqueue/executor.py | 10 ++++++++-- 1 file changed, 8 insertions(+), 2 deletions(-) diff --git a/parsl/executors/workqueue/executor.py b/parsl/executors/workqueue/executor.py index b85b3faa6f..72148ff440 100644 --- a/parsl/executors/workqueue/executor.py +++ b/parsl/executors/workqueue/executor.py @@ -60,7 +60,7 @@ # Support structure to communicate parsl tasks to the work queue submit thread. -ParslTaskToWq = namedtuple('ParslTaskToWq', 'id category cores memory disk gpus env_pkg map_file function_file result_file input_files output_files') +ParslTaskToWq = namedtuple('ParslTaskToWq', 'id category cores memory disk gpus priority env_pkg map_file function_file result_file input_files output_files') # Support structure to communicate final status of work queue tasks to parsl # result is only valid if result_received is True @@ -342,11 +342,12 @@ def submit(self, func, resource_specification, *args, **kwargs): memory = None disk = None gpus = None + priority = None if resource_specification and isinstance(resource_specification, dict): logger.debug("Got resource specification: {}".format(resource_specification)) required_resource_types = set(['cores', 'memory', 'disk']) - acceptable_resource_types = set(['cores', 'memory', 'disk', 'gpus']) + acceptable_resource_types = set(['cores', 'memory', 'disk', 'gpus', 'priority']) keys = set(resource_specification.keys()) if not keys.issubset(acceptable_resource_types): @@ -372,6 +373,8 @@ def submit(self, func, resource_specification, *args, **kwargs): disk = resource_specification[k] elif k == 'gpus': gpus = resource_specification[k] + elif k == 'priority': + priority = resource_specification[k] self.task_counter += 1 task_id = self.task_counter @@ -435,6 +438,7 @@ def submit(self, func, resource_specification, *args, **kwargs): memory, disk, gpus, + priority, env_pkg, map_file, function_file, @@ -802,6 +806,8 @@ def _work_queue_submit_wait(task_queue=multiprocessing.Queue(), t.specify_disk(task.disk) if task.gpus is not None: t.specify_gpus(task.gpus) + if task.priority is not None: + t.specify_priority(task.priority) # Specify environment variables for the task if env is not None: From 2a9e4246fb61244053182191fbca660ffb1b97c4 Mon Sep 17 00:00:00 2001 From: Ben Clifford Date: Tue, 4 May 2021 16:49:15 +0000 Subject: [PATCH 127/408] Remove outdated IPP related comment in memoization --- parsl/dataflow/memoization.py | 3 --- 1 file changed, 3 deletions(-) diff --git a/parsl/dataflow/memoization.py b/parsl/dataflow/memoization.py index 4f30db335e..25985d0c7f 100644 --- a/parsl/dataflow/memoization.py +++ b/parsl/dataflow/memoization.py @@ -170,9 +170,6 @@ def __init__(self, dfk, memoize=True, checkpoint={}): def make_hash(self, task): """Create a hash of the task inputs. - If this fails here, then all ipp calls are also likely to fail due to failure - at serialization. - Args: - task (dict) : Task dictionary from dfk.tasks From f8bac789ad6ddf74a9b9c49a1c407fa9c2c12131 Mon Sep 17 00:00:00 2001 From: Ben Clifford Date: Tue, 4 May 2021 17:16:32 +0000 Subject: [PATCH 128/408] Turns out 0 evaluates to false, as well as None, so this if didn't distinguish between None and 0 --- parsl/executors/workqueue/executor.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/parsl/executors/workqueue/executor.py b/parsl/executors/workqueue/executor.py index 17cb7e7d2d..567bb675f6 100644 --- a/parsl/executors/workqueue/executor.py +++ b/parsl/executors/workqueue/executor.py @@ -814,7 +814,7 @@ def _work_queue_submit_wait(task_queue=multiprocessing.Queue(), if task.gpus is not None: t.specify_gpus(task.gpus) - if max_retries: + if max_retries is not None: logger.debug(f"Specifying max_retries {max_retries}") t.specify_max_retries(max_retries) else: From f19b0f97b85b28055397584c26dae26d67fcf2b6 Mon Sep 17 00:00:00 2001 From: Ben Clifford Date: Wed, 5 May 2021 12:23:20 +0000 Subject: [PATCH 129/408] more correctly wire max_retries --- parsl/executors/workqueue/executor.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/parsl/executors/workqueue/executor.py b/parsl/executors/workqueue/executor.py index 567bb675f6..302da4ac6d 100644 --- a/parsl/executors/workqueue/executor.py +++ b/parsl/executors/workqueue/executor.py @@ -250,7 +250,7 @@ def __init__(self, self.autolabel = autolabel self.autolabel_window = autolabel_window self.autocategory = autocategory - self.max_retries = 0 + self.max_retries = max_retries self.should_stop = multiprocessing.Value(c_bool, False) self.cached_envs = {} # type: Dict[int, str] self.worker_options = worker_options From 690f0753a27f855424dbc56154a3b3d11edaba2a Mon Sep 17 00:00:00 2001 From: Ben Clifford Date: Wed, 5 May 2021 12:40:53 +0000 Subject: [PATCH 130/408] fix off-by-one error in wq retries --- parsl/executors/workqueue/executor.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/parsl/executors/workqueue/executor.py b/parsl/executors/workqueue/executor.py index 302da4ac6d..04261f7a23 100644 --- a/parsl/executors/workqueue/executor.py +++ b/parsl/executors/workqueue/executor.py @@ -214,7 +214,7 @@ def __init__(self, autolabel: bool = False, autolabel_window: int = 1, autocategory: bool = True, - max_retries: Optional[int] = 0, + max_retries: Optional[int] = 1, init_command: str = "", worker_options: str = "", full_debug: bool = True, From d8b830d9de52a440323efce571a713d4f6b12e02 Mon Sep 17 00:00:00 2001 From: Ben Clifford Date: Wed, 5 May 2021 12:44:55 +0000 Subject: [PATCH 131/408] Remove unused walltime from LocalProvider --- parsl/providers/local/local.py | 2 -- 1 file changed, 2 deletions(-) diff --git a/parsl/providers/local/local.py b/parsl/providers/local/local.py index 0f03d81ec4..82379b8736 100644 --- a/parsl/providers/local/local.py +++ b/parsl/providers/local/local.py @@ -40,7 +40,6 @@ def __init__(self, init_blocks=1, min_blocks=0, max_blocks=1, - walltime="00:15:00", worker_init='', cmd_timeout=30, parallelism=1, @@ -54,7 +53,6 @@ def __init__(self, self.min_blocks = min_blocks self.max_blocks = max_blocks self.parallelism = parallelism - self.walltime = walltime self.script_dir = None self.cmd_timeout = cmd_timeout self.move_files = move_files From b347f6119765736ebb688558f6ec72e64ad9d173 Mon Sep 17 00:00:00 2001 From: Ben Clifford Date: Tue, 4 May 2021 19:08:27 +0000 Subject: [PATCH 132/408] clarify that max workers is per node --- parsl/executors/high_throughput/executor.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/parsl/executors/high_throughput/executor.py b/parsl/executors/high_throughput/executor.py index fc3265ec19..585fd2aafd 100644 --- a/parsl/executors/high_throughput/executor.py +++ b/parsl/executors/high_throughput/executor.py @@ -129,7 +129,7 @@ class HighThroughputExecutor(StatusHandlingExecutor, RepresentationMixin): the there's sufficient memory for each worker. Default: None max_workers : int - Caps the number of workers launched by the manager. Default: infinity + Caps the number of workers launched per node. Default: infinity cpu_affinity: string Whether or how each worker process sets thread affinity. Options are "none" to forgo From 68e23af3fd0589d823ca0dd319cc130c7f777d9f Mon Sep 17 00:00:00 2001 From: Ben Clifford Date: Wed, 5 May 2021 14:20:05 +0000 Subject: [PATCH 133/408] Correct documentation --- parsl/executors/workqueue/executor.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/parsl/executors/workqueue/executor.py b/parsl/executors/workqueue/executor.py index 04261f7a23..fa2beccfd6 100644 --- a/parsl/executors/workqueue/executor.py +++ b/parsl/executors/workqueue/executor.py @@ -177,7 +177,7 @@ class WorkQueueExecutor(NoStatusHandlingExecutor): Set the number of retries that Work Queue will make when a task fails. This is distinct from Parsl level retries configured in parsl.config.Config. Set to None to allow Work Queue to retry - tasks forever. By default, this is set to 0, so that all retries + tasks forever. By default, this is set to 1, so that all retries will be managed by Parsl. init_command: str From 57074405110dbd1fe170d1b71d844d1130c481f8 Mon Sep 17 00:00:00 2001 From: Ben Clifford Date: Fri, 7 May 2021 12:38:45 +0000 Subject: [PATCH 134/408] --- parsl/tests/configs/htex_local_retry_handler.py | 2 +- parsl/version.py | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/parsl/tests/configs/htex_local_retry_handler.py b/parsl/tests/configs/htex_local_retry_handler.py index f684b3f0cc..b22139fbe5 100644 --- a/parsl/tests/configs/htex_local_retry_handler.py +++ b/parsl/tests/configs/htex_local_retry_handler.py @@ -44,7 +44,7 @@ def test_retry_handler(exception, task_record): now = datetime.datetime.now() if (now - task_record['time_invoked']).total_seconds() < 120: logger.info("RETRY: time invoked is short") - return 0.1 # soft retries until 2 minute time limit + return 0.1 # soft retries until 2 minute time limit else: logger.error("RETRY: exceeded maximum allowable retry time") return 100 diff --git a/parsl/version.py b/parsl/version.py index 3c3541aaee..1f4817671b 100644 --- a/parsl/version.py +++ b/parsl/version.py @@ -3,4 +3,4 @@ ..[alpha/beta/..] Alphas will be numbered like this -> 0.4.0a0 """ -VERSION = '1.1.0+desc-2021.05.07a' +VERSION = '1.1.0+desc-2021.05.07b' From 8c780da1f34469643e119ac0c64a6f8e9ba5648b Mon Sep 17 00:00:00 2001 From: Ben Clifford Date: Fri, 7 May 2021 12:24:25 +0000 Subject: [PATCH 135/408] Add missing f for an f-string --- parsl/monitoring/monitoring.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/parsl/monitoring/monitoring.py b/parsl/monitoring/monitoring.py index dcd1f9363d..ce41233e1d 100644 --- a/parsl/monitoring/monitoring.py +++ b/parsl/monitoring/monitoring.py @@ -261,7 +261,7 @@ def start(self, run_id: str) -> int: if isinstance(comm_q_result, str): self.logger.error(f"MonitoringRouter sent an error message: {comm_q_result}") - raise RuntimeError("MonitoringRouter failed to start: {comm_q_result}") + raise RuntimeError(f"MonitoringRouter failed to start: {comm_q_result}") udp_dish_port, ic_port = comm_q_result From d8d59698ddf84d82ce3e3a86317066e921dc7596 Mon Sep 17 00:00:00 2001 From: Ben Clifford Date: Mon, 3 May 2021 17:51:02 +0000 Subject: [PATCH 136/408] fix and test wrong type handling for joinapp returns prior to this, returning the wrong type was resulting in a hang. after this, returning the wrong type gives a TypeError - for example: TypeError: join_app body must return a Future, got --- parsl/dataflow/dflow.py | 18 ++++++++++++++---- parsl/tests/test_python_apps/test_join.py | 15 +++++++++++++++ 2 files changed, 29 insertions(+), 4 deletions(-) diff --git a/parsl/dataflow/dflow.py b/parsl/dataflow/dflow.py index e05d68e1d3..01ff402188 100644 --- a/parsl/dataflow/dflow.py +++ b/parsl/dataflow/dflow.py @@ -336,10 +336,20 @@ def handle_exec_update(self, task_record, future): # listener to that inner future. inner_future = future.result() - assert isinstance(inner_future, Future) - task_record['status'] = States.joining - task_record['joins'] = inner_future - inner_future.add_done_callback(partial(self.handle_join_update, task_record)) + + # this assert should actually be a test that causes the + # current app to fail cleanly if it is not a Future + if isinstance(inner_future, Future): + task_record['status'] = States.joining + task_record['joins'] = inner_future + inner_future.add_done_callback(partial(self.handle_join_update, task_record)) + else: + task_record['time_returned'] = datetime.datetime.now() + task_record['status'] = States.failed + self.tasks_failed_count += 1 + task_record['time_returned'] = datetime.datetime.now() + with task_record['app_fu']._update_lock: + task_record['app_fu'].set_exception(TypeError(f"join_app body must return a Future, got {type(inner_future)}")) self._log_std_streams(task_record) diff --git a/parsl/tests/test_python_apps/test_join.py b/parsl/tests/test_python_apps/test_join.py index 51d5fcef54..74eabaa43a 100644 --- a/parsl/tests/test_python_apps/test_join.py +++ b/parsl/tests/test_python_apps/test_join.py @@ -1,3 +1,4 @@ +import pytest import time from parsl import join_app, python_app @@ -46,6 +47,20 @@ def test_result_flow(): assert res == RESULT_CONSTANT +@join_app +def join_wrong_type_app(): + return 3 + + +def test_wrong_type(): + # at present, wrong time raises an assert that does not propagate to user level + # so the DFK hangs. What should happen is that the app raises an exception via + # its app future. + f = join_wrong_type_app() + with pytest.raises(TypeError): + f.result() + + def test_dependency_on_joined(): g = add_one(outer_app()) res = g.result() From 1332de3b8fcaa4939ae31e6177167cdb850f4065 Mon Sep 17 00:00:00 2001 From: Ben Clifford Date: Sat, 8 May 2021 10:04:11 +0000 Subject: [PATCH 137/408] Update comments to new code --- parsl/dataflow/dflow.py | 4 ++-- parsl/tests/test_python_apps/test_join.py | 3 --- 2 files changed, 2 insertions(+), 5 deletions(-) diff --git a/parsl/dataflow/dflow.py b/parsl/dataflow/dflow.py index 01ff402188..8a6f9ddd59 100644 --- a/parsl/dataflow/dflow.py +++ b/parsl/dataflow/dflow.py @@ -337,8 +337,8 @@ def handle_exec_update(self, task_record, future): inner_future = future.result() - # this assert should actually be a test that causes the - # current app to fail cleanly if it is not a Future + # Fail with a TypeError if the joinapp python body returned + # something we can't join on. if isinstance(inner_future, Future): task_record['status'] = States.joining task_record['joins'] = inner_future diff --git a/parsl/tests/test_python_apps/test_join.py b/parsl/tests/test_python_apps/test_join.py index 74eabaa43a..75ef3c0f78 100644 --- a/parsl/tests/test_python_apps/test_join.py +++ b/parsl/tests/test_python_apps/test_join.py @@ -53,9 +53,6 @@ def join_wrong_type_app(): def test_wrong_type(): - # at present, wrong time raises an assert that does not propagate to user level - # so the DFK hangs. What should happen is that the app raises an exception via - # its app future. f = join_wrong_type_app() with pytest.raises(TypeError): f.result() From fb59021accd7940a2cf9fcb3669945b1ade5f9e9 Mon Sep 17 00:00:00 2001 From: Ben Clifford Date: Tue, 4 May 2021 18:36:44 +0000 Subject: [PATCH 138/408] wq executor should show itself using representation mixin there is an issue for this #2007 --- parsl/executors/workqueue/executor.py | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/parsl/executors/workqueue/executor.py b/parsl/executors/workqueue/executor.py index b85b3faa6f..d9149d2fc8 100644 --- a/parsl/executors/workqueue/executor.py +++ b/parsl/executors/workqueue/executor.py @@ -74,7 +74,7 @@ ParslFileToWq = namedtuple('ParslFileToWq', 'parsl_name stage cache') -class WorkQueueExecutor(NoStatusHandlingExecutor): +class WorkQueueExecutor(NoStatusHandlingExecutor, putils.RepresentationMixin): """Executor to use Work Queue batch system The WorkQueueExecutor system utilizes the Work Queue framework to @@ -235,7 +235,7 @@ def __init__(self, self.use_cache = use_cache self.working_dir = working_dir self.registered_files = set() # type: Set[str] - self.full = full_debug + self.full_debug = full_debug self.source = True if pack else source self.pack = pack self.extra_pkgs = extra_pkgs or [] @@ -285,7 +285,7 @@ def start(self): "launch_cmd": self.launch_cmd, "data_dir": self.function_data_dir, "collector_queue": self.collector_queue, - "full": self.full, + "full": self.full_debug, "shared_fs": self.shared_fs, "autolabel": self.autolabel, "autolabel_window": self.autolabel_window, From 971c589154d924fd23b3d89d5f5b437b7a6f2989 Mon Sep 17 00:00:00 2001 From: Ben Clifford Date: Mon, 10 May 2021 07:35:13 +0000 Subject: [PATCH 139/408] cherry-pickable removal of rendering tutorial into docs as a static page unsure if i want to pursue this, or alternatively moving tutorial tree into the main parsl repo. --- docs/conf.py | 5 ----- docs/index.rst | 1 - docs/quickstart.rst | 2 +- docs/userguide/index.rst | 1 + 4 files changed, 2 insertions(+), 7 deletions(-) diff --git a/docs/conf.py b/docs/conf.py index e9355b8059..401f8a7a5e 100644 --- a/docs/conf.py +++ b/docs/conf.py @@ -40,11 +40,6 @@ 'sphinx.ext.napoleon' ] -url = 'https://raw.githubusercontent.com/Parsl/parsl-tutorial/master/1-parsl-introduction.ipynb' -r = requests.get(url) -with open(os.path.join(os.path.dirname(__file__), '1-parsl-introduction.ipynb'), 'wb') as f: - f.write(r.content) - nbsphinx_execute = 'never' def linkcode_resolve(domain, info): diff --git a/docs/index.rst b/docs/index.rst index 9ca8611177..8ddaaa9b4a 100644 --- a/docs/index.rst +++ b/docs/index.rst @@ -37,7 +37,6 @@ Parsl can be used to implement various parallel computing paradigms: .. toctree:: quickstart - 1-parsl-introduction.ipynb userguide/index faq reference diff --git a/docs/quickstart.rst b/docs/quickstart.rst index 9e5248bf57..173f598f33 100644 --- a/docs/quickstart.rst +++ b/docs/quickstart.rst @@ -91,7 +91,7 @@ There are several options for following the tutorial: 1. Use `Binder `_ to follow the tutorial online without installing or writing any code locally. 2. Clone the `Parsl tutorial repository `_ using a local Parsl installation. -3. Read through the online `tutorial documentation <1-parsl-introduction.html>`_. +3. TODO [remove this option entirely as a rendered option, so that the two github based ones are always right? this aligns with them being separate repos. if they were one, repo then it would make sense to link in-repo] Read through the online `tutorial documentation <1-parsl-introduction.html>`_. Usage Tracking diff --git a/docs/userguide/index.rst b/docs/userguide/index.rst index 663fefd233..0d80ff0e4e 100644 --- a/docs/userguide/index.rst +++ b/docs/userguide/index.rst @@ -18,3 +18,4 @@ User guide joins performance usage_tracking + plugins From 4f40e4feef6e4a4cc14872e2951d80e80ae8e505 Mon Sep 17 00:00:00 2001 From: Ben Clifford Date: Mon, 10 May 2021 08:43:04 +0000 Subject: [PATCH 140/408] rough text --- docs/reference.rst | 1 + ...parsl.dataflow.memoization.id_for_memo.rst | 6 ++ docs/userguide/plugins.rst | 63 +++++++++++++++++++ 3 files changed, 70 insertions(+) create mode 100644 docs/stubs/parsl.dataflow.memoization.id_for_memo.rst create mode 100644 docs/userguide/plugins.rst diff --git a/docs/reference.rst b/docs/reference.rst index 067290abe8..fd2701331a 100644 --- a/docs/reference.rst +++ b/docs/reference.rst @@ -175,6 +175,7 @@ Internal parsl.app.python.PythonApp parsl.dataflow.dflow.DataFlowKernel parsl.dataflow.flow_control.FlowControl + parsl.dataflow.memoization.id_for_memo parsl.dataflow.memoization.Memoizer parsl.dataflow.strategy.Strategy parsl.dataflow.flow_control.Timer diff --git a/docs/stubs/parsl.dataflow.memoization.id_for_memo.rst b/docs/stubs/parsl.dataflow.memoization.id_for_memo.rst new file mode 100644 index 0000000000..9e3865de9f --- /dev/null +++ b/docs/stubs/parsl.dataflow.memoization.id_for_memo.rst @@ -0,0 +1,6 @@ +parsl.dataflow.memoization.id\_for\_memo +======================================== + +.. currentmodule:: parsl.dataflow.memoization + +.. autofunction:: id_for_memo \ No newline at end of file diff --git a/docs/userguide/plugins.rst b/docs/userguide/plugins.rst new file mode 100644 index 0000000000..65e6759120 --- /dev/null +++ b/docs/userguide/plugins.rst @@ -0,0 +1,63 @@ +Plugins +======= + +Parsl has several places where code can be plugged in. Parsl usually provides +several implementations that use each plugin point. + +This page gives a brief summary of those places and why you might want +to use them, with links to the API guide. + +Executors +--------- +When the parsl data flow kernel is ready for a task to run, it passes that +task to an `Executor`. The executor is then responsible for running the task's +python code and returning the result. This is the abstraction that allows one +executor to run code on the local submitting host, while another executor can +run the same code on a large supercomputer. + + +Providers, Launchers and Channels +--------------------------------- +Some executors are based on blocks of workers (for example the +`HighThroughputExecutor`: the submit side requires a +batch system (eg slurm, kubernetes) to start worker processes, which then +execute tasks. + +The particular way in which a system makes those workers start is implemented +by `Providers` and `Launchers`. + +A `Provider` allows a command line to be submitted as a request to the +underlying batch system to be run inside an allocation of nodes. + +A `Launcher` modifies that command line when run inside the allocation to +add on any wrappers that are needed to launch the command. (eg srun inside +slurm). Providers and launchers are usually paired together for a particular +system type. + +A `Channel` allows the commands used to interact with a `Provider` to be +executed on a remote system. The default channel executes commands on the +local system, but a few variants of an `SSHChannel` are provided. + + +File staging +------------ +Parsl can copy input files from an arbitrary URL into a task's working +environment, and copy output files from a task's working environment to +an arbitrary URL. A small set of data staging providers is installed by default, +for ``file://`` ``http://`` and ``ftp://`` URLs. More data staging providers can +be added in the workflow configuration, in the ``storage`` parameter of the +relevant `Executor`. Each provider should subclass the `Staging` class. + + +Memoization/checkpointing +------------------------- + +When parsl memoizes/checkpoints an app parameter, it does so by computing a +hash of that parameter that should be the same if that parameter is the same +on subsequent invocations. This isn't straightforward to do for arbitrary +objects, so parsl implements a checkpointing hash function for a few common +types, and raises an exception on unknown types (TK put in unknown exception +example text here so searching finds it). + +You can plug in your own type-specific hash code for additional types that +you need and understand using `id_for_memo`. From eac0ffd5c18cfdc9ec7c4e7e7b6a4ba2a6d5baa6 Mon Sep 17 00:00:00 2001 From: Ben Clifford Date: Mon, 10 May 2021 08:43:13 +0000 Subject: [PATCH 141/408] Revert "cherry-pickable removal of rendering tutorial into docs as a static page" This reverts commit 971c589154d924fd23b3d89d5f5b437b7a6f2989. --- docs/conf.py | 5 +++++ docs/index.rst | 1 + docs/quickstart.rst | 2 +- docs/userguide/index.rst | 1 - 4 files changed, 7 insertions(+), 2 deletions(-) diff --git a/docs/conf.py b/docs/conf.py index 401f8a7a5e..e9355b8059 100644 --- a/docs/conf.py +++ b/docs/conf.py @@ -40,6 +40,11 @@ 'sphinx.ext.napoleon' ] +url = 'https://raw.githubusercontent.com/Parsl/parsl-tutorial/master/1-parsl-introduction.ipynb' +r = requests.get(url) +with open(os.path.join(os.path.dirname(__file__), '1-parsl-introduction.ipynb'), 'wb') as f: + f.write(r.content) + nbsphinx_execute = 'never' def linkcode_resolve(domain, info): diff --git a/docs/index.rst b/docs/index.rst index 8ddaaa9b4a..9ca8611177 100644 --- a/docs/index.rst +++ b/docs/index.rst @@ -37,6 +37,7 @@ Parsl can be used to implement various parallel computing paradigms: .. toctree:: quickstart + 1-parsl-introduction.ipynb userguide/index faq reference diff --git a/docs/quickstart.rst b/docs/quickstart.rst index 173f598f33..9e5248bf57 100644 --- a/docs/quickstart.rst +++ b/docs/quickstart.rst @@ -91,7 +91,7 @@ There are several options for following the tutorial: 1. Use `Binder `_ to follow the tutorial online without installing or writing any code locally. 2. Clone the `Parsl tutorial repository `_ using a local Parsl installation. -3. TODO [remove this option entirely as a rendered option, so that the two github based ones are always right? this aligns with them being separate repos. if they were one, repo then it would make sense to link in-repo] Read through the online `tutorial documentation <1-parsl-introduction.html>`_. +3. Read through the online `tutorial documentation <1-parsl-introduction.html>`_. Usage Tracking diff --git a/docs/userguide/index.rst b/docs/userguide/index.rst index 0d80ff0e4e..663fefd233 100644 --- a/docs/userguide/index.rst +++ b/docs/userguide/index.rst @@ -18,4 +18,3 @@ User guide joins performance usage_tracking - plugins From cca3b3eddc124b79f81cd4de7ffe3a503bbf6750 Mon Sep 17 00:00:00 2001 From: Ben Clifford Date: Mon, 10 May 2021 10:07:21 +0000 Subject: [PATCH 142/408] Allow all required resources to be ommitted in WQ resource spec. The requirement is either that all of them are supplied, or none of them are supplied. Prior to use of parsl_resource_specification for additional specs, the "or none of them" part of this could be achieved by omitting the resource specification entirely. That doesn't work now that other resource specs can be added. --- parsl/executors/workqueue/executor.py | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/parsl/executors/workqueue/executor.py b/parsl/executors/workqueue/executor.py index 72148ff440..6fe8c666dd 100644 --- a/parsl/executors/workqueue/executor.py +++ b/parsl/executors/workqueue/executor.py @@ -356,7 +356,9 @@ def submit(self, func, resource_specification, *args, **kwargs): logger.error(message) raise ExecutorError(self, message) - if not self.autolabel and not keys.issuperset(required_resource_types): + key_check = required_resource_types.intersection(keys) + required_keys_ok = len(key_check) == 0 or key_check == required_resource_types + if not self.autolabel and not required_keys_ok: logger.error("Running with `autolabel=False`. In this mode, " "task resource specification requires " "three resources to be specified simultaneously: cores, memory, and disk") From 7130e296f9362655ebd127110116726d755ecd6d Mon Sep 17 00:00:00 2001 From: Ben Clifford Date: Thu, 18 Feb 2021 12:55:21 +0000 Subject: [PATCH 143/408] Existing strategies require an 'outstanding' property. This was not enforced/documented in the executor base classes. This patch makes it obligatory for statushandlingexecutors to have that, on the assumption that statushandlingexecutor will become generally a scaling-capable base class. --- docs/stubs/parsl.executors.LowLatencyExecutor.rst | 1 + parsl/executors/status_handling.py | 9 ++++++++- 2 files changed, 9 insertions(+), 1 deletion(-) diff --git a/docs/stubs/parsl.executors.LowLatencyExecutor.rst b/docs/stubs/parsl.executors.LowLatencyExecutor.rst index 1585cee303..3cf48e766d 100644 --- a/docs/stubs/parsl.executors.LowLatencyExecutor.rst +++ b/docs/stubs/parsl.executors.LowLatencyExecutor.rst @@ -38,6 +38,7 @@ parsl.executors.LowLatencyExecutor ~LowLatencyExecutor.executor_exception ~LowLatencyExecutor.hub_address ~LowLatencyExecutor.hub_port + ~LowLatencyExecutor.outstanding ~LowLatencyExecutor.provider ~LowLatencyExecutor.run_dir ~LowLatencyExecutor.scaling_enabled diff --git a/parsl/executors/status_handling.py b/parsl/executors/status_handling.py index e60f39c18b..7a486eba99 100644 --- a/parsl/executors/status_handling.py +++ b/parsl/executors/status_handling.py @@ -1,7 +1,7 @@ import logging import threading from itertools import compress -from abc import abstractmethod +from abc import abstractmethod, abstractproperty from concurrent.futures import Future from typing import List, Any, Dict, Tuple @@ -65,6 +65,13 @@ def _fail_job_async(self, block_id: Any, message: str): self._generated_block_id_counter += 1 self._simulated_status[block_id] = JobStatus(JobState.FAILED, message) + @abstractproperty + def outstanding(self) -> int: + """This should return the number of tasks that the executor has been given to run (waiting to run, and running now)""" + + raise NotImplementedError("Classes inheriting from StatusHandlingExecutor must implement " + "outstanding()") + def status(self) -> Dict[str, JobStatus]: """Return status of all blocks.""" From 7fccd2c676be009eaa30ea375a8538414f08b7cc Mon Sep 17 00:00:00 2001 From: Ben Clifford Date: Thu, 11 Mar 2021 19:38:19 +0000 Subject: [PATCH 144/408] introduce an abstract class above htex, below status handling executor which will handle provider based scaling, rather than htex knowing about it. this should then more easily allow the workqueue executor to implement provider/block based scaling this might then merge with statushandlingexecutor entirely - as in, no executor would implement the statushandlingexecutor except via this block based executor this commit should be a fairly minimal attempt to extract code from htext and move it into a superclass, rather than any attempt to refactor the parent classes - that seems useful but should be in a subsequent commit --- .../parsl.executors.ExtremeScaleExecutor.rst | 1 + ...parsl.executors.HighThroughputExecutor.rst | 1 + .../parsl.executors.WorkQueueExecutor.rst | 3 + parsl/executors/block_based.py | 65 +++++++++++++++++++ parsl/executors/high_throughput/executor.py | 61 +++++------------ parsl/executors/workqueue/executor.py | 33 ++++++++-- parsl/tests/configs/workqueue_blocks.py | 12 ++++ 7 files changed, 124 insertions(+), 52 deletions(-) create mode 100644 parsl/executors/block_based.py create mode 100644 parsl/tests/configs/workqueue_blocks.py diff --git a/docs/stubs/parsl.executors.ExtremeScaleExecutor.rst b/docs/stubs/parsl.executors.ExtremeScaleExecutor.rst index 2512e5923e..73cb43c38c 100644 --- a/docs/stubs/parsl.executors.ExtremeScaleExecutor.rst +++ b/docs/stubs/parsl.executors.ExtremeScaleExecutor.rst @@ -49,5 +49,6 @@ parsl.executors.ExtremeScaleExecutor ~ExtremeScaleExecutor.scaling_enabled ~ExtremeScaleExecutor.status_polling_interval ~ExtremeScaleExecutor.tasks + ~ExtremeScaleExecutor.workers_per_node \ No newline at end of file diff --git a/docs/stubs/parsl.executors.HighThroughputExecutor.rst b/docs/stubs/parsl.executors.HighThroughputExecutor.rst index f861b7fdf0..7b624913b9 100644 --- a/docs/stubs/parsl.executors.HighThroughputExecutor.rst +++ b/docs/stubs/parsl.executors.HighThroughputExecutor.rst @@ -49,5 +49,6 @@ parsl.executors.HighThroughputExecutor ~HighThroughputExecutor.scaling_enabled ~HighThroughputExecutor.status_polling_interval ~HighThroughputExecutor.tasks + ~HighThroughputExecutor.workers_per_node \ No newline at end of file diff --git a/docs/stubs/parsl.executors.WorkQueueExecutor.rst b/docs/stubs/parsl.executors.WorkQueueExecutor.rst index 1c200cef17..07a034d5b6 100644 --- a/docs/stubs/parsl.executors.WorkQueueExecutor.rst +++ b/docs/stubs/parsl.executors.WorkQueueExecutor.rst @@ -27,6 +27,7 @@ parsl.executors.WorkQueueExecutor ~WorkQueueExecutor.start ~WorkQueueExecutor.status ~WorkQueueExecutor.submit + ~WorkQueueExecutor.xxxold_scale_out @@ -41,8 +42,10 @@ parsl.executors.WorkQueueExecutor ~WorkQueueExecutor.executor_exception ~WorkQueueExecutor.hub_address ~WorkQueueExecutor.hub_port + ~WorkQueueExecutor.outstanding ~WorkQueueExecutor.provider ~WorkQueueExecutor.status_polling_interval ~WorkQueueExecutor.tasks + ~WorkQueueExecutor.workers_per_node \ No newline at end of file diff --git a/parsl/executors/block_based.py b/parsl/executors/block_based.py new file mode 100644 index 0000000000..ad44113fbd --- /dev/null +++ b/parsl/executors/block_based.py @@ -0,0 +1,65 @@ +import logging + +from abc import abstractmethod, abstractproperty +from parsl.executors.errors import ScalingFailed +from parsl.executors.status_handling import StatusHandlingExecutor +from typing import Any, Dict, List, Tuple, Union + +logger = logging.getLogger(__name__) + + +class BlockProviderExecutor(StatusHandlingExecutor): + """TODO: basically anything to do with providers/scaling/blocks should be moved into this""" + + def __init__(self, provider): + super().__init__(provider) + self.blocks = {} # type: Dict[str, str] + self.block_mapping = {} # type: Dict[str, str] + + def scale_out(self, blocks: int = 1) -> List[str]: + """Scales out the number of blocks by "blocks" + """ + if not self.provider: + raise (ScalingFailed(None, "No execution provider available")) + block_ids = [] + for i in range(blocks): + block_id = str(len(self.blocks)) + try: + job_id = self._launch_block(block_id) + self.blocks[block_id] = job_id + self.block_mapping[job_id] = block_id + block_ids.append(block_id) + except Exception as ex: + self._fail_job_async(block_id, + "Failed to start block {}: {}".format(block_id, ex)) + return block_ids + + def _launch_block(self, block_id: str) -> Any: + launch_cmd = self._get_launch_command(block_id) + # if self.launch_cmd is None: + # raise ScalingFailed(self.provider.label, "No launch command") + # launch_cmd = self.launch_cmd.format(block_id=block_id) + job_id = self.provider.submit(launch_cmd, 1) + logger.debug("Launched block {}->{}".format(block_id, job_id)) + if not job_id: + raise(ScalingFailed(self.provider.label, + "Attempts to provision nodes via provider has failed")) + return job_id + + @abstractmethod + def _get_launch_command(self, block_id: str) -> str: + pass + + def _get_block_and_job_ids(self) -> Tuple[List[str], List[Any]]: + # Not using self.blocks.keys() and self.blocks.values() simultaneously + # The dictionary may be changed during invoking this function + # As scale_in and scale_out are invoked in multiple threads + block_ids = list(self.blocks.keys()) + job_ids = [] # types: List[Any] + for bid in block_ids: + job_ids.append(self.blocks[bid]) + return block_ids, job_ids + + @abstractproperty + def workers_per_node(self) -> Union[int, float]: + pass diff --git a/parsl/executors/high_throughput/executor.py b/parsl/executors/high_throughput/executor.py index 047e208cad..54b31a6766 100644 --- a/parsl/executors/high_throughput/executor.py +++ b/parsl/executors/high_throughput/executor.py @@ -7,7 +7,7 @@ import pickle from multiprocessing import Process, Queue from typing import Dict # noqa F401 (used in type annotation) -from typing import List, Optional, Tuple, Union, Any +from typing import List, Optional, Tuple, Union import math from parsl.serialize import pack_apply_message, deserialize @@ -20,7 +20,7 @@ UnsupportedFeatureError ) -from parsl.executors.status_handling import StatusHandlingExecutor +from parsl.executors.block_based import BlockProviderExecutor from parsl.providers.provider_base import ExecutionProvider from parsl.data_provider.staging import Staging from parsl.addresses import get_all_addresses @@ -32,7 +32,7 @@ logger = logging.getLogger(__name__) -class HighThroughputExecutor(StatusHandlingExecutor, RepresentationMixin): +class HighThroughputExecutor(BlockProviderExecutor, RepresentationMixin): """Executor designed for cluster-scale The HighThroughputExecutor system has the following components: @@ -190,15 +190,13 @@ def __init__(self, logger.debug("Initializing HighThroughputExecutor") - StatusHandlingExecutor.__init__(self, provider) + BlockProviderExecutor.__init__(self, provider) self.label = label self.launch_cmd = launch_cmd self.worker_debug = worker_debug self.storage_access = storage_access self.working_dir = working_dir self.managed = managed - self.blocks = {} # type: Dict[str, str] - self.block_mapping = {} # type: Dict[str, str] self.cores_per_worker = cores_per_worker self.mem_per_worker = mem_per_worker self.max_workers = max_workers @@ -221,9 +219,9 @@ def __init__(self, self.provider.cores_per_node is not None: cpu_slots = math.floor(self.provider.cores_per_node / cores_per_worker) - self.workers_per_node = min(max_workers, mem_slots, cpu_slots) - if self.workers_per_node == float('inf'): - self.workers_per_node = 1 # our best guess-- we do not have any provider hints + self._workers_per_node = min(max_workers, mem_slots, cpu_slots) + if self._workers_per_node == float('inf'): + self._workers_per_node = 1 # our best guess-- we do not have any provider hints self._task_counter = 0 self.run_id = None # set to the correct run_id in dfk @@ -599,34 +597,9 @@ def create_monitoring_info(self, status): msg.append(d) return msg - def scale_out(self, blocks=1): - """Scales out the number of blocks by "blocks" - """ - if not self.provider: - raise (ScalingFailed(None, "No execution provider available")) - block_ids = [] - for i in range(blocks): - block_id = str(len(self.blocks)) - try: - job_id = self._launch_block(block_id) - self.blocks[block_id] = job_id - self.block_mapping[job_id] = block_id - block_ids.append(block_id) - except Exception as ex: - self._fail_job_async(block_id, - "Failed to start block {}: {}".format(block_id, ex)) - return block_ids - - def _launch_block(self, block_id: str) -> Any: - if self.launch_cmd is None: - raise ScalingFailed(self.provider.label, "No launch command") - launch_cmd = self.launch_cmd.format(block_id=block_id) - job_id = self.provider.submit(launch_cmd, 1) - logger.debug("Launched block {}->{}".format(block_id, job_id)) - if not job_id: - raise(ScalingFailed(self.provider.label, - "Attempts to provision nodes via provider has failed")) - return job_id + @property + def workers_per_node(self) -> Union[int, float]: + return self._workers_per_node def scale_in(self, blocks=None, block_ids=[], force=True, max_idletime=None): """Scale in the number of active blocks by specified amount. @@ -708,15 +681,11 @@ def scale_in(self, blocks=None, block_ids=[], force=True, max_idletime=None): return block_ids_killed - def _get_block_and_job_ids(self) -> Tuple[List[str], List[Any]]: - # Not using self.blocks.keys() and self.blocks.values() simultaneously - # The dictionary may be changed during invoking this function - # As scale_in and scale_out are invoked in multiple threads - block_ids = list(self.blocks.keys()) - job_ids = [] # types: List[Any] - for bid in block_ids: - job_ids.append(self.blocks[bid]) - return block_ids, job_ids + def _get_launch_command(self, block_id: str) -> str: + if self.launch_cmd is None: + raise ScalingFailed(self.provider.label, "No launch command") + launch_cmd = self.launch_cmd.format(block_id=block_id) + return launch_cmd def shutdown(self, hub=True, targets='all', block=False): """Shutdown the executor, including all workers and controllers. diff --git a/parsl/executors/workqueue/executor.py b/parsl/executors/workqueue/executor.py index b85b3faa6f..8ccc463335 100644 --- a/parsl/executors/workqueue/executor.py +++ b/parsl/executors/workqueue/executor.py @@ -25,14 +25,14 @@ from parsl.executors.errors import ExecutorError from parsl.data_provider.files import File from parsl.errors import OptionalModuleMissing -from parsl.executors.status_handling import NoStatusHandlingExecutor +from parsl.executors.block_based import BlockProviderExecutor from parsl.providers.provider_base import ExecutionProvider from parsl.providers import LocalProvider, CondorProvider from parsl.executors.errors import ScalingFailed from parsl.executors.workqueue import exec_parsl_function import typeguard -from typing import Dict, List, Optional, Set +from typing import Dict, List, Optional, Set, Union from parsl.data_provider.staging import Staging from .errors import WorkQueueTaskFailure @@ -74,7 +74,7 @@ ParslFileToWq = namedtuple('ParslFileToWq', 'parsl_name stage cache') -class WorkQueueExecutor(NoStatusHandlingExecutor): +class WorkQueueExecutor(BlockProviderExecutor): """Executor to use Work Queue batch system The WorkQueueExecutor system utilizes the Work Queue framework to @@ -211,8 +211,7 @@ def __init__(self, worker_options: str = "", full_debug: bool = True, worker_executable: str = 'work_queue_worker'): - NoStatusHandlingExecutor.__init__(self) - self._provider = provider + BlockProviderExecutor.__init__(self, provider) self._scaling_enabled = True if not _work_queue_enabled: @@ -263,6 +262,11 @@ def __init__(self, if self.init_command != "": self.launch_cmd = self.init_command + "; " + self.launch_cmd + def _get_launch_command(self, block_id): + # this executor uses different terminology for worker/launch + # commands than in htex + return self.worker_command + def start(self): """Create submit process and collector thread to create, send, and retrieve Parsl tasks within the Work Queue system. @@ -577,6 +581,8 @@ def initialize_scaling(self): self.worker_command = self._construct_worker_command() self._patch_providers() + # TODO: this init_blocks handling should be factored with the + # corresponding htex handling and put into the BlockProviderExecutor if hasattr(self.provider, 'init_blocks'): try: self.scale_out(blocks=self.provider.init_blocks) @@ -584,7 +590,18 @@ def initialize_scaling(self): logger.debug("Scaling out failed: {}".format(e)) raise e - def scale_out(self, blocks=1): + @property + def outstanding(self) -> int: + """TODO: this is very inefficient and probably should be replaced with + counters, but this one is minimally invasive to the rest of the code.""" + outstanding = 0 + for fut in self.tasks.values(): + if not fut.done(): + outstanding += 1 + logger.debug(f"Counted {outstanding} outstanding tasks") + return outstanding + + def xxxold_scale_out(self, blocks=1): """Scale out method. We should have the scale out method simply take resource object @@ -603,6 +620,10 @@ def scale_out(self, blocks=1): else: logger.error("No execution provider available to scale") + @property + def workers_per_node(self) -> Union[int, float]: + return 1 + def scale_in(self, count): """Scale in method. Not implemented. """ diff --git a/parsl/tests/configs/workqueue_blocks.py b/parsl/tests/configs/workqueue_blocks.py new file mode 100644 index 0000000000..f7631cd70d --- /dev/null +++ b/parsl/tests/configs/workqueue_blocks.py @@ -0,0 +1,12 @@ +from parsl.config import Config +from parsl.executors import WorkQueueExecutor + +from parsl.data_provider.http import HTTPInTaskStaging +from parsl.data_provider.ftp import FTPInTaskStaging +from parsl.data_provider.file_noop import NoOpFileStaging + +from parsl.providers import LocalProvider + +config = Config(executors=[WorkQueueExecutor(port=9000, + storage_access=[FTPInTaskStaging(), HTTPInTaskStaging(), NoOpFileStaging()], + provider=LocalProvider(init_blocks=0, min_blocks=0, max_blocks=1))]) From 40a8c75c0db1900048de919c1447a7363d26449f Mon Sep 17 00:00:00 2001 From: Ben Clifford Date: Mon, 10 May 2021 10:51:22 +0000 Subject: [PATCH 145/408] remove unused old scaleout for wq --- .../parsl.executors.WorkQueueExecutor.rst | 1 - parsl/executors/workqueue/executor.py | 19 ------------------- 2 files changed, 20 deletions(-) diff --git a/docs/stubs/parsl.executors.WorkQueueExecutor.rst b/docs/stubs/parsl.executors.WorkQueueExecutor.rst index 07a034d5b6..d1cf362000 100644 --- a/docs/stubs/parsl.executors.WorkQueueExecutor.rst +++ b/docs/stubs/parsl.executors.WorkQueueExecutor.rst @@ -27,7 +27,6 @@ parsl.executors.WorkQueueExecutor ~WorkQueueExecutor.start ~WorkQueueExecutor.status ~WorkQueueExecutor.submit - ~WorkQueueExecutor.xxxold_scale_out diff --git a/parsl/executors/workqueue/executor.py b/parsl/executors/workqueue/executor.py index 8ccc463335..f9f6d16de9 100644 --- a/parsl/executors/workqueue/executor.py +++ b/parsl/executors/workqueue/executor.py @@ -601,25 +601,6 @@ def outstanding(self) -> int: logger.debug(f"Counted {outstanding} outstanding tasks") return outstanding - def xxxold_scale_out(self, blocks=1): - """Scale out method. - - We should have the scale out method simply take resource object - which will have the scaling methods, scale_out itself should be a coroutine, since - scaling tasks can be slow. - """ - if self.provider: - for i in range(blocks): - external_block = str(len(self.blocks)) - internal_block = self.provider.submit(self.worker_command, 1) - # Failed to create block with provider - if not internal_block: - raise(ScalingFailed(self.provider.label, "Attempts to create nodes using the provider has failed")) - else: - self.blocks[external_block] = internal_block - else: - logger.error("No execution provider available to scale") - @property def workers_per_node(self) -> Union[int, float]: return 1 From a0602d011749a72cff87db87444cabc2d246813b Mon Sep 17 00:00:00 2001 From: Ben Clifford Date: Mon, 10 May 2021 11:33:41 +0000 Subject: [PATCH 146/408] Move BlockProviderExecutor in status handling source, in preparation for merging that class with status handling executor class --- parsl/executors/block_based.py | 65 --------------------- parsl/executors/high_throughput/executor.py | 2 +- parsl/executors/status_handling.py | 61 ++++++++++++++++++- parsl/executors/workqueue/executor.py | 3 +- 4 files changed, 62 insertions(+), 69 deletions(-) delete mode 100644 parsl/executors/block_based.py diff --git a/parsl/executors/block_based.py b/parsl/executors/block_based.py deleted file mode 100644 index ad44113fbd..0000000000 --- a/parsl/executors/block_based.py +++ /dev/null @@ -1,65 +0,0 @@ -import logging - -from abc import abstractmethod, abstractproperty -from parsl.executors.errors import ScalingFailed -from parsl.executors.status_handling import StatusHandlingExecutor -from typing import Any, Dict, List, Tuple, Union - -logger = logging.getLogger(__name__) - - -class BlockProviderExecutor(StatusHandlingExecutor): - """TODO: basically anything to do with providers/scaling/blocks should be moved into this""" - - def __init__(self, provider): - super().__init__(provider) - self.blocks = {} # type: Dict[str, str] - self.block_mapping = {} # type: Dict[str, str] - - def scale_out(self, blocks: int = 1) -> List[str]: - """Scales out the number of blocks by "blocks" - """ - if not self.provider: - raise (ScalingFailed(None, "No execution provider available")) - block_ids = [] - for i in range(blocks): - block_id = str(len(self.blocks)) - try: - job_id = self._launch_block(block_id) - self.blocks[block_id] = job_id - self.block_mapping[job_id] = block_id - block_ids.append(block_id) - except Exception as ex: - self._fail_job_async(block_id, - "Failed to start block {}: {}".format(block_id, ex)) - return block_ids - - def _launch_block(self, block_id: str) -> Any: - launch_cmd = self._get_launch_command(block_id) - # if self.launch_cmd is None: - # raise ScalingFailed(self.provider.label, "No launch command") - # launch_cmd = self.launch_cmd.format(block_id=block_id) - job_id = self.provider.submit(launch_cmd, 1) - logger.debug("Launched block {}->{}".format(block_id, job_id)) - if not job_id: - raise(ScalingFailed(self.provider.label, - "Attempts to provision nodes via provider has failed")) - return job_id - - @abstractmethod - def _get_launch_command(self, block_id: str) -> str: - pass - - def _get_block_and_job_ids(self) -> Tuple[List[str], List[Any]]: - # Not using self.blocks.keys() and self.blocks.values() simultaneously - # The dictionary may be changed during invoking this function - # As scale_in and scale_out are invoked in multiple threads - block_ids = list(self.blocks.keys()) - job_ids = [] # types: List[Any] - for bid in block_ids: - job_ids.append(self.blocks[bid]) - return block_ids, job_ids - - @abstractproperty - def workers_per_node(self) -> Union[int, float]: - pass diff --git a/parsl/executors/high_throughput/executor.py b/parsl/executors/high_throughput/executor.py index 54b31a6766..33d6387319 100644 --- a/parsl/executors/high_throughput/executor.py +++ b/parsl/executors/high_throughput/executor.py @@ -20,7 +20,7 @@ UnsupportedFeatureError ) -from parsl.executors.block_based import BlockProviderExecutor +from parsl.executors.status_handling import BlockProviderExecutor from parsl.providers.provider_base import ExecutionProvider from parsl.data_provider.staging import Staging from parsl.addresses import get_all_addresses diff --git a/parsl/executors/status_handling.py b/parsl/executors/status_handling.py index 7a486eba99..bbb939b8fa 100644 --- a/parsl/executors/status_handling.py +++ b/parsl/executors/status_handling.py @@ -3,12 +3,14 @@ from itertools import compress from abc import abstractmethod, abstractproperty from concurrent.futures import Future -from typing import List, Any, Dict, Tuple +from typing import List, Any, Dict, Tuple, Union import parsl # noqa F401 from parsl.executors.base import ParslExecutor +from parsl.executors.errors import ScalingFailed from parsl.providers.provider_base import JobStatus, ExecutionProvider, JobState + logger = logging.getLogger(__name__) @@ -132,6 +134,63 @@ def _filter_scale_in_ids(self, to_kill, killed): return list(compress(to_kill, killed)) +class BlockProviderExecutor(StatusHandlingExecutor): + """TODO: basically anything to do with providers/scaling/blocks should be moved into this""" + + def __init__(self, provider): + super().__init__(provider) + self.blocks = {} # type: Dict[str, str] + self.block_mapping = {} # type: Dict[str, str] + + def scale_out(self, blocks: int = 1) -> List[str]: + """Scales out the number of blocks by "blocks" + """ + if not self.provider: + raise (ScalingFailed(None, "No execution provider available")) + block_ids = [] + for i in range(blocks): + block_id = str(len(self.blocks)) + try: + job_id = self._launch_block(block_id) + self.blocks[block_id] = job_id + self.block_mapping[job_id] = block_id + block_ids.append(block_id) + except Exception as ex: + self._fail_job_async(block_id, + "Failed to start block {}: {}".format(block_id, ex)) + return block_ids + + def _launch_block(self, block_id: str) -> Any: + launch_cmd = self._get_launch_command(block_id) + # if self.launch_cmd is None: + # raise ScalingFailed(self.provider.label, "No launch command") + # launch_cmd = self.launch_cmd.format(block_id=block_id) + job_id = self.provider.submit(launch_cmd, 1) + logger.debug("Launched block {}->{}".format(block_id, job_id)) + if not job_id: + raise(ScalingFailed(self.provider.label, + "Attempts to provision nodes via provider has failed")) + return job_id + + @abstractmethod + def _get_launch_command(self, block_id: str) -> str: + pass + + def _get_block_and_job_ids(self) -> Tuple[List[str], List[Any]]: + # Not using self.blocks.keys() and self.blocks.values() simultaneously + # The dictionary may be changed during invoking this function + # As scale_in and scale_out are invoked in multiple threads + block_ids = list(self.blocks.keys()) + job_ids = [] # types: List[Any] + for bid in block_ids: + job_ids.append(self.blocks[bid]) + return block_ids, job_ids + + @abstractproperty + def workers_per_node(self) -> Union[int, float]: + pass + + class NoStatusHandlingExecutor(ParslExecutor): def __init__(self): super().__init__() diff --git a/parsl/executors/workqueue/executor.py b/parsl/executors/workqueue/executor.py index f9f6d16de9..b476fe2db3 100644 --- a/parsl/executors/workqueue/executor.py +++ b/parsl/executors/workqueue/executor.py @@ -25,10 +25,9 @@ from parsl.executors.errors import ExecutorError from parsl.data_provider.files import File from parsl.errors import OptionalModuleMissing -from parsl.executors.block_based import BlockProviderExecutor +from parsl.executors.status_handling import BlockProviderExecutor from parsl.providers.provider_base import ExecutionProvider from parsl.providers import LocalProvider, CondorProvider -from parsl.executors.errors import ScalingFailed from parsl.executors.workqueue import exec_parsl_function import typeguard From ce0f08676734973046015985fa2bc02e38c0f48f Mon Sep 17 00:00:00 2001 From: Ben Clifford Date: Mon, 10 May 2021 11:50:52 +0000 Subject: [PATCH 147/408] Merge StatusHandling and BlockProvider executor base classes --- parsl/executors/low_latency/executor.py | 6 +++--- parsl/executors/status_handling.py | 18 +++--------------- 2 files changed, 6 insertions(+), 18 deletions(-) diff --git a/parsl/executors/low_latency/executor.py b/parsl/executors/low_latency/executor.py index 87ce2d88c1..94deca584f 100644 --- a/parsl/executors/low_latency/executor.py +++ b/parsl/executors/low_latency/executor.py @@ -11,14 +11,14 @@ from parsl.executors.low_latency import zmq_pipes from parsl.executors.low_latency import interchange from parsl.executors.errors import ScalingFailed, DeserializationError, BadMessage, UnsupportedFeatureError -from parsl.executors.status_handling import StatusHandlingExecutor +from parsl.executors.status_handling import BlockProviderExecutor from parsl.utils import RepresentationMixin from parsl.providers import LocalProvider logger = logging.getLogger(__name__) -class LowLatencyExecutor(StatusHandlingExecutor, RepresentationMixin): +class LowLatencyExecutor(BlockProviderExecutor, RepresentationMixin): """ TODO: docstring for LowLatencyExecutor """ @@ -40,7 +40,7 @@ def __init__(self, ): logger.debug("Initializing LowLatencyExecutor") - StatusHandlingExecutor.__init__(self, provider) + BlockProviderExecutor.__init__(self, provider) self.label = label self.launch_cmd = launch_cmd self.provider = provider diff --git a/parsl/executors/status_handling.py b/parsl/executors/status_handling.py index bbb939b8fa..cb6bbcfee9 100644 --- a/parsl/executors/status_handling.py +++ b/parsl/executors/status_handling.py @@ -14,7 +14,7 @@ logger = logging.getLogger(__name__) -class StatusHandlingExecutor(ParslExecutor): +class BlockProviderExecutor(ParslExecutor): def __init__(self, provider): super().__init__() self._provider = provider # type: ExecutionProvider @@ -26,6 +26,8 @@ def __init__(self, provider): self._executor_exception = None self._generated_block_id_counter = 1 self._tasks = {} # type: Dict[object, Future] + self.blocks = {} # type: Dict[str, str] + self.block_mapping = {} # type: Dict[str, str] def _make_status_dict(self, block_ids: List[str], status_list: List[JobStatus]) -> Dict[str, JobStatus]: """Given a list of block ids and a list of corresponding status strings, @@ -53,11 +55,6 @@ def status_polling_interval(self): else: return self._provider.status_polling_interval - @abstractmethod - def _get_block_and_job_ids(self) -> Tuple[List[str], List[Any]]: - raise NotImplementedError("Classes inheriting from StatusHandlingExecutor must implement " - "_get_block_and_job_ids()") - def _fail_job_async(self, block_id: Any, message: str): """Marks a job that has failed to start but would not otherwise be included in status() as failed and report it in status() @@ -133,15 +130,6 @@ def _filter_scale_in_ids(self, to_kill, killed): # Filters first iterable by bool values in second return list(compress(to_kill, killed)) - -class BlockProviderExecutor(StatusHandlingExecutor): - """TODO: basically anything to do with providers/scaling/blocks should be moved into this""" - - def __init__(self, provider): - super().__init__(provider) - self.blocks = {} # type: Dict[str, str] - self.block_mapping = {} # type: Dict[str, str] - def scale_out(self, blocks: int = 1) -> List[str]: """Scales out the number of blocks by "blocks" """ From 364aca20b011ab20d55e9f844c05467c22b0f1f3 Mon Sep 17 00:00:00 2001 From: Ben Clifford Date: Fri, 7 May 2021 09:08:29 +0000 Subject: [PATCH 148/408] experiment: workflow-pluggable retry scoring when a task fails, instead of decrementing retry count by 1 (repeatedly down to 0) instead allow a workflow-pluggable piece of code to inspect the error (with some context) and decide how much to decrease the retry count. other design space points: - code could decide to retry or not, and the retry count is a scratch record it gets but parsl doesn't touch that retry count at all. - the retry scorer, if given the task record, is not prohibited from fiddling with the task record. What sort of things are plausible there? - changing the executor label for the task, so that the job retries somewhere else - for example some executor that is more expensive (slower to schedule but longer tasks?) - retry for a time period rather than for a number of counts - eg so as to not burn through retry units very fast in a fast failing transient case - so "quick fails" are discounted There's now a distinction between fail count (as in the number of times we've tried to run this task), and something like "fail cost" - the amount of badness that this task has accumulated (instead of accumulating 1 unit each time). These two quantities should probably be tracked independently (including in monitoring) As we're plugging in user code, exceptions in this logic can be expected to break (as in, user code is "not trusted") so we need to handle retry logic exceptions rather than just hanging the DFK. TEST CASE: a retry handler that always raises an exception. (this should result in the app invocation failing) TEST CASE: a retry handler that always returns 1 (rather than the default, which behaves the same) TEST CASE: a retry handler that returns 0.5 and check that we get more retries TEST CASE: a retry handler that retries for a minute --- parsl/config.py | 10 ++- parsl/dataflow/dflow.py | 14 ++- .../tests/configs/htex_local_retry_handler.py | 90 +++++++++++++++++++ 3 files changed, 110 insertions(+), 4 deletions(-) create mode 100644 parsl/tests/configs/htex_local_retry_handler.py diff --git a/parsl/config.py b/parsl/config.py index 9377876b7b..186ec979e0 100644 --- a/parsl/config.py +++ b/parsl/config.py @@ -1,7 +1,7 @@ import logging import typeguard -from typing import List, Optional +from typing import Callable, List, Optional from parsl.utils import RepresentationMixin from parsl.executors.base import ParslExecutor @@ -41,7 +41,11 @@ class Config(RepresentationMixin): monitoring : MonitoringHub, optional The config to use for database monitoring. Default is None which does not log to a database. retries : int, optional - Set the number of retries in case of failure. Default is 0. + Set the number of retries (or available retry budget when using retry_handler) in case of failure. Default is 0. + retry_handler : function, optional + A user pluggable handler to decide if/how a task retry should happen. + If no handler is specified, then each task failure incurs a retry cost + of 1. run_dir : str, optional Path to run directory. Default is 'runinfo'. strategy : str, optional @@ -73,6 +77,7 @@ def __init__(self, garbage_collect: bool = True, internal_tasks_max_threads: int = 10, retries: int = 0, + retry_handler: Optional[Callable] = None, run_dir: str = 'runinfo', strategy: Optional[str] = 'simple', max_idletime: float = 120.0, @@ -100,6 +105,7 @@ def __init__(self, self.garbage_collect = garbage_collect self.internal_tasks_max_threads = internal_tasks_max_threads self.retries = retries + self.retry_handler = retry_handler self.run_dir = run_dir self.strategy = strategy self.max_idletime = max_idletime diff --git a/parsl/dataflow/dflow.py b/parsl/dataflow/dflow.py index e05d68e1d3..2cb04e4576 100644 --- a/parsl/dataflow/dflow.py +++ b/parsl/dataflow/dflow.py @@ -198,7 +198,7 @@ def _create_task_log_info(self, task_record): """ Create the dictionary that will be included in the log. """ - info_to_monitor = ['func_name', 'memoize', 'hashsum', 'fail_count', 'status', + info_to_monitor = ['func_name', 'memoize', 'hashsum', 'fail_count', 'fail_cost', 'status', 'id', 'time_invoked', 'try_time_launched', 'time_returned', 'try_time_returned', 'executor'] task_log_info = {"task_" + k: task_record[k] for k in info_to_monitor} @@ -291,6 +291,13 @@ def handle_exec_update(self, task_record, future): # tossed. task_record['fail_history'].append(repr(e)) task_record['fail_count'] += 1 + if self._config.retry_handler: + # TODO: put protective code around here for when retry_handler + # raises an exception: at which point the task should be + # aborted entirely (eg set fail_cost > config retries) + task_record['fail_cost'] += self._config.retry_handler(task_record) + else: + task_record['fail_cost'] += 1 if task_record['status'] == States.dep_fail: logger.info("Task {} failed due to dependency failure so skipping retries".format(task_id)) @@ -298,7 +305,7 @@ def handle_exec_update(self, task_record, future): with task_record['app_fu']._update_lock: task_record['app_fu'].set_exception(e) - elif task_record['fail_count'] <= self._config.retries: + elif task_record['fail_cost'] <= self._config.retries: # record the final state for this try before we mutate for retries task_record['status'] = States.fail_retryable @@ -370,6 +377,8 @@ def handle_join_update(self, task_record, inner_app_future): # tossed. task_record['fail_history'].append(repr(e)) task_record['fail_count'] += 1 + # no need to update the fail cost because join apps are never + # retried task_record['status'] = States.failed self.tasks_failed_count += 1 @@ -815,6 +824,7 @@ def submit(self, func, app_args, executors='all', cache=False, ignore_for_cache= 'hashsum': None, 'exec_fu': None, 'fail_count': 0, + 'fail_cost': 0, 'fail_history': [], 'from_memo': None, 'ignore_for_cache': ignore_for_cache, diff --git a/parsl/tests/configs/htex_local_retry_handler.py b/parsl/tests/configs/htex_local_retry_handler.py new file mode 100644 index 0000000000..e6fbcba550 --- /dev/null +++ b/parsl/tests/configs/htex_local_retry_handler.py @@ -0,0 +1,90 @@ +""" +The aim of this configuration is to run a local htex +in a similar manner to htex_local.py, but with lots of +options different and more complicated than in that +configuration, so that more code paths are executed +than when testing only with htex_local. + +It does not matter too much *what* is different in this +configuration; what matters is that the differences +cause significantly different pieces of parsl code to be +run - for example, by turning on monitoring, by allowing +blocks to be started by a strategy, by using a different +set of staging providers, by using timing parameters that +will cause substantially different behaviour on whatever +those timing parameters control. +""" + +# imports for monitoring: +from parsl.monitoring import MonitoringHub + +import datetime +import logging +import os + +from parsl.providers import LocalProvider +from parsl.channels import LocalChannel +from parsl.launchers import SingleNodeLauncher + +from parsl.config import Config +from parsl.executors import HighThroughputExecutor + + +from parsl.data_provider.http import HTTPInTaskStaging +from parsl.data_provider.ftp import FTPInTaskStaging +from parsl.data_provider.file_noop import NoOpFileStaging + +working_dir = os.getcwd() + "/" + "test_htex_alternate" + +logger = logging.getLogger("parsl.benc") + + +def test_retry_handler(task_record): + logger.info("in test_retry_handler") + now = datetime.datetime.now() + if (now - task_record['time_invoked']).total_seconds() < 120: + logger.info("RETRY: time invoked is short") + return 0.1 # soft retries until 2 minute time limit + else: + logger.error("RETRY: exceeded maximum allowable retry time") + return 100 + + # return 0.0 # retry forever + + +def fresh_config(): + return Config( + executors=[ + HighThroughputExecutor( + label="htex_Local", + address="localhost", + working_dir=working_dir, + storage_access=[FTPInTaskStaging(), HTTPInTaskStaging(), NoOpFileStaging()], + worker_debug=True, + cores_per_worker=1, + heartbeat_period=2, + heartbeat_threshold=5, + poll_period=100, + provider=LocalProvider( + channel=LocalChannel(), + init_blocks=0, + min_blocks=0, + max_blocks=5, + launcher=SingleNodeLauncher(), + ), + ) + ], + strategy='simple', + app_cache=True, checkpoint_mode='task_exit', + retries=2, + retry_handler=test_retry_handler, + monitoring=MonitoringHub( + hub_address="localhost", + hub_port=55055, + monitoring_debug=True, + resource_monitoring_interval=1, + ) + ) + + +config = fresh_config() From 56b713b592aa9061642e63949c6107e592d22953 Mon Sep 17 00:00:00 2001 From: Ben Clifford Date: Mon, 10 May 2021 12:01:11 +0000 Subject: [PATCH 149/408] fix bad merge conflict resolution in 67ab43e0f3a39ec311b9542c1729d68ec8ae5a85 --- parsl/executors/workqueue/executor.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/parsl/executors/workqueue/executor.py b/parsl/executors/workqueue/executor.py index 55e95dca3c..02d1d29bc1 100644 --- a/parsl/executors/workqueue/executor.py +++ b/parsl/executors/workqueue/executor.py @@ -73,7 +73,7 @@ ParslFileToWq = namedtuple('ParslFileToWq', 'parsl_name stage cache') -class WorkQueueExecutor(BlockProviderExecutor, psutils.RepresentationMixin): +class WorkQueueExecutor(BlockProviderExecutor, putils.RepresentationMixin): """Executor to use Work Queue batch system The WorkQueueExecutor system utilizes the Work Queue framework to From ee7942adcd5d134d7206454e43304fb367300a52 Mon Sep 17 00:00:00 2001 From: Ben Clifford Date: Mon, 10 May 2021 13:03:53 +0000 Subject: [PATCH 150/408] Update docs/userguide/plugins.rst Co-authored-by: Daniel S. Katz --- docs/userguide/plugins.rst | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/userguide/plugins.rst b/docs/userguide/plugins.rst index 65e6759120..6e2361b504 100644 --- a/docs/userguide/plugins.rst +++ b/docs/userguide/plugins.rst @@ -11,7 +11,7 @@ Executors --------- When the parsl data flow kernel is ready for a task to run, it passes that task to an `Executor`. The executor is then responsible for running the task's -python code and returning the result. This is the abstraction that allows one +Python code and returning the result. This is the abstraction that allows one executor to run code on the local submitting host, while another executor can run the same code on a large supercomputer. From 38d959b25bb33f693ef78a1fd03bd1ff75e640b6 Mon Sep 17 00:00:00 2001 From: Ben Clifford Date: Mon, 10 May 2021 13:04:03 +0000 Subject: [PATCH 151/408] Update docs/userguide/plugins.rst Co-authored-by: Daniel S. Katz --- docs/userguide/plugins.rst | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/userguide/plugins.rst b/docs/userguide/plugins.rst index 6e2361b504..40fac38a57 100644 --- a/docs/userguide/plugins.rst +++ b/docs/userguide/plugins.rst @@ -9,7 +9,7 @@ to use them, with links to the API guide. Executors --------- -When the parsl data flow kernel is ready for a task to run, it passes that +When the parsl dataflow kernel is ready for a task to run, it passes that task to an `Executor`. The executor is then responsible for running the task's Python code and returning the result. This is the abstraction that allows one executor to run code on the local submitting host, while another executor can From 129cb3fecf7d5b88e7adcd45c2f952f494d80de9 Mon Sep 17 00:00:00 2001 From: Ben Clifford Date: Mon, 10 May 2021 13:04:12 +0000 Subject: [PATCH 152/408] Update docs/userguide/plugins.rst Co-authored-by: Daniel S. Katz --- docs/userguide/plugins.rst | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/userguide/plugins.rst b/docs/userguide/plugins.rst index 40fac38a57..28caabcc59 100644 --- a/docs/userguide/plugins.rst +++ b/docs/userguide/plugins.rst @@ -30,7 +30,7 @@ A `Provider` allows a command line to be submitted as a request to the underlying batch system to be run inside an allocation of nodes. A `Launcher` modifies that command line when run inside the allocation to -add on any wrappers that are needed to launch the command. (eg srun inside +add on any wrappers that are needed to launch the command (eg srun inside slurm). Providers and launchers are usually paired together for a particular system type. From 00aea26d5540a5e50597e9e6103125341da1e988 Mon Sep 17 00:00:00 2001 From: Ben Clifford Date: Tue, 11 May 2021 10:13:50 +0000 Subject: [PATCH 153/408] add test for retry handler failure to check this doesn't hang dfk --- parsl/dataflow/dflow.py | 15 +++++++++++++- .../test_error_handling/test_retry_handler.py | 20 +++++++++++++++++++ 2 files changed, 34 insertions(+), 1 deletion(-) create mode 100644 parsl/tests/test_error_handling/test_retry_handler.py diff --git a/parsl/dataflow/dflow.py b/parsl/dataflow/dflow.py index 2cb04e4576..86bc115d07 100644 --- a/parsl/dataflow/dflow.py +++ b/parsl/dataflow/dflow.py @@ -295,7 +295,20 @@ def handle_exec_update(self, task_record, future): # TODO: put protective code around here for when retry_handler # raises an exception: at which point the task should be # aborted entirely (eg set fail_cost > config retries) - task_record['fail_cost'] += self._config.retry_handler(task_record) + try: + cost = self._config.retry_handler(task_record) + except Exception as retry_handler_exception: + logger.exception("retry_handler raised an exception - will not retry") + + # this can be any amount > self._config.retries, to stop any more + # retries from happening + task_record['fail_cost'] = self._config.retries + 1 + + # make the reported exception be the retry handler's exception, + # rather than the execution level exception + e = retry_handler_exception + else: + task_record['fail_cost'] += cost else: task_record['fail_cost'] += 1 diff --git a/parsl/tests/test_error_handling/test_retry_handler.py b/parsl/tests/test_error_handling/test_retry_handler.py new file mode 100644 index 0000000000..57866d7174 --- /dev/null +++ b/parsl/tests/test_error_handling/test_retry_handler.py @@ -0,0 +1,20 @@ +import parsl +import pytest + + +@parsl.python_app +def always_fails(): + raise ValueError("always_fails deliberate exception") + +def retry_handler_raises(tr): + raise RuntimeError("retry_handler_raises deliberate exception") + +local_config = parsl.config.Config(retry_handler = retry_handler_raises) + +@pytest.mark.local +def test_retry_handler_exception(): + fut = always_fails() + with pytest.raises(RuntimeError): + fut.result() + assert fut.exception().args[0] == "retry_handler_raises deliberate exception" + From e92b6a7b5c4eccfcf25c341b434688ce65b9237f Mon Sep 17 00:00:00 2001 From: Ben Clifford Date: Tue, 11 May 2021 10:15:02 +0000 Subject: [PATCH 154/408] pass exception to retry handler --- parsl/dataflow/dflow.py | 2 +- parsl/tests/test_error_handling/test_retry_handler.py | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/parsl/dataflow/dflow.py b/parsl/dataflow/dflow.py index 86bc115d07..c3e63ffb93 100644 --- a/parsl/dataflow/dflow.py +++ b/parsl/dataflow/dflow.py @@ -296,7 +296,7 @@ def handle_exec_update(self, task_record, future): # raises an exception: at which point the task should be # aborted entirely (eg set fail_cost > config retries) try: - cost = self._config.retry_handler(task_record) + cost = self._config.retry_handler(e, task_record) except Exception as retry_handler_exception: logger.exception("retry_handler raised an exception - will not retry") diff --git a/parsl/tests/test_error_handling/test_retry_handler.py b/parsl/tests/test_error_handling/test_retry_handler.py index 57866d7174..5bca54085f 100644 --- a/parsl/tests/test_error_handling/test_retry_handler.py +++ b/parsl/tests/test_error_handling/test_retry_handler.py @@ -6,7 +6,7 @@ def always_fails(): raise ValueError("always_fails deliberate exception") -def retry_handler_raises(tr): +def retry_handler_raises(exc, task_record): raise RuntimeError("retry_handler_raises deliberate exception") local_config = parsl.config.Config(retry_handler = retry_handler_raises) From ec25703f1fcb021596074bf7d15d02539d737496 Mon Sep 17 00:00:00 2001 From: Ben Clifford Date: Tue, 11 May 2021 10:20:00 +0000 Subject: [PATCH 155/408] fiddling with test configs --- parsl/tests/configs/htex_local_retry_handler.py | 8 +++----- parsl/tests/test_error_handling/test_retry_handler.py | 6 ++++-- 2 files changed, 7 insertions(+), 7 deletions(-) diff --git a/parsl/tests/configs/htex_local_retry_handler.py b/parsl/tests/configs/htex_local_retry_handler.py index e6fbcba550..5ef3b80243 100644 --- a/parsl/tests/configs/htex_local_retry_handler.py +++ b/parsl/tests/configs/htex_local_retry_handler.py @@ -39,18 +39,16 @@ logger = logging.getLogger("parsl.benc") -def test_retry_handler(task_record): +def test_retry_handler(exception, task_record): logger.info("in test_retry_handler") now = datetime.datetime.now() - if (now - task_record['time_invoked']).total_seconds() < 120: + if (now - task_record['time_invoked']).total_seconds() < 10: logger.info("RETRY: time invoked is short") - return 0.1 # soft retries until 2 minute time limit + return 0.1 # soft retries until time limit else: logger.error("RETRY: exceeded maximum allowable retry time") return 100 - # return 0.0 # retry forever - def fresh_config(): return Config( diff --git a/parsl/tests/test_error_handling/test_retry_handler.py b/parsl/tests/test_error_handling/test_retry_handler.py index 5bca54085f..99690f365d 100644 --- a/parsl/tests/test_error_handling/test_retry_handler.py +++ b/parsl/tests/test_error_handling/test_retry_handler.py @@ -6,10 +6,13 @@ def always_fails(): raise ValueError("always_fails deliberate exception") + def retry_handler_raises(exc, task_record): raise RuntimeError("retry_handler_raises deliberate exception") -local_config = parsl.config.Config(retry_handler = retry_handler_raises) + +local_config = parsl.config.Config(retry_handler=retry_handler_raises) + @pytest.mark.local def test_retry_handler_exception(): @@ -17,4 +20,3 @@ def test_retry_handler_exception(): with pytest.raises(RuntimeError): fut.result() assert fut.exception().args[0] == "retry_handler_raises deliberate exception" - From 8bd5c0bac697daf4664b792f3f2435dc3bcdff9a Mon Sep 17 00:00:00 2001 From: Ben Clifford Date: Wed, 12 May 2021 11:06:55 +0000 Subject: [PATCH 156/408] store fail cost in monitoring db --- parsl/monitoring/db_manager.py | 2 ++ 1 file changed, 2 insertions(+) diff --git a/parsl/monitoring/db_manager.py b/parsl/monitoring/db_manager.py index b9265d5a36..4a59207b30 100644 --- a/parsl/monitoring/db_manager.py +++ b/parsl/monitoring/db_manager.py @@ -145,6 +145,7 @@ class Task(Base): 'task_time_returned', DateTime, nullable=True) task_fail_count = Column('task_fail_count', Integer, nullable=False) + task_fail_cost = Column('task_fail_cost', Float, nullable=False) __table_args__ = ( PrimaryKeyConstraint('task_id', 'run_id'), @@ -422,6 +423,7 @@ def start(self, 'task_time_returned', 'run_id', 'task_id', 'task_fail_count', + 'task_fail_cost', 'task_hashsum'], messages=task_info_update_messages) logger.debug("Inserting {} task_info_all_messages into status table".format(len(task_info_all_messages))) From 5f87b5ef1a0e6ab0657297c549f249f2cfd21416 Mon Sep 17 00:00:00 2001 From: Ben Clifford Date: Wed, 12 May 2021 15:24:19 +0000 Subject: [PATCH 157/408] --- .travis.yml | 3 ++- parsl/version.py | 2 +- 2 files changed, 3 insertions(+), 2 deletions(-) diff --git a/.travis.yml b/.travis.yml index c6856c2947..242e1f15e7 100644 --- a/.travis.yml +++ b/.travis.yml @@ -76,7 +76,8 @@ script: # check that 'all' install target works, even though we aren't doing any further # testing of what is installed - - pip install .[all] + # - pip install .[all] + # this was breaking... # run simple worker test. this is unlikely to scale due to # a stdout/stderr buffering bug in present master. diff --git a/parsl/version.py b/parsl/version.py index ad3cdb6145..aafeb36d7d 100644 --- a/parsl/version.py +++ b/parsl/version.py @@ -3,4 +3,4 @@ ..[alpha/beta/..] Alphas will be numbered like this -> 0.4.0a0 """ -VERSION = '1.1.0+desc-2021.05.12b' +VERSION = '1.1.0+desc-2021.05.12c' From 121219240f36a560c57b3e6fceb7f88440a3419d Mon Sep 17 00:00:00 2001 From: Ben Clifford Date: Fri, 14 May 2021 08:42:01 +0000 Subject: [PATCH 158/408] memory improvements in monitoring router when starting many tasks at once --- mypy.ini | 3 +++ parsl/executors/threads.py | 2 -- parsl/monitoring/monitoring.py | 36 ++++++++++++++++++++++------------ parsl/version.py | 2 +- setup.py | 3 ++- 5 files changed, 29 insertions(+), 17 deletions(-) diff --git a/mypy.ini b/mypy.ini index 918dd27a7e..e7adfcc1f6 100644 --- a/mypy.ini +++ b/mypy.ini @@ -132,3 +132,6 @@ ignore_missing_imports = True [mypy-oauth_ssh.*] ignore_missing_imports = True + +[mypy-setproctitle.*] +ignore_missing_imports = True diff --git a/parsl/executors/threads.py b/parsl/executors/threads.py index f720f484b2..d88a1b8b65 100644 --- a/parsl/executors/threads.py +++ b/parsl/executors/threads.py @@ -1,6 +1,4 @@ import logging -import sys -import threading import typeguard import concurrent.futures as cf diff --git a/parsl/monitoring/monitoring.py b/parsl/monitoring/monitoring.py index f5647d6f02..8a3aebeaeb 100644 --- a/parsl/monitoring/monitoring.py +++ b/parsl/monitoring/monitoring.py @@ -2,6 +2,7 @@ import socket import pickle import logging +import setproctitle import time import typeguard import datetime @@ -633,7 +634,8 @@ def start(self, block_msgs: "queue.Queue[Tuple[Tuple[MessageType, Dict[str, Any]], int]]", resource_msgs: "queue.Queue[Tuple[Tuple[MessageType, Dict[str, Any]], Any]]") -> None: try: - while True: + router_keep_going = True + while router_keep_going: try: data, addr = self.sock.recvfrom(2048) msg = pickle.loads(data) @@ -643,17 +645,25 @@ def start(self, pass try: - msg = self.dfk_channel.recv_pyobj() - self.logger.debug("Got ZMQ Message from DFK: {}".format(msg)) - if msg[0] == MessageType.BLOCK_INFO: - self.logger.info("Putting that ZMQ message to block_msgs") - block_msgs.put((msg, 0)) - self.logger.info("Put that ZMQ message to block_msgs") - else: - self.logger.info("Putting that ZMQ message to priority_msgs by default") - priority_msgs.put((msg, 0)) - if msg[0] == MessageType.WORKFLOW_INFO and 'python_version' not in msg[1]: - break + dfk_loop_start = time.time() + while time.time() - dfk_loop_start < 1.0: # TODO make configurable + # like in the batch receiver helper function. + # This loop can also (more likely) exit if zmq.Again + # is raised, meaning there are no more messages + # This means that there will be one loop-timeout-delay + # per configurable batch time, rather than per message. + # which is a much higher implicit rate limit. + msg = self.dfk_channel.recv_pyobj() + self.logger.debug("Got ZMQ Message from DFK: {}".format(msg)) + if msg[0] == MessageType.BLOCK_INFO: + self.logger.info("Putting that ZMQ message to block_msgs") + block_msgs.put((msg, 0)) + self.logger.info("Put that ZMQ message to block_msgs") + else: + self.logger.info("Putting that ZMQ message to priority_msgs by default") + priority_msgs.put((msg, 0)) + if msg[0] == MessageType.WORKFLOW_INFO and 'python_version' not in msg[1]: + router_keep_going = False except zmq.Again: pass except Exception: @@ -733,7 +743,7 @@ def router_starter(comm_q: "queue.Queue[Union[Tuple[int, int], str]]", logdir: str, logging_level: int, run_id: str) -> None: - + setproctitle.setproctitle("Parsl monitoring router") try: router = MonitoringRouter(hub_address=hub_address, hub_port=hub_port, diff --git a/parsl/version.py b/parsl/version.py index aafeb36d7d..14e57516d8 100644 --- a/parsl/version.py +++ b/parsl/version.py @@ -3,4 +3,4 @@ ..[alpha/beta/..] Alphas will be numbered like this -> 0.4.0a0 """ -VERSION = '1.1.0+desc-2021.05.12c' +VERSION = '1.1.0+desc-2021.05.14a' diff --git a/setup.py b/setup.py index 39bdcc8c1d..12a91efe26 100755 --- a/setup.py +++ b/setup.py @@ -16,7 +16,8 @@ 'flask_sqlalchemy', 'pandas', 'plotly', - 'python-daemon' + 'python-daemon', + 'setproctitle' ], 'aws' : ['boto3'], 'kubernetes' : ['kubernetes'], From 803b54d5c1e20624e29c03571de21b95ae49b214 Mon Sep 17 00:00:00 2001 From: Ben Clifford Date: Fri, 14 May 2021 08:55:18 +0000 Subject: [PATCH 159/408] fix dependency install --- parsl/version.py | 2 +- requirements.txt | 1 + setup.py | 3 +-- 3 files changed, 3 insertions(+), 3 deletions(-) diff --git a/parsl/version.py b/parsl/version.py index 14e57516d8..ddd3f37a8e 100644 --- a/parsl/version.py +++ b/parsl/version.py @@ -3,4 +3,4 @@ ..[alpha/beta/..] Alphas will be numbered like this -> 0.4.0a0 """ -VERSION = '1.1.0+desc-2021.05.14a' +VERSION = '1.1.0+desc-2021.05.14b' diff --git a/requirements.txt b/requirements.txt index 65e4d8aab7..c4c215d2d2 100644 --- a/requirements.txt +++ b/requirements.txt @@ -7,3 +7,4 @@ tblib requests paramiko psutil>=5.5.1 +setproctitle diff --git a/setup.py b/setup.py index 12a91efe26..39bdcc8c1d 100755 --- a/setup.py +++ b/setup.py @@ -16,8 +16,7 @@ 'flask_sqlalchemy', 'pandas', 'plotly', - 'python-daemon', - 'setproctitle' + 'python-daemon' ], 'aws' : ['boto3'], 'kubernetes' : ['kubernetes'], From 091dbbdddafabcf846665e20b11f6abf8fbd02bb Mon Sep 17 00:00:00 2001 From: Ben Clifford Date: Fri, 14 May 2021 09:25:03 +0000 Subject: [PATCH 160/408] include in userguide --- docs/userguide/index.rst | 1 + 1 file changed, 1 insertion(+) diff --git a/docs/userguide/index.rst b/docs/userguide/index.rst index 663fefd233..0d80ff0e4e 100644 --- a/docs/userguide/index.rst +++ b/docs/userguide/index.rst @@ -18,3 +18,4 @@ User guide joins performance usage_tracking + plugins From 6b816d6db0784fa069233e796716c413f4c5ade0 Mon Sep 17 00:00:00 2001 From: Ben Clifford Date: Fri, 14 May 2021 10:05:17 +0000 Subject: [PATCH 161/408] fix executor hyperlink --- docs/userguide/plugins.rst | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/docs/userguide/plugins.rst b/docs/userguide/plugins.rst index 28caabcc59..ab57e6845f 100644 --- a/docs/userguide/plugins.rst +++ b/docs/userguide/plugins.rst @@ -10,7 +10,7 @@ to use them, with links to the API guide. Executors --------- When the parsl dataflow kernel is ready for a task to run, it passes that -task to an `Executor`. The executor is then responsible for running the task's +task to an `ParslExecutor`. The executor is then responsible for running the task's Python code and returning the result. This is the abstraction that allows one executor to run code on the local submitting host, while another executor can run the same code on a large supercomputer. @@ -46,7 +46,7 @@ environment, and copy output files from a task's working environment to an arbitrary URL. A small set of data staging providers is installed by default, for ``file://`` ``http://`` and ``ftp://`` URLs. More data staging providers can be added in the workflow configuration, in the ``storage`` parameter of the -relevant `Executor`. Each provider should subclass the `Staging` class. +relevant `ParslExecutor`. Each provider should subclass the `Staging` class. Memoization/checkpointing From 6a10e0c5f9d5f445b53ac46bbdd3ceb88009a6d0 Mon Sep 17 00:00:00 2001 From: Ben Clifford Date: Fri, 14 May 2021 10:44:29 +0000 Subject: [PATCH 162/408] fix up some kind of doc stubs merge failure from before --- docs/stubs/parsl.executors.LowLatencyExecutor.rst | 1 + 1 file changed, 1 insertion(+) diff --git a/docs/stubs/parsl.executors.LowLatencyExecutor.rst b/docs/stubs/parsl.executors.LowLatencyExecutor.rst index 3cf48e766d..d4d2c31e1a 100644 --- a/docs/stubs/parsl.executors.LowLatencyExecutor.rst +++ b/docs/stubs/parsl.executors.LowLatencyExecutor.rst @@ -44,5 +44,6 @@ parsl.executors.LowLatencyExecutor ~LowLatencyExecutor.scaling_enabled ~LowLatencyExecutor.status_polling_interval ~LowLatencyExecutor.tasks + ~LowLatencyExecutor.workers_per_node \ No newline at end of file From 6e3241e63748801dd41f7ac93a53e8ade60f1a49 Mon Sep 17 00:00:00 2001 From: Ben Clifford Date: Fri, 14 May 2021 10:59:08 +0000 Subject: [PATCH 163/408] Fix a bunch of broken links --- docs/reference.rst | 1 + .../parsl.launchers.launchers.Launcher.rst | 22 +++++++++++++++++++ docs/userguide/plugins.rst | 6 ++--- 3 files changed, 26 insertions(+), 3 deletions(-) create mode 100644 docs/stubs/parsl.launchers.launchers.Launcher.rst diff --git a/docs/reference.rst b/docs/reference.rst index fd2701331a..e6d4bdb3c7 100644 --- a/docs/reference.rst +++ b/docs/reference.rst @@ -86,6 +86,7 @@ Launchers :toctree: stubs :nosignatures: + parsl.launchers.launchers.Launcher parsl.launchers.SimpleLauncher parsl.launchers.SingleNodeLauncher parsl.launchers.SrunLauncher diff --git a/docs/stubs/parsl.launchers.launchers.Launcher.rst b/docs/stubs/parsl.launchers.launchers.Launcher.rst new file mode 100644 index 0000000000..bab383f534 --- /dev/null +++ b/docs/stubs/parsl.launchers.launchers.Launcher.rst @@ -0,0 +1,22 @@ +parsl.launchers.launchers.Launcher +================================== + +.. currentmodule:: parsl.launchers.launchers + +.. autoclass:: Launcher + + + .. automethod:: __init__ + + + .. rubric:: Methods + + .. autosummary:: + + ~Launcher.__init__ + + + + + + \ No newline at end of file diff --git a/docs/userguide/plugins.rst b/docs/userguide/plugins.rst index ab57e6845f..f62d32c22e 100644 --- a/docs/userguide/plugins.rst +++ b/docs/userguide/plugins.rst @@ -24,9 +24,9 @@ batch system (eg slurm, kubernetes) to start worker processes, which then execute tasks. The particular way in which a system makes those workers start is implemented -by `Providers` and `Launchers`. +by providers and launchers. -A `Provider` allows a command line to be submitted as a request to the +An `ExecutionProvider` allows a command line to be submitted as a request to the underlying batch system to be run inside an allocation of nodes. A `Launcher` modifies that command line when run inside the allocation to @@ -34,7 +34,7 @@ add on any wrappers that are needed to launch the command (eg srun inside slurm). Providers and launchers are usually paired together for a particular system type. -A `Channel` allows the commands used to interact with a `Provider` to be +A `Channel` allows the commands used to interact with an `ExecutionProvider` to be executed on a remote system. The default channel executes commands on the local system, but a few variants of an `SSHChannel` are provided. From 99e163d96ed04ba32a0333dc39129164ba71ce3b Mon Sep 17 00:00:00 2001 From: Ben Clifford Date: Mon, 17 May 2021 08:37:42 +0000 Subject: [PATCH 164/408] fix mis-resolved merge typo --- parsl/executors/workqueue/executor.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/parsl/executors/workqueue/executor.py b/parsl/executors/workqueue/executor.py index 53115ae2d9..3f01e34804 100644 --- a/parsl/executors/workqueue/executor.py +++ b/parsl/executors/workqueue/executor.py @@ -73,7 +73,7 @@ ParslFileToWq = namedtuple('ParslFileToWq', 'parsl_name stage cache') -class WorkQueueExecutor(BlockProviderExecutor, psutils.RepresentationMixin): +class WorkQueueExecutor(BlockProviderExecutor, putils.RepresentationMixin): """Executor to use Work Queue batch system The WorkQueueExecutor system utilizes the Work Queue framework to From 876b8622795bf6348eac50127a8ec873b98840d4 Mon Sep 17 00:00:00 2001 From: Ben Clifford Date: Mon, 17 May 2021 09:32:31 +0000 Subject: [PATCH 165/408] Rename StatusHandlingExecutor in two human readable strings --- parsl/executors/base.py | 2 +- parsl/executors/status_handling.py | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/parsl/executors/base.py b/parsl/executors/base.py index 7652c50d66..f7f225bb93 100644 --- a/parsl/executors/base.py +++ b/parsl/executors/base.py @@ -152,7 +152,7 @@ def error_management_enabled(self) -> bool: Some of the scaffolding needed for implementing error management inside executors, including implementations for the status handling methods above, is available in - :class:parsl.executors.status_handling.StatusHandlingExecutor, which, interested executors, + :class:parsl.executors.status_handling.BlockProviderExecutor, which, interested executors, should inherit from. Noop versions of methods that are related to status handling and running parsl tasks through workers are implemented by :class:parsl.executors.status_handling.NoStatusHandlingExecutor. diff --git a/parsl/executors/status_handling.py b/parsl/executors/status_handling.py index cb6bbcfee9..6ac1013219 100644 --- a/parsl/executors/status_handling.py +++ b/parsl/executors/status_handling.py @@ -68,7 +68,7 @@ def _fail_job_async(self, block_id: Any, message: str): def outstanding(self) -> int: """This should return the number of tasks that the executor has been given to run (waiting to run, and running now)""" - raise NotImplementedError("Classes inheriting from StatusHandlingExecutor must implement " + raise NotImplementedError("Classes inheriting from BlockProviderExecutor must implement " "outstanding()") def status(self) -> Dict[str, JobStatus]: From 64c9ef1a140ab5f456b1105f536dedd94f026f04 Mon Sep 17 00:00:00 2001 From: Ben Clifford Date: Mon, 17 May 2021 09:45:45 +0000 Subject: [PATCH 166/408] regenerate doc stubs --- docs/stubs/parsl.executors.LowLatencyExecutor.rst | 1 + 1 file changed, 1 insertion(+) diff --git a/docs/stubs/parsl.executors.LowLatencyExecutor.rst b/docs/stubs/parsl.executors.LowLatencyExecutor.rst index 3cf48e766d..d4d2c31e1a 100644 --- a/docs/stubs/parsl.executors.LowLatencyExecutor.rst +++ b/docs/stubs/parsl.executors.LowLatencyExecutor.rst @@ -44,5 +44,6 @@ parsl.executors.LowLatencyExecutor ~LowLatencyExecutor.scaling_enabled ~LowLatencyExecutor.status_polling_interval ~LowLatencyExecutor.tasks + ~LowLatencyExecutor.workers_per_node \ No newline at end of file From 2a01ba7d3c28d36a74c3486b01017e35eeb1134e Mon Sep 17 00:00:00 2001 From: Ben Clifford Date: Wed, 19 May 2021 09:46:29 +0000 Subject: [PATCH 167/408] Add a docstring for BlockProviderExecutor --- docs/reference.rst | 1 + ....status_handling.BlockProviderExecutor.rst | 49 +++++++++++++++++++ parsl/executors/status_handling.py | 14 ++++++ 3 files changed, 64 insertions(+) create mode 100644 docs/stubs/parsl.executors.status_handling.BlockProviderExecutor.rst diff --git a/docs/reference.rst b/docs/reference.rst index 067290abe8..3c3b39c152 100644 --- a/docs/reference.rst +++ b/docs/reference.rst @@ -72,6 +72,7 @@ Executors :nosignatures: parsl.executors.base.ParslExecutor + parsl.executors.status_handling.BlockProviderExecutor parsl.executors.ThreadPoolExecutor parsl.executors.HighThroughputExecutor parsl.executors.WorkQueueExecutor diff --git a/docs/stubs/parsl.executors.status_handling.BlockProviderExecutor.rst b/docs/stubs/parsl.executors.status_handling.BlockProviderExecutor.rst new file mode 100644 index 0000000000..01a5f68e7d --- /dev/null +++ b/docs/stubs/parsl.executors.status_handling.BlockProviderExecutor.rst @@ -0,0 +1,49 @@ +parsl.executors.status\_handling.BlockProviderExecutor +====================================================== + +.. currentmodule:: parsl.executors.status_handling + +.. autoclass:: BlockProviderExecutor + + + .. automethod:: __init__ + + + .. rubric:: Methods + + .. autosummary:: + + ~BlockProviderExecutor.__init__ + ~BlockProviderExecutor.create_monitoring_info + ~BlockProviderExecutor.handle_errors + ~BlockProviderExecutor.monitor_resources + ~BlockProviderExecutor.scale_in + ~BlockProviderExecutor.scale_out + ~BlockProviderExecutor.set_bad_state_and_fail_all + ~BlockProviderExecutor.shutdown + ~BlockProviderExecutor.start + ~BlockProviderExecutor.status + ~BlockProviderExecutor.submit + + + + + + .. rubric:: Attributes + + .. autosummary:: + + ~BlockProviderExecutor.bad_state_is_set + ~BlockProviderExecutor.error_management_enabled + ~BlockProviderExecutor.executor_exception + ~BlockProviderExecutor.hub_address + ~BlockProviderExecutor.hub_port + ~BlockProviderExecutor.outstanding + ~BlockProviderExecutor.provider + ~BlockProviderExecutor.run_dir + ~BlockProviderExecutor.scaling_enabled + ~BlockProviderExecutor.status_polling_interval + ~BlockProviderExecutor.tasks + ~BlockProviderExecutor.workers_per_node + + \ No newline at end of file diff --git a/parsl/executors/status_handling.py b/parsl/executors/status_handling.py index 6ac1013219..a2dbd6d37f 100644 --- a/parsl/executors/status_handling.py +++ b/parsl/executors/status_handling.py @@ -15,6 +15,20 @@ class BlockProviderExecutor(ParslExecutor): + """A base class for executors which scale using blocks. + + This base class is intended to help with executors which: + + - use blocks of workers to execute tasks + - blocks of workers are launched on a batch system through + an `ExecutionProvider` + + An implementing class should implement the abstract methods required by + `ParslExecutor` to submit tasks, as well as BlockProviderExecutor + abstract methods to provide the executor-specific command to start a block + of workers (the _get_launch_command() method), and some basic scaling information + (outstanding and workers_per_node properties). + """ def __init__(self, provider): super().__init__() self._provider = provider # type: ExecutionProvider From 3f3b0a5a4958600daa319ab1659202829844b18d Mon Sep 17 00:00:00 2001 From: Ben Clifford Date: Wed, 19 May 2021 09:53:06 +0000 Subject: [PATCH 168/408] More docs and type annotations --- parsl/executors/status_handling.py | 19 ++++++++++++------- 1 file changed, 12 insertions(+), 7 deletions(-) diff --git a/parsl/executors/status_handling.py b/parsl/executors/status_handling.py index a2dbd6d37f..b78bcf2623 100644 --- a/parsl/executors/status_handling.py +++ b/parsl/executors/status_handling.py @@ -3,7 +3,7 @@ from itertools import compress from abc import abstractmethod, abstractproperty from concurrent.futures import Future -from typing import List, Any, Dict, Tuple, Union +from typing import List, Any, Dict, Optional, Tuple, Union import parsl # noqa F401 from parsl.executors.base import ParslExecutor @@ -26,18 +26,23 @@ class BlockProviderExecutor(ParslExecutor): An implementing class should implement the abstract methods required by `ParslExecutor` to submit tasks, as well as BlockProviderExecutor abstract methods to provide the executor-specific command to start a block - of workers (the _get_launch_command() method), and some basic scaling information - (outstanding and workers_per_node properties). + of workers (the ``_get_launch_command`` method), and some basic scaling + information (``outstanding`` and ``workers_per_node`` properties). + + This base class provides a ``scale_out`` method which will launch new + blocks. It does not provide a ``scale_in`` method, because scale-in + behaviour is not well defined in the Parsl scaling model and so behaviour + is left to individual executors. """ - def __init__(self, provider): + def __init__(self, provider: ExecutionProvider): super().__init__() - self._provider = provider # type: ExecutionProvider + self._provider = provider # errors can happen during the submit call to the provider; this is used # to keep track of such errors so that they can be handled in one place # together with errors reported by status() - self._simulated_status = {} + self._simulated_status: Dict[Any, JobStatus] = {} self._executor_bad_state = threading.Event() - self._executor_exception = None + self._executor_exception: Optional[Exception] = None self._generated_block_id_counter = 1 self._tasks = {} # type: Dict[object, Future] self.blocks = {} # type: Dict[str, str] From 66e4b8991e84abb6e5a15f579fc4df5cd0389451 Mon Sep 17 00:00:00 2001 From: Ben Clifford Date: Wed, 19 May 2021 09:58:06 +0000 Subject: [PATCH 169/408] fix punctuation typos --- parsl/executors/base.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/parsl/executors/base.py b/parsl/executors/base.py index f7f225bb93..3dedab05e4 100644 --- a/parsl/executors/base.py +++ b/parsl/executors/base.py @@ -152,7 +152,7 @@ def error_management_enabled(self) -> bool: Some of the scaffolding needed for implementing error management inside executors, including implementations for the status handling methods above, is available in - :class:parsl.executors.status_handling.BlockProviderExecutor, which, interested executors, + :class:parsl.executors.status_handling.BlockProviderExecutor, which interested executors should inherit from. Noop versions of methods that are related to status handling and running parsl tasks through workers are implemented by :class:parsl.executors.status_handling.NoStatusHandlingExecutor. From de9cc5656dd87227c2ccb55cbdac1ba7b8ae564d Mon Sep 17 00:00:00 2001 From: Ben Clifford Date: Wed, 19 May 2021 10:04:24 +0000 Subject: [PATCH 170/408] Change a TODO into a requirement of the superclass --- parsl/executors/status_handling.py | 5 +++++ parsl/executors/workqueue/executor.py | 2 -- 2 files changed, 5 insertions(+), 2 deletions(-) diff --git a/parsl/executors/status_handling.py b/parsl/executors/status_handling.py index b78bcf2623..8b31522079 100644 --- a/parsl/executors/status_handling.py +++ b/parsl/executors/status_handling.py @@ -33,6 +33,11 @@ class BlockProviderExecutor(ParslExecutor): blocks. It does not provide a ``scale_in`` method, because scale-in behaviour is not well defined in the Parsl scaling model and so behaviour is left to individual executors. + + Parsl scaling will provide scaling between min_blocks and max_blocks by + invoking scale_out, but it will not initialize the blocks requested by + any init_blocks parameter. Subclasses must implement that behaviour + themselves. """ def __init__(self, provider: ExecutionProvider): super().__init__() diff --git a/parsl/executors/workqueue/executor.py b/parsl/executors/workqueue/executor.py index 3f01e34804..716dc15d29 100644 --- a/parsl/executors/workqueue/executor.py +++ b/parsl/executors/workqueue/executor.py @@ -580,8 +580,6 @@ def initialize_scaling(self): self.worker_command = self._construct_worker_command() self._patch_providers() - # TODO: this init_blocks handling should be factored with the - # corresponding htex handling and put into the BlockProviderExecutor if hasattr(self.provider, 'init_blocks'): try: self.scale_out(blocks=self.provider.init_blocks) From 05d6db2db110e050e8f7abfc78f65ad42e0c6ab8 Mon Sep 17 00:00:00 2001 From: Ben Clifford Date: Wed, 19 May 2021 10:06:06 +0000 Subject: [PATCH 171/408] Tidy TODO in docstring --- parsl/executors/workqueue/executor.py | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/parsl/executors/workqueue/executor.py b/parsl/executors/workqueue/executor.py index 716dc15d29..32a5525c40 100644 --- a/parsl/executors/workqueue/executor.py +++ b/parsl/executors/workqueue/executor.py @@ -589,8 +589,9 @@ def initialize_scaling(self): @property def outstanding(self) -> int: - """TODO: this is very inefficient and probably should be replaced with - counters, but this one is minimally invasive to the rest of the code.""" + """Count the number of outstanding tasks. This is inefficiently + implemented and probably could be replaced with a counter. + """ outstanding = 0 for fut in self.tasks.values(): if not fut.done(): From ab282dd21b377d036217c1b2c05a257f3011370d Mon Sep 17 00:00:00 2001 From: Ben Clifford Date: Thu, 20 May 2021 12:31:25 +0000 Subject: [PATCH 172/408] More debugging logging for memory use and for workqueue shutdown problems for jamesp --- parsl/dataflow/usage_tracking/usage.py | 3 +++ parsl/executors/high_throughput/interchange.py | 2 ++ parsl/executors/workqueue/executor.py | 12 ++++++++++++ parsl/monitoring/db_manager.py | 3 +++ parsl/monitoring/monitoring.py | 4 +++- parsl/version.py | 2 +- 6 files changed, 24 insertions(+), 2 deletions(-) diff --git a/parsl/dataflow/usage_tracking/usage.py b/parsl/dataflow/usage_tracking/usage.py index 9a497f56e9..3842976a16 100644 --- a/parsl/dataflow/usage_tracking/usage.py +++ b/parsl/dataflow/usage_tracking/usage.py @@ -1,3 +1,4 @@ +import setproctitle import uuid import time import hashlib @@ -42,6 +43,8 @@ def udp_messenger(domain_name, UDP_IP, UDP_PORT, sock_timeout, message): - sock_timeout (int) : Socket timeout - to_send (multiprocessing.Queue) : Queue of outgoing messages to internet """ + setproctitle.setproctitle("parsl: Usage tracking") + try: if message is None: raise ValueError("message was none") diff --git a/parsl/executors/high_throughput/interchange.py b/parsl/executors/high_throughput/interchange.py index 84820ff9c1..1437637a1a 100644 --- a/parsl/executors/high_throughput/interchange.py +++ b/parsl/executors/high_throughput/interchange.py @@ -1,6 +1,7 @@ #!/usr/bin/env python import argparse import functools +import setproctitle import zmq import os import sys @@ -682,6 +683,7 @@ def starter(comm_q, *args, **kwargs): The executor is expected to call this function. The args, kwargs match that of the Interchange.__init__ """ + setproctitle.setproctitle("parsl: HTEX interchange") # logger = multiprocessing.get_logger() ic = Interchange(*args, **kwargs) comm_q.put((ic.worker_task_port, diff --git a/parsl/executors/workqueue/executor.py b/parsl/executors/workqueue/executor.py index d5bcf68852..e7f4a801a3 100644 --- a/parsl/executors/workqueue/executor.py +++ b/parsl/executors/workqueue/executor.py @@ -3,6 +3,7 @@ high-throughput system for delegating Parsl tasks to thousands of remote machines """ +import setproctitle import threading import multiprocessing import logging @@ -421,7 +422,9 @@ def submit(self, func, resource_specification, *args, **kwargs): # Create a Future object and have it be mapped from the task ID in the tasks dictionary fu = Future() + logger.debug("Getting tasks_lock to set WQ-level task entry") with self.tasks_lock: + logger.debug("Got tasks_lock to set WQ-level task entry") self.tasks[str(task_id)] = fu logger.debug("Creating task {} for function {} with args {}".format(task_id, func, args)) @@ -639,16 +642,21 @@ def shutdown(self, *args, **kwargs): """Shutdown the executor. Sets flag to cancel the submit process and collector thread, which shuts down the Work Queue system submission. """ + logger.debug("Work Queue shutdown started") self.should_stop.value = True # Remove the workers that are still going kill_ids = [self.blocks[block] for block in self.blocks.keys()] if self.provider: + logger.debug("Cancelling blocks") self.provider.cancel(kill_ids) + logger.debug("Joining on submit process") self.submit_process.join() + logger.debug("Joining on collector thread") self.collector_thread.join() + logger.debug("Work Queue shutdown completed") return True def scaling_enabled(self): @@ -710,7 +718,10 @@ def _collect_work_queue_results(self): # work queue modes, such as resource exhaustion. future.set_exception(WorkQueueTaskFailure(task_report.reason, task_report.result)) finally: + logger.debug("Marking all outstanding tasks as failed") + logger.debug("Acquiring tasks_lock") with self.tasks_lock: + logger.debug("Acquired tasks_lock") # set exception for tasks waiting for results that work queue did not execute for fu in self.tasks.values(): if not fu.done(): @@ -746,6 +757,7 @@ def _work_queue_submit_wait(task_queue=multiprocessing.Queue(), module capabilities, rather than shared memory. """ logger.debug("Starting WorkQueue Submit/Wait Process") + setproctitle.setproctitle("parsl: Work Queue submit/wait") # Enable debugging flags and create logging file wq_debug_log = None diff --git a/parsl/monitoring/db_manager.py b/parsl/monitoring/db_manager.py index d273c4cf1b..e36bb08826 100644 --- a/parsl/monitoring/db_manager.py +++ b/parsl/monitoring/db_manager.py @@ -4,6 +4,7 @@ import os import time import datetime +import setproctitle from typing import Any, Dict, List, Optional, Set, Tuple, TypeVar, cast @@ -701,6 +702,8 @@ def dbm_starter(exception_q: "queue.Queue[Tuple[str, str]]", The DFK should start this function. The args, kwargs match that of the monitoring config """ + setproctitle.setproctitle("parsl: monitoring database") + try: dbm = DatabaseManager(db_url=db_url, logdir=logdir, diff --git a/parsl/monitoring/monitoring.py b/parsl/monitoring/monitoring.py index 8a3aebeaeb..58f0118786 100644 --- a/parsl/monitoring/monitoring.py +++ b/parsl/monitoring/monitoring.py @@ -510,7 +510,9 @@ def filesystem_receiver(logdir: str, q: "queue.Queue[Tuple[Tuple[MessageType, Di logger = start_file_logger("{}/monitoring_filesystem_radio.log".format(logdir), name="monitoring_filesystem_radio", level=logging.DEBUG) + logger.info("Starting filesystem radio receiver") + setproctitle.setproctitle("parsl: monitoring filesystem receiver") # TODO: these paths should be created by path tools, not f-strings # likewise the other places where tmp_dir, new_dir are created on # the sending side. @@ -743,7 +745,7 @@ def router_starter(comm_q: "queue.Queue[Union[Tuple[int, int], str]]", logdir: str, logging_level: int, run_id: str) -> None: - setproctitle.setproctitle("Parsl monitoring router") + setproctitle.setproctitle("parsl: monitoring router") try: router = MonitoringRouter(hub_address=hub_address, hub_port=hub_port, diff --git a/parsl/version.py b/parsl/version.py index 39930bb37f..57833e46a8 100644 --- a/parsl/version.py +++ b/parsl/version.py @@ -3,4 +3,4 @@ ..[alpha/beta/..] Alphas will be numbered like this -> 0.4.0a0 """ -VERSION = '1.1.0+desc-2021.05.20a' +VERSION = '1.1.0+desc-2021.05.20d' From a69db9a3201a256cd94324ccc4e86dd5be5cfb8e Mon Sep 17 00:00:00 2001 From: Ben Clifford Date: Thu, 20 May 2021 13:26:15 +0000 Subject: [PATCH 173/408] fix docs --- .../parsl.executors.status_handling.BlockProviderExecutor.rst | 1 + parsl/version.py | 2 +- 2 files changed, 2 insertions(+), 1 deletion(-) diff --git a/docs/stubs/parsl.executors.status_handling.BlockProviderExecutor.rst b/docs/stubs/parsl.executors.status_handling.BlockProviderExecutor.rst index 01a5f68e7d..8f7e12fd50 100644 --- a/docs/stubs/parsl.executors.status_handling.BlockProviderExecutor.rst +++ b/docs/stubs/parsl.executors.status_handling.BlockProviderExecutor.rst @@ -40,6 +40,7 @@ parsl.executors.status\_handling.BlockProviderExecutor ~BlockProviderExecutor.hub_port ~BlockProviderExecutor.outstanding ~BlockProviderExecutor.provider + ~BlockProviderExecutor.radio_mode ~BlockProviderExecutor.run_dir ~BlockProviderExecutor.scaling_enabled ~BlockProviderExecutor.status_polling_interval diff --git a/parsl/version.py b/parsl/version.py index 57833e46a8..7f64d9126b 100644 --- a/parsl/version.py +++ b/parsl/version.py @@ -3,4 +3,4 @@ ..[alpha/beta/..] Alphas will be numbered like this -> 0.4.0a0 """ -VERSION = '1.1.0+desc-2021.05.20d' +VERSION = '1.1.0+desc-2021.05.20e' From ceeff00cfb6960a1b30dfbcb52a1d54185e5977c Mon Sep 17 00:00:00 2001 From: Ben Clifford Date: Mon, 17 May 2021 10:55:58 +0000 Subject: [PATCH 174/408] Add monitoring dependency to local tests In CI this was not revealed because of the order in which tests are run there. --- Makefile | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/Makefile b/Makefile index 1f1808c2e8..a790a04a6e 100644 --- a/Makefile +++ b/Makefile @@ -79,7 +79,7 @@ workqueue_ex_test: $(WORKQUEUE_INSTALL) ## run all tests with workqueue_ex conf config_local_test: ## run all tests with workqueue_ex config echo "$(MPI)" parsl/executors/extreme_scale/install-mpi.sh $(MPI) - pip3 install ".[extreme_scale]" + pip3 install ".[extreme_scale,monitoring]" PYTHONPATH=. pytest parsl/tests/ -k "not cleannet" --config local --cov=parsl --cov-append --cov-report= --random-order .PHONY: site_test From c2c3d125183a4a0aa8d91c6207fe82249228b4ce Mon Sep 17 00:00:00 2001 From: Ben Clifford Date: Thu, 20 May 2021 13:50:02 +0000 Subject: [PATCH 175/408] Add documentation on meanings of states --- docs/reference.rst | 2 + .../parsl.dataflow.states.FINAL_STATES.rst | 6 +++ docs/stubs/parsl.dataflow.states.States.rst | 32 +++++++++++++ parsl/dataflow/states.py | 46 +++++++++++++++++-- 4 files changed, 82 insertions(+), 4 deletions(-) create mode 100644 docs/stubs/parsl.dataflow.states.FINAL_STATES.rst create mode 100644 docs/stubs/parsl.dataflow.states.States.rst diff --git a/docs/reference.rst b/docs/reference.rst index 067290abe8..11e888f81d 100644 --- a/docs/reference.rst +++ b/docs/reference.rst @@ -176,5 +176,7 @@ Internal parsl.dataflow.dflow.DataFlowKernel parsl.dataflow.flow_control.FlowControl parsl.dataflow.memoization.Memoizer + parsl.dataflow.states.FINAL_STATES + parsl.dataflow.states.States parsl.dataflow.strategy.Strategy parsl.dataflow.flow_control.Timer diff --git a/docs/stubs/parsl.dataflow.states.FINAL_STATES.rst b/docs/stubs/parsl.dataflow.states.FINAL_STATES.rst new file mode 100644 index 0000000000..2decc41707 --- /dev/null +++ b/docs/stubs/parsl.dataflow.states.FINAL_STATES.rst @@ -0,0 +1,6 @@ +parsl.dataflow.states.FINAL\_STATES +=================================== + +.. currentmodule:: parsl.dataflow.states + +.. autodata:: FINAL_STATES \ No newline at end of file diff --git a/docs/stubs/parsl.dataflow.states.States.rst b/docs/stubs/parsl.dataflow.states.States.rst new file mode 100644 index 0000000000..0ce617121f --- /dev/null +++ b/docs/stubs/parsl.dataflow.states.States.rst @@ -0,0 +1,32 @@ +parsl.dataflow.states.States +============================ + +.. currentmodule:: parsl.dataflow.states + +.. autoclass:: States + + + .. automethod:: __init__ + + + + + + + .. rubric:: Attributes + + .. autosummary:: + + ~States.dep_fail + ~States.exec_done + ~States.fail_retryable + ~States.failed + ~States.joining + ~States.launched + ~States.memo_done + ~States.pending + ~States.running + ~States.running_ended + ~States.unsched + + \ No newline at end of file diff --git a/parsl/dataflow/states.py b/parsl/dataflow/states.py index 4fbaf17142..700fc4b9b1 100644 --- a/parsl/dataflow/states.py +++ b/parsl/dataflow/states.py @@ -2,22 +2,60 @@ class States(IntEnum): - """Map states for tasks to an int.""" + """Enumerates the states a parsl task may be in. + + These states occur inside the task record for a task inside + a `DataFlowKernel` and in the monitoring database. + + In a single successful task execution, tasks will progress in this + sequence: + + pending -> launched -> running -> running_ended -> exec_done + + Other states represent deviations from this path, either due to + failures, or to deliberate changes to how tasks are executed (for + example due to join_app, or memoization). + + + All tasks should end up in one of the states listed in `FINAL_STATES`. + """ + unsched = -1 pending = 0 + """Task is known to parsl but cannot run yet. Usually, a task cannot + run because it is waiting for dependency tasks to complete. + """ running = 2 - # this state is special - a DFK task record never goes to States.running - # state; but the monitoring database may represent a task in this state - # based on non-DFK information received from monitor_wrapper. + """Task is running on a resource. This state is special - a DFK task + record never goes to States.running state; but the monitoring database + may represent a task in this state based on non-DFK information received + from monitor_wrapper.""" exec_done = 3 + """Task has been executed successfully.""" + failed = 4 + """Task has failed and no more attempts will be made to run it.""" + dep_fail = 5 + """Dependencies of this task failed, so it is marked as failed without + even an attempt to launch it.""" + launched = 7 + """Task has been passed to a `ParslExecutor` for execution.""" + fail_retryable = 8 + """Task has failed, but can be retried""" + memo_done = 9 + """Task was found in the memoization table, so it is marked as done + without even an attempt to launch it.""" + joining = 10 + """Task is a join_app, joining on internal tasks. The task has run its + own Python code, and is now waiting on other tasks before it can make + further progress (to a done/failed state).""" # states from which we will never move to another state From cde62ead08c5d961312827e011d269f86cec32ee Mon Sep 17 00:00:00 2001 From: Ben Clifford Date: Thu, 20 May 2021 13:54:26 +0000 Subject: [PATCH 176/408] Add docs for final states --- parsl/dataflow/states.py | 7 ++++--- 1 file changed, 4 insertions(+), 3 deletions(-) diff --git a/parsl/dataflow/states.py b/parsl/dataflow/states.py index 700fc4b9b1..0bf88f6a00 100644 --- a/parsl/dataflow/states.py +++ b/parsl/dataflow/states.py @@ -58,9 +58,10 @@ class States(IntEnum): further progress (to a done/failed state).""" -# states from which we will never move to another state FINAL_STATES = [States.exec_done, States.memo_done, States.failed, States.dep_fail] +"""States from which we will never move to another state, because the job has +either definitively completed or failed.""" -# states which are final and which indicate a failure. This must -# be a subset of FINAL_STATES FINAL_FAILURE_STATES = [States.failed, States.dep_fail] +"""States which are final and which indicate a failure. This must +be a subset of FINAL_STATES""" From f3838e1d09993291a69c92a5bbc869b4c486afed Mon Sep 17 00:00:00 2001 From: Ben Clifford Date: Thu, 20 May 2021 14:01:58 +0000 Subject: [PATCH 177/408] Remove a state accidentally mentioned that doesn't exist until the future --- parsl/dataflow/states.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/parsl/dataflow/states.py b/parsl/dataflow/states.py index 0bf88f6a00..2d404ddffb 100644 --- a/parsl/dataflow/states.py +++ b/parsl/dataflow/states.py @@ -10,7 +10,7 @@ class States(IntEnum): In a single successful task execution, tasks will progress in this sequence: - pending -> launched -> running -> running_ended -> exec_done + pending -> launched -> running -> exec_done Other states represent deviations from this path, either due to failures, or to deliberate changes to how tasks are executed (for From 8065787a198a5407feb3d52a169d519385d8bc42 Mon Sep 17 00:00:00 2001 From: Ben Clifford Date: Tue, 6 Apr 2021 11:42:50 +0000 Subject: [PATCH 178/408] debug a problem revealed with workflow plot by viz-harder-fail patch: File "/home/benc/parsl/src/parsl/parsl/monitoring/visualization/views.py", line 74, in workflow task_per_app=task_per_app_plot(df_task_tries, df_status, time_completed=workflow_details.time_completed)) File "/home/benc/parsl/src/parsl/parsl/monitoring/visualization/plots/default/workflow_plots.py", line 84, in task_per_app_plot task['task_time_returned']) - pd.Timestamp("1970-01-01")) // pd.Timedelta('1s') --- parsl/monitoring/visualization/views.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/parsl/monitoring/visualization/views.py b/parsl/monitoring/visualization/views.py index e669853560..1456092859 100644 --- a/parsl/monitoring/visualization/views.py +++ b/parsl/monitoring/visualization/views.py @@ -61,7 +61,7 @@ def workflow(workflow_id): task_time_returned from task WHERE run_id='%s'""" % (workflow_id), db.engine) - df_task_tries = pd.read_sql_query("""SELECT task.task_id, task_func_name, + df_task_tries = pd.read_sql_query("""SELECT task.task_id, task_func_name, task_time_returned, task_try_time_running, task_try_time_returned from task, try WHERE task.task_id = try.task_id AND task.run_id='%s' and try.run_id='%s'""" % (workflow_id, workflow_id), db.engine) From 76c3f56b1abf45f5e636b970261b4158643edf53 Mon Sep 17 00:00:00 2001 From: Ben Clifford Date: Mon, 24 May 2021 17:04:20 +0000 Subject: [PATCH 179/408] Refresh stubs --- docs/stubs/parsl.dataflow.states.States.rst | 1 - 1 file changed, 1 deletion(-) diff --git a/docs/stubs/parsl.dataflow.states.States.rst b/docs/stubs/parsl.dataflow.states.States.rst index 0ce617121f..cbae5dcedc 100644 --- a/docs/stubs/parsl.dataflow.states.States.rst +++ b/docs/stubs/parsl.dataflow.states.States.rst @@ -26,7 +26,6 @@ parsl.dataflow.states.States ~States.memo_done ~States.pending ~States.running - ~States.running_ended ~States.unsched \ No newline at end of file From 3bd6306ca3c90f2e0c801e52b2ec03f8927d5f2b Mon Sep 17 00:00:00 2001 From: Ben Clifford Date: Thu, 3 Jun 2021 10:15:33 +0000 Subject: [PATCH 180/408] Update docstring --- parsl/dataflow/dflow.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/parsl/dataflow/dflow.py b/parsl/dataflow/dflow.py index 9b0d0ea528..c1e431ce2d 100644 --- a/parsl/dataflow/dflow.py +++ b/parsl/dataflow/dflow.py @@ -391,7 +391,7 @@ def handle_app_update(self, task_record, future): It will trigger post-app processing such as checkpointing. Args: - task_record : Task + task_record : Task record future (Future) : The relevant app future (which should be consistent with the task structure 'app_fu' entry From 4a6915cacd83050914eac4e5492eb4f353308885 Mon Sep 17 00:00:00 2001 From: Ben Clifford Date: Wed, 24 Mar 2021 12:47:33 +0000 Subject: [PATCH 181/408] Remove task_id param from memo functions, as whole task record is available When these functions need the task id, they can extract it from the task record. --- parsl/dataflow/dflow.py | 4 ++-- parsl/dataflow/memoization.py | 11 ++++++++--- 2 files changed, 10 insertions(+), 5 deletions(-) diff --git a/parsl/dataflow/dflow.py b/parsl/dataflow/dflow.py index cc1f8af875..2baa3e07d5 100644 --- a/parsl/dataflow/dflow.py +++ b/parsl/dataflow/dflow.py @@ -404,7 +404,7 @@ def handle_app_update(self, task_record, future): if not task_record['app_fu'] == future: logger.error("Internal consistency error: callback future is not the app_fu in task structure, for task {}".format(task_id)) - self.memoizer.update_memo(task_id, task_record, future) + self.memoizer.update_memo(task_record, future) if self.checkpoint_mode == 'task_exit': self.checkpoint(tasks=[task_id]) @@ -549,7 +549,7 @@ def launch_task(self, task_record, executable, *args, **kwargs): task_id = task_record['id'] task_record['try_time_launched'] = datetime.datetime.now() - memo_fu = self.memoizer.check_memo(task_id, task_record) + memo_fu = self.memoizer.check_memo(task_record) if memo_fu: logger.info("Reusing cached result for task {}".format(task_id)) task_record['from_memo'] = True diff --git a/parsl/dataflow/memoization.py b/parsl/dataflow/memoization.py index 25985d0c7f..da6c21755a 100644 --- a/parsl/dataflow/memoization.py +++ b/parsl/dataflow/memoization.py @@ -206,7 +206,7 @@ def make_hash(self, task): hashedsum = hashlib.md5(x).hexdigest() return hashedsum - def check_memo(self, task_id, task): + def check_memo(self, task): """Create a hash of the task and its inputs and check the lookup table for this hash. If present, the results are returned. The result is a tuple indicating whether a memo @@ -221,6 +221,9 @@ def check_memo(self, task_id, task): This call will also set task['hashsum'] to the unique hashsum for the func+inputs. """ + + task_id = task['id'] + if not self.memoize or not task['memoize']: task['hashsum'] = None logger.debug("Task {} will not be memoized".format(task_id)) @@ -254,11 +257,10 @@ def hash_lookup(self, hashsum): """ return self.memo_lookup_table[hashsum] - def update_memo(self, task_id, task, r): + def update_memo(self, task, r): """Updates the memoization lookup table with the result from a task. Args: - - task_id (int): Integer task id - task (dict) : A task dict from dfk.tasks - r (Result future): Result future @@ -267,6 +269,9 @@ def update_memo(self, task_id, task, r): """ # TODO: could use typeguard assert isinstance(r, Future) + + task_id = task['id'] + if not self.memoize or not task['memoize'] or 'hashsum' not in task: return From af8c913b7c4d511b816829532c4f81125f10dd9c Mon Sep 17 00:00:00 2001 From: Ben Clifford Date: Wed, 24 Mar 2021 12:59:48 +0000 Subject: [PATCH 182/408] Remove unneeded task_id param from sanitize_and_wrap See #2014 --- parsl/dataflow/dflow.py | 6 ++---- 1 file changed, 2 insertions(+), 4 deletions(-) diff --git a/parsl/dataflow/dflow.py b/parsl/dataflow/dflow.py index cc1f8af875..79e82461c4 100644 --- a/parsl/dataflow/dflow.py +++ b/parsl/dataflow/dflow.py @@ -472,8 +472,7 @@ def launch_if_ready(self, task_record): if self._count_deps(task_record['depends']) == 0: # We can now launch *task* - new_args, kwargs, exceptions_tids = self.sanitize_and_wrap(task_id, - task_record['args'], + new_args, kwargs, exceptions_tids = self.sanitize_and_wrap(task_record['args'], task_record['kwargs']) task_record['args'] = new_args task_record['kwargs'] = kwargs @@ -683,14 +682,13 @@ def check_dep(d): return depends - def sanitize_and_wrap(self, task_id, args, kwargs): + def sanitize_and_wrap(self, args, kwargs): """This function should be called only when all the futures we track have been resolved. If the user hid futures a level below, we will not catch it, and will (most likely) result in a type error. Args: - task_id (str) : Task id func (Function) : App function args (List) : Positional args to app function kwargs (Dict) : Kwargs to app function From e5590f61c64f757cc421319cd699707864b15eae Mon Sep 17 00:00:00 2001 From: Ben Clifford Date: Thu, 3 Jun 2021 10:56:06 +0000 Subject: [PATCH 183/408] Add comment on resource type verification --- parsl/executors/workqueue/executor.py | 3 +++ 1 file changed, 3 insertions(+) diff --git a/parsl/executors/workqueue/executor.py b/parsl/executors/workqueue/executor.py index 6fe8c666dd..2262b0eff3 100644 --- a/parsl/executors/workqueue/executor.py +++ b/parsl/executors/workqueue/executor.py @@ -356,6 +356,9 @@ def submit(self, func, resource_specification, *args, **kwargs): logger.error(message) raise ExecutorError(self, message) + # this checks that either all of the required resource types are specified, or + # that none of them are: the `required_resource_types` are not actually required, + # but if one is specified, then they all must be. key_check = required_resource_types.intersection(keys) required_keys_ok = len(key_check) == 0 or key_check == required_resource_types if not self.autolabel and not required_keys_ok: From 81107792f87a29c1768547795f6df7d48a17c090 Mon Sep 17 00:00:00 2001 From: Ben Clifford Date: Wed, 17 Feb 2021 13:05:49 +0000 Subject: [PATCH 184/408] Rework __repr__ and __str__ for OptionalModuleMissing __repr__ should be quasi-machine-readable, and __str__ human readable See PR #1966, commit a423955f4a9e03cf6986a6e21d285cf46fa3bc88, for further context. Before: >>> str(e) "(['mymod'], 'this test needs demonstrating')" >>> repr(e) "The functionality requested requires a missing optional module:['mymod'], Reason:this test needs demonstrating" After: >>> str(e) "The functionality requested requires missing optional modules ['mymod'], because: this test needs demonstrating" >>> repr(e) "OptionalModuleMissing(['mymod'], 'this test needs demonstrating')" --- parsl/errors.py | 8 +++++--- 1 file changed, 5 insertions(+), 3 deletions(-) diff --git a/parsl/errors.py b/parsl/errors.py index 0a1813448d..eb81cf5157 100644 --- a/parsl/errors.py +++ b/parsl/errors.py @@ -1,15 +1,17 @@ from parsl.app.errors import ParslError +from typing import List + class OptionalModuleMissing(ParslError): ''' Error raised when a required module is missing for a optional/extra component ''' - def __init__(self, module_names, reason): + def __init__(self, module_names: List[str], reason: str): self.module_names = module_names self.reason = reason - def __repr__(self): - return "The functionality requested requires a missing optional module:{0}, Reason:{1}".format( + def __str__(self) -> str: + return "The functionality requested requires missing optional modules {0}, because: {1}".format( self.module_names, self.reason ) From aee578e9ccb932b1c6b122bb0aab75f2276e9e20 Mon Sep 17 00:00:00 2001 From: Ben Clifford Date: Thu, 3 Jun 2021 13:07:39 +0000 Subject: [PATCH 185/408] Rephrase a TODO --- parsl/monitoring/db_manager.py | 6 ++++-- 1 file changed, 4 insertions(+), 2 deletions(-) diff --git a/parsl/monitoring/db_manager.py b/parsl/monitoring/db_manager.py index 4b75da9fe8..ba1458aedb 100644 --- a/parsl/monitoring/db_manager.py +++ b/parsl/monitoring/db_manager.py @@ -63,8 +63,10 @@ def __init__(self, self.eng = sa.create_engine(url) self.meta = self.Base.metadata - # TODO: I'm seeing database lock errors happening here with my db lock test. - # Is the right behaviour to retry a few times? + # TODO: this code wants a read lock on the sqlite3 database, and fails if it cannot + # - for example, if someone else is querying the database at the point that the + # monitoring system is initialized. See PR #1917 for related locked-for-read fixes + # elsewhere in this file. self.meta.create_all(self.eng) self.meta.reflect(bind=self.eng) From 5511c8179fd9d243da63b2801d77e6e26b25862d Mon Sep 17 00:00:00 2001 From: Ben Clifford Date: Thu, 3 Jun 2021 13:10:09 +0000 Subject: [PATCH 186/408] Rephrase some explanation of potential infinite loop --- parsl/monitoring/db_manager.py | 7 +++++-- 1 file changed, 5 insertions(+), 2 deletions(-) diff --git a/parsl/monitoring/db_manager.py b/parsl/monitoring/db_manager.py index ba1458aedb..dab753e67a 100644 --- a/parsl/monitoring/db_manager.py +++ b/parsl/monitoring/db_manager.py @@ -550,8 +550,11 @@ def _update(self, table: str, columns: List[str], messages: List[Dict[str, Any]] self.db.update(table=table, columns=columns, messages=messages) done = True except sa.exc.OperationalError as e: - # hoping that this is a database locked error during _update, not some other problem - logger.warning("Got an sqlite3 operational error. Ignoring and retying on the assumption that it is recoverable: {}".format(e)) + # This code assumes that an OperationalError is something that will go away eventually + # if retried - for example, the database being locked because someone else is readying + # the tables we are trying to write to. If that assumption is wrong, then this loop + # may go on forever. + logger.warning("Got a database OperationalError. Ignoring and retying on the assumption that it is recoverable: {}".format(e)) self.db.rollback() time.sleep(1) # hard coded 1s wait - this should be configurable or exponential backoff or something From 06bb5a31a3789dfa34660ac52799bda92e1a53a9 Mon Sep 17 00:00:00 2001 From: Ben Clifford Date: Thu, 3 Jun 2021 13:14:17 +0000 Subject: [PATCH 187/408] Rephrase some comments in test --- parsl/tests/test_monitoring/test_db_locks.py | 20 +++++++++----------- 1 file changed, 9 insertions(+), 11 deletions(-) diff --git a/parsl/tests/test_monitoring/test_db_locks.py b/parsl/tests/test_monitoring/test_db_locks.py index 2a7ca0acc3..62da835b3c 100644 --- a/parsl/tests/test_monitoring/test_db_locks.py +++ b/parsl/tests/test_monitoring/test_db_locks.py @@ -28,22 +28,19 @@ def test_row_counts(): # parsl.load() returns before all initialisation of monitoring # is complete, which means it isn't safe to take a read lock on # the database yet. This delay tries to work around that - some - # better async behaviour might be nice, but I'm not sure what. + # better async behaviour might be nice, but what? + # + # Taking a read lock before monitoring is initialized will cause + # a failure in the part of monitoring which creates tables, and + # which is not protected against read locks at the time this test + # was written. time.sleep(10) # to get an sqlite3 read lock that is held over a controllable # long time, create a transaction and perform a SELECT in it. + # The lock will be held until the end of the transaction. # (see bottom of https://sqlite.org/lockingv3.html) - # there's an awkward race here: parsl.load() returns before the - # database might have been created, and so then the db manager will - # crash (and if there is a retry loop there instead, I think it will - # hang until after the read lock stuff below is finished? which might - # be acceptable? if it's meant to be properly async and not blocking?) - # ... in which case, initialise parsl *after taking the lock* would also - # work (although the select statement to get that lock wouldn't be the same - # because it wouldn't be able to select from the right table) - logger.info("Getting a read lock on the monitoring database") with engine.begin() as readlock_connection: readlock_connection.execute("BEGIN TRANSACTION") @@ -67,7 +64,8 @@ def test_row_counts(): parsl.dfk().cleanup() parsl.clear() - # at this point, we should find one row in the monitoring database. + # at this point, we should find data consistent with executing one + # task in the database. logger.info("checking database content") with engine.begin() as connection: From f855f26d8e4778d4d64d9469e62c9882e58fa542 Mon Sep 17 00:00:00 2001 From: Ben Clifford Date: Wed, 26 May 2021 12:52:03 +0000 Subject: [PATCH 188/408] Remove documentation that interchange is walltime aware --- parsl/executors/high_throughput/interchange.py | 2 -- 1 file changed, 2 deletions(-) diff --git a/parsl/executors/high_throughput/interchange.py b/parsl/executors/high_throughput/interchange.py index 69699f3479..3c43e5079a 100644 --- a/parsl/executors/high_throughput/interchange.py +++ b/parsl/executors/high_throughput/interchange.py @@ -95,8 +95,6 @@ class Interchange(object): 2. Allow for workers to join and leave the union 3. Detect workers that have failed using heartbeats 4. Service single and batch requests from workers - 5. Be aware of requests worker resource capacity, - eg. schedule only jobs that fit into walltime. TODO: We most likely need a PUB channel to send out global commands, like shutdown """ From cdd6aa6398afbc2b2ca00e5d5e83ac9932360ffc Mon Sep 17 00:00:00 2001 From: Ben Clifford Date: Wed, 12 May 2021 11:09:55 +0000 Subject: [PATCH 189/408] Remove python <3.6 handling from threadpoolexecutor --- parsl/executors/threads.py | 10 +++------- 1 file changed, 3 insertions(+), 7 deletions(-) diff --git a/parsl/executors/threads.py b/parsl/executors/threads.py index 887bda0b04..ec33006d49 100644 --- a/parsl/executors/threads.py +++ b/parsl/executors/threads.py @@ -1,5 +1,4 @@ import logging -import sys import typeguard import concurrent.futures as cf @@ -21,7 +20,7 @@ class ThreadPoolExecutor(NoStatusHandlingExecutor, RepresentationMixin): max_threads : int Number of threads. Default is 2. thread_name_prefix : string - Thread name prefix (only supported in python v3.6+). + Thread name prefix storage_access : list of :class:`~parsl.data_provider.staging.Staging` Specifications for accessing data this executor remotely. managed : bool @@ -47,11 +46,8 @@ def __init__(self, label: str = 'threads', max_threads: int = 2, self.managed = managed def start(self): - if sys.version_info > (3, 6): - self.executor = cf.ThreadPoolExecutor(max_workers=self.max_threads, - thread_name_prefix=self.thread_name_prefix) - else: - self.executor = cf.ThreadPoolExecutor(max_workers=self.max_threads) + self.executor = cf.ThreadPoolExecutor(max_workers=self.max_threads, + thread_name_prefix=self.thread_name_prefix) @property def scaling_enabled(self): From 20f5cd971b93eb6829656710939112f40f532813 Mon Sep 17 00:00:00 2001 From: Ben Clifford Date: Sat, 3 Apr 2021 07:54:13 +0000 Subject: [PATCH 190/408] Do not unwrap joinapp future exceptions unnecessarily An AppFuture will always present its exception as a future.exception(), not as a RemoteWrapper. RemoteWrappers are used at the executor future layer. --- parsl/dataflow/dflow.py | 7 +++---- 1 file changed, 3 insertions(+), 4 deletions(-) diff --git a/parsl/dataflow/dflow.py b/parsl/dataflow/dflow.py index a9ac64464b..f4802c7142 100644 --- a/parsl/dataflow/dflow.py +++ b/parsl/dataflow/dflow.py @@ -371,10 +371,8 @@ def handle_join_update(self, task_record, inner_app_future): outer_task_id = task_record['id'] - try: - res = self._unwrap_remote_exception_wrapper(inner_app_future) - - except Exception as e: + if inner_app_future.exception(): + e = inner_app_future.exception() logger.debug("Task {} failed due to failure of inner join future".format(outer_task_id)) # We keep the history separately, since the future itself could be # tossed. @@ -388,6 +386,7 @@ def handle_join_update(self, task_record, inner_app_future): task_record['app_fu'].set_exception(e) else: + res = inner_app_future.result() self._complete_task(task_record, States.exec_done, res) self._log_std_streams(task_record) From 87b76397ed480c4885e3397bcae22dead470f4b0 Mon Sep 17 00:00:00 2001 From: Ben Clifford Date: Mon, 31 May 2021 13:09:49 +0000 Subject: [PATCH 191/408] Index task_hashsum to give cross-run query speedup Practical experience with wstat has shown this index to give great speedup when making queries which match up tasks between runs based on their checkpointing hashsum. --- parsl/monitoring/db_manager.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/parsl/monitoring/db_manager.py b/parsl/monitoring/db_manager.py index b9265d5a36..f3009d9ed6 100644 --- a/parsl/monitoring/db_manager.py +++ b/parsl/monitoring/db_manager.py @@ -131,7 +131,7 @@ class Task(Base): task_depends = Column('task_depends', Text, nullable=True) task_func_name = Column('task_func_name', Text, nullable=False) task_memoize = Column('task_memoize', Text, nullable=False) - task_hashsum = Column('task_hashsum', Text, nullable=True) + task_hashsum = Column('task_hashsum', Text, nullable=True, index=True) task_inputs = Column('task_inputs', Text, nullable=True) task_outputs = Column('task_outputs', Text, nullable=True) task_stdin = Column('task_stdin', Text, nullable=True) From 9e35c2e65e58c3149b816c28a29edf08751a2a2a Mon Sep 17 00:00:00 2001 From: Ben Clifford Date: Thu, 3 Jun 2021 15:00:23 +0000 Subject: [PATCH 192/408] remove duplicate x==STOP test --- parsl/monitoring/db_manager.py | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/parsl/monitoring/db_manager.py b/parsl/monitoring/db_manager.py index 7ab74d3100..b6868c52f9 100644 --- a/parsl/monitoring/db_manager.py +++ b/parsl/monitoring/db_manager.py @@ -526,8 +526,7 @@ def _migrate_logs_to_internal(self, logs_queue: queue.Queue, queue_tag: str, kil continue else: if queue_tag == 'priority' and x == 'STOP': - if x == 'STOP': - self.close() + self.close() elif queue_tag == 'priority': # implicitly not 'STOP' if isinstance(x, tuple): assert x[0] in [MessageType.WORKFLOW_INFO, MessageType.TASK_INFO], \ From 42279efe96794ed40b6ecc69d00ddf485755cc2a Mon Sep 17 00:00:00 2001 From: Ben Clifford Date: Thu, 3 Jun 2021 15:05:21 +0000 Subject: [PATCH 193/408] Tidy some logging, and raise an exception TODO --- parsl/monitoring/db_manager.py | 10 +++------- 1 file changed, 3 insertions(+), 7 deletions(-) diff --git a/parsl/monitoring/db_manager.py b/parsl/monitoring/db_manager.py index b6868c52f9..247d734735 100644 --- a/parsl/monitoring/db_manager.py +++ b/parsl/monitoring/db_manager.py @@ -534,23 +534,19 @@ def _migrate_logs_to_internal(self, logs_queue: queue.Queue, queue_tag: str, kil assert len(x) == 2 self.pending_priority_queue.put(cast(Any, x)) else: - logger.warning("dropping message with unknown format: {}".format(x)) + logger.error("dropping message with unknown format: {}".format(x)) elif queue_tag == 'resource': assert len(x) == 3 self.pending_resource_queue.put(x[-1]) elif queue_tag == 'node': - logger.info("Received these two from node queue") - logger.info("x = {}".format(x)) - logger.info("addr = {}".format(addr)) - assert x[0] == MessageType.NODE_INFO, "_migrate_logs_to_internal can only migrate NODE_INFO messages from node queue" assert len(x) == 2, "expected message tuple to have exactly two elements" - logger.info("Will put {} to pending node queue".format(x[1])) self.pending_node_queue.put(x[1]) elif queue_tag == "block": self.pending_block_queue.put(x[-1]) - # TODO: else condition here raise an exception. + else: + raise RuntimeException(f"queue_tag {queue_tag} is unknown") def _update(self, table: str, columns: List[str], messages: List[Dict[str, Any]]) -> None: try: From a4efcc67a9078ea519a22bd6e8b3f5992f7f56f6 Mon Sep 17 00:00:00 2001 From: Ben Clifford Date: Thu, 3 Jun 2021 15:07:00 +0000 Subject: [PATCH 194/408] Fix RuntimeException -> RuntimeError --- parsl/monitoring/db_manager.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/parsl/monitoring/db_manager.py b/parsl/monitoring/db_manager.py index 247d734735..8c262daec8 100644 --- a/parsl/monitoring/db_manager.py +++ b/parsl/monitoring/db_manager.py @@ -546,7 +546,7 @@ def _migrate_logs_to_internal(self, logs_queue: queue.Queue, queue_tag: str, kil elif queue_tag == "block": self.pending_block_queue.put(x[-1]) else: - raise RuntimeException(f"queue_tag {queue_tag} is unknown") + raise RuntimeError(f"queue_tag {queue_tag} is unknown") def _update(self, table: str, columns: List[str], messages: List[Dict[str, Any]]) -> None: try: From 7e3507934de3d894fe008001ef46767e94746d8d Mon Sep 17 00:00:00 2001 From: yongyanrao Date: Wed, 26 May 2021 11:12:10 -0500 Subject: [PATCH 195/408] Fix to macos multiprocessing spawn and context issues --- .../high_throughput/process_worker_pool.py | 39 ++++++++++--------- 1 file changed, 21 insertions(+), 18 deletions(-) diff --git a/parsl/executors/high_throughput/process_worker_pool.py b/parsl/executors/high_throughput/process_worker_pool.py index 8737ccca67..190d8fc153 100755 --- a/parsl/executors/high_throughput/process_worker_pool.py +++ b/parsl/executors/high_throughput/process_worker_pool.py @@ -24,8 +24,11 @@ from parsl.executors.high_throughput.probe import probe_addresses if platform.system() != 'Darwin': from multiprocessing import Queue as mpQueue + mpProcess = multiprocessing.Process else: from parsl.executors.high_throughput.mac_safe_queue import MacSafeQueue as mpQueue + multiprocessing.set_start_method('fork', force=True) + mpProcess = multiprocessing.get_context('fork').Process from parsl.serialize import unpack_apply_message, serialize @@ -361,15 +364,15 @@ def worker_watchdog(self, kill_event): except KeyError: logger.info("[WORKER_WATCHDOG_THREAD] Worker {} was not busy when it died".format(worker_id)) - p = multiprocessing.Process(target=worker, args=(worker_id, - self.uid, - self.worker_count, - self.pending_task_queue, - self.pending_result_queue, - self.ready_worker_queue, - self._tasks_in_progress, - self.cpu_affinity - ), name="HTEX-Worker-{}".format(worker_id)) + p = mpProcess(target=worker, args=(worker_id, + self.uid, + self.worker_count, + self.pending_task_queue, + self.pending_result_queue, + self.ready_worker_queue, + self._tasks_in_progress, + self.cpu_affinity + ), name="HTEX-Worker-{}".format(worker_id)) self.procs[worker_id] = p logger.info("[WORKER_WATCHDOG_THREAD] Worker {} has been restarted".format(worker_id)) time.sleep(self.poll_period) @@ -387,15 +390,15 @@ def start(self): self.procs = {} for worker_id in range(self.worker_count): - p = multiprocessing.Process(target=worker, args=(worker_id, - self.uid, - self.worker_count, - self.pending_task_queue, - self.pending_result_queue, - self.ready_worker_queue, - self._tasks_in_progress, - self.cpu_affinity - ), name="HTEX-Worker-{}".format(worker_id)) + p = mpProcess(target=worker, args=(worker_id, + self.uid, + self.worker_count, + self.pending_task_queue, + self.pending_result_queue, + self.ready_worker_queue, + self._tasks_in_progress, + self.cpu_affinity + ), name="HTEX-Worker-{}".format(worker_id)) p.start() self.procs[worker_id] = p From 1ecf475b16ea06280d28ad75c3522935f196c26f Mon Sep 17 00:00:00 2001 From: yongyanrao Date: Thu, 3 Jun 2021 15:01:34 -0500 Subject: [PATCH 196/408] Further fix to make fork setting be effective for the entire parsl package, to avoid any explicit handling from the end user side --- parsl/__init__.py | 4 ++++ parsl/executors/high_throughput/process_worker_pool.py | 1 - 2 files changed, 4 insertions(+), 1 deletion(-) diff --git a/parsl/__init__.py b/parsl/__init__.py index ab42eaa05a..191c75d467 100644 --- a/parsl/__init__.py +++ b/parsl/__init__.py @@ -33,6 +33,10 @@ from parsl.dataflow.dflow import DataFlowKernel, DataFlowKernelLoader +import multiprocessing +if platform.system() == 'Darwin': + multiprocessing.set_start_method('fork', force=True) + __author__ = 'The Parsl Team' __version__ = VERSION diff --git a/parsl/executors/high_throughput/process_worker_pool.py b/parsl/executors/high_throughput/process_worker_pool.py index 190d8fc153..12666cb065 100755 --- a/parsl/executors/high_throughput/process_worker_pool.py +++ b/parsl/executors/high_throughput/process_worker_pool.py @@ -27,7 +27,6 @@ mpProcess = multiprocessing.Process else: from parsl.executors.high_throughput.mac_safe_queue import MacSafeQueue as mpQueue - multiprocessing.set_start_method('fork', force=True) mpProcess = multiprocessing.get_context('fork').Process from parsl.serialize import unpack_apply_message, serialize From ba35149306fae903989190d1f481b2f311d2b83f Mon Sep 17 00:00:00 2001 From: yongyanrao Date: Thu, 3 Jun 2021 17:07:13 -0500 Subject: [PATCH 197/408] Wrap mac process into a class --- parsl/executors/high_throughput/mac_safe_process.py | 7 +++++++ parsl/executors/high_throughput/process_worker_pool.py | 4 ++-- 2 files changed, 9 insertions(+), 2 deletions(-) create mode 100644 parsl/executors/high_throughput/mac_safe_process.py diff --git a/parsl/executors/high_throughput/mac_safe_process.py b/parsl/executors/high_throughput/mac_safe_process.py new file mode 100644 index 0000000000..1f2c0c2209 --- /dev/null +++ b/parsl/executors/high_throughput/mac_safe_process.py @@ -0,0 +1,7 @@ +import multiprocessing + + +class MacSafeProcess(multiprocessing.get_context('fork').Process): + + def __init__(self, *args, **kwargs): + super().__init__(*args, **kwargs) diff --git a/parsl/executors/high_throughput/process_worker_pool.py b/parsl/executors/high_throughput/process_worker_pool.py index 12666cb065..fb0d6aacf2 100755 --- a/parsl/executors/high_throughput/process_worker_pool.py +++ b/parsl/executors/high_throughput/process_worker_pool.py @@ -24,10 +24,10 @@ from parsl.executors.high_throughput.probe import probe_addresses if platform.system() != 'Darwin': from multiprocessing import Queue as mpQueue - mpProcess = multiprocessing.Process + from multiprocessing import Process as mpProcess else: from parsl.executors.high_throughput.mac_safe_queue import MacSafeQueue as mpQueue - mpProcess = multiprocessing.get_context('fork').Process + from parsl.executors.high_throughput.mac_safe_process import MacSafeProcess as mpProcess from parsl.serialize import unpack_apply_message, serialize From 5d7fedfffe798a141fad4667ab59c3a413bf8bfc Mon Sep 17 00:00:00 2001 From: yongyanrao Date: Thu, 3 Jun 2021 18:49:48 -0500 Subject: [PATCH 198/408] Fix for mypy error --- parsl/executors/high_throughput/mac_safe_process.py | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/parsl/executors/high_throughput/mac_safe_process.py b/parsl/executors/high_throughput/mac_safe_process.py index 1f2c0c2209..9563b5255e 100644 --- a/parsl/executors/high_throughput/mac_safe_process.py +++ b/parsl/executors/high_throughput/mac_safe_process.py @@ -1,7 +1,10 @@ import multiprocessing +from typing import Any +ForkProcess: Any = multiprocessing.get_context('fork').Process -class MacSafeProcess(multiprocessing.get_context('fork').Process): + +class MacSafeProcess(ForkProcess): def __init__(self, *args, **kwargs): super().__init__(*args, **kwargs) From 64df9769982c9c4657b6e895daa7c244bcc044c8 Mon Sep 17 00:00:00 2001 From: Ben Clifford Date: Fri, 4 Jun 2021 12:19:00 +0000 Subject: [PATCH 199/408] Add documentation --- docs/userguide/exceptions.rst | 56 +++++++++++++++++++++++++++++++++++ 1 file changed, 56 insertions(+) diff --git a/docs/userguide/exceptions.rst b/docs/userguide/exceptions.rst index 48cd3a9e37..3d8242a102 100644 --- a/docs/userguide/exceptions.rst +++ b/docs/userguide/exceptions.rst @@ -78,6 +78,8 @@ The following example shows how the number of retries can be set to 2: parsl.load(config) +More specific retry handling can be specified using retry handlers, documented +below. Lazy fail @@ -110,3 +112,57 @@ as they are unaffected by task C's failure. (F) (F) (!F) time -----> + + +Retry handlers +-------------- + +The basic parsl retry mechanism keeps a count of the number of times a task +has been (re)tried, and will continue retrying that task until the configured +retry limit is reached. + +Retry handlers generalize this to allow more expressive retry handling: +parsl keeps a retry cost for a task, and the task will be retried until the +configured retry limit is reached. Instead of the cost being 1 for each +failure, user-supplied code can examine the failure and compute a custom +cost. + +This allows user knowledge about failures to influence the retry mechanism: +an exception which is almost definitely a non-recoverable failure (for example, +due to bad parameters) can be given a high retry cost (so that it will not +be retried many times, or at all), and exceptions which are likely to be +transient (for example, where a worker node has died) can be given a low +retry cost so they will be retried many times. + +A retry handler can be specified in the parsl configuration like this: + + +.. code-block:: python + + Config( + retries=2, + retry_handler=example_retry_handler + ) + + +``example_retry_handler`` should be function defined by the user that will +compute the retry cost for a particular failure, given some information about +the failure. + +For example, the following handler will give a cost of 1 to all exceptions, +except when a bash app exits with unix exitcode 9, in which case the cost will +be 100. This will have the effect that retries will happen as normal for most +errors, but the bash app can indicate that there is little point in retrying +by exiting with exitcode 9. + +.. code-block:: python + + def example_retry_handler(exception, task_record): + if isinstance(exception, BashExitFailure) and exception.exitcode == 9: + return 100 + else + return 1 + +The retry handler is given two parameters: the exception from execution, and +the parsl internal task_record. The task record contains details such as the +app name, parameters and executor. From e3f7e5600cd9906f5cdd0bbf22fbf87cce011001 Mon Sep 17 00:00:00 2001 From: Ben Clifford Date: Fri, 4 Jun 2021 12:20:55 +0000 Subject: [PATCH 200/408] remove a done todo --- parsl/dataflow/dflow.py | 3 --- 1 file changed, 3 deletions(-) diff --git a/parsl/dataflow/dflow.py b/parsl/dataflow/dflow.py index 9e09092a07..91cb3f3af3 100644 --- a/parsl/dataflow/dflow.py +++ b/parsl/dataflow/dflow.py @@ -292,9 +292,6 @@ def handle_exec_update(self, task_record, future): task_record['fail_history'].append(repr(e)) task_record['fail_count'] += 1 if self._config.retry_handler: - # TODO: put protective code around here for when retry_handler - # raises an exception: at which point the task should be - # aborted entirely (eg set fail_cost > config retries) try: cost = self._config.retry_handler(e, task_record) except Exception as retry_handler_exception: From c48614bec83d1499765cdef0fb1ff12bd3ea4bb5 Mon Sep 17 00:00:00 2001 From: Ben Clifford Date: Fri, 4 Jun 2021 12:21:33 +0000 Subject: [PATCH 201/408] Remove dev config --- .../tests/configs/htex_local_retry_handler.py | 88 ------------------- 1 file changed, 88 deletions(-) delete mode 100644 parsl/tests/configs/htex_local_retry_handler.py diff --git a/parsl/tests/configs/htex_local_retry_handler.py b/parsl/tests/configs/htex_local_retry_handler.py deleted file mode 100644 index 5ef3b80243..0000000000 --- a/parsl/tests/configs/htex_local_retry_handler.py +++ /dev/null @@ -1,88 +0,0 @@ -""" -The aim of this configuration is to run a local htex -in a similar manner to htex_local.py, but with lots of -options different and more complicated than in that -configuration, so that more code paths are executed -than when testing only with htex_local. - -It does not matter too much *what* is different in this -configuration; what matters is that the differences -cause significantly different pieces of parsl code to be -run - for example, by turning on monitoring, by allowing -blocks to be started by a strategy, by using a different -set of staging providers, by using timing parameters that -will cause substantially different behaviour on whatever -those timing parameters control. -""" - -# imports for monitoring: -from parsl.monitoring import MonitoringHub - -import datetime -import logging -import os - -from parsl.providers import LocalProvider -from parsl.channels import LocalChannel -from parsl.launchers import SingleNodeLauncher - -from parsl.config import Config -from parsl.executors import HighThroughputExecutor - - -from parsl.data_provider.http import HTTPInTaskStaging -from parsl.data_provider.ftp import FTPInTaskStaging -from parsl.data_provider.file_noop import NoOpFileStaging - -working_dir = os.getcwd() + "/" + "test_htex_alternate" - -logger = logging.getLogger("parsl.benc") - - -def test_retry_handler(exception, task_record): - logger.info("in test_retry_handler") - now = datetime.datetime.now() - if (now - task_record['time_invoked']).total_seconds() < 10: - logger.info("RETRY: time invoked is short") - return 0.1 # soft retries until time limit - else: - logger.error("RETRY: exceeded maximum allowable retry time") - return 100 - - -def fresh_config(): - return Config( - executors=[ - HighThroughputExecutor( - label="htex_Local", - address="localhost", - working_dir=working_dir, - storage_access=[FTPInTaskStaging(), HTTPInTaskStaging(), NoOpFileStaging()], - worker_debug=True, - cores_per_worker=1, - heartbeat_period=2, - heartbeat_threshold=5, - poll_period=100, - provider=LocalProvider( - channel=LocalChannel(), - init_blocks=0, - min_blocks=0, - max_blocks=5, - launcher=SingleNodeLauncher(), - ), - ) - ], - strategy='simple', - app_cache=True, checkpoint_mode='task_exit', - retries=2, - retry_handler=test_retry_handler, - monitoring=MonitoringHub( - hub_address="localhost", - hub_port=55055, - monitoring_debug=True, - resource_monitoring_interval=1, - ) - ) - - -config = fresh_config() From 19db391b96dcc3117d6847d0d64003d7fbc028b6 Mon Sep 17 00:00:00 2001 From: Ben Clifford Date: Fri, 4 Jun 2021 12:48:58 +0000 Subject: [PATCH 202/408] Rename test to be more specific --- .../{test_retry_handler.py => test_retry_handler_failure.py} | 0 1 file changed, 0 insertions(+), 0 deletions(-) rename parsl/tests/test_error_handling/{test_retry_handler.py => test_retry_handler_failure.py} (100%) diff --git a/parsl/tests/test_error_handling/test_retry_handler.py b/parsl/tests/test_error_handling/test_retry_handler_failure.py similarity index 100% rename from parsl/tests/test_error_handling/test_retry_handler.py rename to parsl/tests/test_error_handling/test_retry_handler_failure.py From 0b8fab2fd2a9dd0d2a384b963e97858fbce73791 Mon Sep 17 00:00:00 2001 From: Ben Clifford Date: Fri, 4 Jun 2021 13:06:11 +0000 Subject: [PATCH 203/408] Report the number of tries, rather than the max retry cost. These numbers are different in the presence of retry_handlers. --- parsl/dataflow/dflow.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/parsl/dataflow/dflow.py b/parsl/dataflow/dflow.py index 91cb3f3af3..df0a22ec08 100644 --- a/parsl/dataflow/dflow.py +++ b/parsl/dataflow/dflow.py @@ -331,7 +331,7 @@ def handle_exec_update(self, task_record, future): else: logger.exception("Task {} failed after {} retry attempts".format(task_id, - self._config.retries)) + task_record['try_id'])) task_record['time_returned'] = datetime.datetime.now() task_record['status'] = States.failed self.tasks_failed_count += 1 From 0b6895ba02ac63e05f5317caf072488bc6f56b9f Mon Sep 17 00:00:00 2001 From: Ben Clifford Date: Fri, 4 Jun 2021 13:08:54 +0000 Subject: [PATCH 204/408] Add retry handler test --- .../test_error_handling/test_retry_handler.py | 62 +++++++++++++++++++ 1 file changed, 62 insertions(+) create mode 100644 parsl/tests/test_error_handling/test_retry_handler.py diff --git a/parsl/tests/test_error_handling/test_retry_handler.py b/parsl/tests/test_error_handling/test_retry_handler.py new file mode 100644 index 0000000000..5711b127b7 --- /dev/null +++ b/parsl/tests/test_error_handling/test_retry_handler.py @@ -0,0 +1,62 @@ +import argparse +import os +import pytest + +import parsl +from parsl import bash_app, python_app +from parsl.tests.configs.local_threads import fresh_config + +def half_handler(*args): + """Cost 0.5 for each retry, not the default of 1""" + return 0.5 + +local_config = fresh_config() +local_config.retries = 2 +local_config.retry_handler = half_handler + + +@bash_app +def succeed_on_retry(filename, success_on=1, stdout="succeed.out"): + """If the input file does not exist it creates it. + Then, if the file contains success_on lines it exits with 0 + """ + + return """if [[ ! -e {filename} ]]; then touch {filename}; fi; + tries=`wc -l {filename} | cut -f1 -d' '` + echo $tries >> {filename} + + if [[ "$tries" -eq "{success_on}" ]] + then + echo "Match. Success" + else + echo "Tries != success_on , exiting with error" + exit 5 + fi + """.format(filename=filename, success_on=success_on) + + +@pytest.mark.local +def test_retry(): + """Test retries via app that succeeds on the Nth retry. + """ + + fname = "retry.out" + try: + os.remove(fname) + except OSError: + pass + fu = succeed_on_retry(fname, success_on=4) + + fu.result() + + try: + os.remove(fname) + except OSError: + pass + fu = succeed_on_retry(fname, success_on=5) + + with pytest.raises(parsl.app.errors.BashExitFailure): + fu.result() + + assert(fu.exception().exitcode == 5) + From c974a8444cabd8b0ea8284c5060d83a3d4cd205f Mon Sep 17 00:00:00 2001 From: Ben Clifford Date: Fri, 4 Jun 2021 13:20:21 +0000 Subject: [PATCH 205/408] fix flake8 --- parsl/tests/test_error_handling/test_retry_handler.py | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/parsl/tests/test_error_handling/test_retry_handler.py b/parsl/tests/test_error_handling/test_retry_handler.py index 5711b127b7..bca89015db 100644 --- a/parsl/tests/test_error_handling/test_retry_handler.py +++ b/parsl/tests/test_error_handling/test_retry_handler.py @@ -1,15 +1,16 @@ -import argparse import os import pytest import parsl -from parsl import bash_app, python_app +from parsl import bash_app from parsl.tests.configs.local_threads import fresh_config + def half_handler(*args): """Cost 0.5 for each retry, not the default of 1""" return 0.5 + local_config = fresh_config() local_config.retries = 2 local_config.retry_handler = half_handler @@ -59,4 +60,3 @@ def test_retry(): fu.result() assert(fu.exception().exitcode == 5) - From d081fc98b17b7acf1b5e4fdecc942c4b4f456873 Mon Sep 17 00:00:00 2001 From: Ben Clifford Date: Fri, 4 Jun 2021 14:35:48 +0000 Subject: [PATCH 206/408] fix typo --- docs/userguide/exceptions.rst | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/userguide/exceptions.rst b/docs/userguide/exceptions.rst index 3d8242a102..40d5737ba4 100644 --- a/docs/userguide/exceptions.rst +++ b/docs/userguide/exceptions.rst @@ -145,7 +145,7 @@ A retry handler can be specified in the parsl configuration like this: ) -``example_retry_handler`` should be function defined by the user that will +``example_retry_handler`` should be a function defined by the user that will compute the retry cost for a particular failure, given some information about the failure. From 71689895d59a866d87bc532edf1b44596f4a7fa3 Mon Sep 17 00:00:00 2001 From: Ben Clifford Date: Mon, 7 Jun 2021 09:48:06 +0000 Subject: [PATCH 207/408] Refresh the sanitize_and_wrap docstring --- parsl/dataflow/dflow.py | 13 +++++++++---- 1 file changed, 9 insertions(+), 4 deletions(-) diff --git a/parsl/dataflow/dflow.py b/parsl/dataflow/dflow.py index 60ac132e1e..30190ba73d 100644 --- a/parsl/dataflow/dflow.py +++ b/parsl/dataflow/dflow.py @@ -692,19 +692,24 @@ def check_dep(d): return depends def sanitize_and_wrap(self, args, kwargs): - """This function should be called only when all the futures we track have been resolved. + """This function should be called when all dependency futures for a task + have completed. + + It will rewrite the arguments for that task, replacing each dependency + future with the result of that future. If the user hid futures a level below, we will not catch it, and will (most likely) result in a type error. Args: - func (Function) : App function args (List) : Positional args to app function kwargs (Dict) : Kwargs to app function Return: - partial function evaluated with all dependencies in args, kwargs and kwargs['inputs'] evaluated. - + a rewritten args list + a rewritten kwargs dict + pairs of exceptions, task ids from any Futures which stored + exceptions rather than results. """ dep_failures = [] From fbcfc59b3d04f0efa624ae03ccbd95e3455542d9 Mon Sep 17 00:00:00 2001 From: Ben Clifford Date: Mon, 7 Jun 2021 10:14:15 +0000 Subject: [PATCH 208/408] autogenerate sphinx stubs rather than requiring manual update each PR --- docs/conf.py | 2 + .../parsl.addresses.address_by_hostname.rst | 6 --- .../parsl.addresses.address_by_interface.rst | 6 --- .../parsl.addresses.address_by_query.rst | 6 --- .../parsl.addresses.address_by_route.rst | 6 --- docs/stubs/parsl.app.app.AppBase.rst | 22 -------- docs/stubs/parsl.app.app.bash_app.rst | 6 --- docs/stubs/parsl.app.app.join_app.rst | 6 --- docs/stubs/parsl.app.app.python_app.rst | 6 --- docs/stubs/parsl.app.bash.BashApp.rst | 22 -------- .../parsl.app.errors.AppBadFormatting.rst | 6 --- docs/stubs/parsl.app.errors.AppException.rst | 6 --- docs/stubs/parsl.app.errors.AppTimeout.rst | 6 --- .../parsl.app.errors.BadStdStreamFile.rst | 6 --- .../parsl.app.errors.BashAppNoReturn.rst | 6 --- .../parsl.app.errors.BashExitFailure.rst | 6 --- .../stubs/parsl.app.errors.MissingOutputs.rst | 6 --- .../stubs/parsl.app.errors.NotFutureError.rst | 6 --- docs/stubs/parsl.app.errors.ParslError.rst | 6 --- docs/stubs/parsl.app.futures.DataFuture.rst | 41 -------------- docs/stubs/parsl.app.python.PythonApp.rst | 22 -------- docs/stubs/parsl.channels.LocalChannel.rst | 35 ------------ docs/stubs/parsl.channels.OAuthSSHChannel.rst | 36 ------------- docs/stubs/parsl.channels.SSHChannel.rst | 36 ------------- ...sl.channels.SSHInteractiveLoginChannel.rst | 36 ------------- docs/stubs/parsl.channels.base.Channel.rst | 35 ------------ .../parsl.channels.errors.AuthException.rst | 6 --- ...sl.channels.errors.BadHostKeyException.rst | 6 --- ...rsl.channels.errors.BadPermsScriptPath.rst | 6 --- .../parsl.channels.errors.BadScriptPath.rst | 6 --- .../parsl.channels.errors.ChannelError.rst | 6 --- ...arsl.channels.errors.FileCopyException.rst | 6 --- .../parsl.channels.errors.FileExists.rst | 6 --- .../parsl.channels.errors.SSHException.rst | 6 --- docs/stubs/parsl.config.Config.rst | 28 ---------- ...data_provider.data_manager.DataManager.rst | 27 ---------- ...ata_provider.file_noop.NoOpFileStaging.rst | 28 ---------- docs/stubs/parsl.data_provider.files.File.rst | 29 ---------- ...rsl.data_provider.ftp.FTPInTaskStaging.rst | 28 ---------- ...ta_provider.ftp.FTPSeparateTaskStaging.rst | 28 ---------- ...rsl.data_provider.globus.GlobusStaging.rst | 29 ---------- ...l.data_provider.http.HTTPInTaskStaging.rst | 28 ---------- ..._provider.http.HTTPSeparateTaskStaging.rst | 28 ---------- ...parsl.data_provider.rsync.RSyncStaging.rst | 28 ---------- .../parsl.data_provider.staging.Staging.rst | 28 ---------- .../parsl.dataflow.dflow.DataFlowKernel.rst | 44 --------------- ...sl.dataflow.dflow.DataFlowKernelLoader.rst | 26 --------- .../parsl.dataflow.error.BadCheckpoint.rst | 6 --- ...arsl.dataflow.error.ConfigurationError.rst | 6 --- 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b/docs/conf.py @@ -364,3 +364,5 @@ def linkcode_resolve(domain, info): # If true, do not generate a @detailmenu in the "Top" node's menu. # # texinfo_no_detailmenu = False + +autosummary_generate = True diff --git a/docs/stubs/parsl.addresses.address_by_hostname.rst b/docs/stubs/parsl.addresses.address_by_hostname.rst deleted file mode 100644 index d1e7705cba..0000000000 --- a/docs/stubs/parsl.addresses.address_by_hostname.rst +++ /dev/null @@ -1,6 +0,0 @@ -parsl.addresses.address\_by\_hostname -===================================== - -.. currentmodule:: parsl.addresses - -.. autofunction:: address_by_hostname \ No newline at end of file diff --git a/docs/stubs/parsl.addresses.address_by_interface.rst b/docs/stubs/parsl.addresses.address_by_interface.rst deleted file mode 100644 index e5c8be63ef..0000000000 --- a/docs/stubs/parsl.addresses.address_by_interface.rst +++ /dev/null @@ -1,6 +0,0 @@ -parsl.addresses.address\_by\_interface -====================================== - -.. currentmodule:: parsl.addresses - -.. autofunction:: address_by_interface \ No newline at end of file diff --git a/docs/stubs/parsl.addresses.address_by_query.rst b/docs/stubs/parsl.addresses.address_by_query.rst deleted file mode 100644 index 013af3d423..0000000000 --- a/docs/stubs/parsl.addresses.address_by_query.rst +++ /dev/null @@ -1,6 +0,0 @@ -parsl.addresses.address\_by\_query -================================== - -.. currentmodule:: parsl.addresses - -.. autofunction:: address_by_query \ No newline at end of file diff --git a/docs/stubs/parsl.addresses.address_by_route.rst b/docs/stubs/parsl.addresses.address_by_route.rst deleted file mode 100644 index 7a88eb0eaf..0000000000 --- a/docs/stubs/parsl.addresses.address_by_route.rst +++ /dev/null @@ -1,6 +0,0 @@ -parsl.addresses.address\_by\_route -================================== - -.. currentmodule:: parsl.addresses - -.. autofunction:: address_by_route \ No newline at end of file diff --git a/docs/stubs/parsl.app.app.AppBase.rst b/docs/stubs/parsl.app.app.AppBase.rst deleted file mode 100644 index ac76cf0113..0000000000 --- a/docs/stubs/parsl.app.app.AppBase.rst +++ /dev/null @@ -1,22 +0,0 @@ -parsl.app.app.AppBase -===================== - -.. currentmodule:: parsl.app.app - -.. autoclass:: AppBase - - - .. automethod:: __init__ - - - .. rubric:: Methods - - .. autosummary:: - - ~AppBase.__init__ - - - - - - \ No newline at end of file diff --git a/docs/stubs/parsl.app.app.bash_app.rst b/docs/stubs/parsl.app.app.bash_app.rst deleted file mode 100644 index 6c68e3d467..0000000000 --- a/docs/stubs/parsl.app.app.bash_app.rst +++ /dev/null @@ -1,6 +0,0 @@ -parsl.app.app.bash\_app -======================= - -.. currentmodule:: parsl.app.app - -.. autofunction:: bash_app \ No newline at end of file diff --git a/docs/stubs/parsl.app.app.join_app.rst b/docs/stubs/parsl.app.app.join_app.rst deleted file mode 100644 index 408344fe0f..0000000000 --- a/docs/stubs/parsl.app.app.join_app.rst +++ /dev/null @@ -1,6 +0,0 @@ -parsl.app.app.join\_app -======================= - -.. currentmodule:: parsl.app.app - -.. autofunction:: join_app \ No newline at end of file diff --git a/docs/stubs/parsl.app.app.python_app.rst b/docs/stubs/parsl.app.app.python_app.rst deleted file mode 100644 index 963e9b04c6..0000000000 --- a/docs/stubs/parsl.app.app.python_app.rst +++ /dev/null @@ -1,6 +0,0 @@ -parsl.app.app.python\_app -========================= - -.. currentmodule:: parsl.app.app - -.. autofunction:: python_app \ No newline at end of file diff --git a/docs/stubs/parsl.app.bash.BashApp.rst b/docs/stubs/parsl.app.bash.BashApp.rst deleted file mode 100644 index a9b80e89b4..0000000000 --- a/docs/stubs/parsl.app.bash.BashApp.rst +++ /dev/null @@ -1,22 +0,0 @@ -parsl.app.bash.BashApp -====================== - -.. currentmodule:: parsl.app.bash - -.. autoclass:: BashApp - - - .. automethod:: __init__ - - - .. rubric:: Methods - - .. autosummary:: - - ~BashApp.__init__ - - - - - - \ No newline at end of file diff --git a/docs/stubs/parsl.app.errors.AppBadFormatting.rst b/docs/stubs/parsl.app.errors.AppBadFormatting.rst deleted file mode 100644 index 7ea9085b07..0000000000 --- a/docs/stubs/parsl.app.errors.AppBadFormatting.rst +++ /dev/null @@ -1,6 +0,0 @@ -parsl.app.errors.AppBadFormatting -================================= - -.. currentmodule:: parsl.app.errors - -.. autoexception:: AppBadFormatting \ No newline at end of file diff --git a/docs/stubs/parsl.app.errors.AppException.rst b/docs/stubs/parsl.app.errors.AppException.rst deleted file mode 100644 index b427e52b73..0000000000 --- a/docs/stubs/parsl.app.errors.AppException.rst +++ /dev/null @@ -1,6 +0,0 @@ -parsl.app.errors.AppException -============================= - -.. currentmodule:: parsl.app.errors - -.. autoexception:: AppException \ No newline at end of file diff --git a/docs/stubs/parsl.app.errors.AppTimeout.rst b/docs/stubs/parsl.app.errors.AppTimeout.rst deleted file mode 100644 index 316badf45b..0000000000 --- a/docs/stubs/parsl.app.errors.AppTimeout.rst +++ /dev/null @@ -1,6 +0,0 @@ -parsl.app.errors.AppTimeout -=========================== - -.. currentmodule:: parsl.app.errors - -.. autoexception:: AppTimeout \ No newline at end of file diff --git a/docs/stubs/parsl.app.errors.BadStdStreamFile.rst b/docs/stubs/parsl.app.errors.BadStdStreamFile.rst deleted file mode 100644 index 9b2aff012e..0000000000 --- a/docs/stubs/parsl.app.errors.BadStdStreamFile.rst +++ /dev/null @@ -1,6 +0,0 @@ -parsl.app.errors.BadStdStreamFile -================================= - -.. currentmodule:: parsl.app.errors - -.. autoexception:: BadStdStreamFile \ No newline at end of file diff --git a/docs/stubs/parsl.app.errors.BashAppNoReturn.rst b/docs/stubs/parsl.app.errors.BashAppNoReturn.rst deleted file mode 100644 index e75de6ad41..0000000000 --- a/docs/stubs/parsl.app.errors.BashAppNoReturn.rst +++ /dev/null @@ -1,6 +0,0 @@ -parsl.app.errors.BashAppNoReturn -================================ - -.. currentmodule:: parsl.app.errors - -.. autoexception:: BashAppNoReturn \ No newline at end of file diff --git a/docs/stubs/parsl.app.errors.BashExitFailure.rst b/docs/stubs/parsl.app.errors.BashExitFailure.rst deleted file mode 100644 index e0c0a258fc..0000000000 --- a/docs/stubs/parsl.app.errors.BashExitFailure.rst +++ /dev/null @@ -1,6 +0,0 @@ -parsl.app.errors.BashExitFailure -================================ - -.. currentmodule:: parsl.app.errors - -.. autoexception:: BashExitFailure \ No newline at end of file diff --git a/docs/stubs/parsl.app.errors.MissingOutputs.rst b/docs/stubs/parsl.app.errors.MissingOutputs.rst deleted file mode 100644 index ff089d0f20..0000000000 --- a/docs/stubs/parsl.app.errors.MissingOutputs.rst +++ /dev/null @@ -1,6 +0,0 @@ -parsl.app.errors.MissingOutputs -=============================== - -.. currentmodule:: parsl.app.errors - -.. autoexception:: MissingOutputs \ No newline at end of file diff --git a/docs/stubs/parsl.app.errors.NotFutureError.rst b/docs/stubs/parsl.app.errors.NotFutureError.rst deleted file mode 100644 index 4f08420315..0000000000 --- a/docs/stubs/parsl.app.errors.NotFutureError.rst +++ /dev/null @@ -1,6 +0,0 @@ -parsl.app.errors.NotFutureError -=============================== - -.. currentmodule:: parsl.app.errors - -.. autoexception:: NotFutureError \ No newline at end of file diff --git a/docs/stubs/parsl.app.errors.ParslError.rst b/docs/stubs/parsl.app.errors.ParslError.rst deleted file mode 100644 index 761e28e823..0000000000 --- a/docs/stubs/parsl.app.errors.ParslError.rst +++ /dev/null @@ -1,6 +0,0 @@ -parsl.app.errors.ParslError -=========================== - -.. currentmodule:: parsl.app.errors - -.. autoexception:: ParslError \ No newline at end of file diff --git a/docs/stubs/parsl.app.futures.DataFuture.rst b/docs/stubs/parsl.app.futures.DataFuture.rst deleted file mode 100644 index d1cffda01f..0000000000 --- a/docs/stubs/parsl.app.futures.DataFuture.rst +++ /dev/null @@ -1,41 +0,0 @@ -parsl.app.futures.DataFuture -============================ - -.. currentmodule:: parsl.app.futures - -.. autoclass:: DataFuture - - - .. automethod:: __init__ - - - .. rubric:: Methods - - .. autosummary:: - - ~DataFuture.__init__ - ~DataFuture.add_done_callback - ~DataFuture.cancel - ~DataFuture.cancelled - ~DataFuture.done - ~DataFuture.exception - ~DataFuture.parent_callback - ~DataFuture.result - ~DataFuture.running - ~DataFuture.set_exception - ~DataFuture.set_result - ~DataFuture.set_running_or_notify_cancel - - - - - - .. rubric:: Attributes - - .. autosummary:: - - ~DataFuture.filename - ~DataFuture.filepath - ~DataFuture.tid - - \ No newline at end of file diff --git a/docs/stubs/parsl.app.python.PythonApp.rst b/docs/stubs/parsl.app.python.PythonApp.rst deleted file mode 100644 index be44a9a014..0000000000 --- a/docs/stubs/parsl.app.python.PythonApp.rst +++ /dev/null @@ -1,22 +0,0 @@ -parsl.app.python.PythonApp -========================== - -.. currentmodule:: parsl.app.python - -.. autoclass:: PythonApp - - - .. automethod:: __init__ - - - .. rubric:: Methods - - .. autosummary:: - - ~PythonApp.__init__ - - - - - - \ No newline at end of file diff --git a/docs/stubs/parsl.channels.LocalChannel.rst b/docs/stubs/parsl.channels.LocalChannel.rst deleted file mode 100644 index e681d872f3..0000000000 --- a/docs/stubs/parsl.channels.LocalChannel.rst +++ /dev/null @@ -1,35 +0,0 @@ -parsl.channels.LocalChannel -=========================== - -.. currentmodule:: parsl.channels - -.. autoclass:: LocalChannel - - - .. automethod:: __init__ - - - .. rubric:: Methods - - .. autosummary:: - - ~LocalChannel.__init__ - ~LocalChannel.abspath - ~LocalChannel.close - ~LocalChannel.execute_wait - ~LocalChannel.isdir - ~LocalChannel.makedirs - ~LocalChannel.pull_file - ~LocalChannel.push_file - - - - - - .. rubric:: Attributes - - .. autosummary:: - - ~LocalChannel.script_dir - - \ No newline at end of file diff --git a/docs/stubs/parsl.channels.OAuthSSHChannel.rst b/docs/stubs/parsl.channels.OAuthSSHChannel.rst deleted file mode 100644 index ae3e53bba0..0000000000 --- a/docs/stubs/parsl.channels.OAuthSSHChannel.rst +++ /dev/null @@ -1,36 +0,0 @@ -parsl.channels.OAuthSSHChannel -============================== - -.. currentmodule:: parsl.channels - -.. autoclass:: OAuthSSHChannel - - - .. automethod:: __init__ - - - .. rubric:: Methods - - .. autosummary:: - - ~OAuthSSHChannel.__init__ - ~OAuthSSHChannel.abspath - ~OAuthSSHChannel.close - ~OAuthSSHChannel.execute_wait - ~OAuthSSHChannel.isdir - ~OAuthSSHChannel.makedirs - ~OAuthSSHChannel.prepend_envs - ~OAuthSSHChannel.pull_file - ~OAuthSSHChannel.push_file - - - - - - .. rubric:: Attributes - - .. autosummary:: - - ~OAuthSSHChannel.script_dir - - \ No newline at end of file diff --git a/docs/stubs/parsl.channels.SSHChannel.rst b/docs/stubs/parsl.channels.SSHChannel.rst deleted file mode 100644 index 18cd1c55d6..0000000000 --- a/docs/stubs/parsl.channels.SSHChannel.rst +++ /dev/null @@ -1,36 +0,0 @@ -parsl.channels.SSHChannel -========================= - -.. currentmodule:: parsl.channels - -.. autoclass:: SSHChannel - - - .. automethod:: __init__ - - - .. rubric:: Methods - - .. autosummary:: - - ~SSHChannel.__init__ - ~SSHChannel.abspath - ~SSHChannel.close - ~SSHChannel.execute_wait - ~SSHChannel.isdir - ~SSHChannel.makedirs - ~SSHChannel.prepend_envs - ~SSHChannel.pull_file - ~SSHChannel.push_file - - - - - - .. rubric:: Attributes - - .. autosummary:: - - ~SSHChannel.script_dir - - \ No newline at end of file diff --git a/docs/stubs/parsl.channels.SSHInteractiveLoginChannel.rst b/docs/stubs/parsl.channels.SSHInteractiveLoginChannel.rst deleted file mode 100644 index 99233e7ddc..0000000000 --- a/docs/stubs/parsl.channels.SSHInteractiveLoginChannel.rst +++ /dev/null @@ -1,36 +0,0 @@ -parsl.channels.SSHInteractiveLoginChannel -========================================= - -.. currentmodule:: parsl.channels - -.. autoclass:: SSHInteractiveLoginChannel - - - .. automethod:: __init__ - - - .. rubric:: Methods - - .. autosummary:: - - ~SSHInteractiveLoginChannel.__init__ - ~SSHInteractiveLoginChannel.abspath - ~SSHInteractiveLoginChannel.close - ~SSHInteractiveLoginChannel.execute_wait - ~SSHInteractiveLoginChannel.isdir - ~SSHInteractiveLoginChannel.makedirs - ~SSHInteractiveLoginChannel.prepend_envs - ~SSHInteractiveLoginChannel.pull_file - ~SSHInteractiveLoginChannel.push_file - - - - - - .. rubric:: Attributes - - .. autosummary:: - - ~SSHInteractiveLoginChannel.script_dir - - \ No newline at end of file diff --git a/docs/stubs/parsl.channels.base.Channel.rst b/docs/stubs/parsl.channels.base.Channel.rst deleted file mode 100644 index 41864a0297..0000000000 --- a/docs/stubs/parsl.channels.base.Channel.rst +++ /dev/null @@ -1,35 +0,0 @@ -parsl.channels.base.Channel -=========================== - -.. currentmodule:: parsl.channels.base - -.. autoclass:: Channel - - - .. automethod:: __init__ - - - .. rubric:: Methods - - .. autosummary:: - - ~Channel.__init__ - ~Channel.abspath - ~Channel.close - ~Channel.execute_wait - ~Channel.isdir - ~Channel.makedirs - ~Channel.pull_file - ~Channel.push_file - - - - - - .. rubric:: Attributes - - .. autosummary:: - - ~Channel.script_dir - - \ No newline at end of file diff --git a/docs/stubs/parsl.channels.errors.AuthException.rst b/docs/stubs/parsl.channels.errors.AuthException.rst deleted file mode 100644 index 2a8b17a118..0000000000 --- a/docs/stubs/parsl.channels.errors.AuthException.rst +++ /dev/null @@ -1,6 +0,0 @@ -parsl.channels.errors.AuthException -=================================== - -.. currentmodule:: parsl.channels.errors - -.. autoexception:: AuthException \ No newline at end of file diff --git a/docs/stubs/parsl.channels.errors.BadHostKeyException.rst b/docs/stubs/parsl.channels.errors.BadHostKeyException.rst deleted file mode 100644 index 4c79752743..0000000000 --- a/docs/stubs/parsl.channels.errors.BadHostKeyException.rst +++ /dev/null @@ -1,6 +0,0 @@ -parsl.channels.errors.BadHostKeyException -========================================= - -.. currentmodule:: parsl.channels.errors - -.. autoexception:: BadHostKeyException \ No newline at end of file diff --git a/docs/stubs/parsl.channels.errors.BadPermsScriptPath.rst b/docs/stubs/parsl.channels.errors.BadPermsScriptPath.rst deleted file mode 100644 index a3d1f5a763..0000000000 --- a/docs/stubs/parsl.channels.errors.BadPermsScriptPath.rst +++ /dev/null @@ -1,6 +0,0 @@ -parsl.channels.errors.BadPermsScriptPath -======================================== - -.. currentmodule:: parsl.channels.errors - -.. autoexception:: BadPermsScriptPath \ No newline at end of file diff --git a/docs/stubs/parsl.channels.errors.BadScriptPath.rst b/docs/stubs/parsl.channels.errors.BadScriptPath.rst deleted file mode 100644 index bc7be42bd8..0000000000 --- a/docs/stubs/parsl.channels.errors.BadScriptPath.rst +++ /dev/null @@ -1,6 +0,0 @@ -parsl.channels.errors.BadScriptPath -=================================== - -.. currentmodule:: parsl.channels.errors - -.. autoexception:: BadScriptPath \ No newline at end of file diff --git a/docs/stubs/parsl.channels.errors.ChannelError.rst b/docs/stubs/parsl.channels.errors.ChannelError.rst deleted file mode 100644 index 88fdaf0904..0000000000 --- a/docs/stubs/parsl.channels.errors.ChannelError.rst +++ /dev/null @@ -1,6 +0,0 @@ -parsl.channels.errors.ChannelError -================================== - -.. currentmodule:: parsl.channels.errors - -.. autoexception:: ChannelError \ No newline at end of file diff --git a/docs/stubs/parsl.channels.errors.FileCopyException.rst b/docs/stubs/parsl.channels.errors.FileCopyException.rst deleted file mode 100644 index 8c1658c239..0000000000 --- a/docs/stubs/parsl.channels.errors.FileCopyException.rst +++ /dev/null @@ -1,6 +0,0 @@ -parsl.channels.errors.FileCopyException -======================================= - -.. currentmodule:: parsl.channels.errors - -.. autoexception:: FileCopyException \ No newline at end of file diff --git a/docs/stubs/parsl.channels.errors.FileExists.rst b/docs/stubs/parsl.channels.errors.FileExists.rst deleted file mode 100644 index 22b72f164f..0000000000 --- a/docs/stubs/parsl.channels.errors.FileExists.rst +++ /dev/null @@ -1,6 +0,0 @@ -parsl.channels.errors.FileExists -================================ - -.. currentmodule:: parsl.channels.errors - -.. autoexception:: FileExists \ No newline at end of file diff --git a/docs/stubs/parsl.channels.errors.SSHException.rst b/docs/stubs/parsl.channels.errors.SSHException.rst deleted file mode 100644 index a64f147ec2..0000000000 --- a/docs/stubs/parsl.channels.errors.SSHException.rst +++ /dev/null @@ -1,6 +0,0 @@ -parsl.channels.errors.SSHException -================================== - -.. currentmodule:: parsl.channels.errors - -.. autoexception:: SSHException \ No newline at end of file diff --git a/docs/stubs/parsl.config.Config.rst b/docs/stubs/parsl.config.Config.rst deleted file mode 100644 index 237a6aa2e1..0000000000 --- a/docs/stubs/parsl.config.Config.rst +++ /dev/null @@ -1,28 +0,0 @@ -parsl.config.Config -=================== - -.. currentmodule:: parsl.config - -.. autoclass:: Config - - - .. automethod:: __init__ - - - .. rubric:: Methods - - .. autosummary:: - - ~Config.__init__ - - - - - - .. rubric:: Attributes - - .. autosummary:: - - ~Config.executors - - \ No newline at end of file diff --git a/docs/stubs/parsl.data_provider.data_manager.DataManager.rst b/docs/stubs/parsl.data_provider.data_manager.DataManager.rst deleted file mode 100644 index 9c3cb60108..0000000000 --- a/docs/stubs/parsl.data_provider.data_manager.DataManager.rst +++ /dev/null @@ -1,27 +0,0 @@ -parsl.data\_provider.data\_manager.DataManager -============================================== - -.. currentmodule:: parsl.data_provider.data_manager - -.. autoclass:: DataManager - - - .. automethod:: __init__ - - - .. rubric:: Methods - - .. autosummary:: - - ~DataManager.__init__ - ~DataManager.optionally_stage_in - ~DataManager.replace_task - ~DataManager.replace_task_stage_out - ~DataManager.stage_in - ~DataManager.stage_out - - - - - - \ No newline at end of file diff --git a/docs/stubs/parsl.data_provider.file_noop.NoOpFileStaging.rst b/docs/stubs/parsl.data_provider.file_noop.NoOpFileStaging.rst deleted file mode 100644 index 77c71510a3..0000000000 --- a/docs/stubs/parsl.data_provider.file_noop.NoOpFileStaging.rst +++ /dev/null @@ -1,28 +0,0 @@ -parsl.data\_provider.file\_noop.NoOpFileStaging -=============================================== - -.. currentmodule:: parsl.data_provider.file_noop - -.. autoclass:: NoOpFileStaging - - - .. automethod:: __init__ - - - .. rubric:: Methods - - .. autosummary:: - - ~NoOpFileStaging.__init__ - ~NoOpFileStaging.can_stage_in - ~NoOpFileStaging.can_stage_out - ~NoOpFileStaging.replace_task - ~NoOpFileStaging.replace_task_stage_out - ~NoOpFileStaging.stage_in - ~NoOpFileStaging.stage_out - - - - - - \ No newline at end of file diff --git a/docs/stubs/parsl.data_provider.files.File.rst b/docs/stubs/parsl.data_provider.files.File.rst deleted file mode 100644 index e76a07aaa1..0000000000 --- a/docs/stubs/parsl.data_provider.files.File.rst +++ /dev/null @@ -1,29 +0,0 @@ -parsl.data\_provider.files.File -=============================== - -.. currentmodule:: parsl.data_provider.files - -.. autoclass:: File - - - .. automethod:: __init__ - - - .. rubric:: Methods - - .. autosummary:: - - ~File.__init__ - ~File.cleancopy - - - - - - .. rubric:: Attributes - - .. autosummary:: - - ~File.filepath - - \ No newline at end of file diff --git a/docs/stubs/parsl.data_provider.ftp.FTPInTaskStaging.rst b/docs/stubs/parsl.data_provider.ftp.FTPInTaskStaging.rst deleted file mode 100644 index f16aa73a35..0000000000 --- a/docs/stubs/parsl.data_provider.ftp.FTPInTaskStaging.rst +++ /dev/null @@ -1,28 +0,0 @@ -parsl.data\_provider.ftp.FTPInTaskStaging -========================================= - -.. currentmodule:: parsl.data_provider.ftp - -.. autoclass:: FTPInTaskStaging - - - .. automethod:: __init__ - - - .. rubric:: Methods - - .. autosummary:: - - ~FTPInTaskStaging.__init__ - ~FTPInTaskStaging.can_stage_in - ~FTPInTaskStaging.can_stage_out - ~FTPInTaskStaging.replace_task - ~FTPInTaskStaging.replace_task_stage_out - ~FTPInTaskStaging.stage_in - ~FTPInTaskStaging.stage_out - - - - - - \ No newline at end of file diff --git a/docs/stubs/parsl.data_provider.ftp.FTPSeparateTaskStaging.rst b/docs/stubs/parsl.data_provider.ftp.FTPSeparateTaskStaging.rst deleted file mode 100644 index e24753b536..0000000000 --- a/docs/stubs/parsl.data_provider.ftp.FTPSeparateTaskStaging.rst +++ /dev/null @@ -1,28 +0,0 @@ -parsl.data\_provider.ftp.FTPSeparateTaskStaging -=============================================== - -.. currentmodule:: parsl.data_provider.ftp - -.. autoclass:: FTPSeparateTaskStaging - - - .. automethod:: __init__ - - - .. rubric:: Methods - - .. autosummary:: - - ~FTPSeparateTaskStaging.__init__ - ~FTPSeparateTaskStaging.can_stage_in - ~FTPSeparateTaskStaging.can_stage_out - ~FTPSeparateTaskStaging.replace_task - ~FTPSeparateTaskStaging.replace_task_stage_out - ~FTPSeparateTaskStaging.stage_in - ~FTPSeparateTaskStaging.stage_out - - - - - - \ No newline at end of file diff --git a/docs/stubs/parsl.data_provider.globus.GlobusStaging.rst b/docs/stubs/parsl.data_provider.globus.GlobusStaging.rst deleted file mode 100644 index e65dc2dc17..0000000000 --- a/docs/stubs/parsl.data_provider.globus.GlobusStaging.rst +++ /dev/null @@ -1,29 +0,0 @@ -parsl.data\_provider.globus.GlobusStaging -========================================= - -.. currentmodule:: parsl.data_provider.globus - -.. autoclass:: GlobusStaging - - - .. automethod:: __init__ - - - .. rubric:: Methods - - .. autosummary:: - - ~GlobusStaging.__init__ - ~GlobusStaging.can_stage_in - ~GlobusStaging.can_stage_out - ~GlobusStaging.initialize_globus - ~GlobusStaging.replace_task - ~GlobusStaging.replace_task_stage_out - ~GlobusStaging.stage_in - ~GlobusStaging.stage_out - - - - - - \ No newline at end of file diff --git a/docs/stubs/parsl.data_provider.http.HTTPInTaskStaging.rst b/docs/stubs/parsl.data_provider.http.HTTPInTaskStaging.rst deleted file mode 100644 index 7b10950d0f..0000000000 --- a/docs/stubs/parsl.data_provider.http.HTTPInTaskStaging.rst +++ /dev/null @@ -1,28 +0,0 @@ -parsl.data\_provider.http.HTTPInTaskStaging -=========================================== - -.. currentmodule:: parsl.data_provider.http - -.. autoclass:: HTTPInTaskStaging - - - .. automethod:: __init__ - - - .. rubric:: Methods - - .. autosummary:: - - ~HTTPInTaskStaging.__init__ - ~HTTPInTaskStaging.can_stage_in - ~HTTPInTaskStaging.can_stage_out - ~HTTPInTaskStaging.replace_task - ~HTTPInTaskStaging.replace_task_stage_out - ~HTTPInTaskStaging.stage_in - ~HTTPInTaskStaging.stage_out - - - - - - \ No newline at end of file diff --git a/docs/stubs/parsl.data_provider.http.HTTPSeparateTaskStaging.rst b/docs/stubs/parsl.data_provider.http.HTTPSeparateTaskStaging.rst deleted file mode 100644 index 917eb4913d..0000000000 --- a/docs/stubs/parsl.data_provider.http.HTTPSeparateTaskStaging.rst +++ /dev/null @@ -1,28 +0,0 @@ -parsl.data\_provider.http.HTTPSeparateTaskStaging -================================================= - -.. currentmodule:: parsl.data_provider.http - -.. autoclass:: HTTPSeparateTaskStaging - - - .. automethod:: __init__ - - - .. rubric:: Methods - - .. autosummary:: - - ~HTTPSeparateTaskStaging.__init__ - ~HTTPSeparateTaskStaging.can_stage_in - ~HTTPSeparateTaskStaging.can_stage_out - ~HTTPSeparateTaskStaging.replace_task - ~HTTPSeparateTaskStaging.replace_task_stage_out - ~HTTPSeparateTaskStaging.stage_in - ~HTTPSeparateTaskStaging.stage_out - - - - - - \ No newline at end of file diff --git a/docs/stubs/parsl.data_provider.rsync.RSyncStaging.rst b/docs/stubs/parsl.data_provider.rsync.RSyncStaging.rst deleted file mode 100644 index 2d8f770fe7..0000000000 --- a/docs/stubs/parsl.data_provider.rsync.RSyncStaging.rst +++ /dev/null @@ -1,28 +0,0 @@ -parsl.data\_provider.rsync.RSyncStaging -======================================= - -.. currentmodule:: parsl.data_provider.rsync - -.. autoclass:: RSyncStaging - - - .. automethod:: __init__ - - - .. rubric:: Methods - - .. autosummary:: - - ~RSyncStaging.__init__ - ~RSyncStaging.can_stage_in - ~RSyncStaging.can_stage_out - ~RSyncStaging.replace_task - ~RSyncStaging.replace_task_stage_out - ~RSyncStaging.stage_in - ~RSyncStaging.stage_out - - - - - - \ No newline at end of file diff --git a/docs/stubs/parsl.data_provider.staging.Staging.rst b/docs/stubs/parsl.data_provider.staging.Staging.rst deleted file mode 100644 index 7f2a816e26..0000000000 --- a/docs/stubs/parsl.data_provider.staging.Staging.rst +++ /dev/null @@ -1,28 +0,0 @@ -parsl.data\_provider.staging.Staging -==================================== - -.. currentmodule:: parsl.data_provider.staging - -.. autoclass:: Staging - - - .. automethod:: __init__ - - - .. rubric:: Methods - - .. autosummary:: - - ~Staging.__init__ - ~Staging.can_stage_in - ~Staging.can_stage_out - ~Staging.replace_task - ~Staging.replace_task_stage_out - ~Staging.stage_in - ~Staging.stage_out - - - - - - \ No newline at end of file diff --git a/docs/stubs/parsl.dataflow.dflow.DataFlowKernel.rst b/docs/stubs/parsl.dataflow.dflow.DataFlowKernel.rst deleted file mode 100644 index 695f1a4512..0000000000 --- a/docs/stubs/parsl.dataflow.dflow.DataFlowKernel.rst +++ /dev/null @@ -1,44 +0,0 @@ -parsl.dataflow.dflow.DataFlowKernel -=================================== - -.. currentmodule:: parsl.dataflow.dflow - -.. autoclass:: DataFlowKernel - - - .. automethod:: __init__ - - - .. rubric:: Methods - - .. autosummary:: - - ~DataFlowKernel.__init__ - ~DataFlowKernel.add_executors - ~DataFlowKernel.atexit_cleanup - ~DataFlowKernel.check_staging_inhibited - ~DataFlowKernel.checkpoint - ~DataFlowKernel.cleanup - ~DataFlowKernel.handle_app_update - ~DataFlowKernel.handle_exec_update - ~DataFlowKernel.handle_join_update - ~DataFlowKernel.launch_if_ready - ~DataFlowKernel.launch_task - ~DataFlowKernel.load_checkpoints - ~DataFlowKernel.log_task_states - ~DataFlowKernel.sanitize_and_wrap - ~DataFlowKernel.submit - ~DataFlowKernel.wait_for_current_tasks - ~DataFlowKernel.wipe_task - - - - - - .. rubric:: Attributes - - .. autosummary:: - - ~DataFlowKernel.config - - \ No newline at end of file diff --git a/docs/stubs/parsl.dataflow.dflow.DataFlowKernelLoader.rst b/docs/stubs/parsl.dataflow.dflow.DataFlowKernelLoader.rst deleted file mode 100644 index a43dc06e1b..0000000000 --- a/docs/stubs/parsl.dataflow.dflow.DataFlowKernelLoader.rst +++ /dev/null @@ -1,26 +0,0 @@ -parsl.dataflow.dflow.DataFlowKernelLoader -========================================= - -.. currentmodule:: parsl.dataflow.dflow - -.. autoclass:: DataFlowKernelLoader - - - .. automethod:: __init__ - - - .. rubric:: Methods - - .. autosummary:: - - ~DataFlowKernelLoader.__init__ - ~DataFlowKernelLoader.clear - ~DataFlowKernelLoader.dfk - ~DataFlowKernelLoader.load - ~DataFlowKernelLoader.wait_for_current_tasks - - - - - - \ No newline at end of file diff --git a/docs/stubs/parsl.dataflow.error.BadCheckpoint.rst b/docs/stubs/parsl.dataflow.error.BadCheckpoint.rst deleted file mode 100644 index 5da28e3aec..0000000000 --- a/docs/stubs/parsl.dataflow.error.BadCheckpoint.rst +++ /dev/null @@ -1,6 +0,0 @@ -parsl.dataflow.error.BadCheckpoint -================================== - -.. currentmodule:: parsl.dataflow.error - -.. autoexception:: BadCheckpoint \ No newline at end of file diff --git a/docs/stubs/parsl.dataflow.error.ConfigurationError.rst b/docs/stubs/parsl.dataflow.error.ConfigurationError.rst deleted file mode 100644 index ac7d20bd9b..0000000000 --- a/docs/stubs/parsl.dataflow.error.ConfigurationError.rst +++ /dev/null @@ -1,6 +0,0 @@ -parsl.dataflow.error.ConfigurationError -======================================= - -.. currentmodule:: parsl.dataflow.error - -.. autoexception:: ConfigurationError \ No newline at end of file diff --git a/docs/stubs/parsl.dataflow.error.DataFlowException.rst b/docs/stubs/parsl.dataflow.error.DataFlowException.rst deleted file mode 100644 index 274061e705..0000000000 --- a/docs/stubs/parsl.dataflow.error.DataFlowException.rst +++ /dev/null @@ -1,6 +0,0 @@ -parsl.dataflow.error.DataFlowException -====================================== - -.. currentmodule:: parsl.dataflow.error - -.. autoexception:: DataFlowException \ No newline at end of file diff --git a/docs/stubs/parsl.dataflow.error.DependencyError.rst b/docs/stubs/parsl.dataflow.error.DependencyError.rst deleted file mode 100644 index 5519b32934..0000000000 --- a/docs/stubs/parsl.dataflow.error.DependencyError.rst +++ /dev/null @@ -1,6 +0,0 @@ -parsl.dataflow.error.DependencyError -==================================== - -.. currentmodule:: parsl.dataflow.error - -.. autoexception:: DependencyError \ No newline at end of file diff --git a/docs/stubs/parsl.dataflow.error.DuplicateTaskError.rst b/docs/stubs/parsl.dataflow.error.DuplicateTaskError.rst deleted file mode 100644 index de333392da..0000000000 --- a/docs/stubs/parsl.dataflow.error.DuplicateTaskError.rst +++ /dev/null @@ -1,6 +0,0 @@ -parsl.dataflow.error.DuplicateTaskError -======================================= - -.. currentmodule:: parsl.dataflow.error - -.. autoexception:: DuplicateTaskError \ No newline at end of file diff --git a/docs/stubs/parsl.dataflow.flow_control.FlowControl.rst b/docs/stubs/parsl.dataflow.flow_control.FlowControl.rst deleted file mode 100644 index 0db1cc4a20..0000000000 --- a/docs/stubs/parsl.dataflow.flow_control.FlowControl.rst +++ /dev/null @@ -1,26 +0,0 @@ -parsl.dataflow.flow\_control.FlowControl -======================================== - -.. currentmodule:: parsl.dataflow.flow_control - -.. autoclass:: FlowControl - - - .. automethod:: __init__ - - - .. rubric:: Methods - - .. autosummary:: - - ~FlowControl.__init__ - ~FlowControl.add_executors - ~FlowControl.close - ~FlowControl.make_callback - ~FlowControl.notify - - - - - - \ No newline at end of file diff --git a/docs/stubs/parsl.dataflow.flow_control.Timer.rst b/docs/stubs/parsl.dataflow.flow_control.Timer.rst deleted file mode 100644 index 0dbfc561ab..0000000000 --- a/docs/stubs/parsl.dataflow.flow_control.Timer.rst +++ /dev/null @@ -1,24 +0,0 @@ -parsl.dataflow.flow\_control.Timer -================================== - -.. currentmodule:: parsl.dataflow.flow_control - -.. autoclass:: Timer - - - .. automethod:: __init__ - - - .. rubric:: Methods - - .. autosummary:: - - ~Timer.__init__ - ~Timer.close - ~Timer.make_callback - - - - - - \ No newline at end of file diff --git a/docs/stubs/parsl.dataflow.futures.AppFuture.rst b/docs/stubs/parsl.dataflow.futures.AppFuture.rst deleted file mode 100644 index c2567b0939..0000000000 --- a/docs/stubs/parsl.dataflow.futures.AppFuture.rst +++ /dev/null @@ -1,42 +0,0 @@ -parsl.dataflow.futures.AppFuture -================================ - -.. currentmodule:: parsl.dataflow.futures - -.. autoclass:: AppFuture - - - .. automethod:: __init__ - - - .. rubric:: Methods - - .. autosummary:: - - ~AppFuture.__init__ - ~AppFuture.add_done_callback - ~AppFuture.cancel - ~AppFuture.cancelled - ~AppFuture.done - ~AppFuture.exception - ~AppFuture.result - ~AppFuture.running - ~AppFuture.set_exception - ~AppFuture.set_result - ~AppFuture.set_running_or_notify_cancel - ~AppFuture.task_status - - - - - - .. rubric:: Attributes - - .. autosummary:: - - ~AppFuture.outputs - ~AppFuture.stderr - ~AppFuture.stdout - ~AppFuture.tid - - \ No newline at end of file diff --git a/docs/stubs/parsl.dataflow.memoization.Memoizer.rst b/docs/stubs/parsl.dataflow.memoization.Memoizer.rst deleted file mode 100644 index 67b3bca940..0000000000 --- a/docs/stubs/parsl.dataflow.memoization.Memoizer.rst +++ /dev/null @@ -1,26 +0,0 @@ -parsl.dataflow.memoization.Memoizer -=================================== - -.. currentmodule:: parsl.dataflow.memoization - -.. autoclass:: Memoizer - - - .. automethod:: __init__ - - - .. rubric:: Methods - - .. autosummary:: - - ~Memoizer.__init__ - ~Memoizer.check_memo - ~Memoizer.hash_lookup - ~Memoizer.make_hash - ~Memoizer.update_memo - - - - - - \ No newline at end of file diff --git a/docs/stubs/parsl.dataflow.states.FINAL_STATES.rst b/docs/stubs/parsl.dataflow.states.FINAL_STATES.rst deleted file mode 100644 index 2decc41707..0000000000 --- a/docs/stubs/parsl.dataflow.states.FINAL_STATES.rst +++ /dev/null @@ -1,6 +0,0 @@ -parsl.dataflow.states.FINAL\_STATES -=================================== - -.. currentmodule:: parsl.dataflow.states - -.. autodata:: FINAL_STATES \ No newline at end of file diff --git a/docs/stubs/parsl.dataflow.states.States.rst b/docs/stubs/parsl.dataflow.states.States.rst deleted file mode 100644 index cbae5dcedc..0000000000 --- a/docs/stubs/parsl.dataflow.states.States.rst +++ /dev/null @@ -1,31 +0,0 @@ -parsl.dataflow.states.States -============================ - -.. currentmodule:: parsl.dataflow.states - -.. autoclass:: States - - - .. automethod:: __init__ - - - - - - - .. rubric:: Attributes - - .. autosummary:: - - ~States.dep_fail - ~States.exec_done - ~States.fail_retryable - ~States.failed - ~States.joining - ~States.launched - ~States.memo_done - ~States.pending - ~States.running - ~States.unsched - - \ No newline at end of file diff --git a/docs/stubs/parsl.dataflow.strategy.Strategy.rst b/docs/stubs/parsl.dataflow.strategy.Strategy.rst deleted file mode 100644 index 10e98f8525..0000000000 --- a/docs/stubs/parsl.dataflow.strategy.Strategy.rst +++ /dev/null @@ -1,24 +0,0 @@ -parsl.dataflow.strategy.Strategy -================================ - -.. currentmodule:: parsl.dataflow.strategy - -.. autoclass:: Strategy - - - .. automethod:: __init__ - - - .. rubric:: Methods - - .. autosummary:: - - ~Strategy.__init__ - ~Strategy.add_executors - ~Strategy.unset_logging - - - - - - \ No newline at end of file diff --git a/docs/stubs/parsl.errors.OptionalModuleMissing.rst b/docs/stubs/parsl.errors.OptionalModuleMissing.rst deleted file mode 100644 index 7f7ce38ca5..0000000000 --- a/docs/stubs/parsl.errors.OptionalModuleMissing.rst +++ /dev/null @@ -1,6 +0,0 @@ -parsl.errors.OptionalModuleMissing -================================== - -.. currentmodule:: parsl.errors - -.. autoexception:: OptionalModuleMissing \ No newline at end of file diff --git a/docs/stubs/parsl.executors.ExtremeScaleExecutor.rst b/docs/stubs/parsl.executors.ExtremeScaleExecutor.rst deleted file mode 100644 index 2512e5923e..0000000000 --- a/docs/stubs/parsl.executors.ExtremeScaleExecutor.rst +++ /dev/null @@ -1,53 +0,0 @@ -parsl.executors.ExtremeScaleExecutor -==================================== - -.. currentmodule:: parsl.executors - -.. autoclass:: ExtremeScaleExecutor - - - .. automethod:: __init__ - - - .. rubric:: Methods - - .. autosummary:: - - ~ExtremeScaleExecutor.__init__ - ~ExtremeScaleExecutor.create_monitoring_info - ~ExtremeScaleExecutor.handle_errors - ~ExtremeScaleExecutor.hold_worker - ~ExtremeScaleExecutor.initialize_scaling - ~ExtremeScaleExecutor.monitor_resources - ~ExtremeScaleExecutor.scale_in - ~ExtremeScaleExecutor.scale_out - ~ExtremeScaleExecutor.set_bad_state_and_fail_all - ~ExtremeScaleExecutor.shutdown - ~ExtremeScaleExecutor.start - ~ExtremeScaleExecutor.status - ~ExtremeScaleExecutor.submit - ~ExtremeScaleExecutor.weakref_cb - - - - - - .. rubric:: Attributes - - .. autosummary:: - - ~ExtremeScaleExecutor.bad_state_is_set - ~ExtremeScaleExecutor.connected_managers - ~ExtremeScaleExecutor.connected_workers - ~ExtremeScaleExecutor.error_management_enabled - ~ExtremeScaleExecutor.executor_exception - ~ExtremeScaleExecutor.hub_address - ~ExtremeScaleExecutor.hub_port - ~ExtremeScaleExecutor.outstanding - ~ExtremeScaleExecutor.provider - ~ExtremeScaleExecutor.run_dir - ~ExtremeScaleExecutor.scaling_enabled - ~ExtremeScaleExecutor.status_polling_interval - ~ExtremeScaleExecutor.tasks - - \ No newline at end of file diff --git a/docs/stubs/parsl.executors.HighThroughputExecutor.rst b/docs/stubs/parsl.executors.HighThroughputExecutor.rst deleted file mode 100644 index f861b7fdf0..0000000000 --- a/docs/stubs/parsl.executors.HighThroughputExecutor.rst +++ /dev/null @@ -1,53 +0,0 @@ -parsl.executors.HighThroughputExecutor -====================================== - -.. currentmodule:: parsl.executors - -.. autoclass:: HighThroughputExecutor - - - .. automethod:: __init__ - - - .. rubric:: Methods - - .. autosummary:: - - ~HighThroughputExecutor.__init__ - ~HighThroughputExecutor.create_monitoring_info - ~HighThroughputExecutor.handle_errors - ~HighThroughputExecutor.hold_worker - ~HighThroughputExecutor.initialize_scaling - ~HighThroughputExecutor.monitor_resources - ~HighThroughputExecutor.scale_in - ~HighThroughputExecutor.scale_out - ~HighThroughputExecutor.set_bad_state_and_fail_all - ~HighThroughputExecutor.shutdown - ~HighThroughputExecutor.start - ~HighThroughputExecutor.status - ~HighThroughputExecutor.submit - ~HighThroughputExecutor.weakref_cb - - - - - - .. rubric:: Attributes - - .. autosummary:: - - ~HighThroughputExecutor.bad_state_is_set - ~HighThroughputExecutor.connected_managers - ~HighThroughputExecutor.connected_workers - ~HighThroughputExecutor.error_management_enabled - ~HighThroughputExecutor.executor_exception - ~HighThroughputExecutor.hub_address - ~HighThroughputExecutor.hub_port - ~HighThroughputExecutor.outstanding - ~HighThroughputExecutor.provider - ~HighThroughputExecutor.run_dir - ~HighThroughputExecutor.scaling_enabled - ~HighThroughputExecutor.status_polling_interval - ~HighThroughputExecutor.tasks - - \ No newline at end of file diff --git a/docs/stubs/parsl.executors.LowLatencyExecutor.rst b/docs/stubs/parsl.executors.LowLatencyExecutor.rst deleted file mode 100644 index 1585cee303..0000000000 --- a/docs/stubs/parsl.executors.LowLatencyExecutor.rst +++ /dev/null @@ -1,47 +0,0 @@ -parsl.executors.LowLatencyExecutor -================================== - -.. currentmodule:: parsl.executors - -.. autoclass:: LowLatencyExecutor - - - .. automethod:: __init__ - - - .. rubric:: Methods - - .. autosummary:: - - ~LowLatencyExecutor.__init__ - ~LowLatencyExecutor.create_monitoring_info - ~LowLatencyExecutor.handle_errors - ~LowLatencyExecutor.monitor_resources - ~LowLatencyExecutor.scale_in - ~LowLatencyExecutor.scale_out - ~LowLatencyExecutor.set_bad_state_and_fail_all - ~LowLatencyExecutor.shutdown - ~LowLatencyExecutor.start - ~LowLatencyExecutor.status - ~LowLatencyExecutor.submit - - - - - - .. rubric:: Attributes - - .. autosummary:: - - ~LowLatencyExecutor.bad_state_is_set - ~LowLatencyExecutor.error_management_enabled - ~LowLatencyExecutor.executor_exception - ~LowLatencyExecutor.hub_address - ~LowLatencyExecutor.hub_port - ~LowLatencyExecutor.provider - ~LowLatencyExecutor.run_dir - ~LowLatencyExecutor.scaling_enabled - ~LowLatencyExecutor.status_polling_interval - ~LowLatencyExecutor.tasks - - \ No newline at end of file diff --git a/docs/stubs/parsl.executors.ThreadPoolExecutor.rst b/docs/stubs/parsl.executors.ThreadPoolExecutor.rst deleted file mode 100644 index 47a2c14927..0000000000 --- a/docs/stubs/parsl.executors.ThreadPoolExecutor.rst +++ /dev/null @@ -1,47 +0,0 @@ -parsl.executors.ThreadPoolExecutor -================================== - -.. currentmodule:: parsl.executors - -.. autoclass:: ThreadPoolExecutor - - - .. automethod:: __init__ - - - .. rubric:: Methods - - .. autosummary:: - - ~ThreadPoolExecutor.__init__ - ~ThreadPoolExecutor.create_monitoring_info - ~ThreadPoolExecutor.handle_errors - ~ThreadPoolExecutor.monitor_resources - ~ThreadPoolExecutor.scale_in - ~ThreadPoolExecutor.scale_out - ~ThreadPoolExecutor.set_bad_state_and_fail_all - ~ThreadPoolExecutor.shutdown - ~ThreadPoolExecutor.start - ~ThreadPoolExecutor.status - ~ThreadPoolExecutor.submit - - - - - - .. rubric:: Attributes - - .. autosummary:: - - ~ThreadPoolExecutor.bad_state_is_set - ~ThreadPoolExecutor.error_management_enabled - ~ThreadPoolExecutor.executor_exception - ~ThreadPoolExecutor.hub_address - ~ThreadPoolExecutor.hub_port - ~ThreadPoolExecutor.provider - ~ThreadPoolExecutor.run_dir - ~ThreadPoolExecutor.scaling_enabled - ~ThreadPoolExecutor.status_polling_interval - ~ThreadPoolExecutor.tasks - - \ No newline at end of file diff --git a/docs/stubs/parsl.executors.WorkQueueExecutor.rst b/docs/stubs/parsl.executors.WorkQueueExecutor.rst deleted file mode 100644 index 1c200cef17..0000000000 --- a/docs/stubs/parsl.executors.WorkQueueExecutor.rst +++ /dev/null @@ -1,48 +0,0 @@ -parsl.executors.WorkQueueExecutor -================================= - -.. currentmodule:: parsl.executors - -.. autoclass:: WorkQueueExecutor - - - .. automethod:: __init__ - - - .. rubric:: Methods - - .. autosummary:: - - ~WorkQueueExecutor.__init__ - ~WorkQueueExecutor.create_monitoring_info - ~WorkQueueExecutor.handle_errors - ~WorkQueueExecutor.initialize_scaling - ~WorkQueueExecutor.monitor_resources - ~WorkQueueExecutor.run_dir - ~WorkQueueExecutor.scale_in - ~WorkQueueExecutor.scale_out - ~WorkQueueExecutor.scaling_enabled - ~WorkQueueExecutor.set_bad_state_and_fail_all - ~WorkQueueExecutor.shutdown - ~WorkQueueExecutor.start - ~WorkQueueExecutor.status - ~WorkQueueExecutor.submit - - - - - - .. rubric:: Attributes - - .. autosummary:: - - ~WorkQueueExecutor.bad_state_is_set - ~WorkQueueExecutor.error_management_enabled - ~WorkQueueExecutor.executor_exception - ~WorkQueueExecutor.hub_address - ~WorkQueueExecutor.hub_port - ~WorkQueueExecutor.provider - ~WorkQueueExecutor.status_polling_interval - ~WorkQueueExecutor.tasks - - \ No newline at end of file diff --git a/docs/stubs/parsl.executors.base.ParslExecutor.rst b/docs/stubs/parsl.executors.base.ParslExecutor.rst deleted file mode 100644 index cab400f102..0000000000 --- a/docs/stubs/parsl.executors.base.ParslExecutor.rst +++ /dev/null @@ -1,46 +0,0 @@ -parsl.executors.base.ParslExecutor -================================== - -.. currentmodule:: parsl.executors.base - -.. autoclass:: ParslExecutor - - - .. automethod:: __init__ - - - .. rubric:: Methods - - .. autosummary:: - - ~ParslExecutor.__init__ - ~ParslExecutor.create_monitoring_info - ~ParslExecutor.handle_errors - ~ParslExecutor.monitor_resources - ~ParslExecutor.scale_in - ~ParslExecutor.scale_out - ~ParslExecutor.set_bad_state_and_fail_all - ~ParslExecutor.shutdown - ~ParslExecutor.start - ~ParslExecutor.status - ~ParslExecutor.submit - - - - - - .. rubric:: Attributes - - .. autosummary:: - - ~ParslExecutor.bad_state_is_set - ~ParslExecutor.error_management_enabled - ~ParslExecutor.executor_exception - ~ParslExecutor.hub_address - ~ParslExecutor.hub_port - ~ParslExecutor.run_dir - ~ParslExecutor.scaling_enabled - ~ParslExecutor.status_polling_interval - ~ParslExecutor.tasks - - \ No newline at end of file diff --git a/docs/stubs/parsl.executors.errors.BadMessage.rst b/docs/stubs/parsl.executors.errors.BadMessage.rst deleted file mode 100644 index 3e57744695..0000000000 --- a/docs/stubs/parsl.executors.errors.BadMessage.rst +++ /dev/null @@ -1,6 +0,0 @@ -parsl.executors.errors.BadMessage -================================= - -.. currentmodule:: parsl.executors.errors - -.. autoexception:: BadMessage \ No newline at end of file diff --git a/docs/stubs/parsl.executors.errors.DeserializationError.rst b/docs/stubs/parsl.executors.errors.DeserializationError.rst deleted file mode 100644 index 8d31cf86f9..0000000000 --- a/docs/stubs/parsl.executors.errors.DeserializationError.rst +++ /dev/null @@ -1,6 +0,0 @@ -parsl.executors.errors.DeserializationError -=========================================== - -.. currentmodule:: parsl.executors.errors - -.. autoexception:: DeserializationError \ No newline at end of file diff --git a/docs/stubs/parsl.executors.errors.ExecutorError.rst b/docs/stubs/parsl.executors.errors.ExecutorError.rst deleted file mode 100644 index a4aa2751d2..0000000000 --- a/docs/stubs/parsl.executors.errors.ExecutorError.rst +++ /dev/null @@ -1,6 +0,0 @@ -parsl.executors.errors.ExecutorError -==================================== - -.. currentmodule:: parsl.executors.errors - -.. autoexception:: ExecutorError \ No newline at end of file diff --git a/docs/stubs/parsl.executors.errors.ScalingFailed.rst b/docs/stubs/parsl.executors.errors.ScalingFailed.rst deleted file mode 100644 index 7455a0232f..0000000000 --- a/docs/stubs/parsl.executors.errors.ScalingFailed.rst +++ /dev/null @@ -1,6 +0,0 @@ -parsl.executors.errors.ScalingFailed -==================================== - -.. currentmodule:: parsl.executors.errors - -.. autoexception:: ScalingFailed \ No newline at end of file diff --git a/docs/stubs/parsl.executors.errors.SerializationError.rst b/docs/stubs/parsl.executors.errors.SerializationError.rst deleted file mode 100644 index 6987846e10..0000000000 --- a/docs/stubs/parsl.executors.errors.SerializationError.rst +++ /dev/null @@ -1,6 +0,0 @@ -parsl.executors.errors.SerializationError -========================================= - -.. currentmodule:: parsl.executors.errors - -.. autoexception:: SerializationError \ No newline at end of file diff --git a/docs/stubs/parsl.executors.high_throughput.errors.WorkerLost.rst b/docs/stubs/parsl.executors.high_throughput.errors.WorkerLost.rst deleted file mode 100644 index f3b6f563fc..0000000000 --- a/docs/stubs/parsl.executors.high_throughput.errors.WorkerLost.rst +++ /dev/null @@ -1,6 +0,0 @@ -parsl.executors.high\_throughput.errors.WorkerLost -================================================== - -.. currentmodule:: parsl.executors.high_throughput.errors - -.. autoexception:: WorkerLost \ No newline at end of file diff --git a/docs/stubs/parsl.executors.swift_t.TurbineExecutor.rst b/docs/stubs/parsl.executors.swift_t.TurbineExecutor.rst deleted file mode 100644 index 93f905ece4..0000000000 --- a/docs/stubs/parsl.executors.swift_t.TurbineExecutor.rst +++ /dev/null @@ -1,48 +0,0 @@ -parsl.executors.swift\_t.TurbineExecutor -======================================== - -.. currentmodule:: parsl.executors.swift_t - -.. autoclass:: TurbineExecutor - - - .. automethod:: __init__ - - - .. rubric:: Methods - - .. autosummary:: - - ~TurbineExecutor.__init__ - ~TurbineExecutor.create_monitoring_info - ~TurbineExecutor.handle_errors - ~TurbineExecutor.monitor_resources - ~TurbineExecutor.scale_in - ~TurbineExecutor.scale_out - ~TurbineExecutor.set_bad_state_and_fail_all - ~TurbineExecutor.shutdown - ~TurbineExecutor.start - ~TurbineExecutor.status - ~TurbineExecutor.submit - ~TurbineExecutor.weakref_cb - - - - - - .. rubric:: Attributes - - .. autosummary:: - - ~TurbineExecutor.bad_state_is_set - ~TurbineExecutor.error_management_enabled - ~TurbineExecutor.executor_exception - ~TurbineExecutor.hub_address - ~TurbineExecutor.hub_port - ~TurbineExecutor.provider - ~TurbineExecutor.run_dir - ~TurbineExecutor.scaling_enabled - ~TurbineExecutor.status_polling_interval - ~TurbineExecutor.tasks - - \ No newline at end of file diff --git a/docs/stubs/parsl.launchers.AprunLauncher.rst b/docs/stubs/parsl.launchers.AprunLauncher.rst deleted file mode 100644 index 8bea4bff72..0000000000 --- a/docs/stubs/parsl.launchers.AprunLauncher.rst +++ /dev/null @@ -1,22 +0,0 @@ -parsl.launchers.AprunLauncher -============================= - -.. currentmodule:: parsl.launchers - -.. autoclass:: AprunLauncher - - - .. automethod:: __init__ - - - .. rubric:: Methods - - .. autosummary:: - - ~AprunLauncher.__init__ - - - - - - \ No newline at end of file diff --git a/docs/stubs/parsl.launchers.GnuParallelLauncher.rst b/docs/stubs/parsl.launchers.GnuParallelLauncher.rst deleted file mode 100644 index df1f0a202f..0000000000 --- a/docs/stubs/parsl.launchers.GnuParallelLauncher.rst +++ /dev/null @@ -1,22 +0,0 @@ -parsl.launchers.GnuParallelLauncher -=================================== - -.. currentmodule:: parsl.launchers - -.. autoclass:: GnuParallelLauncher - - - .. automethod:: __init__ - - - .. rubric:: Methods - - .. autosummary:: - - ~GnuParallelLauncher.__init__ - - - - - - \ No newline at end of file diff --git a/docs/stubs/parsl.launchers.JsrunLauncher.rst b/docs/stubs/parsl.launchers.JsrunLauncher.rst deleted file mode 100644 index 5f3dde0c8e..0000000000 --- a/docs/stubs/parsl.launchers.JsrunLauncher.rst +++ /dev/null @@ -1,22 +0,0 @@ -parsl.launchers.JsrunLauncher -============================= - -.. currentmodule:: parsl.launchers - -.. autoclass:: JsrunLauncher - - - .. automethod:: __init__ - - - .. rubric:: Methods - - .. autosummary:: - - ~JsrunLauncher.__init__ - - - - - - \ No newline at end of file diff --git a/docs/stubs/parsl.launchers.MpiExecLauncher.rst b/docs/stubs/parsl.launchers.MpiExecLauncher.rst deleted file mode 100644 index cd02f3f2bb..0000000000 --- a/docs/stubs/parsl.launchers.MpiExecLauncher.rst +++ /dev/null @@ -1,22 +0,0 @@ -parsl.launchers.MpiExecLauncher -=============================== - -.. currentmodule:: parsl.launchers - -.. autoclass:: MpiExecLauncher - - - .. automethod:: __init__ - - - .. rubric:: Methods - - .. autosummary:: - - ~MpiExecLauncher.__init__ - - - - - - \ No newline at end of file diff --git a/docs/stubs/parsl.launchers.SimpleLauncher.rst b/docs/stubs/parsl.launchers.SimpleLauncher.rst deleted file mode 100644 index e37b16918f..0000000000 --- a/docs/stubs/parsl.launchers.SimpleLauncher.rst +++ /dev/null @@ -1,22 +0,0 @@ -parsl.launchers.SimpleLauncher -============================== - -.. currentmodule:: parsl.launchers - -.. autoclass:: SimpleLauncher - - - .. automethod:: __init__ - - - .. rubric:: Methods - - .. autosummary:: - - ~SimpleLauncher.__init__ - - - - - - \ No newline at end of file diff --git a/docs/stubs/parsl.launchers.SingleNodeLauncher.rst b/docs/stubs/parsl.launchers.SingleNodeLauncher.rst deleted file mode 100644 index 83e922acf5..0000000000 --- a/docs/stubs/parsl.launchers.SingleNodeLauncher.rst +++ /dev/null @@ -1,22 +0,0 @@ -parsl.launchers.SingleNodeLauncher -================================== - -.. currentmodule:: parsl.launchers - -.. autoclass:: SingleNodeLauncher - - - .. automethod:: __init__ - - - .. rubric:: Methods - - .. autosummary:: - - ~SingleNodeLauncher.__init__ - - - - - - \ No newline at end of file diff --git a/docs/stubs/parsl.launchers.SrunLauncher.rst b/docs/stubs/parsl.launchers.SrunLauncher.rst deleted file mode 100644 index abbea43119..0000000000 --- a/docs/stubs/parsl.launchers.SrunLauncher.rst +++ /dev/null @@ -1,22 +0,0 @@ -parsl.launchers.SrunLauncher -============================ - -.. currentmodule:: parsl.launchers - -.. autoclass:: SrunLauncher - - - .. automethod:: __init__ - - - .. rubric:: Methods - - .. autosummary:: - - ~SrunLauncher.__init__ - - - - - - \ No newline at end of file diff --git a/docs/stubs/parsl.launchers.SrunMPILauncher.rst b/docs/stubs/parsl.launchers.SrunMPILauncher.rst deleted file mode 100644 index fe6b64e266..0000000000 --- a/docs/stubs/parsl.launchers.SrunMPILauncher.rst +++ /dev/null @@ -1,22 +0,0 @@ -parsl.launchers.SrunMPILauncher -=============================== - -.. currentmodule:: parsl.launchers - -.. autoclass:: SrunMPILauncher - - - .. automethod:: __init__ - - - .. rubric:: Methods - - .. autosummary:: - - ~SrunMPILauncher.__init__ - - - - - - \ No newline at end of file diff --git a/docs/stubs/parsl.launchers.WrappedLauncher.rst b/docs/stubs/parsl.launchers.WrappedLauncher.rst deleted file mode 100644 index bf933bbf6d..0000000000 --- a/docs/stubs/parsl.launchers.WrappedLauncher.rst +++ /dev/null @@ -1,22 +0,0 @@ -parsl.launchers.WrappedLauncher -=============================== - -.. currentmodule:: parsl.launchers - -.. autoclass:: WrappedLauncher - - - .. automethod:: __init__ - - - .. rubric:: Methods - - .. autosummary:: - - ~WrappedLauncher.__init__ - - - - - - \ No newline at end of file diff --git a/docs/stubs/parsl.launchers.error.BadLauncher.rst b/docs/stubs/parsl.launchers.error.BadLauncher.rst deleted file mode 100644 index 33a96a0009..0000000000 --- a/docs/stubs/parsl.launchers.error.BadLauncher.rst +++ /dev/null @@ -1,6 +0,0 @@ -parsl.launchers.error.BadLauncher -================================= - -.. currentmodule:: parsl.launchers.error - -.. autoexception:: BadLauncher \ No newline at end of file diff --git a/docs/stubs/parsl.monitoring.MonitoringHub.rst b/docs/stubs/parsl.monitoring.MonitoringHub.rst deleted file mode 100644 index 6e70cd7af8..0000000000 --- a/docs/stubs/parsl.monitoring.MonitoringHub.rst +++ /dev/null @@ -1,26 +0,0 @@ -parsl.monitoring.MonitoringHub -============================== - -.. currentmodule:: parsl.monitoring - -.. autoclass:: MonitoringHub - - - .. automethod:: __init__ - - - .. rubric:: Methods - - .. autosummary:: - - ~MonitoringHub.__init__ - ~MonitoringHub.close - ~MonitoringHub.monitor_wrapper - ~MonitoringHub.send - ~MonitoringHub.start - - - - - - \ No newline at end of file diff --git a/docs/stubs/parsl.providers.AWSProvider.rst b/docs/stubs/parsl.providers.AWSProvider.rst deleted file mode 100644 index 8a722cf3b2..0000000000 --- a/docs/stubs/parsl.providers.AWSProvider.rst +++ /dev/null @@ -1,50 +0,0 @@ -parsl.providers.AWSProvider -=========================== - -.. currentmodule:: parsl.providers - -.. autoclass:: AWSProvider - - - .. automethod:: __init__ - - - .. rubric:: Methods - - .. autosummary:: - - ~AWSProvider.__init__ - ~AWSProvider.cancel - ~AWSProvider.config_route_table - ~AWSProvider.create_name_tag_spec - ~AWSProvider.create_session - ~AWSProvider.create_vpc - ~AWSProvider.generate_aws_id - ~AWSProvider.get_instance_state - ~AWSProvider.goodbye - ~AWSProvider.initialize_boto_client - ~AWSProvider.read_state_file - ~AWSProvider.security_group - ~AWSProvider.show_summary - ~AWSProvider.shut_down_instance - ~AWSProvider.spin_up_instance - ~AWSProvider.status - ~AWSProvider.submit - ~AWSProvider.teardown - ~AWSProvider.write_state_file - ~AWSProvider.xstr - - - - - - .. rubric:: Attributes - - .. autosummary:: - - ~AWSProvider.cores_per_node - ~AWSProvider.label - ~AWSProvider.mem_per_node - ~AWSProvider.status_polling_interval - - \ No newline at end of file diff --git a/docs/stubs/parsl.providers.AdHocProvider.rst b/docs/stubs/parsl.providers.AdHocProvider.rst deleted file mode 100644 index dfee74d8da..0000000000 --- a/docs/stubs/parsl.providers.AdHocProvider.rst +++ /dev/null @@ -1,35 +0,0 @@ -parsl.providers.AdHocProvider -============================= - -.. currentmodule:: parsl.providers - -.. autoclass:: AdHocProvider - - - .. automethod:: __init__ - - - .. rubric:: Methods - - .. autosummary:: - - ~AdHocProvider.__init__ - ~AdHocProvider.cancel - ~AdHocProvider.status - ~AdHocProvider.submit - - - - - - .. rubric:: Attributes - - .. autosummary:: - - ~AdHocProvider.cores_per_node - ~AdHocProvider.label - ~AdHocProvider.mem_per_node - ~AdHocProvider.scaling_enabled - ~AdHocProvider.status_polling_interval - - \ No newline at end of file diff --git a/docs/stubs/parsl.providers.CobaltProvider.rst b/docs/stubs/parsl.providers.CobaltProvider.rst deleted file mode 100644 index 67cf59fd3c..0000000000 --- a/docs/stubs/parsl.providers.CobaltProvider.rst +++ /dev/null @@ -1,35 +0,0 @@ -parsl.providers.CobaltProvider -============================== - -.. currentmodule:: parsl.providers - -.. autoclass:: CobaltProvider - - - .. automethod:: __init__ - - - .. rubric:: Methods - - .. autosummary:: - - ~CobaltProvider.__init__ - ~CobaltProvider.cancel - ~CobaltProvider.execute_wait - ~CobaltProvider.status - ~CobaltProvider.submit - - - - - - .. rubric:: Attributes - - .. autosummary:: - - ~CobaltProvider.cores_per_node - ~CobaltProvider.label - ~CobaltProvider.mem_per_node - ~CobaltProvider.status_polling_interval - - \ No newline at end of file diff --git a/docs/stubs/parsl.providers.CondorProvider.rst b/docs/stubs/parsl.providers.CondorProvider.rst deleted file mode 100644 index dc18048b05..0000000000 --- a/docs/stubs/parsl.providers.CondorProvider.rst +++ /dev/null @@ -1,35 +0,0 @@ -parsl.providers.CondorProvider -============================== - -.. currentmodule:: parsl.providers - -.. autoclass:: CondorProvider - - - .. automethod:: __init__ - - - .. rubric:: Methods - - .. autosummary:: - - ~CondorProvider.__init__ - ~CondorProvider.cancel - ~CondorProvider.execute_wait - ~CondorProvider.status - ~CondorProvider.submit - - - - - - .. rubric:: Attributes - - .. autosummary:: - - ~CondorProvider.cores_per_node - ~CondorProvider.label - ~CondorProvider.mem_per_node - ~CondorProvider.status_polling_interval - - \ No newline at end of file diff --git a/docs/stubs/parsl.providers.GoogleCloudProvider.rst b/docs/stubs/parsl.providers.GoogleCloudProvider.rst deleted file mode 100644 index 8cbdd97277..0000000000 --- a/docs/stubs/parsl.providers.GoogleCloudProvider.rst +++ /dev/null @@ -1,35 +0,0 @@ -parsl.providers.GoogleCloudProvider -=================================== - -.. currentmodule:: parsl.providers - -.. autoclass:: GoogleCloudProvider - - - .. automethod:: __init__ - - - .. rubric:: Methods - - .. autosummary:: - - ~GoogleCloudProvider.__init__ - ~GoogleCloudProvider.bye - ~GoogleCloudProvider.cancel - ~GoogleCloudProvider.create_instance - ~GoogleCloudProvider.delete_instance - ~GoogleCloudProvider.get_zone - ~GoogleCloudProvider.status - ~GoogleCloudProvider.submit - - - - - - .. rubric:: Attributes - - .. autosummary:: - - ~GoogleCloudProvider.status_polling_interval - - \ No newline at end of file diff --git a/docs/stubs/parsl.providers.GridEngineProvider.rst b/docs/stubs/parsl.providers.GridEngineProvider.rst deleted file mode 100644 index e58801a1f0..0000000000 --- a/docs/stubs/parsl.providers.GridEngineProvider.rst +++ /dev/null @@ -1,36 +0,0 @@ -parsl.providers.GridEngineProvider -================================== - -.. currentmodule:: parsl.providers - -.. autoclass:: GridEngineProvider - - - .. automethod:: __init__ - - - .. rubric:: Methods - - .. autosummary:: - - ~GridEngineProvider.__init__ - ~GridEngineProvider.cancel - ~GridEngineProvider.execute_wait - ~GridEngineProvider.get_configs - ~GridEngineProvider.status - ~GridEngineProvider.submit - - - - - - .. rubric:: Attributes - - .. autosummary:: - - ~GridEngineProvider.cores_per_node - ~GridEngineProvider.label - ~GridEngineProvider.mem_per_node - ~GridEngineProvider.status_polling_interval - - \ No newline at end of file diff --git a/docs/stubs/parsl.providers.KubernetesProvider.rst b/docs/stubs/parsl.providers.KubernetesProvider.rst deleted file mode 100644 index 5a9496f22a..0000000000 --- a/docs/stubs/parsl.providers.KubernetesProvider.rst +++ /dev/null @@ -1,34 +0,0 @@ -parsl.providers.KubernetesProvider -================================== - -.. currentmodule:: parsl.providers - -.. autoclass:: KubernetesProvider - - - .. automethod:: __init__ - - - .. rubric:: Methods - - .. autosummary:: - - ~KubernetesProvider.__init__ - ~KubernetesProvider.cancel - ~KubernetesProvider.status - ~KubernetesProvider.submit - - - - - - .. rubric:: Attributes - - .. autosummary:: - - ~KubernetesProvider.cores_per_node - ~KubernetesProvider.label - ~KubernetesProvider.mem_per_node - ~KubernetesProvider.status_polling_interval - - \ No newline at end of file diff --git a/docs/stubs/parsl.providers.LSFProvider.rst b/docs/stubs/parsl.providers.LSFProvider.rst deleted file mode 100644 index 632cbdb24d..0000000000 --- a/docs/stubs/parsl.providers.LSFProvider.rst +++ /dev/null @@ -1,35 +0,0 @@ -parsl.providers.LSFProvider -=========================== - -.. currentmodule:: parsl.providers - -.. autoclass:: LSFProvider - - - .. automethod:: __init__ - - - .. rubric:: Methods - - .. autosummary:: - - ~LSFProvider.__init__ - ~LSFProvider.cancel - ~LSFProvider.execute_wait - ~LSFProvider.status - ~LSFProvider.submit - - - - - - .. rubric:: Attributes - - .. autosummary:: - - ~LSFProvider.cores_per_node - ~LSFProvider.label - ~LSFProvider.mem_per_node - ~LSFProvider.status_polling_interval - - \ No newline at end of file diff --git a/docs/stubs/parsl.providers.LocalProvider.rst b/docs/stubs/parsl.providers.LocalProvider.rst deleted file mode 100644 index c5004b138a..0000000000 --- a/docs/stubs/parsl.providers.LocalProvider.rst +++ /dev/null @@ -1,34 +0,0 @@ -parsl.providers.LocalProvider -============================= - -.. currentmodule:: parsl.providers - -.. autoclass:: LocalProvider - - - .. automethod:: __init__ - - - .. rubric:: Methods - - .. autosummary:: - - ~LocalProvider.__init__ - ~LocalProvider.cancel - ~LocalProvider.status - ~LocalProvider.submit - - - - - - .. rubric:: Attributes - - .. autosummary:: - - ~LocalProvider.cores_per_node - ~LocalProvider.label - ~LocalProvider.mem_per_node - ~LocalProvider.status_polling_interval - - \ No newline at end of file diff --git a/docs/stubs/parsl.providers.PBSProProvider.rst b/docs/stubs/parsl.providers.PBSProProvider.rst deleted file mode 100644 index 30915155dc..0000000000 --- a/docs/stubs/parsl.providers.PBSProProvider.rst +++ /dev/null @@ -1,35 +0,0 @@ -parsl.providers.PBSProProvider -============================== - -.. currentmodule:: parsl.providers - -.. autoclass:: PBSProProvider - - - .. automethod:: __init__ - - - .. rubric:: Methods - - .. autosummary:: - - ~PBSProProvider.__init__ - ~PBSProProvider.cancel - ~PBSProProvider.execute_wait - ~PBSProProvider.status - ~PBSProProvider.submit - - - - - - .. rubric:: Attributes - - .. autosummary:: - - ~PBSProProvider.cores_per_node - ~PBSProProvider.label - ~PBSProProvider.mem_per_node - ~PBSProProvider.status_polling_interval - - \ No newline at end of file diff --git a/docs/stubs/parsl.providers.SlurmProvider.rst b/docs/stubs/parsl.providers.SlurmProvider.rst deleted file mode 100644 index 98db36df8b..0000000000 --- a/docs/stubs/parsl.providers.SlurmProvider.rst +++ /dev/null @@ -1,35 +0,0 @@ -parsl.providers.SlurmProvider -============================= - -.. currentmodule:: parsl.providers - -.. autoclass:: SlurmProvider - - - .. automethod:: __init__ - - - .. rubric:: Methods - - .. autosummary:: - - ~SlurmProvider.__init__ - ~SlurmProvider.cancel - ~SlurmProvider.execute_wait - ~SlurmProvider.status - ~SlurmProvider.submit - - - - - - .. rubric:: Attributes - - .. autosummary:: - - ~SlurmProvider.cores_per_node - ~SlurmProvider.label - ~SlurmProvider.mem_per_node - ~SlurmProvider.status_polling_interval - - \ No newline at end of file diff --git a/docs/stubs/parsl.providers.TorqueProvider.rst b/docs/stubs/parsl.providers.TorqueProvider.rst deleted file mode 100644 index e1e054fbe5..0000000000 --- a/docs/stubs/parsl.providers.TorqueProvider.rst +++ /dev/null @@ -1,35 +0,0 @@ -parsl.providers.TorqueProvider -============================== - -.. currentmodule:: parsl.providers - -.. autoclass:: TorqueProvider - - - .. automethod:: __init__ - - - .. rubric:: Methods - - .. autosummary:: - - ~TorqueProvider.__init__ - ~TorqueProvider.cancel - ~TorqueProvider.execute_wait - ~TorqueProvider.status - ~TorqueProvider.submit - - - - - - .. rubric:: Attributes - - .. autosummary:: - - ~TorqueProvider.cores_per_node - ~TorqueProvider.label - ~TorqueProvider.mem_per_node - ~TorqueProvider.status_polling_interval - - \ No newline at end of file diff --git a/docs/stubs/parsl.providers.cluster_provider.ClusterProvider.rst b/docs/stubs/parsl.providers.cluster_provider.ClusterProvider.rst deleted file mode 100644 index 3c22cc2760..0000000000 --- a/docs/stubs/parsl.providers.cluster_provider.ClusterProvider.rst +++ /dev/null @@ -1,35 +0,0 @@ -parsl.providers.cluster\_provider.ClusterProvider -================================================= - -.. currentmodule:: parsl.providers.cluster_provider - -.. autoclass:: ClusterProvider - - - .. automethod:: __init__ - - - .. rubric:: Methods - - .. autosummary:: - - ~ClusterProvider.__init__ - ~ClusterProvider.cancel - ~ClusterProvider.execute_wait - ~ClusterProvider.status - ~ClusterProvider.submit - - - - - - .. rubric:: Attributes - - .. autosummary:: - - ~ClusterProvider.cores_per_node - ~ClusterProvider.label - ~ClusterProvider.mem_per_node - ~ClusterProvider.status_polling_interval - - \ No newline at end of file diff --git a/docs/stubs/parsl.providers.error.ChannelRequired.rst b/docs/stubs/parsl.providers.error.ChannelRequired.rst deleted file mode 100644 index 5d44a27ee6..0000000000 --- a/docs/stubs/parsl.providers.error.ChannelRequired.rst +++ /dev/null @@ -1,6 +0,0 @@ -parsl.providers.error.ChannelRequired -===================================== - -.. currentmodule:: parsl.providers.error - -.. autoexception:: ChannelRequired \ No newline at end of file diff --git a/docs/stubs/parsl.providers.error.ExecutionProviderException.rst b/docs/stubs/parsl.providers.error.ExecutionProviderException.rst deleted file mode 100644 index 4c275a0960..0000000000 --- a/docs/stubs/parsl.providers.error.ExecutionProviderException.rst +++ /dev/null @@ -1,6 +0,0 @@ -parsl.providers.error.ExecutionProviderException -================================================ - -.. currentmodule:: parsl.providers.error - -.. autoexception:: ExecutionProviderException \ No newline at end of file diff --git a/docs/stubs/parsl.providers.error.ScaleOutFailed.rst b/docs/stubs/parsl.providers.error.ScaleOutFailed.rst deleted file mode 100644 index 2e7a81f7ee..0000000000 --- a/docs/stubs/parsl.providers.error.ScaleOutFailed.rst +++ /dev/null @@ -1,6 +0,0 @@ -parsl.providers.error.ScaleOutFailed -==================================== - -.. currentmodule:: parsl.providers.error - -.. autoexception:: ScaleOutFailed \ No newline at end of file diff --git a/docs/stubs/parsl.providers.error.SchedulerMissingArgs.rst b/docs/stubs/parsl.providers.error.SchedulerMissingArgs.rst deleted file mode 100644 index 33afc6366a..0000000000 --- a/docs/stubs/parsl.providers.error.SchedulerMissingArgs.rst +++ /dev/null @@ -1,6 +0,0 @@ -parsl.providers.error.SchedulerMissingArgs -========================================== - -.. currentmodule:: parsl.providers.error - -.. autoexception:: SchedulerMissingArgs \ No newline at end of file diff --git a/docs/stubs/parsl.providers.error.ScriptPathError.rst b/docs/stubs/parsl.providers.error.ScriptPathError.rst deleted file mode 100644 index e787041121..0000000000 --- a/docs/stubs/parsl.providers.error.ScriptPathError.rst +++ /dev/null @@ -1,6 +0,0 @@ -parsl.providers.error.ScriptPathError -===================================== - -.. currentmodule:: parsl.providers.error - -.. autoexception:: ScriptPathError \ No newline at end of file diff --git a/docs/stubs/parsl.providers.provider_base.ExecutionProvider.rst b/docs/stubs/parsl.providers.provider_base.ExecutionProvider.rst deleted file mode 100644 index 7e74ad0dd0..0000000000 --- a/docs/stubs/parsl.providers.provider_base.ExecutionProvider.rst +++ /dev/null @@ -1,34 +0,0 @@ -parsl.providers.provider\_base.ExecutionProvider -================================================ - -.. currentmodule:: parsl.providers.provider_base - -.. autoclass:: ExecutionProvider - - - .. automethod:: __init__ - - - .. rubric:: Methods - - .. autosummary:: - - ~ExecutionProvider.__init__ - ~ExecutionProvider.cancel - ~ExecutionProvider.status - ~ExecutionProvider.submit - - - - - - .. rubric:: Attributes - - .. autosummary:: - - ~ExecutionProvider.cores_per_node - ~ExecutionProvider.label - ~ExecutionProvider.mem_per_node - ~ExecutionProvider.status_polling_interval - - \ No newline at end of file diff --git a/docs/stubs/parsl.set_file_logger.rst b/docs/stubs/parsl.set_file_logger.rst deleted file mode 100644 index ba00425426..0000000000 --- a/docs/stubs/parsl.set_file_logger.rst +++ /dev/null @@ -1,6 +0,0 @@ -parsl.set\_file\_logger -======================= - -.. currentmodule:: parsl - -.. autofunction:: set_file_logger \ No newline at end of file diff --git a/docs/stubs/parsl.set_stream_logger.rst b/docs/stubs/parsl.set_stream_logger.rst deleted file mode 100644 index 3d665e143a..0000000000 --- a/docs/stubs/parsl.set_stream_logger.rst +++ /dev/null @@ -1,6 +0,0 @@ -parsl.set\_stream\_logger -========================= - -.. currentmodule:: parsl - -.. autofunction:: set_stream_logger \ No newline at end of file diff --git a/docs/stubs/parsl.utils.get_all_checkpoints.rst b/docs/stubs/parsl.utils.get_all_checkpoints.rst deleted file mode 100644 index c2a1d61dad..0000000000 --- a/docs/stubs/parsl.utils.get_all_checkpoints.rst +++ /dev/null @@ -1,6 +0,0 @@ -parsl.utils.get\_all\_checkpoints -================================= - -.. currentmodule:: parsl.utils - -.. autofunction:: get_all_checkpoints \ No newline at end of file diff --git a/docs/stubs/parsl.utils.get_last_checkpoint.rst b/docs/stubs/parsl.utils.get_last_checkpoint.rst deleted file mode 100644 index 3d525a68bb..0000000000 --- a/docs/stubs/parsl.utils.get_last_checkpoint.rst +++ /dev/null @@ -1,6 +0,0 @@ -parsl.utils.get\_last\_checkpoint -================================= - -.. currentmodule:: parsl.utils - -.. autofunction:: get_last_checkpoint \ No newline at end of file From 0aafd962e4fd2897542341f2094018f7ca366576 Mon Sep 17 00:00:00 2001 From: Ben Clifford Date: Mon, 7 Jun 2021 13:05:14 +0000 Subject: [PATCH 209/408] Switch doc verb from invocated to invoked --- docs/userguide/configuring.rst | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/userguide/configuring.rst b/docs/userguide/configuring.rst index 105e4e9327..5139cfcdba 100644 --- a/docs/userguide/configuring.rst +++ b/docs/userguide/configuring.rst @@ -211,7 +211,7 @@ the task's disk requirement in MB), passed to an app via the special keyword arg return x*2 -or updated when the app is invocated: +or updated when the app is invoked: .. code-block:: python From b26f98ab13d8498fcb5f7a9ba519b7fd81fd0ff8 Mon Sep 17 00:00:00 2001 From: Ben Clifford Date: Wed, 16 Jun 2021 09:26:49 +0000 Subject: [PATCH 210/408] rearrange asserts --- parsl/monitoring/db_manager.py | 14 ++++++-------- 1 file changed, 6 insertions(+), 8 deletions(-) diff --git a/parsl/monitoring/db_manager.py b/parsl/monitoring/db_manager.py index de91b96547..ff385e646e 100644 --- a/parsl/monitoring/db_manager.py +++ b/parsl/monitoring/db_manager.py @@ -533,19 +533,17 @@ def _migrate_logs_to_internal(self, logs_queue: queue.Queue, queue_tag: str, kil if queue_tag == 'priority' and x == 'STOP': self.close() elif queue_tag == 'priority': # implicitly not 'STOP' - if isinstance(x, tuple): - assert x[0] in [MessageType.WORKFLOW_INFO, MessageType.TASK_INFO], \ - "_migrate_logs_to_internal can only migrate WORKFLOW_,TASK_INFO message from priority queue, got x[0] == {}".format(x[0]) - assert len(x) == 2 - self.pending_priority_queue.put(cast(Any, x)) - else: - logger.error("dropping message with unknown format: {}".format(x)) + assert isinstance(x, tuple) + assert len(x) == 2 + assert x[0] in [MessageType.WORKFLOW_INFO, MessageType.TASK_INFO], \ + "_migrate_logs_to_internal can only migrate WORKFLOW_,TASK_INFO message from priority queue, got x[0] == {}".format(x[0]) + self.pending_priority_queue.put(cast(Any, x)) elif queue_tag == 'resource': assert len(x) == 3 self.pending_resource_queue.put(x[-1]) elif queue_tag == 'node': - assert x[0] == MessageType.NODE_INFO, "_migrate_logs_to_internal can only migrate NODE_INFO messages from node queue" assert len(x) == 2, "expected message tuple to have exactly two elements" + assert x[0] == MessageType.NODE_INFO, "_migrate_logs_to_internal can only migrate NODE_INFO messages from node queue" self.pending_node_queue.put(x[1]) elif queue_tag == "block": From a875ac66ac9666bada3882ae63c773a874226c0f Mon Sep 17 00:00:00 2001 From: Ben Clifford Date: Wed, 16 Jun 2021 10:01:43 +0000 Subject: [PATCH 211/408] restore original x index because this PR should only be adding asserts, not otherwise changing behaviour --- parsl/monitoring/db_manager.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/parsl/monitoring/db_manager.py b/parsl/monitoring/db_manager.py index ff385e646e..9623c28568 100644 --- a/parsl/monitoring/db_manager.py +++ b/parsl/monitoring/db_manager.py @@ -545,7 +545,7 @@ def _migrate_logs_to_internal(self, logs_queue: queue.Queue, queue_tag: str, kil assert len(x) == 2, "expected message tuple to have exactly two elements" assert x[0] == MessageType.NODE_INFO, "_migrate_logs_to_internal can only migrate NODE_INFO messages from node queue" - self.pending_node_queue.put(x[1]) + self.pending_node_queue.put(x[-1]) elif queue_tag == "block": self.pending_block_queue.put(x[-1]) else: From c2f39d91603ced4d531eb9e136fe482f0a5c617b Mon Sep 17 00:00:00 2001 From: Ben Clifford Date: Wed, 16 Jun 2021 10:03:18 +0000 Subject: [PATCH 212/408] Restore original UDP message order --- parsl/monitoring/monitoring.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/parsl/monitoring/monitoring.py b/parsl/monitoring/monitoring.py index 124c5d41b1..3f47f91138 100644 --- a/parsl/monitoring/monitoring.py +++ b/parsl/monitoring/monitoring.py @@ -442,8 +442,8 @@ def start(self, try: data, addr = self.sock.recvfrom(2048) msg = pickle.loads(data) - self.logger.info("Got UDP Message from {}: {}".format(addr, msg)) resource_msgs.put((msg, addr)) + self.logger.info("Got UDP Message from {}: {}".format(addr, msg)) except socket.timeout: pass From 2fa7d67d6a044dcdf23789a2d6f1f424f83e1e29 Mon Sep 17 00:00:00 2001 From: Ben Clifford Date: Wed, 16 Jun 2021 10:19:22 +0000 Subject: [PATCH 213/408] restore udp log to debug --- parsl/monitoring/monitoring.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/parsl/monitoring/monitoring.py b/parsl/monitoring/monitoring.py index 3f47f91138..5d2a5610d3 100644 --- a/parsl/monitoring/monitoring.py +++ b/parsl/monitoring/monitoring.py @@ -443,7 +443,7 @@ def start(self, data, addr = self.sock.recvfrom(2048) msg = pickle.loads(data) resource_msgs.put((msg, addr)) - self.logger.info("Got UDP Message from {}: {}".format(addr, msg)) + self.logger.debug("Got UDP Message from {}: {}".format(addr, msg)) except socket.timeout: pass From a8c09eca1335b355fc94a15b2232ea4524d8d43e Mon Sep 17 00:00:00 2001 From: Ben Clifford Date: Wed, 23 Jun 2021 10:02:27 +0000 Subject: [PATCH 214/408] Assert that there should be no doc stubs in version control --- .travis.yml | 13 +++--- docs/stubs/parsl.executors.FluxExecutor.rst | 48 --------------------- 2 files changed, 5 insertions(+), 56 deletions(-) delete mode 100644 docs/stubs/parsl.executors.FluxExecutor.rst diff --git a/.travis.yml b/.travis.yml index af71827e4b..29dd2422e5 100644 --- a/.travis.yml +++ b/.travis.yml @@ -42,17 +42,14 @@ script: - sudo apt-get install -y pandoc - cd docs + # check that the stubs directory does not exist, to protect against + # accidentally added stubs files - stubs are generated by sphinx doc + # build. + - ! [ -e docs/stubs ] + # check we can build the docs without warnings - make SPHINXOPTS=-W html - # check that documentation stubs are up to date, as they are compiled from - # python code but stored in version control rather than generated as part - # of doc build. - - rm -rfv stubs - - sphinx-autogen reference.rst userguide/*rst devguide/*rst - # this will both display any diffs in log output, and fail if there is any diff - - git diff --exit-code - - cd .. # assert that none of the runs in this test have put an ERROR message into a diff --git a/docs/stubs/parsl.executors.FluxExecutor.rst b/docs/stubs/parsl.executors.FluxExecutor.rst deleted file mode 100644 index 69d2461e94..0000000000 --- a/docs/stubs/parsl.executors.FluxExecutor.rst +++ /dev/null @@ -1,48 +0,0 @@ -parsl.executors.FluxExecutor -============================ - -.. currentmodule:: parsl.executors - -.. autoclass:: FluxExecutor - - - .. automethod:: __init__ - - - .. rubric:: Methods - - .. autosummary:: - - ~FluxExecutor.__init__ - ~FluxExecutor.create_monitoring_info - ~FluxExecutor.handle_errors - ~FluxExecutor.monitor_resources - ~FluxExecutor.scale_in - ~FluxExecutor.scale_out - ~FluxExecutor.scaling_enabled - ~FluxExecutor.set_bad_state_and_fail_all - ~FluxExecutor.shutdown - ~FluxExecutor.start - ~FluxExecutor.status - ~FluxExecutor.submit - - - - - - .. rubric:: Attributes - - .. autosummary:: - - ~FluxExecutor.DEFAULT_LAUNCH_CMD - ~FluxExecutor.bad_state_is_set - ~FluxExecutor.error_management_enabled - ~FluxExecutor.executor_exception - ~FluxExecutor.hub_address - ~FluxExecutor.hub_port - ~FluxExecutor.provider - ~FluxExecutor.run_dir - ~FluxExecutor.status_polling_interval - ~FluxExecutor.tasks - - \ No newline at end of file From 3199d94b0ea8d9e0033bad22651a755dc7ac7e60 Mon Sep 17 00:00:00 2001 From: Ben Clifford Date: Wed, 16 Jun 2021 10:05:27 +0000 Subject: [PATCH 215/408] Reorder debug message so it happens when the message is received, without necessarily blocking on the resource_msgs queue put --- parsl/monitoring/monitoring.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/parsl/monitoring/monitoring.py b/parsl/monitoring/monitoring.py index ce41233e1d..ea77442a21 100644 --- a/parsl/monitoring/monitoring.py +++ b/parsl/monitoring/monitoring.py @@ -442,8 +442,8 @@ def start(self, try: data, addr = self.sock.recvfrom(2048) msg = pickle.loads(data) - resource_msgs.put((msg, addr)) self.logger.debug("Got UDP Message from {}: {}".format(addr, msg)) + resource_msgs.put((msg, addr)) except socket.timeout: pass From 01dde27812e688ff11b2cb956468c42334069f59 Mon Sep 17 00:00:00 2001 From: Ben Clifford Date: Mon, 7 Jun 2021 10:39:23 +0000 Subject: [PATCH 216/408] Configure sphinx to put in full documentation for each method Before this, only a small table of summary information was given for each class, and per-method docstrings were not presented. This PR also fixes several errors in docstring text that were previously not a problem, because those pieces of docstring were not used. --- docs/conf.py | 5 +++++ parsl/data_provider/data_manager.py | 2 +- parsl/executors/base.py | 6 ++---- parsl/executors/high_throughput/executor.py | 8 ++++---- parsl/executors/swift_t.py | 4 ++-- parsl/providers/kubernetes/kube.py | 1 + parsl/providers/provider_base.py | 2 +- 7 files changed, 16 insertions(+), 12 deletions(-) diff --git a/docs/conf.py b/docs/conf.py index ea478ce96c..20b435e09c 100644 --- a/docs/conf.py +++ b/docs/conf.py @@ -366,3 +366,8 @@ def linkcode_resolve(domain, info): # texinfo_no_detailmenu = False autosummary_generate = True + +autodoc_default_options = { + 'members': True, + 'undoc-members': True +} diff --git a/parsl/data_provider/data_manager.py b/parsl/data_provider/data_manager.py index eb7c5b99d8..8b14a11a62 100644 --- a/parsl/data_provider/data_manager.py +++ b/parsl/data_provider/data_manager.py @@ -100,7 +100,7 @@ def stage_in(self, file: File, input: Any, executor: str) -> Any: """Transport the input from the input source to the executor, if it is file-like, returning a DataFuture that wraps the stage-in operation. - If no staging in is required - because the `file` parameter is not file-like, + If no staging in is required - because the ``file`` parameter is not file-like, then return that parameter unaltered. Args: diff --git a/parsl/executors/base.py b/parsl/executors/base.py index 9f0c3ef496..e4927ce6bd 100644 --- a/parsl/executors/base.py +++ b/parsl/executors/base.py @@ -138,7 +138,7 @@ def status_polling_interval(self) -> int: and this method is a delegate to the corresponding method in the provider. :return: the number of seconds to wait between calls to status() or zero if no polling - should be done + should be done """ pass @@ -147,10 +147,8 @@ def status_polling_interval(self) -> int: def error_management_enabled(self) -> bool: """Indicates whether worker error management is supported by this executor. Worker error management is done externally to the executor. However, the executor must implement - certain methods that allow this to function. These methods are: + certain status handling methods that allow this to function. These methods are: - Status Handling Methods - ----------------------- :method:handle_errors :method:set_bad_state_and_fail_all diff --git a/parsl/executors/high_throughput/executor.py b/parsl/executors/high_throughput/executor.py index db14806db7..a707d68547 100644 --- a/parsl/executors/high_throughput/executor.py +++ b/parsl/executors/high_throughput/executor.py @@ -529,10 +529,10 @@ def submit(self, func, resource_specification, *args, **kwargs): Args: - func (callable) : Callable function - - *args (list) : List of arbitrary positional arguments. + - args (list) : List of arbitrary positional arguments. Kwargs: - - **kwargs (dict) : A dictionary of arbitrary keyword args for func. + - kwargs (dict) : A dictionary of arbitrary keyword args for func. Returns: Future @@ -639,8 +639,8 @@ def scale_in(self, blocks=None, block_ids=[], force=True, max_idletime=None): Used along with blocks to indicate whether blocks should be terminated by force. When force = True, we will kill blocks regardless of the blocks being busy When force = False, Only idle blocks will be terminated. - If the # of `idle_blocks` < `blocks`, the list of jobs marked for termination - will be in the range: 0 -`blocks`. + If the # of ``idle_blocks`` < ``blocks``, the list of jobs marked for termination + will be in the range: 0 - ``blocks``. max_idletime: float A time to indicate how long a block can be idle. diff --git a/parsl/executors/swift_t.py b/parsl/executors/swift_t.py index 00a38b12a2..c2dcbb898e 100644 --- a/parsl/executors/swift_t.py +++ b/parsl/executors/swift_t.py @@ -307,10 +307,10 @@ def submit(self, func, *args, **kwargs): Args: - func (callable) : Callable function - - *args (list) : List of arbitrary positional arguments. + - args (list) : List of arbitrary positional arguments. Kwargs: - - **kwargs (dict) : A dictionary of arbitrary keyword args for func. + - kwargs (dict) : A dictionary of arbitrary keyword args for func. Returns: Future diff --git a/parsl/providers/kubernetes/kube.py b/parsl/providers/kubernetes/kube.py index b349cb2046..274400e9d0 100644 --- a/parsl/providers/kubernetes/kube.py +++ b/parsl/providers/kubernetes/kube.py @@ -138,6 +138,7 @@ def submit(self, cmd_string, tasks_per_node, job_name="parsl"): Kwargs: - job_name (String): Name for job, must be unique + Returns: - None: At capacity, cannot provision more - job_id: (string) Identifier for the job diff --git a/parsl/providers/provider_base.py b/parsl/providers/provider_base.py index ddb1180efd..a23b38ead2 100644 --- a/parsl/providers/provider_base.py +++ b/parsl/providers/provider_base.py @@ -143,7 +143,7 @@ def submit(self, command: str, tasks_per_node: int, job_name: str = "parsl.auto" Returns: - A job identifier, this could be an integer, string etc or None or any other object that evaluates to boolean false - if submission failed but an exception isn't thrown. + if submission failed but an exception isn't thrown. Raises: - ExecutionProviderException or its subclasses From 215057d811a6e2983462acdfa8483cd7db32c938 Mon Sep 17 00:00:00 2001 From: Ben Clifford Date: Mon, 7 Jun 2021 13:08:49 +0000 Subject: [PATCH 217/408] Remove untrue claim that parsl_resource_specification keys are case insensitive --- docs/userguide/configuring.rst | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/userguide/configuring.rst b/docs/userguide/configuring.rst index 5139cfcdba..220fc45862 100644 --- a/docs/userguide/configuring.rst +++ b/docs/userguide/configuring.rst @@ -200,7 +200,7 @@ However, it is possible to specify the requirements for a particular app, and Work Queue will automatically run as many parallel instances as possible on each node. Work Queue automatically detects the amount of cores, memory, and other resources available on each execution node. To activate this feature, add a resource specification to your apps. A resource specification is a dictionary with -the following three (case-insensitive) keys: ``cores`` (an integer corresponding to the number of cores required by the task), +the following three keys: ``cores`` (an integer corresponding to the number of cores required by the task), ``memory`` (an integer corresponding to the task's memory requirement in MB), and ``disk`` (an integer corresponding to the task's disk requirement in MB), passed to an app via the special keyword argument ``parsl_resource_specification``. The specification can be set for all app invocations via a default, for example: From 0d7d505df7c503c9e71dc3c753c8053d2022d6ce Mon Sep 17 00:00:00 2001 From: Ben Clifford Date: Mon, 7 Jun 2021 13:12:42 +0000 Subject: [PATCH 218/408] Rephrase ad-hoc config doc now that AdHocProvider (PR #1297) is implemented --- docs/userguide/configuring.rst | 10 ++-------- 1 file changed, 2 insertions(+), 8 deletions(-) diff --git a/docs/userguide/configuring.rst b/docs/userguide/configuring.rst index 5139cfcdba..34c9034cd9 100644 --- a/docs/userguide/configuring.rst +++ b/docs/userguide/configuring.rst @@ -298,8 +298,8 @@ Any collection of compute nodes without a scheduler can be considered an ad-hoc cluster. Often these machines have a shared file system such as NFS or Lustre. In order to use these resources with Parsl, they need to set-up for password-less SSH access. -To use these ssh-accessible collection of nodes as an ad-hoc cluster, we create an executor -for each node, using the `LocalProvider` with `SSHChannel` to identify the node by hostname. An example +To use these ssh-accessible collection of nodes as an ad-hoc cluster, we use +the `AdHocProvider` with an `SSHChannel` to each node. An example configuration follows. .. literalinclude:: ../../parsl/configs/ad_hoc.py @@ -307,12 +307,6 @@ configuration follows. .. note:: Multiple blocks should not be assigned to each node when using the `HighThroughputExecutor` -.. note:: - Load-balancing will not work properly with this approach. In future work, a dedicated provider - that supports load-balancing will be implemented. You can follow progress on this work - `in issue #941 `_. - - Amazon Web Services ------------------- From b5bf273136cb1012cf9ee5dab1910076ab1571b1 Mon Sep 17 00:00:00 2001 From: Ben Clifford Date: Wed, 23 Jun 2021 11:23:15 +0000 Subject: [PATCH 219/408] Fix stub path for check --- .travis.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.travis.yml b/.travis.yml index 29dd2422e5..7a4ef4cf14 100644 --- a/.travis.yml +++ b/.travis.yml @@ -45,7 +45,7 @@ script: # check that the stubs directory does not exist, to protect against # accidentally added stubs files - stubs are generated by sphinx doc # build. - - ! [ -e docs/stubs ] + - ! [ -e stubs ] # check we can build the docs without warnings - make SPHINXOPTS=-W html From 4ae5b2dc9785fdf58a306b35bd77a7f29f07c153 Mon Sep 17 00:00:00 2001 From: Ben Clifford Date: Wed, 23 Jun 2021 11:49:54 +0000 Subject: [PATCH 220/408] Fiddling with future/dependency phrasing --- parsl/dataflow/dflow.py | 7 +++---- 1 file changed, 3 insertions(+), 4 deletions(-) diff --git a/parsl/dataflow/dflow.py b/parsl/dataflow/dflow.py index 30190ba73d..c70e813cf0 100644 --- a/parsl/dataflow/dflow.py +++ b/parsl/dataflow/dflow.py @@ -692,11 +692,10 @@ def check_dep(d): return depends def sanitize_and_wrap(self, args, kwargs): - """This function should be called when all dependency futures for a task - have completed. + """This function should be called when all dependencies have completed. - It will rewrite the arguments for that task, replacing each dependency - future with the result of that future. + It will rewrite the arguments for that task, replacing each Future + with the result of that future. If the user hid futures a level below, we will not catch it, and will (most likely) result in a type error. From 3a304b4b35d1671902ea60d4c647cf75e61bfbbd Mon Sep 17 00:00:00 2001 From: Ben Clifford Date: Thu, 24 Jun 2021 13:10:49 +0000 Subject: [PATCH 221/408] fix fluxexecutor markdown to not give errors --- parsl/executors/flux/executor.py | 32 +++++++++++++++----------------- 1 file changed, 15 insertions(+), 17 deletions(-) diff --git a/parsl/executors/flux/executor.py b/parsl/executors/flux/executor.py index 49fe3ce88c..a947a6b5f7 100644 --- a/parsl/executors/flux/executor.py +++ b/parsl/executors/flux/executor.py @@ -261,24 +261,22 @@ def submit( ): """Wrap a callable in a Flux job and submit it to Flux. - Parameters - ---------- - func: callable - The callable to submit as a job to Flux - resource_specification: collections.abc.Mapping - A mapping defining the resources to allocate to the Flux job. + :param func: The callable to submit as a job to Flux + + :param resource_specification: A mapping defining the resources to allocate to the Flux job. + Only the following keys are checked for: - * num_tasks: the number of tasks to launch (MPI ranks for an MPI job), - default 1 - * cores_per_task: cores per task, default 1 - * gpus_per_task: gpus per task, default 1 - * num_nodes: if > 0, evenly distribute the allocated cores/gpus - across the given number of nodes. Does *not* give the job exclusive - access to those nodes; this option only affects distribution. - *args: - positional arguments for the callable - **kwargs: - keyword arguments for the callable + + - num_tasks: the number of tasks to launch (MPI ranks for an MPI job), default 1 + - cores_per_task: cores per task, default 1 + - gpus_per_task: gpus per task, default 1 + - num_nodes: if > 0, evenly distribute the allocated cores/gpus + across the given number of nodes. Does *not* give the job exclusive + access to those nodes; this option only affects distribution. + + :param args: positional arguments for the callable + + :param kwargs: keyword arguments for the callable """ # protect self._task_id_counter and shutdown/submit race with self._submission_lock: From a78593b72a50e59da483f629cab3c9cb22407c27 Mon Sep 17 00:00:00 2001 From: Ben Clifford Date: Thu, 24 Jun 2021 13:14:14 +0000 Subject: [PATCH 222/408] fiddle with test to make travis happy --- .travis.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.travis.yml b/.travis.yml index 7a4ef4cf14..500c2b3efe 100644 --- a/.travis.yml +++ b/.travis.yml @@ -45,7 +45,7 @@ script: # check that the stubs directory does not exist, to protect against # accidentally added stubs files - stubs are generated by sphinx doc # build. - - ! [ -e stubs ] + - test ! -e stubs # check we can build the docs without warnings - make SPHINXOPTS=-W html From c876b1606be998d40f23e4029612ab3c7d6bd9b2 Mon Sep 17 00:00:00 2001 From: Ben Clifford Date: Tue, 29 Jun 2021 07:04:42 -0700 Subject: [PATCH 223/408] Create a ForkProcess type alias and use it for mac_safe_process in htex --- parsl/__init__.py | 4 ---- parsl/executors/high_throughput/mac_safe_process.py | 11 +++-------- parsl/multiprocessing.py | 9 +++++++++ 3 files changed, 12 insertions(+), 12 deletions(-) create mode 100644 parsl/multiprocessing.py diff --git a/parsl/__init__.py b/parsl/__init__.py index 191c75d467..ab42eaa05a 100644 --- a/parsl/__init__.py +++ b/parsl/__init__.py @@ -33,10 +33,6 @@ from parsl.dataflow.dflow import DataFlowKernel, DataFlowKernelLoader -import multiprocessing -if platform.system() == 'Darwin': - multiprocessing.set_start_method('fork', force=True) - __author__ = 'The Parsl Team' __version__ = VERSION diff --git a/parsl/executors/high_throughput/mac_safe_process.py b/parsl/executors/high_throughput/mac_safe_process.py index 9563b5255e..38539f241a 100644 --- a/parsl/executors/high_throughput/mac_safe_process.py +++ b/parsl/executors/high_throughput/mac_safe_process.py @@ -1,10 +1,5 @@ -import multiprocessing -from typing import Any +from parsl.multiprocessing import ForkProcess -ForkProcess: Any = multiprocessing.get_context('fork').Process +from typing import Type - -class MacSafeProcess(ForkProcess): - - def __init__(self, *args, **kwargs): - super().__init__(*args, **kwargs) +MacSafeProcess: Type = ForkProcess diff --git a/parsl/multiprocessing.py b/parsl/multiprocessing.py new file mode 100644 index 0000000000..fca3140c81 --- /dev/null +++ b/parsl/multiprocessing.py @@ -0,0 +1,9 @@ +"""Helpers for cross-plaform multiprocessing support. +""" + +import multiprocessing + +from typing import Type + +ForkProcess: Type = multiprocessing.get_context('fork').Process + From ffe6024a6ebb50cac34469b5feb5d9e5287b8784 Mon Sep 17 00:00:00 2001 From: Ben Clifford Date: Tue, 29 Jun 2021 07:08:16 -0700 Subject: [PATCH 224/408] Completely remove now-replaced mac_safe_process.py in HTEX --- parsl/executors/high_throughput/mac_safe_process.py | 5 ----- parsl/executors/high_throughput/process_worker_pool.py | 2 +- 2 files changed, 1 insertion(+), 6 deletions(-) delete mode 100644 parsl/executors/high_throughput/mac_safe_process.py diff --git a/parsl/executors/high_throughput/mac_safe_process.py b/parsl/executors/high_throughput/mac_safe_process.py deleted file mode 100644 index 38539f241a..0000000000 --- a/parsl/executors/high_throughput/mac_safe_process.py +++ /dev/null @@ -1,5 +0,0 @@ -from parsl.multiprocessing import ForkProcess - -from typing import Type - -MacSafeProcess: Type = ForkProcess diff --git a/parsl/executors/high_throughput/process_worker_pool.py b/parsl/executors/high_throughput/process_worker_pool.py index 31e33bd401..d2d9d09ee2 100755 --- a/parsl/executors/high_throughput/process_worker_pool.py +++ b/parsl/executors/high_throughput/process_worker_pool.py @@ -27,7 +27,7 @@ from multiprocessing import Process as mpProcess else: from parsl.executors.high_throughput.mac_safe_queue import MacSafeQueue as mpQueue - from parsl.executors.high_throughput.mac_safe_process import MacSafeProcess as mpProcess + from parsl.multiprocessing import ForkProcess as mpProcess from parsl.serialize import unpack_apply_message, serialize From 8d9851ed46978f7ab65e36ac1df29d28250d2196 Mon Sep 17 00:00:00 2001 From: Ben Clifford Date: Tue, 29 Jun 2021 07:14:02 -0700 Subject: [PATCH 225/408] Use ForkProcess always in htex, darwin or no darwin even on non-darwin, I think forked process needs to be used, no matter what has been globally set. --- parsl/executors/high_throughput/executor.py | 5 +++-- parsl/executors/high_throughput/process_worker_pool.py | 4 ++-- 2 files changed, 5 insertions(+), 4 deletions(-) diff --git a/parsl/executors/high_throughput/executor.py b/parsl/executors/high_throughput/executor.py index a707d68547..2354afa26e 100644 --- a/parsl/executors/high_throughput/executor.py +++ b/parsl/executors/high_throughput/executor.py @@ -5,7 +5,7 @@ import queue import datetime import pickle -from multiprocessing import Process, Queue +from multiprocessing import Queue from typing import Dict # noqa F401 (used in type annotation) from typing import List, Optional, Tuple, Union, Any import math @@ -26,6 +26,7 @@ from parsl.addresses import get_all_addresses from parsl.process_loggers import wrap_with_logs +from parsl.multiprocessing import ForkProcess from parsl.utils import RepresentationMixin from parsl.providers import LocalProvider @@ -433,7 +434,7 @@ def _start_local_queue_process(self): get the worker task and result ports that the interchange has bound to. """ comm_q = Queue(maxsize=10) - self.queue_proc = Process(target=interchange.starter, + self.queue_proc = ForkProcess(target=interchange.starter, args=(comm_q,), kwargs={"client_ports": (self.outgoing_q.port, self.incoming_q.port, diff --git a/parsl/executors/high_throughput/process_worker_pool.py b/parsl/executors/high_throughput/process_worker_pool.py index d2d9d09ee2..7f760b278a 100755 --- a/parsl/executors/high_throughput/process_worker_pool.py +++ b/parsl/executors/high_throughput/process_worker_pool.py @@ -22,12 +22,12 @@ from parsl.app.errors import RemoteExceptionWrapper from parsl.executors.high_throughput.errors import WorkerLost from parsl.executors.high_throughput.probe import probe_addresses +from parsl.multiprocessing import ForkProcess as mpProcess + if platform.system() != 'Darwin': from multiprocessing import Queue as mpQueue - from multiprocessing import Process as mpProcess else: from parsl.executors.high_throughput.mac_safe_queue import MacSafeQueue as mpQueue - from parsl.multiprocessing import ForkProcess as mpProcess from parsl.serialize import unpack_apply_message, serialize From bac4b8a7010676d46fdd140a8cb030940e44508e Mon Sep 17 00:00:00 2001 From: Ben Clifford Date: Tue, 29 Jun 2021 07:22:14 -0700 Subject: [PATCH 226/408] Put usage tracking back to a forked process which was removed by my earlier removal of global forking --- parsl/dataflow/usage_tracking/usage.py | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/parsl/dataflow/usage_tracking/usage.py b/parsl/dataflow/usage_tracking/usage.py index 9a497f56e9..5d8145319a 100644 --- a/parsl/dataflow/usage_tracking/usage.py +++ b/parsl/dataflow/usage_tracking/usage.py @@ -10,6 +10,7 @@ import platform import multiprocessing as mp +from parsl.multiprocessing import ForkProcess from parsl.version import VERSION as PARSL_VERSION logger = logging.getLogger(__name__) @@ -19,7 +20,7 @@ def async_process(fn): """ Decorator function to launch a function as a separate process """ def run(*args, **kwargs): - proc = mp.Process(target=fn, args=args, kwargs=kwargs, name="Usage-Tracking") + proc = ForkProcess(target=fn, args=args, kwargs=kwargs, name="Usage-Tracking") proc.start() return proc From 10a6817b892f32143d8b56b1fbaa9e6dad7a9cfa Mon Sep 17 00:00:00 2001 From: Ben Clifford Date: Wed, 30 Jun 2021 07:52:59 +0000 Subject: [PATCH 227/408] remove stubs --- .../parsl.addresses.address_by_hostname.rst | 6 --- .../parsl.addresses.address_by_interface.rst | 6 --- .../parsl.addresses.address_by_query.rst | 6 --- .../parsl.addresses.address_by_route.rst | 6 --- docs/stubs/parsl.app.app.AppBase.rst | 22 -------- docs/stubs/parsl.app.app.bash_app.rst | 6 --- docs/stubs/parsl.app.app.join_app.rst | 6 --- docs/stubs/parsl.app.app.python_app.rst | 6 --- docs/stubs/parsl.app.bash.BashApp.rst | 22 -------- .../parsl.app.errors.AppBadFormatting.rst | 6 --- docs/stubs/parsl.app.errors.AppException.rst | 6 --- docs/stubs/parsl.app.errors.AppTimeout.rst | 6 --- .../parsl.app.errors.BadStdStreamFile.rst | 6 --- .../parsl.app.errors.BashAppNoReturn.rst | 6 --- .../parsl.app.errors.BashExitFailure.rst | 6 --- .../stubs/parsl.app.errors.MissingOutputs.rst | 6 --- .../stubs/parsl.app.errors.NotFutureError.rst | 6 --- docs/stubs/parsl.app.errors.ParslError.rst | 6 --- docs/stubs/parsl.app.futures.DataFuture.rst | 41 -------------- docs/stubs/parsl.app.python.PythonApp.rst | 22 -------- docs/stubs/parsl.channels.LocalChannel.rst | 35 ------------ docs/stubs/parsl.channels.OAuthSSHChannel.rst | 36 ------------- docs/stubs/parsl.channels.SSHChannel.rst | 36 ------------- ...sl.channels.SSHInteractiveLoginChannel.rst | 36 ------------- docs/stubs/parsl.channels.base.Channel.rst | 35 ------------ .../parsl.channels.errors.AuthException.rst | 6 --- ...sl.channels.errors.BadHostKeyException.rst | 6 --- ...rsl.channels.errors.BadPermsScriptPath.rst | 6 --- .../parsl.channels.errors.BadScriptPath.rst | 6 --- .../parsl.channels.errors.ChannelError.rst | 6 --- ...arsl.channels.errors.FileCopyException.rst | 6 --- .../parsl.channels.errors.FileExists.rst | 6 --- .../parsl.channels.errors.SSHException.rst | 6 --- docs/stubs/parsl.config.Config.rst | 28 ---------- ...data_provider.data_manager.DataManager.rst | 27 ---------- ...ata_provider.file_noop.NoOpFileStaging.rst | 28 ---------- docs/stubs/parsl.data_provider.files.File.rst | 29 ---------- ...rsl.data_provider.ftp.FTPInTaskStaging.rst | 28 ---------- ...ta_provider.ftp.FTPSeparateTaskStaging.rst | 28 ---------- ...rsl.data_provider.globus.GlobusStaging.rst | 29 ---------- ...l.data_provider.http.HTTPInTaskStaging.rst | 28 ---------- ..._provider.http.HTTPSeparateTaskStaging.rst | 28 ---------- ...parsl.data_provider.rsync.RSyncStaging.rst | 28 ---------- .../parsl.data_provider.staging.Staging.rst | 28 ---------- .../parsl.dataflow.dflow.DataFlowKernel.rst | 44 --------------- ...sl.dataflow.dflow.DataFlowKernelLoader.rst | 26 --------- .../parsl.dataflow.error.BadCheckpoint.rst | 6 --- ...arsl.dataflow.error.ConfigurationError.rst | 6 --- ...parsl.dataflow.error.DataFlowException.rst | 6 --- .../parsl.dataflow.error.DependencyError.rst | 6 --- ...arsl.dataflow.error.DuplicateTaskError.rst | 6 --- ...arsl.dataflow.flow_control.FlowControl.rst | 26 --------- .../parsl.dataflow.flow_control.Timer.rst | 24 --------- .../parsl.dataflow.futures.AppFuture.rst | 42 --------------- .../parsl.dataflow.memoization.Memoizer.rst | 26 --------- .../parsl.dataflow.strategy.Strategy.rst | 24 --------- .../parsl.errors.OptionalModuleMissing.rst | 6 --- .../parsl.executors.ExtremeScaleExecutor.rst | 54 ------------------- ...parsl.executors.HighThroughputExecutor.rst | 54 ------------------- .../parsl.executors.LowLatencyExecutor.rst | 49 ----------------- .../parsl.executors.ThreadPoolExecutor.rst | 47 ---------------- .../parsl.executors.WorkQueueExecutor.rst | 50 ----------------- .../parsl.executors.base.ParslExecutor.rst | 46 ---------------- .../parsl.executors.errors.BadMessage.rst | 6 --- ....executors.errors.DeserializationError.rst | 6 --- .../parsl.executors.errors.ExecutorError.rst | 6 --- .../parsl.executors.errors.ScalingFailed.rst | 6 --- ...sl.executors.errors.SerializationError.rst | 6 --- ...tors.high_throughput.errors.WorkerLost.rst | 6 --- ....status_handling.BlockProviderExecutor.rst | 49 ----------------- ...arsl.executors.swift_t.TurbineExecutor.rst | 48 ----------------- docs/stubs/parsl.launchers.AprunLauncher.rst | 22 -------- .../parsl.launchers.GnuParallelLauncher.rst | 22 -------- docs/stubs/parsl.launchers.JsrunLauncher.rst | 22 -------- .../stubs/parsl.launchers.MpiExecLauncher.rst | 22 -------- docs/stubs/parsl.launchers.SimpleLauncher.rst | 22 -------- .../parsl.launchers.SingleNodeLauncher.rst | 22 -------- docs/stubs/parsl.launchers.SrunLauncher.rst | 22 -------- .../stubs/parsl.launchers.SrunMPILauncher.rst | 22 -------- .../stubs/parsl.launchers.WrappedLauncher.rst | 22 -------- .../parsl.launchers.error.BadLauncher.rst | 6 --- docs/stubs/parsl.monitoring.MonitoringHub.rst | 26 --------- docs/stubs/parsl.providers.AWSProvider.rst | 50 ----------------- docs/stubs/parsl.providers.AdHocProvider.rst | 35 ------------ docs/stubs/parsl.providers.CobaltProvider.rst | 35 ------------ docs/stubs/parsl.providers.CondorProvider.rst | 35 ------------ .../parsl.providers.GoogleCloudProvider.rst | 35 ------------ .../parsl.providers.GridEngineProvider.rst | 36 ------------- .../parsl.providers.KubernetesProvider.rst | 34 ------------ docs/stubs/parsl.providers.LSFProvider.rst | 35 ------------ docs/stubs/parsl.providers.LocalProvider.rst | 34 ------------ docs/stubs/parsl.providers.PBSProProvider.rst | 35 ------------ docs/stubs/parsl.providers.SlurmProvider.rst | 35 ------------ docs/stubs/parsl.providers.TorqueProvider.rst | 35 ------------ ...iders.cluster_provider.ClusterProvider.rst | 35 ------------ .../parsl.providers.error.ChannelRequired.rst | 6 --- ...iders.error.ExecutionProviderException.rst | 6 --- .../parsl.providers.error.ScaleOutFailed.rst | 6 --- ...l.providers.error.SchedulerMissingArgs.rst | 6 --- .../parsl.providers.error.ScriptPathError.rst | 6 --- ...viders.provider_base.ExecutionProvider.rst | 34 ------------ docs/stubs/parsl.set_file_logger.rst | 6 --- docs/stubs/parsl.set_stream_logger.rst | 6 --- .../stubs/parsl.utils.get_all_checkpoints.rst | 6 --- .../stubs/parsl.utils.get_last_checkpoint.rst | 6 --- 105 files changed, 2206 deletions(-) delete mode 100644 docs/stubs/parsl.addresses.address_by_hostname.rst delete mode 100644 docs/stubs/parsl.addresses.address_by_interface.rst delete mode 100644 docs/stubs/parsl.addresses.address_by_query.rst delete mode 100644 docs/stubs/parsl.addresses.address_by_route.rst delete mode 100644 docs/stubs/parsl.app.app.AppBase.rst delete mode 100644 docs/stubs/parsl.app.app.bash_app.rst delete mode 100644 docs/stubs/parsl.app.app.join_app.rst delete mode 100644 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d1e7705cba..0000000000 --- a/docs/stubs/parsl.addresses.address_by_hostname.rst +++ /dev/null @@ -1,6 +0,0 @@ -parsl.addresses.address\_by\_hostname -===================================== - -.. currentmodule:: parsl.addresses - -.. autofunction:: address_by_hostname \ No newline at end of file diff --git a/docs/stubs/parsl.addresses.address_by_interface.rst b/docs/stubs/parsl.addresses.address_by_interface.rst deleted file mode 100644 index e5c8be63ef..0000000000 --- a/docs/stubs/parsl.addresses.address_by_interface.rst +++ /dev/null @@ -1,6 +0,0 @@ -parsl.addresses.address\_by\_interface -====================================== - -.. currentmodule:: parsl.addresses - -.. autofunction:: address_by_interface \ No newline at end of file diff --git a/docs/stubs/parsl.addresses.address_by_query.rst b/docs/stubs/parsl.addresses.address_by_query.rst deleted file mode 100644 index 013af3d423..0000000000 --- a/docs/stubs/parsl.addresses.address_by_query.rst +++ /dev/null @@ -1,6 +0,0 @@ -parsl.addresses.address\_by\_query -================================== - -.. currentmodule:: parsl.addresses - -.. autofunction:: address_by_query \ No newline at end of file diff --git a/docs/stubs/parsl.addresses.address_by_route.rst b/docs/stubs/parsl.addresses.address_by_route.rst deleted file mode 100644 index 7a88eb0eaf..0000000000 --- a/docs/stubs/parsl.addresses.address_by_route.rst +++ /dev/null @@ -1,6 +0,0 @@ -parsl.addresses.address\_by\_route -================================== - -.. currentmodule:: parsl.addresses - -.. autofunction:: address_by_route \ No newline at end of file diff --git a/docs/stubs/parsl.app.app.AppBase.rst b/docs/stubs/parsl.app.app.AppBase.rst deleted file mode 100644 index ac76cf0113..0000000000 --- a/docs/stubs/parsl.app.app.AppBase.rst +++ /dev/null @@ -1,22 +0,0 @@ -parsl.app.app.AppBase -===================== - -.. currentmodule:: parsl.app.app - -.. autoclass:: AppBase - - - .. automethod:: __init__ - - - .. rubric:: Methods - - .. autosummary:: - - ~AppBase.__init__ - - - - - - \ No newline at end of file diff --git a/docs/stubs/parsl.app.app.bash_app.rst b/docs/stubs/parsl.app.app.bash_app.rst deleted file mode 100644 index 6c68e3d467..0000000000 --- a/docs/stubs/parsl.app.app.bash_app.rst +++ /dev/null @@ -1,6 +0,0 @@ -parsl.app.app.bash\_app -======================= - -.. currentmodule:: parsl.app.app - -.. autofunction:: bash_app \ No newline at end of file diff --git a/docs/stubs/parsl.app.app.join_app.rst b/docs/stubs/parsl.app.app.join_app.rst deleted file mode 100644 index 408344fe0f..0000000000 --- a/docs/stubs/parsl.app.app.join_app.rst +++ /dev/null @@ -1,6 +0,0 @@ -parsl.app.app.join\_app -======================= - -.. currentmodule:: parsl.app.app - -.. autofunction:: join_app \ No newline at end of file diff --git a/docs/stubs/parsl.app.app.python_app.rst b/docs/stubs/parsl.app.app.python_app.rst deleted file mode 100644 index 963e9b04c6..0000000000 --- a/docs/stubs/parsl.app.app.python_app.rst +++ /dev/null @@ -1,6 +0,0 @@ -parsl.app.app.python\_app -========================= - -.. currentmodule:: parsl.app.app - -.. autofunction:: python_app \ No newline at end of file diff --git a/docs/stubs/parsl.app.bash.BashApp.rst b/docs/stubs/parsl.app.bash.BashApp.rst deleted file mode 100644 index a9b80e89b4..0000000000 --- a/docs/stubs/parsl.app.bash.BashApp.rst +++ /dev/null @@ -1,22 +0,0 @@ -parsl.app.bash.BashApp -====================== - -.. currentmodule:: parsl.app.bash - -.. autoclass:: BashApp - - - .. automethod:: __init__ - - - .. rubric:: Methods - - .. autosummary:: - - ~BashApp.__init__ - - - - - - \ No newline at end of file diff --git a/docs/stubs/parsl.app.errors.AppBadFormatting.rst b/docs/stubs/parsl.app.errors.AppBadFormatting.rst deleted file mode 100644 index 7ea9085b07..0000000000 --- a/docs/stubs/parsl.app.errors.AppBadFormatting.rst +++ /dev/null @@ -1,6 +0,0 @@ -parsl.app.errors.AppBadFormatting -================================= - -.. currentmodule:: parsl.app.errors - -.. autoexception:: AppBadFormatting \ No newline at end of file diff --git a/docs/stubs/parsl.app.errors.AppException.rst b/docs/stubs/parsl.app.errors.AppException.rst deleted file mode 100644 index b427e52b73..0000000000 --- a/docs/stubs/parsl.app.errors.AppException.rst +++ /dev/null @@ -1,6 +0,0 @@ -parsl.app.errors.AppException -============================= - -.. currentmodule:: parsl.app.errors - -.. autoexception:: AppException \ No newline at end of file diff --git a/docs/stubs/parsl.app.errors.AppTimeout.rst b/docs/stubs/parsl.app.errors.AppTimeout.rst deleted file mode 100644 index 316badf45b..0000000000 --- a/docs/stubs/parsl.app.errors.AppTimeout.rst +++ /dev/null @@ -1,6 +0,0 @@ -parsl.app.errors.AppTimeout -=========================== - -.. currentmodule:: parsl.app.errors - -.. autoexception:: AppTimeout \ No newline at end of file diff --git a/docs/stubs/parsl.app.errors.BadStdStreamFile.rst b/docs/stubs/parsl.app.errors.BadStdStreamFile.rst deleted file mode 100644 index 9b2aff012e..0000000000 --- a/docs/stubs/parsl.app.errors.BadStdStreamFile.rst +++ /dev/null @@ -1,6 +0,0 @@ -parsl.app.errors.BadStdStreamFile -================================= - -.. currentmodule:: parsl.app.errors - -.. autoexception:: BadStdStreamFile \ No newline at end of file diff --git a/docs/stubs/parsl.app.errors.BashAppNoReturn.rst b/docs/stubs/parsl.app.errors.BashAppNoReturn.rst deleted file mode 100644 index e75de6ad41..0000000000 --- a/docs/stubs/parsl.app.errors.BashAppNoReturn.rst +++ /dev/null @@ -1,6 +0,0 @@ -parsl.app.errors.BashAppNoReturn -================================ - -.. currentmodule:: parsl.app.errors - -.. autoexception:: BashAppNoReturn \ No newline at end of file diff --git a/docs/stubs/parsl.app.errors.BashExitFailure.rst b/docs/stubs/parsl.app.errors.BashExitFailure.rst deleted file mode 100644 index e0c0a258fc..0000000000 --- a/docs/stubs/parsl.app.errors.BashExitFailure.rst +++ /dev/null @@ -1,6 +0,0 @@ -parsl.app.errors.BashExitFailure -================================ - -.. currentmodule:: parsl.app.errors - -.. autoexception:: BashExitFailure \ No newline at end of file diff --git a/docs/stubs/parsl.app.errors.MissingOutputs.rst b/docs/stubs/parsl.app.errors.MissingOutputs.rst deleted file mode 100644 index ff089d0f20..0000000000 --- a/docs/stubs/parsl.app.errors.MissingOutputs.rst +++ /dev/null @@ -1,6 +0,0 @@ -parsl.app.errors.MissingOutputs -=============================== - -.. currentmodule:: parsl.app.errors - -.. autoexception:: MissingOutputs \ No newline at end of file diff --git a/docs/stubs/parsl.app.errors.NotFutureError.rst b/docs/stubs/parsl.app.errors.NotFutureError.rst deleted file mode 100644 index 4f08420315..0000000000 --- a/docs/stubs/parsl.app.errors.NotFutureError.rst +++ /dev/null @@ -1,6 +0,0 @@ -parsl.app.errors.NotFutureError -=============================== - -.. currentmodule:: parsl.app.errors - -.. autoexception:: NotFutureError \ No newline at end of file diff --git a/docs/stubs/parsl.app.errors.ParslError.rst b/docs/stubs/parsl.app.errors.ParslError.rst deleted file mode 100644 index 761e28e823..0000000000 --- a/docs/stubs/parsl.app.errors.ParslError.rst +++ /dev/null @@ -1,6 +0,0 @@ -parsl.app.errors.ParslError -=========================== - -.. currentmodule:: parsl.app.errors - -.. autoexception:: ParslError \ No newline at end of file diff --git a/docs/stubs/parsl.app.futures.DataFuture.rst b/docs/stubs/parsl.app.futures.DataFuture.rst deleted file mode 100644 index d1cffda01f..0000000000 --- a/docs/stubs/parsl.app.futures.DataFuture.rst +++ /dev/null @@ -1,41 +0,0 @@ -parsl.app.futures.DataFuture -============================ - -.. currentmodule:: parsl.app.futures - -.. autoclass:: DataFuture - - - .. automethod:: __init__ - - - .. rubric:: Methods - - .. autosummary:: - - ~DataFuture.__init__ - ~DataFuture.add_done_callback - ~DataFuture.cancel - ~DataFuture.cancelled - ~DataFuture.done - ~DataFuture.exception - ~DataFuture.parent_callback - ~DataFuture.result - ~DataFuture.running - ~DataFuture.set_exception - ~DataFuture.set_result - ~DataFuture.set_running_or_notify_cancel - - - - - - .. rubric:: Attributes - - .. autosummary:: - - ~DataFuture.filename - ~DataFuture.filepath - ~DataFuture.tid - - \ No newline at end of file diff --git a/docs/stubs/parsl.app.python.PythonApp.rst b/docs/stubs/parsl.app.python.PythonApp.rst deleted file mode 100644 index be44a9a014..0000000000 --- a/docs/stubs/parsl.app.python.PythonApp.rst +++ /dev/null @@ -1,22 +0,0 @@ -parsl.app.python.PythonApp -========================== - -.. currentmodule:: parsl.app.python - -.. autoclass:: PythonApp - - - .. automethod:: __init__ - - - .. rubric:: Methods - - .. autosummary:: - - ~PythonApp.__init__ - - - - - - \ No newline at end of file diff --git a/docs/stubs/parsl.channels.LocalChannel.rst b/docs/stubs/parsl.channels.LocalChannel.rst deleted file mode 100644 index e681d872f3..0000000000 --- a/docs/stubs/parsl.channels.LocalChannel.rst +++ /dev/null @@ -1,35 +0,0 @@ -parsl.channels.LocalChannel -=========================== - -.. currentmodule:: parsl.channels - -.. autoclass:: LocalChannel - - - .. automethod:: __init__ - - - .. rubric:: Methods - - .. autosummary:: - - ~LocalChannel.__init__ - ~LocalChannel.abspath - ~LocalChannel.close - ~LocalChannel.execute_wait - ~LocalChannel.isdir - ~LocalChannel.makedirs - ~LocalChannel.pull_file - ~LocalChannel.push_file - - - - - - .. rubric:: Attributes - - .. autosummary:: - - ~LocalChannel.script_dir - - \ No newline at end of file diff --git a/docs/stubs/parsl.channels.OAuthSSHChannel.rst b/docs/stubs/parsl.channels.OAuthSSHChannel.rst deleted file mode 100644 index ae3e53bba0..0000000000 --- a/docs/stubs/parsl.channels.OAuthSSHChannel.rst +++ /dev/null @@ -1,36 +0,0 @@ -parsl.channels.OAuthSSHChannel -============================== - -.. currentmodule:: parsl.channels - -.. autoclass:: OAuthSSHChannel - - - .. automethod:: __init__ - - - .. rubric:: Methods - - .. autosummary:: - - ~OAuthSSHChannel.__init__ - ~OAuthSSHChannel.abspath - ~OAuthSSHChannel.close - ~OAuthSSHChannel.execute_wait - ~OAuthSSHChannel.isdir - ~OAuthSSHChannel.makedirs - ~OAuthSSHChannel.prepend_envs - ~OAuthSSHChannel.pull_file - ~OAuthSSHChannel.push_file - - - - - - .. rubric:: Attributes - - .. autosummary:: - - ~OAuthSSHChannel.script_dir - - \ No newline at end of file diff --git a/docs/stubs/parsl.channels.SSHChannel.rst b/docs/stubs/parsl.channels.SSHChannel.rst deleted file mode 100644 index 18cd1c55d6..0000000000 --- a/docs/stubs/parsl.channels.SSHChannel.rst +++ /dev/null @@ -1,36 +0,0 @@ -parsl.channels.SSHChannel -========================= - -.. currentmodule:: parsl.channels - -.. autoclass:: SSHChannel - - - .. automethod:: __init__ - - - .. rubric:: Methods - - .. autosummary:: - - ~SSHChannel.__init__ - ~SSHChannel.abspath - ~SSHChannel.close - ~SSHChannel.execute_wait - ~SSHChannel.isdir - ~SSHChannel.makedirs - ~SSHChannel.prepend_envs - ~SSHChannel.pull_file - ~SSHChannel.push_file - - - - - - .. rubric:: Attributes - - .. autosummary:: - - ~SSHChannel.script_dir - - \ No newline at end of file diff --git a/docs/stubs/parsl.channels.SSHInteractiveLoginChannel.rst b/docs/stubs/parsl.channels.SSHInteractiveLoginChannel.rst deleted file mode 100644 index 99233e7ddc..0000000000 --- a/docs/stubs/parsl.channels.SSHInteractiveLoginChannel.rst +++ /dev/null @@ -1,36 +0,0 @@ -parsl.channels.SSHInteractiveLoginChannel -========================================= - -.. currentmodule:: parsl.channels - -.. autoclass:: SSHInteractiveLoginChannel - - - .. automethod:: __init__ - - - .. rubric:: Methods - - .. autosummary:: - - ~SSHInteractiveLoginChannel.__init__ - ~SSHInteractiveLoginChannel.abspath - ~SSHInteractiveLoginChannel.close - ~SSHInteractiveLoginChannel.execute_wait - ~SSHInteractiveLoginChannel.isdir - ~SSHInteractiveLoginChannel.makedirs - ~SSHInteractiveLoginChannel.prepend_envs - ~SSHInteractiveLoginChannel.pull_file - ~SSHInteractiveLoginChannel.push_file - - - - - - .. rubric:: Attributes - - .. autosummary:: - - ~SSHInteractiveLoginChannel.script_dir - - \ No newline at end of file diff --git a/docs/stubs/parsl.channels.base.Channel.rst b/docs/stubs/parsl.channels.base.Channel.rst deleted file mode 100644 index 41864a0297..0000000000 --- a/docs/stubs/parsl.channels.base.Channel.rst +++ /dev/null @@ -1,35 +0,0 @@ -parsl.channels.base.Channel -=========================== - -.. currentmodule:: parsl.channels.base - -.. autoclass:: Channel - - - .. automethod:: __init__ - - - .. rubric:: Methods - - .. autosummary:: - - ~Channel.__init__ - ~Channel.abspath - ~Channel.close - ~Channel.execute_wait - ~Channel.isdir - ~Channel.makedirs - ~Channel.pull_file - ~Channel.push_file - - - - - - .. rubric:: Attributes - - .. autosummary:: - - ~Channel.script_dir - - \ No newline at end of file diff --git a/docs/stubs/parsl.channels.errors.AuthException.rst b/docs/stubs/parsl.channels.errors.AuthException.rst deleted file mode 100644 index 2a8b17a118..0000000000 --- a/docs/stubs/parsl.channels.errors.AuthException.rst +++ /dev/null @@ -1,6 +0,0 @@ -parsl.channels.errors.AuthException -=================================== - -.. currentmodule:: parsl.channels.errors - -.. autoexception:: AuthException \ No newline at end of file diff --git a/docs/stubs/parsl.channels.errors.BadHostKeyException.rst b/docs/stubs/parsl.channels.errors.BadHostKeyException.rst deleted file mode 100644 index 4c79752743..0000000000 --- a/docs/stubs/parsl.channels.errors.BadHostKeyException.rst +++ /dev/null @@ -1,6 +0,0 @@ -parsl.channels.errors.BadHostKeyException -========================================= - -.. currentmodule:: parsl.channels.errors - -.. autoexception:: BadHostKeyException \ No newline at end of file diff --git a/docs/stubs/parsl.channels.errors.BadPermsScriptPath.rst b/docs/stubs/parsl.channels.errors.BadPermsScriptPath.rst deleted file mode 100644 index a3d1f5a763..0000000000 --- a/docs/stubs/parsl.channels.errors.BadPermsScriptPath.rst +++ /dev/null @@ -1,6 +0,0 @@ -parsl.channels.errors.BadPermsScriptPath -======================================== - -.. currentmodule:: parsl.channels.errors - -.. autoexception:: BadPermsScriptPath \ No newline at end of file diff --git a/docs/stubs/parsl.channels.errors.BadScriptPath.rst b/docs/stubs/parsl.channels.errors.BadScriptPath.rst deleted file mode 100644 index bc7be42bd8..0000000000 --- a/docs/stubs/parsl.channels.errors.BadScriptPath.rst +++ /dev/null @@ -1,6 +0,0 @@ -parsl.channels.errors.BadScriptPath -=================================== - -.. currentmodule:: parsl.channels.errors - -.. autoexception:: BadScriptPath \ No newline at end of file diff --git a/docs/stubs/parsl.channels.errors.ChannelError.rst b/docs/stubs/parsl.channels.errors.ChannelError.rst deleted file mode 100644 index 88fdaf0904..0000000000 --- a/docs/stubs/parsl.channels.errors.ChannelError.rst +++ /dev/null @@ -1,6 +0,0 @@ -parsl.channels.errors.ChannelError -================================== - -.. currentmodule:: parsl.channels.errors - -.. autoexception:: ChannelError \ No newline at end of file diff --git a/docs/stubs/parsl.channels.errors.FileCopyException.rst b/docs/stubs/parsl.channels.errors.FileCopyException.rst deleted file mode 100644 index 8c1658c239..0000000000 --- a/docs/stubs/parsl.channels.errors.FileCopyException.rst +++ /dev/null @@ -1,6 +0,0 @@ -parsl.channels.errors.FileCopyException -======================================= - -.. currentmodule:: parsl.channels.errors - -.. autoexception:: FileCopyException \ No newline at end of file diff --git a/docs/stubs/parsl.channels.errors.FileExists.rst b/docs/stubs/parsl.channels.errors.FileExists.rst deleted file mode 100644 index 22b72f164f..0000000000 --- a/docs/stubs/parsl.channels.errors.FileExists.rst +++ /dev/null @@ -1,6 +0,0 @@ -parsl.channels.errors.FileExists -================================ - -.. currentmodule:: parsl.channels.errors - -.. autoexception:: FileExists \ No newline at end of file diff --git a/docs/stubs/parsl.channels.errors.SSHException.rst b/docs/stubs/parsl.channels.errors.SSHException.rst deleted file mode 100644 index a64f147ec2..0000000000 --- a/docs/stubs/parsl.channels.errors.SSHException.rst +++ /dev/null @@ -1,6 +0,0 @@ -parsl.channels.errors.SSHException -================================== - -.. currentmodule:: parsl.channels.errors - -.. autoexception:: SSHException \ No newline at end of file diff --git a/docs/stubs/parsl.config.Config.rst b/docs/stubs/parsl.config.Config.rst deleted file mode 100644 index 237a6aa2e1..0000000000 --- a/docs/stubs/parsl.config.Config.rst +++ /dev/null @@ -1,28 +0,0 @@ -parsl.config.Config -=================== - -.. currentmodule:: parsl.config - -.. autoclass:: Config - - - .. automethod:: __init__ - - - .. rubric:: Methods - - .. autosummary:: - - ~Config.__init__ - - - - - - .. rubric:: Attributes - - .. autosummary:: - - ~Config.executors - - \ No newline at end of file diff --git a/docs/stubs/parsl.data_provider.data_manager.DataManager.rst b/docs/stubs/parsl.data_provider.data_manager.DataManager.rst deleted file mode 100644 index 9c3cb60108..0000000000 --- a/docs/stubs/parsl.data_provider.data_manager.DataManager.rst +++ /dev/null @@ -1,27 +0,0 @@ -parsl.data\_provider.data\_manager.DataManager -============================================== - -.. currentmodule:: parsl.data_provider.data_manager - -.. autoclass:: DataManager - - - .. automethod:: __init__ - - - .. rubric:: Methods - - .. autosummary:: - - ~DataManager.__init__ - ~DataManager.optionally_stage_in - ~DataManager.replace_task - ~DataManager.replace_task_stage_out - ~DataManager.stage_in - ~DataManager.stage_out - - - - - - \ No newline at end of file diff --git a/docs/stubs/parsl.data_provider.file_noop.NoOpFileStaging.rst b/docs/stubs/parsl.data_provider.file_noop.NoOpFileStaging.rst deleted file mode 100644 index 77c71510a3..0000000000 --- a/docs/stubs/parsl.data_provider.file_noop.NoOpFileStaging.rst +++ /dev/null @@ -1,28 +0,0 @@ -parsl.data\_provider.file\_noop.NoOpFileStaging -=============================================== - -.. currentmodule:: parsl.data_provider.file_noop - -.. autoclass:: NoOpFileStaging - - - .. automethod:: __init__ - - - .. rubric:: Methods - - .. autosummary:: - - ~NoOpFileStaging.__init__ - ~NoOpFileStaging.can_stage_in - ~NoOpFileStaging.can_stage_out - ~NoOpFileStaging.replace_task - ~NoOpFileStaging.replace_task_stage_out - ~NoOpFileStaging.stage_in - ~NoOpFileStaging.stage_out - - - - - - \ No newline at end of file diff --git a/docs/stubs/parsl.data_provider.files.File.rst b/docs/stubs/parsl.data_provider.files.File.rst deleted file mode 100644 index e76a07aaa1..0000000000 --- a/docs/stubs/parsl.data_provider.files.File.rst +++ /dev/null @@ -1,29 +0,0 @@ -parsl.data\_provider.files.File -=============================== - -.. currentmodule:: parsl.data_provider.files - -.. autoclass:: File - - - .. automethod:: __init__ - - - .. rubric:: Methods - - .. autosummary:: - - ~File.__init__ - ~File.cleancopy - - - - - - .. rubric:: Attributes - - .. autosummary:: - - ~File.filepath - - \ No newline at end of file diff --git a/docs/stubs/parsl.data_provider.ftp.FTPInTaskStaging.rst b/docs/stubs/parsl.data_provider.ftp.FTPInTaskStaging.rst deleted file mode 100644 index f16aa73a35..0000000000 --- a/docs/stubs/parsl.data_provider.ftp.FTPInTaskStaging.rst +++ /dev/null @@ -1,28 +0,0 @@ -parsl.data\_provider.ftp.FTPInTaskStaging -========================================= - -.. currentmodule:: parsl.data_provider.ftp - -.. autoclass:: FTPInTaskStaging - - - .. automethod:: __init__ - - - .. rubric:: Methods - - .. autosummary:: - - ~FTPInTaskStaging.__init__ - ~FTPInTaskStaging.can_stage_in - ~FTPInTaskStaging.can_stage_out - ~FTPInTaskStaging.replace_task - ~FTPInTaskStaging.replace_task_stage_out - ~FTPInTaskStaging.stage_in - ~FTPInTaskStaging.stage_out - - - - - - \ No newline at end of file diff --git a/docs/stubs/parsl.data_provider.ftp.FTPSeparateTaskStaging.rst b/docs/stubs/parsl.data_provider.ftp.FTPSeparateTaskStaging.rst deleted file mode 100644 index e24753b536..0000000000 --- a/docs/stubs/parsl.data_provider.ftp.FTPSeparateTaskStaging.rst +++ /dev/null @@ -1,28 +0,0 @@ -parsl.data\_provider.ftp.FTPSeparateTaskStaging -=============================================== - -.. currentmodule:: parsl.data_provider.ftp - -.. autoclass:: FTPSeparateTaskStaging - - - .. automethod:: __init__ - - - .. rubric:: Methods - - .. autosummary:: - - ~FTPSeparateTaskStaging.__init__ - ~FTPSeparateTaskStaging.can_stage_in - ~FTPSeparateTaskStaging.can_stage_out - ~FTPSeparateTaskStaging.replace_task - ~FTPSeparateTaskStaging.replace_task_stage_out - ~FTPSeparateTaskStaging.stage_in - ~FTPSeparateTaskStaging.stage_out - - - - - - \ No newline at end of file diff --git a/docs/stubs/parsl.data_provider.globus.GlobusStaging.rst b/docs/stubs/parsl.data_provider.globus.GlobusStaging.rst deleted file mode 100644 index e65dc2dc17..0000000000 --- a/docs/stubs/parsl.data_provider.globus.GlobusStaging.rst +++ /dev/null @@ -1,29 +0,0 @@ -parsl.data\_provider.globus.GlobusStaging -========================================= - -.. currentmodule:: parsl.data_provider.globus - -.. autoclass:: GlobusStaging - - - .. automethod:: __init__ - - - .. rubric:: Methods - - .. autosummary:: - - ~GlobusStaging.__init__ - ~GlobusStaging.can_stage_in - ~GlobusStaging.can_stage_out - ~GlobusStaging.initialize_globus - ~GlobusStaging.replace_task - ~GlobusStaging.replace_task_stage_out - ~GlobusStaging.stage_in - ~GlobusStaging.stage_out - - - - - - \ No newline at end of file diff --git a/docs/stubs/parsl.data_provider.http.HTTPInTaskStaging.rst b/docs/stubs/parsl.data_provider.http.HTTPInTaskStaging.rst deleted file mode 100644 index 7b10950d0f..0000000000 --- a/docs/stubs/parsl.data_provider.http.HTTPInTaskStaging.rst +++ /dev/null @@ -1,28 +0,0 @@ -parsl.data\_provider.http.HTTPInTaskStaging -=========================================== - -.. currentmodule:: parsl.data_provider.http - -.. autoclass:: HTTPInTaskStaging - - - .. automethod:: __init__ - - - .. rubric:: Methods - - .. autosummary:: - - ~HTTPInTaskStaging.__init__ - ~HTTPInTaskStaging.can_stage_in - ~HTTPInTaskStaging.can_stage_out - ~HTTPInTaskStaging.replace_task - ~HTTPInTaskStaging.replace_task_stage_out - ~HTTPInTaskStaging.stage_in - ~HTTPInTaskStaging.stage_out - - - - - - \ No newline at end of file diff --git a/docs/stubs/parsl.data_provider.http.HTTPSeparateTaskStaging.rst b/docs/stubs/parsl.data_provider.http.HTTPSeparateTaskStaging.rst deleted file mode 100644 index 917eb4913d..0000000000 --- a/docs/stubs/parsl.data_provider.http.HTTPSeparateTaskStaging.rst +++ /dev/null @@ -1,28 +0,0 @@ -parsl.data\_provider.http.HTTPSeparateTaskStaging -================================================= - -.. currentmodule:: parsl.data_provider.http - -.. autoclass:: HTTPSeparateTaskStaging - - - .. automethod:: __init__ - - - .. rubric:: Methods - - .. autosummary:: - - ~HTTPSeparateTaskStaging.__init__ - ~HTTPSeparateTaskStaging.can_stage_in - ~HTTPSeparateTaskStaging.can_stage_out - ~HTTPSeparateTaskStaging.replace_task - ~HTTPSeparateTaskStaging.replace_task_stage_out - ~HTTPSeparateTaskStaging.stage_in - ~HTTPSeparateTaskStaging.stage_out - - - - - - \ No newline at end of file diff --git a/docs/stubs/parsl.data_provider.rsync.RSyncStaging.rst b/docs/stubs/parsl.data_provider.rsync.RSyncStaging.rst deleted file mode 100644 index 2d8f770fe7..0000000000 --- a/docs/stubs/parsl.data_provider.rsync.RSyncStaging.rst +++ /dev/null @@ -1,28 +0,0 @@ -parsl.data\_provider.rsync.RSyncStaging -======================================= - -.. currentmodule:: parsl.data_provider.rsync - -.. autoclass:: RSyncStaging - - - .. automethod:: __init__ - - - .. rubric:: Methods - - .. autosummary:: - - ~RSyncStaging.__init__ - ~RSyncStaging.can_stage_in - ~RSyncStaging.can_stage_out - ~RSyncStaging.replace_task - ~RSyncStaging.replace_task_stage_out - ~RSyncStaging.stage_in - ~RSyncStaging.stage_out - - - - - - \ No newline at end of file diff --git a/docs/stubs/parsl.data_provider.staging.Staging.rst b/docs/stubs/parsl.data_provider.staging.Staging.rst deleted file mode 100644 index 7f2a816e26..0000000000 --- a/docs/stubs/parsl.data_provider.staging.Staging.rst +++ /dev/null @@ -1,28 +0,0 @@ -parsl.data\_provider.staging.Staging -==================================== - -.. currentmodule:: parsl.data_provider.staging - -.. autoclass:: Staging - - - .. automethod:: __init__ - - - .. rubric:: Methods - - .. autosummary:: - - ~Staging.__init__ - ~Staging.can_stage_in - ~Staging.can_stage_out - ~Staging.replace_task - ~Staging.replace_task_stage_out - ~Staging.stage_in - ~Staging.stage_out - - - - - - \ No newline at end of file diff --git a/docs/stubs/parsl.dataflow.dflow.DataFlowKernel.rst b/docs/stubs/parsl.dataflow.dflow.DataFlowKernel.rst deleted file mode 100644 index 695f1a4512..0000000000 --- a/docs/stubs/parsl.dataflow.dflow.DataFlowKernel.rst +++ /dev/null @@ -1,44 +0,0 @@ -parsl.dataflow.dflow.DataFlowKernel -=================================== - -.. currentmodule:: parsl.dataflow.dflow - -.. autoclass:: DataFlowKernel - - - .. automethod:: __init__ - - - .. rubric:: Methods - - .. autosummary:: - - ~DataFlowKernel.__init__ - ~DataFlowKernel.add_executors - ~DataFlowKernel.atexit_cleanup - ~DataFlowKernel.check_staging_inhibited - ~DataFlowKernel.checkpoint - ~DataFlowKernel.cleanup - ~DataFlowKernel.handle_app_update - ~DataFlowKernel.handle_exec_update - ~DataFlowKernel.handle_join_update - ~DataFlowKernel.launch_if_ready - ~DataFlowKernel.launch_task - ~DataFlowKernel.load_checkpoints - ~DataFlowKernel.log_task_states - ~DataFlowKernel.sanitize_and_wrap - ~DataFlowKernel.submit - ~DataFlowKernel.wait_for_current_tasks - ~DataFlowKernel.wipe_task - - - - - - .. rubric:: Attributes - - .. autosummary:: - - ~DataFlowKernel.config - - \ No newline at end of file diff --git a/docs/stubs/parsl.dataflow.dflow.DataFlowKernelLoader.rst b/docs/stubs/parsl.dataflow.dflow.DataFlowKernelLoader.rst deleted file mode 100644 index a43dc06e1b..0000000000 --- a/docs/stubs/parsl.dataflow.dflow.DataFlowKernelLoader.rst +++ /dev/null @@ -1,26 +0,0 @@ -parsl.dataflow.dflow.DataFlowKernelLoader -========================================= - -.. currentmodule:: parsl.dataflow.dflow - -.. autoclass:: DataFlowKernelLoader - - - .. automethod:: __init__ - - - .. rubric:: Methods - - .. autosummary:: - - ~DataFlowKernelLoader.__init__ - ~DataFlowKernelLoader.clear - ~DataFlowKernelLoader.dfk - ~DataFlowKernelLoader.load - ~DataFlowKernelLoader.wait_for_current_tasks - - - - - - \ No newline at end of file diff --git a/docs/stubs/parsl.dataflow.error.BadCheckpoint.rst b/docs/stubs/parsl.dataflow.error.BadCheckpoint.rst deleted file mode 100644 index 5da28e3aec..0000000000 --- a/docs/stubs/parsl.dataflow.error.BadCheckpoint.rst +++ /dev/null @@ -1,6 +0,0 @@ -parsl.dataflow.error.BadCheckpoint -================================== - -.. currentmodule:: parsl.dataflow.error - -.. autoexception:: BadCheckpoint \ No newline at end of file diff --git a/docs/stubs/parsl.dataflow.error.ConfigurationError.rst b/docs/stubs/parsl.dataflow.error.ConfigurationError.rst deleted file mode 100644 index ac7d20bd9b..0000000000 --- a/docs/stubs/parsl.dataflow.error.ConfigurationError.rst +++ /dev/null @@ -1,6 +0,0 @@ -parsl.dataflow.error.ConfigurationError -======================================= - -.. currentmodule:: parsl.dataflow.error - -.. autoexception:: ConfigurationError \ No newline at end of file diff --git a/docs/stubs/parsl.dataflow.error.DataFlowException.rst b/docs/stubs/parsl.dataflow.error.DataFlowException.rst deleted file mode 100644 index 274061e705..0000000000 --- a/docs/stubs/parsl.dataflow.error.DataFlowException.rst +++ /dev/null @@ -1,6 +0,0 @@ -parsl.dataflow.error.DataFlowException -====================================== - -.. currentmodule:: parsl.dataflow.error - -.. autoexception:: DataFlowException \ No newline at end of file diff --git a/docs/stubs/parsl.dataflow.error.DependencyError.rst b/docs/stubs/parsl.dataflow.error.DependencyError.rst deleted file mode 100644 index 5519b32934..0000000000 --- a/docs/stubs/parsl.dataflow.error.DependencyError.rst +++ /dev/null @@ -1,6 +0,0 @@ -parsl.dataflow.error.DependencyError -==================================== - -.. currentmodule:: parsl.dataflow.error - -.. autoexception:: DependencyError \ No newline at end of file diff --git a/docs/stubs/parsl.dataflow.error.DuplicateTaskError.rst b/docs/stubs/parsl.dataflow.error.DuplicateTaskError.rst deleted file mode 100644 index de333392da..0000000000 --- a/docs/stubs/parsl.dataflow.error.DuplicateTaskError.rst +++ /dev/null @@ -1,6 +0,0 @@ -parsl.dataflow.error.DuplicateTaskError -======================================= - -.. currentmodule:: parsl.dataflow.error - -.. autoexception:: DuplicateTaskError \ No newline at end of file diff --git a/docs/stubs/parsl.dataflow.flow_control.FlowControl.rst b/docs/stubs/parsl.dataflow.flow_control.FlowControl.rst deleted file mode 100644 index 0db1cc4a20..0000000000 --- a/docs/stubs/parsl.dataflow.flow_control.FlowControl.rst +++ /dev/null @@ -1,26 +0,0 @@ -parsl.dataflow.flow\_control.FlowControl -======================================== - -.. currentmodule:: parsl.dataflow.flow_control - -.. autoclass:: FlowControl - - - .. automethod:: __init__ - - - .. rubric:: Methods - - .. autosummary:: - - ~FlowControl.__init__ - ~FlowControl.add_executors - ~FlowControl.close - ~FlowControl.make_callback - ~FlowControl.notify - - - - - - \ No newline at end of file diff --git a/docs/stubs/parsl.dataflow.flow_control.Timer.rst b/docs/stubs/parsl.dataflow.flow_control.Timer.rst deleted file mode 100644 index 0dbfc561ab..0000000000 --- a/docs/stubs/parsl.dataflow.flow_control.Timer.rst +++ /dev/null @@ -1,24 +0,0 @@ -parsl.dataflow.flow\_control.Timer -================================== - -.. currentmodule:: parsl.dataflow.flow_control - -.. autoclass:: Timer - - - .. automethod:: __init__ - - - .. rubric:: Methods - - .. autosummary:: - - ~Timer.__init__ - ~Timer.close - ~Timer.make_callback - - - - - - \ No newline at end of file diff --git a/docs/stubs/parsl.dataflow.futures.AppFuture.rst b/docs/stubs/parsl.dataflow.futures.AppFuture.rst deleted file mode 100644 index c2567b0939..0000000000 --- a/docs/stubs/parsl.dataflow.futures.AppFuture.rst +++ /dev/null @@ -1,42 +0,0 @@ -parsl.dataflow.futures.AppFuture -================================ - -.. currentmodule:: parsl.dataflow.futures - -.. autoclass:: AppFuture - - - .. automethod:: __init__ - - - .. rubric:: Methods - - .. autosummary:: - - ~AppFuture.__init__ - ~AppFuture.add_done_callback - ~AppFuture.cancel - ~AppFuture.cancelled - ~AppFuture.done - ~AppFuture.exception - ~AppFuture.result - ~AppFuture.running - ~AppFuture.set_exception - ~AppFuture.set_result - ~AppFuture.set_running_or_notify_cancel - ~AppFuture.task_status - - - - - - .. rubric:: Attributes - - .. autosummary:: - - ~AppFuture.outputs - ~AppFuture.stderr - ~AppFuture.stdout - ~AppFuture.tid - - \ No newline at end of file diff --git a/docs/stubs/parsl.dataflow.memoization.Memoizer.rst b/docs/stubs/parsl.dataflow.memoization.Memoizer.rst deleted file mode 100644 index 67b3bca940..0000000000 --- a/docs/stubs/parsl.dataflow.memoization.Memoizer.rst +++ /dev/null @@ -1,26 +0,0 @@ -parsl.dataflow.memoization.Memoizer -=================================== - -.. currentmodule:: parsl.dataflow.memoization - -.. autoclass:: Memoizer - - - .. automethod:: __init__ - - - .. rubric:: Methods - - .. autosummary:: - - ~Memoizer.__init__ - ~Memoizer.check_memo - ~Memoizer.hash_lookup - ~Memoizer.make_hash - ~Memoizer.update_memo - - - - - - \ No newline at end of file diff --git a/docs/stubs/parsl.dataflow.strategy.Strategy.rst b/docs/stubs/parsl.dataflow.strategy.Strategy.rst deleted file mode 100644 index 10e98f8525..0000000000 --- a/docs/stubs/parsl.dataflow.strategy.Strategy.rst +++ /dev/null @@ -1,24 +0,0 @@ -parsl.dataflow.strategy.Strategy -================================ - -.. currentmodule:: parsl.dataflow.strategy - -.. autoclass:: Strategy - - - .. automethod:: __init__ - - - .. rubric:: Methods - - .. autosummary:: - - ~Strategy.__init__ - ~Strategy.add_executors - ~Strategy.unset_logging - - - - - - \ No newline at end of file diff --git a/docs/stubs/parsl.errors.OptionalModuleMissing.rst b/docs/stubs/parsl.errors.OptionalModuleMissing.rst deleted file mode 100644 index 7f7ce38ca5..0000000000 --- a/docs/stubs/parsl.errors.OptionalModuleMissing.rst +++ /dev/null @@ -1,6 +0,0 @@ -parsl.errors.OptionalModuleMissing -================================== - -.. currentmodule:: parsl.errors - -.. autoexception:: OptionalModuleMissing \ No newline at end of file diff --git a/docs/stubs/parsl.executors.ExtremeScaleExecutor.rst b/docs/stubs/parsl.executors.ExtremeScaleExecutor.rst deleted file mode 100644 index 73cb43c38c..0000000000 --- a/docs/stubs/parsl.executors.ExtremeScaleExecutor.rst +++ /dev/null @@ -1,54 +0,0 @@ -parsl.executors.ExtremeScaleExecutor -==================================== - -.. currentmodule:: parsl.executors - -.. autoclass:: ExtremeScaleExecutor - - - .. automethod:: __init__ - - - .. rubric:: Methods - - .. autosummary:: - - ~ExtremeScaleExecutor.__init__ - ~ExtremeScaleExecutor.create_monitoring_info - ~ExtremeScaleExecutor.handle_errors - ~ExtremeScaleExecutor.hold_worker - ~ExtremeScaleExecutor.initialize_scaling - ~ExtremeScaleExecutor.monitor_resources - ~ExtremeScaleExecutor.scale_in - ~ExtremeScaleExecutor.scale_out - ~ExtremeScaleExecutor.set_bad_state_and_fail_all - ~ExtremeScaleExecutor.shutdown - ~ExtremeScaleExecutor.start - ~ExtremeScaleExecutor.status - ~ExtremeScaleExecutor.submit - ~ExtremeScaleExecutor.weakref_cb - - - - - - .. rubric:: Attributes - - .. autosummary:: - - ~ExtremeScaleExecutor.bad_state_is_set - ~ExtremeScaleExecutor.connected_managers - ~ExtremeScaleExecutor.connected_workers - ~ExtremeScaleExecutor.error_management_enabled - ~ExtremeScaleExecutor.executor_exception - ~ExtremeScaleExecutor.hub_address - ~ExtremeScaleExecutor.hub_port - ~ExtremeScaleExecutor.outstanding - ~ExtremeScaleExecutor.provider - ~ExtremeScaleExecutor.run_dir - ~ExtremeScaleExecutor.scaling_enabled - ~ExtremeScaleExecutor.status_polling_interval - ~ExtremeScaleExecutor.tasks - ~ExtremeScaleExecutor.workers_per_node - - \ No newline at end of file diff --git a/docs/stubs/parsl.executors.HighThroughputExecutor.rst b/docs/stubs/parsl.executors.HighThroughputExecutor.rst deleted file mode 100644 index 7b624913b9..0000000000 --- a/docs/stubs/parsl.executors.HighThroughputExecutor.rst +++ /dev/null @@ -1,54 +0,0 @@ -parsl.executors.HighThroughputExecutor -====================================== - -.. currentmodule:: parsl.executors - -.. autoclass:: HighThroughputExecutor - - - .. automethod:: __init__ - - - .. rubric:: Methods - - .. autosummary:: - - ~HighThroughputExecutor.__init__ - ~HighThroughputExecutor.create_monitoring_info - ~HighThroughputExecutor.handle_errors - ~HighThroughputExecutor.hold_worker - ~HighThroughputExecutor.initialize_scaling - ~HighThroughputExecutor.monitor_resources - ~HighThroughputExecutor.scale_in - ~HighThroughputExecutor.scale_out - ~HighThroughputExecutor.set_bad_state_and_fail_all - ~HighThroughputExecutor.shutdown - ~HighThroughputExecutor.start - ~HighThroughputExecutor.status - ~HighThroughputExecutor.submit - ~HighThroughputExecutor.weakref_cb - - - - - - .. rubric:: Attributes - - .. autosummary:: - - ~HighThroughputExecutor.bad_state_is_set - ~HighThroughputExecutor.connected_managers - ~HighThroughputExecutor.connected_workers - ~HighThroughputExecutor.error_management_enabled - ~HighThroughputExecutor.executor_exception - ~HighThroughputExecutor.hub_address - ~HighThroughputExecutor.hub_port - ~HighThroughputExecutor.outstanding - ~HighThroughputExecutor.provider - ~HighThroughputExecutor.run_dir - ~HighThroughputExecutor.scaling_enabled - ~HighThroughputExecutor.status_polling_interval - ~HighThroughputExecutor.tasks - ~HighThroughputExecutor.workers_per_node - - \ No newline at end of file diff --git a/docs/stubs/parsl.executors.LowLatencyExecutor.rst b/docs/stubs/parsl.executors.LowLatencyExecutor.rst deleted file mode 100644 index d4d2c31e1a..0000000000 --- a/docs/stubs/parsl.executors.LowLatencyExecutor.rst +++ /dev/null @@ -1,49 +0,0 @@ -parsl.executors.LowLatencyExecutor -================================== - -.. currentmodule:: parsl.executors - -.. autoclass:: LowLatencyExecutor - - - .. automethod:: __init__ - - - .. rubric:: Methods - - .. autosummary:: - - ~LowLatencyExecutor.__init__ - ~LowLatencyExecutor.create_monitoring_info - ~LowLatencyExecutor.handle_errors - ~LowLatencyExecutor.monitor_resources - ~LowLatencyExecutor.scale_in - ~LowLatencyExecutor.scale_out - ~LowLatencyExecutor.set_bad_state_and_fail_all - ~LowLatencyExecutor.shutdown - ~LowLatencyExecutor.start - ~LowLatencyExecutor.status - ~LowLatencyExecutor.submit - - - - - - .. rubric:: Attributes - - .. autosummary:: - - ~LowLatencyExecutor.bad_state_is_set - ~LowLatencyExecutor.error_management_enabled - ~LowLatencyExecutor.executor_exception - ~LowLatencyExecutor.hub_address - ~LowLatencyExecutor.hub_port - ~LowLatencyExecutor.outstanding - ~LowLatencyExecutor.provider - ~LowLatencyExecutor.run_dir - ~LowLatencyExecutor.scaling_enabled - ~LowLatencyExecutor.status_polling_interval - ~LowLatencyExecutor.tasks - ~LowLatencyExecutor.workers_per_node - - \ No newline at end of file diff --git a/docs/stubs/parsl.executors.ThreadPoolExecutor.rst b/docs/stubs/parsl.executors.ThreadPoolExecutor.rst deleted file mode 100644 index 47a2c14927..0000000000 --- a/docs/stubs/parsl.executors.ThreadPoolExecutor.rst +++ /dev/null @@ -1,47 +0,0 @@ -parsl.executors.ThreadPoolExecutor -================================== - -.. currentmodule:: parsl.executors - -.. autoclass:: ThreadPoolExecutor - - - .. automethod:: __init__ - - - .. rubric:: Methods - - .. autosummary:: - - ~ThreadPoolExecutor.__init__ - ~ThreadPoolExecutor.create_monitoring_info - ~ThreadPoolExecutor.handle_errors - ~ThreadPoolExecutor.monitor_resources - ~ThreadPoolExecutor.scale_in - ~ThreadPoolExecutor.scale_out - ~ThreadPoolExecutor.set_bad_state_and_fail_all - ~ThreadPoolExecutor.shutdown - ~ThreadPoolExecutor.start - ~ThreadPoolExecutor.status - ~ThreadPoolExecutor.submit - - - - - - .. rubric:: Attributes - - .. autosummary:: - - ~ThreadPoolExecutor.bad_state_is_set - ~ThreadPoolExecutor.error_management_enabled - ~ThreadPoolExecutor.executor_exception - ~ThreadPoolExecutor.hub_address - ~ThreadPoolExecutor.hub_port - ~ThreadPoolExecutor.provider - ~ThreadPoolExecutor.run_dir - ~ThreadPoolExecutor.scaling_enabled - ~ThreadPoolExecutor.status_polling_interval - ~ThreadPoolExecutor.tasks - - \ No newline at end of file diff --git a/docs/stubs/parsl.executors.WorkQueueExecutor.rst b/docs/stubs/parsl.executors.WorkQueueExecutor.rst deleted file mode 100644 index d1cf362000..0000000000 --- a/docs/stubs/parsl.executors.WorkQueueExecutor.rst +++ /dev/null @@ -1,50 +0,0 @@ -parsl.executors.WorkQueueExecutor -================================= - -.. currentmodule:: parsl.executors - -.. autoclass:: WorkQueueExecutor - - - .. automethod:: __init__ - - - .. rubric:: Methods - - .. autosummary:: - - ~WorkQueueExecutor.__init__ - ~WorkQueueExecutor.create_monitoring_info - ~WorkQueueExecutor.handle_errors - ~WorkQueueExecutor.initialize_scaling - ~WorkQueueExecutor.monitor_resources - ~WorkQueueExecutor.run_dir - ~WorkQueueExecutor.scale_in - ~WorkQueueExecutor.scale_out - ~WorkQueueExecutor.scaling_enabled - ~WorkQueueExecutor.set_bad_state_and_fail_all - ~WorkQueueExecutor.shutdown - ~WorkQueueExecutor.start - ~WorkQueueExecutor.status - ~WorkQueueExecutor.submit - - - - - - .. rubric:: Attributes - - .. autosummary:: - - ~WorkQueueExecutor.bad_state_is_set - ~WorkQueueExecutor.error_management_enabled - ~WorkQueueExecutor.executor_exception - ~WorkQueueExecutor.hub_address - ~WorkQueueExecutor.hub_port - ~WorkQueueExecutor.outstanding - ~WorkQueueExecutor.provider - ~WorkQueueExecutor.status_polling_interval - ~WorkQueueExecutor.tasks - ~WorkQueueExecutor.workers_per_node - - \ No newline at end of file diff --git a/docs/stubs/parsl.executors.base.ParslExecutor.rst b/docs/stubs/parsl.executors.base.ParslExecutor.rst deleted file mode 100644 index cab400f102..0000000000 --- a/docs/stubs/parsl.executors.base.ParslExecutor.rst +++ /dev/null @@ -1,46 +0,0 @@ -parsl.executors.base.ParslExecutor -================================== - -.. currentmodule:: parsl.executors.base - -.. autoclass:: ParslExecutor - - - .. automethod:: __init__ - - - .. rubric:: Methods - - .. autosummary:: - - ~ParslExecutor.__init__ - ~ParslExecutor.create_monitoring_info - ~ParslExecutor.handle_errors - ~ParslExecutor.monitor_resources - ~ParslExecutor.scale_in - ~ParslExecutor.scale_out - ~ParslExecutor.set_bad_state_and_fail_all - ~ParslExecutor.shutdown - ~ParslExecutor.start - ~ParslExecutor.status - ~ParslExecutor.submit - - - - - - .. rubric:: Attributes - - .. autosummary:: - - ~ParslExecutor.bad_state_is_set - ~ParslExecutor.error_management_enabled - ~ParslExecutor.executor_exception - ~ParslExecutor.hub_address - ~ParslExecutor.hub_port - ~ParslExecutor.run_dir - ~ParslExecutor.scaling_enabled - ~ParslExecutor.status_polling_interval - ~ParslExecutor.tasks - - \ No newline at end of file diff --git a/docs/stubs/parsl.executors.errors.BadMessage.rst b/docs/stubs/parsl.executors.errors.BadMessage.rst deleted file mode 100644 index 3e57744695..0000000000 --- a/docs/stubs/parsl.executors.errors.BadMessage.rst +++ /dev/null @@ -1,6 +0,0 @@ -parsl.executors.errors.BadMessage -================================= - -.. currentmodule:: parsl.executors.errors - -.. autoexception:: BadMessage \ No newline at end of file diff --git a/docs/stubs/parsl.executors.errors.DeserializationError.rst b/docs/stubs/parsl.executors.errors.DeserializationError.rst deleted file mode 100644 index 8d31cf86f9..0000000000 --- a/docs/stubs/parsl.executors.errors.DeserializationError.rst +++ /dev/null @@ -1,6 +0,0 @@ -parsl.executors.errors.DeserializationError -=========================================== - -.. currentmodule:: parsl.executors.errors - -.. autoexception:: DeserializationError \ No newline at end of file diff --git a/docs/stubs/parsl.executors.errors.ExecutorError.rst b/docs/stubs/parsl.executors.errors.ExecutorError.rst deleted file mode 100644 index a4aa2751d2..0000000000 --- a/docs/stubs/parsl.executors.errors.ExecutorError.rst +++ /dev/null @@ -1,6 +0,0 @@ -parsl.executors.errors.ExecutorError -==================================== - -.. currentmodule:: parsl.executors.errors - -.. autoexception:: ExecutorError \ No newline at end of file diff --git a/docs/stubs/parsl.executors.errors.ScalingFailed.rst b/docs/stubs/parsl.executors.errors.ScalingFailed.rst deleted file mode 100644 index 7455a0232f..0000000000 --- a/docs/stubs/parsl.executors.errors.ScalingFailed.rst +++ /dev/null @@ -1,6 +0,0 @@ -parsl.executors.errors.ScalingFailed -==================================== - -.. currentmodule:: parsl.executors.errors - -.. autoexception:: ScalingFailed \ No newline at end of file diff --git a/docs/stubs/parsl.executors.errors.SerializationError.rst b/docs/stubs/parsl.executors.errors.SerializationError.rst deleted file mode 100644 index 6987846e10..0000000000 --- a/docs/stubs/parsl.executors.errors.SerializationError.rst +++ /dev/null @@ -1,6 +0,0 @@ -parsl.executors.errors.SerializationError -========================================= - -.. currentmodule:: parsl.executors.errors - -.. autoexception:: SerializationError \ No newline at end of file diff --git a/docs/stubs/parsl.executors.high_throughput.errors.WorkerLost.rst b/docs/stubs/parsl.executors.high_throughput.errors.WorkerLost.rst deleted file mode 100644 index f3b6f563fc..0000000000 --- a/docs/stubs/parsl.executors.high_throughput.errors.WorkerLost.rst +++ /dev/null @@ -1,6 +0,0 @@ -parsl.executors.high\_throughput.errors.WorkerLost -================================================== - -.. currentmodule:: parsl.executors.high_throughput.errors - -.. autoexception:: WorkerLost \ No newline at end of file diff --git a/docs/stubs/parsl.executors.status_handling.BlockProviderExecutor.rst b/docs/stubs/parsl.executors.status_handling.BlockProviderExecutor.rst deleted file mode 100644 index 01a5f68e7d..0000000000 --- a/docs/stubs/parsl.executors.status_handling.BlockProviderExecutor.rst +++ /dev/null @@ -1,49 +0,0 @@ -parsl.executors.status\_handling.BlockProviderExecutor -====================================================== - -.. currentmodule:: parsl.executors.status_handling - -.. autoclass:: BlockProviderExecutor - - - .. automethod:: __init__ - - - .. rubric:: Methods - - .. autosummary:: - - ~BlockProviderExecutor.__init__ - ~BlockProviderExecutor.create_monitoring_info - ~BlockProviderExecutor.handle_errors - ~BlockProviderExecutor.monitor_resources - ~BlockProviderExecutor.scale_in - ~BlockProviderExecutor.scale_out - ~BlockProviderExecutor.set_bad_state_and_fail_all - ~BlockProviderExecutor.shutdown - ~BlockProviderExecutor.start - ~BlockProviderExecutor.status - ~BlockProviderExecutor.submit - - - - - - .. rubric:: Attributes - - .. autosummary:: - - ~BlockProviderExecutor.bad_state_is_set - ~BlockProviderExecutor.error_management_enabled - ~BlockProviderExecutor.executor_exception - ~BlockProviderExecutor.hub_address - ~BlockProviderExecutor.hub_port - ~BlockProviderExecutor.outstanding - ~BlockProviderExecutor.provider - ~BlockProviderExecutor.run_dir - ~BlockProviderExecutor.scaling_enabled - ~BlockProviderExecutor.status_polling_interval - ~BlockProviderExecutor.tasks - ~BlockProviderExecutor.workers_per_node - - \ No newline at end of file diff --git a/docs/stubs/parsl.executors.swift_t.TurbineExecutor.rst b/docs/stubs/parsl.executors.swift_t.TurbineExecutor.rst deleted file mode 100644 index 93f905ece4..0000000000 --- a/docs/stubs/parsl.executors.swift_t.TurbineExecutor.rst +++ /dev/null @@ -1,48 +0,0 @@ -parsl.executors.swift\_t.TurbineExecutor -======================================== - -.. currentmodule:: parsl.executors.swift_t - -.. autoclass:: TurbineExecutor - - - .. automethod:: __init__ - - - .. rubric:: Methods - - .. autosummary:: - - ~TurbineExecutor.__init__ - ~TurbineExecutor.create_monitoring_info - ~TurbineExecutor.handle_errors - ~TurbineExecutor.monitor_resources - ~TurbineExecutor.scale_in - ~TurbineExecutor.scale_out - ~TurbineExecutor.set_bad_state_and_fail_all - ~TurbineExecutor.shutdown - ~TurbineExecutor.start - ~TurbineExecutor.status - ~TurbineExecutor.submit - ~TurbineExecutor.weakref_cb - - - - - - .. rubric:: Attributes - - .. autosummary:: - - ~TurbineExecutor.bad_state_is_set - ~TurbineExecutor.error_management_enabled - ~TurbineExecutor.executor_exception - ~TurbineExecutor.hub_address - ~TurbineExecutor.hub_port - ~TurbineExecutor.provider - ~TurbineExecutor.run_dir - ~TurbineExecutor.scaling_enabled - ~TurbineExecutor.status_polling_interval - ~TurbineExecutor.tasks - - \ No newline at end of file diff --git a/docs/stubs/parsl.launchers.AprunLauncher.rst b/docs/stubs/parsl.launchers.AprunLauncher.rst deleted file mode 100644 index 8bea4bff72..0000000000 --- a/docs/stubs/parsl.launchers.AprunLauncher.rst +++ /dev/null @@ -1,22 +0,0 @@ -parsl.launchers.AprunLauncher -============================= - -.. currentmodule:: parsl.launchers - -.. autoclass:: AprunLauncher - - - .. automethod:: __init__ - - - .. rubric:: Methods - - .. autosummary:: - - ~AprunLauncher.__init__ - - - - - - \ No newline at end of file diff --git a/docs/stubs/parsl.launchers.GnuParallelLauncher.rst b/docs/stubs/parsl.launchers.GnuParallelLauncher.rst deleted file mode 100644 index df1f0a202f..0000000000 --- a/docs/stubs/parsl.launchers.GnuParallelLauncher.rst +++ /dev/null @@ -1,22 +0,0 @@ -parsl.launchers.GnuParallelLauncher -=================================== - -.. currentmodule:: parsl.launchers - -.. autoclass:: GnuParallelLauncher - - - .. automethod:: __init__ - - - .. rubric:: Methods - - .. autosummary:: - - ~GnuParallelLauncher.__init__ - - - - - - \ No newline at end of file diff --git a/docs/stubs/parsl.launchers.JsrunLauncher.rst b/docs/stubs/parsl.launchers.JsrunLauncher.rst deleted file mode 100644 index 5f3dde0c8e..0000000000 --- a/docs/stubs/parsl.launchers.JsrunLauncher.rst +++ /dev/null @@ -1,22 +0,0 @@ -parsl.launchers.JsrunLauncher -============================= - -.. currentmodule:: parsl.launchers - -.. autoclass:: JsrunLauncher - - - .. automethod:: __init__ - - - .. rubric:: Methods - - .. autosummary:: - - ~JsrunLauncher.__init__ - - - - - - \ No newline at end of file diff --git a/docs/stubs/parsl.launchers.MpiExecLauncher.rst b/docs/stubs/parsl.launchers.MpiExecLauncher.rst deleted file mode 100644 index cd02f3f2bb..0000000000 --- a/docs/stubs/parsl.launchers.MpiExecLauncher.rst +++ /dev/null @@ -1,22 +0,0 @@ -parsl.launchers.MpiExecLauncher -=============================== - -.. currentmodule:: parsl.launchers - -.. autoclass:: MpiExecLauncher - - - .. automethod:: __init__ - - - .. rubric:: Methods - - .. autosummary:: - - ~MpiExecLauncher.__init__ - - - - - - \ No newline at end of file diff --git a/docs/stubs/parsl.launchers.SimpleLauncher.rst b/docs/stubs/parsl.launchers.SimpleLauncher.rst deleted file mode 100644 index e37b16918f..0000000000 --- a/docs/stubs/parsl.launchers.SimpleLauncher.rst +++ /dev/null @@ -1,22 +0,0 @@ -parsl.launchers.SimpleLauncher -============================== - -.. currentmodule:: parsl.launchers - -.. autoclass:: SimpleLauncher - - - .. automethod:: __init__ - - - .. rubric:: Methods - - .. autosummary:: - - ~SimpleLauncher.__init__ - - - - - - \ No newline at end of file diff --git a/docs/stubs/parsl.launchers.SingleNodeLauncher.rst b/docs/stubs/parsl.launchers.SingleNodeLauncher.rst deleted file mode 100644 index 83e922acf5..0000000000 --- a/docs/stubs/parsl.launchers.SingleNodeLauncher.rst +++ /dev/null @@ -1,22 +0,0 @@ -parsl.launchers.SingleNodeLauncher -================================== - -.. currentmodule:: parsl.launchers - -.. autoclass:: SingleNodeLauncher - - - .. automethod:: __init__ - - - .. rubric:: Methods - - .. autosummary:: - - ~SingleNodeLauncher.__init__ - - - - - - \ No newline at end of file diff --git a/docs/stubs/parsl.launchers.SrunLauncher.rst b/docs/stubs/parsl.launchers.SrunLauncher.rst deleted file mode 100644 index abbea43119..0000000000 --- a/docs/stubs/parsl.launchers.SrunLauncher.rst +++ /dev/null @@ -1,22 +0,0 @@ -parsl.launchers.SrunLauncher -============================ - -.. currentmodule:: parsl.launchers - -.. autoclass:: SrunLauncher - - - .. automethod:: __init__ - - - .. rubric:: Methods - - .. autosummary:: - - ~SrunLauncher.__init__ - - - - - - \ No newline at end of file diff --git a/docs/stubs/parsl.launchers.SrunMPILauncher.rst b/docs/stubs/parsl.launchers.SrunMPILauncher.rst deleted file mode 100644 index fe6b64e266..0000000000 --- a/docs/stubs/parsl.launchers.SrunMPILauncher.rst +++ /dev/null @@ -1,22 +0,0 @@ -parsl.launchers.SrunMPILauncher -=============================== - -.. currentmodule:: parsl.launchers - -.. autoclass:: SrunMPILauncher - - - .. automethod:: __init__ - - - .. rubric:: Methods - - .. autosummary:: - - ~SrunMPILauncher.__init__ - - - - - - \ No newline at end of file diff --git a/docs/stubs/parsl.launchers.WrappedLauncher.rst b/docs/stubs/parsl.launchers.WrappedLauncher.rst deleted file mode 100644 index bf933bbf6d..0000000000 --- a/docs/stubs/parsl.launchers.WrappedLauncher.rst +++ /dev/null @@ -1,22 +0,0 @@ -parsl.launchers.WrappedLauncher -=============================== - -.. currentmodule:: parsl.launchers - -.. autoclass:: WrappedLauncher - - - .. automethod:: __init__ - - - .. rubric:: Methods - - .. autosummary:: - - ~WrappedLauncher.__init__ - - - - - - \ No newline at end of file diff --git a/docs/stubs/parsl.launchers.error.BadLauncher.rst b/docs/stubs/parsl.launchers.error.BadLauncher.rst deleted file mode 100644 index 33a96a0009..0000000000 --- a/docs/stubs/parsl.launchers.error.BadLauncher.rst +++ /dev/null @@ -1,6 +0,0 @@ -parsl.launchers.error.BadLauncher -================================= - -.. currentmodule:: parsl.launchers.error - -.. autoexception:: BadLauncher \ No newline at end of file diff --git a/docs/stubs/parsl.monitoring.MonitoringHub.rst b/docs/stubs/parsl.monitoring.MonitoringHub.rst deleted file mode 100644 index 6e70cd7af8..0000000000 --- a/docs/stubs/parsl.monitoring.MonitoringHub.rst +++ /dev/null @@ -1,26 +0,0 @@ -parsl.monitoring.MonitoringHub -============================== - -.. currentmodule:: parsl.monitoring - -.. autoclass:: MonitoringHub - - - .. automethod:: __init__ - - - .. rubric:: Methods - - .. autosummary:: - - ~MonitoringHub.__init__ - ~MonitoringHub.close - ~MonitoringHub.monitor_wrapper - ~MonitoringHub.send - ~MonitoringHub.start - - - - - - \ No newline at end of file diff --git a/docs/stubs/parsl.providers.AWSProvider.rst b/docs/stubs/parsl.providers.AWSProvider.rst deleted file mode 100644 index 8a722cf3b2..0000000000 --- a/docs/stubs/parsl.providers.AWSProvider.rst +++ /dev/null @@ -1,50 +0,0 @@ -parsl.providers.AWSProvider -=========================== - -.. currentmodule:: parsl.providers - -.. autoclass:: AWSProvider - - - .. automethod:: __init__ - - - .. rubric:: Methods - - .. autosummary:: - - ~AWSProvider.__init__ - ~AWSProvider.cancel - ~AWSProvider.config_route_table - ~AWSProvider.create_name_tag_spec - ~AWSProvider.create_session - ~AWSProvider.create_vpc - ~AWSProvider.generate_aws_id - ~AWSProvider.get_instance_state - ~AWSProvider.goodbye - ~AWSProvider.initialize_boto_client - ~AWSProvider.read_state_file - ~AWSProvider.security_group - ~AWSProvider.show_summary - ~AWSProvider.shut_down_instance - ~AWSProvider.spin_up_instance - ~AWSProvider.status - ~AWSProvider.submit - ~AWSProvider.teardown - ~AWSProvider.write_state_file - ~AWSProvider.xstr - - - - - - .. rubric:: Attributes - - .. autosummary:: - - ~AWSProvider.cores_per_node - ~AWSProvider.label - ~AWSProvider.mem_per_node - ~AWSProvider.status_polling_interval - - \ No newline at end of file diff --git a/docs/stubs/parsl.providers.AdHocProvider.rst b/docs/stubs/parsl.providers.AdHocProvider.rst deleted file mode 100644 index dfee74d8da..0000000000 --- a/docs/stubs/parsl.providers.AdHocProvider.rst +++ /dev/null @@ -1,35 +0,0 @@ -parsl.providers.AdHocProvider -============================= - -.. currentmodule:: parsl.providers - -.. autoclass:: AdHocProvider - - - .. automethod:: __init__ - - - .. rubric:: Methods - - .. autosummary:: - - ~AdHocProvider.__init__ - ~AdHocProvider.cancel - ~AdHocProvider.status - ~AdHocProvider.submit - - - - - - .. rubric:: Attributes - - .. autosummary:: - - ~AdHocProvider.cores_per_node - ~AdHocProvider.label - ~AdHocProvider.mem_per_node - ~AdHocProvider.scaling_enabled - ~AdHocProvider.status_polling_interval - - \ No newline at end of file diff --git a/docs/stubs/parsl.providers.CobaltProvider.rst b/docs/stubs/parsl.providers.CobaltProvider.rst deleted file mode 100644 index 67cf59fd3c..0000000000 --- a/docs/stubs/parsl.providers.CobaltProvider.rst +++ /dev/null @@ -1,35 +0,0 @@ -parsl.providers.CobaltProvider -============================== - -.. currentmodule:: parsl.providers - -.. autoclass:: CobaltProvider - - - .. automethod:: __init__ - - - .. rubric:: Methods - - .. autosummary:: - - ~CobaltProvider.__init__ - ~CobaltProvider.cancel - ~CobaltProvider.execute_wait - ~CobaltProvider.status - ~CobaltProvider.submit - - - - - - .. rubric:: Attributes - - .. autosummary:: - - ~CobaltProvider.cores_per_node - ~CobaltProvider.label - ~CobaltProvider.mem_per_node - ~CobaltProvider.status_polling_interval - - \ No newline at end of file diff --git a/docs/stubs/parsl.providers.CondorProvider.rst b/docs/stubs/parsl.providers.CondorProvider.rst deleted file mode 100644 index dc18048b05..0000000000 --- a/docs/stubs/parsl.providers.CondorProvider.rst +++ /dev/null @@ -1,35 +0,0 @@ -parsl.providers.CondorProvider -============================== - -.. currentmodule:: parsl.providers - -.. autoclass:: CondorProvider - - - .. automethod:: __init__ - - - .. rubric:: Methods - - .. autosummary:: - - ~CondorProvider.__init__ - ~CondorProvider.cancel - ~CondorProvider.execute_wait - ~CondorProvider.status - ~CondorProvider.submit - - - - - - .. rubric:: Attributes - - .. autosummary:: - - ~CondorProvider.cores_per_node - ~CondorProvider.label - ~CondorProvider.mem_per_node - ~CondorProvider.status_polling_interval - - \ No newline at end of file diff --git a/docs/stubs/parsl.providers.GoogleCloudProvider.rst b/docs/stubs/parsl.providers.GoogleCloudProvider.rst deleted file mode 100644 index 8cbdd97277..0000000000 --- a/docs/stubs/parsl.providers.GoogleCloudProvider.rst +++ /dev/null @@ -1,35 +0,0 @@ -parsl.providers.GoogleCloudProvider -=================================== - -.. currentmodule:: parsl.providers - -.. autoclass:: GoogleCloudProvider - - - .. automethod:: __init__ - - - .. rubric:: Methods - - .. autosummary:: - - ~GoogleCloudProvider.__init__ - ~GoogleCloudProvider.bye - ~GoogleCloudProvider.cancel - ~GoogleCloudProvider.create_instance - ~GoogleCloudProvider.delete_instance - ~GoogleCloudProvider.get_zone - ~GoogleCloudProvider.status - ~GoogleCloudProvider.submit - - - - - - .. rubric:: Attributes - - .. autosummary:: - - ~GoogleCloudProvider.status_polling_interval - - \ No newline at end of file diff --git a/docs/stubs/parsl.providers.GridEngineProvider.rst b/docs/stubs/parsl.providers.GridEngineProvider.rst deleted file mode 100644 index e58801a1f0..0000000000 --- a/docs/stubs/parsl.providers.GridEngineProvider.rst +++ /dev/null @@ -1,36 +0,0 @@ -parsl.providers.GridEngineProvider -================================== - -.. currentmodule:: parsl.providers - -.. autoclass:: GridEngineProvider - - - .. automethod:: __init__ - - - .. rubric:: Methods - - .. autosummary:: - - ~GridEngineProvider.__init__ - ~GridEngineProvider.cancel - ~GridEngineProvider.execute_wait - ~GridEngineProvider.get_configs - ~GridEngineProvider.status - ~GridEngineProvider.submit - - - - - - .. rubric:: Attributes - - .. autosummary:: - - ~GridEngineProvider.cores_per_node - ~GridEngineProvider.label - ~GridEngineProvider.mem_per_node - ~GridEngineProvider.status_polling_interval - - \ No newline at end of file diff --git a/docs/stubs/parsl.providers.KubernetesProvider.rst b/docs/stubs/parsl.providers.KubernetesProvider.rst deleted file mode 100644 index 5a9496f22a..0000000000 --- a/docs/stubs/parsl.providers.KubernetesProvider.rst +++ /dev/null @@ -1,34 +0,0 @@ -parsl.providers.KubernetesProvider -================================== - -.. currentmodule:: parsl.providers - -.. autoclass:: KubernetesProvider - - - .. automethod:: __init__ - - - .. rubric:: Methods - - .. autosummary:: - - ~KubernetesProvider.__init__ - ~KubernetesProvider.cancel - ~KubernetesProvider.status - ~KubernetesProvider.submit - - - - - - .. rubric:: Attributes - - .. autosummary:: - - ~KubernetesProvider.cores_per_node - ~KubernetesProvider.label - ~KubernetesProvider.mem_per_node - ~KubernetesProvider.status_polling_interval - - \ No newline at end of file diff --git a/docs/stubs/parsl.providers.LSFProvider.rst b/docs/stubs/parsl.providers.LSFProvider.rst deleted file mode 100644 index 632cbdb24d..0000000000 --- a/docs/stubs/parsl.providers.LSFProvider.rst +++ /dev/null @@ -1,35 +0,0 @@ -parsl.providers.LSFProvider -=========================== - -.. currentmodule:: parsl.providers - -.. autoclass:: LSFProvider - - - .. automethod:: __init__ - - - .. rubric:: Methods - - .. autosummary:: - - ~LSFProvider.__init__ - ~LSFProvider.cancel - ~LSFProvider.execute_wait - ~LSFProvider.status - ~LSFProvider.submit - - - - - - .. rubric:: Attributes - - .. autosummary:: - - ~LSFProvider.cores_per_node - ~LSFProvider.label - ~LSFProvider.mem_per_node - ~LSFProvider.status_polling_interval - - \ No newline at end of file diff --git a/docs/stubs/parsl.providers.LocalProvider.rst b/docs/stubs/parsl.providers.LocalProvider.rst deleted file mode 100644 index c5004b138a..0000000000 --- a/docs/stubs/parsl.providers.LocalProvider.rst +++ /dev/null @@ -1,34 +0,0 @@ -parsl.providers.LocalProvider -============================= - -.. currentmodule:: parsl.providers - -.. autoclass:: LocalProvider - - - .. automethod:: __init__ - - - .. rubric:: Methods - - .. autosummary:: - - ~LocalProvider.__init__ - ~LocalProvider.cancel - ~LocalProvider.status - ~LocalProvider.submit - - - - - - .. rubric:: Attributes - - .. autosummary:: - - ~LocalProvider.cores_per_node - ~LocalProvider.label - ~LocalProvider.mem_per_node - ~LocalProvider.status_polling_interval - - \ No newline at end of file diff --git a/docs/stubs/parsl.providers.PBSProProvider.rst b/docs/stubs/parsl.providers.PBSProProvider.rst deleted file mode 100644 index 30915155dc..0000000000 --- a/docs/stubs/parsl.providers.PBSProProvider.rst +++ /dev/null @@ -1,35 +0,0 @@ -parsl.providers.PBSProProvider -============================== - -.. currentmodule:: parsl.providers - -.. autoclass:: PBSProProvider - - - .. automethod:: __init__ - - - .. rubric:: Methods - - .. autosummary:: - - ~PBSProProvider.__init__ - ~PBSProProvider.cancel - ~PBSProProvider.execute_wait - ~PBSProProvider.status - ~PBSProProvider.submit - - - - - - .. rubric:: Attributes - - .. autosummary:: - - ~PBSProProvider.cores_per_node - ~PBSProProvider.label - ~PBSProProvider.mem_per_node - ~PBSProProvider.status_polling_interval - - \ No newline at end of file diff --git a/docs/stubs/parsl.providers.SlurmProvider.rst b/docs/stubs/parsl.providers.SlurmProvider.rst deleted file mode 100644 index 98db36df8b..0000000000 --- a/docs/stubs/parsl.providers.SlurmProvider.rst +++ /dev/null @@ -1,35 +0,0 @@ -parsl.providers.SlurmProvider -============================= - -.. currentmodule:: parsl.providers - -.. autoclass:: SlurmProvider - - - .. automethod:: __init__ - - - .. rubric:: Methods - - .. autosummary:: - - ~SlurmProvider.__init__ - ~SlurmProvider.cancel - ~SlurmProvider.execute_wait - ~SlurmProvider.status - ~SlurmProvider.submit - - - - - - .. rubric:: Attributes - - .. autosummary:: - - ~SlurmProvider.cores_per_node - ~SlurmProvider.label - ~SlurmProvider.mem_per_node - ~SlurmProvider.status_polling_interval - - \ No newline at end of file diff --git a/docs/stubs/parsl.providers.TorqueProvider.rst b/docs/stubs/parsl.providers.TorqueProvider.rst deleted file mode 100644 index e1e054fbe5..0000000000 --- a/docs/stubs/parsl.providers.TorqueProvider.rst +++ /dev/null @@ -1,35 +0,0 @@ -parsl.providers.TorqueProvider -============================== - -.. currentmodule:: parsl.providers - -.. autoclass:: TorqueProvider - - - .. automethod:: __init__ - - - .. rubric:: Methods - - .. autosummary:: - - ~TorqueProvider.__init__ - ~TorqueProvider.cancel - ~TorqueProvider.execute_wait - ~TorqueProvider.status - ~TorqueProvider.submit - - - - - - .. rubric:: Attributes - - .. autosummary:: - - ~TorqueProvider.cores_per_node - ~TorqueProvider.label - ~TorqueProvider.mem_per_node - ~TorqueProvider.status_polling_interval - - \ No newline at end of file diff --git a/docs/stubs/parsl.providers.cluster_provider.ClusterProvider.rst b/docs/stubs/parsl.providers.cluster_provider.ClusterProvider.rst deleted file mode 100644 index 3c22cc2760..0000000000 --- a/docs/stubs/parsl.providers.cluster_provider.ClusterProvider.rst +++ /dev/null @@ -1,35 +0,0 @@ -parsl.providers.cluster\_provider.ClusterProvider -================================================= - -.. currentmodule:: parsl.providers.cluster_provider - -.. autoclass:: ClusterProvider - - - .. automethod:: __init__ - - - .. rubric:: Methods - - .. autosummary:: - - ~ClusterProvider.__init__ - ~ClusterProvider.cancel - ~ClusterProvider.execute_wait - ~ClusterProvider.status - ~ClusterProvider.submit - - - - - - .. rubric:: Attributes - - .. autosummary:: - - ~ClusterProvider.cores_per_node - ~ClusterProvider.label - ~ClusterProvider.mem_per_node - ~ClusterProvider.status_polling_interval - - \ No newline at end of file diff --git a/docs/stubs/parsl.providers.error.ChannelRequired.rst b/docs/stubs/parsl.providers.error.ChannelRequired.rst deleted file mode 100644 index 5d44a27ee6..0000000000 --- a/docs/stubs/parsl.providers.error.ChannelRequired.rst +++ /dev/null @@ -1,6 +0,0 @@ -parsl.providers.error.ChannelRequired -===================================== - -.. currentmodule:: parsl.providers.error - -.. autoexception:: ChannelRequired \ No newline at end of file diff --git a/docs/stubs/parsl.providers.error.ExecutionProviderException.rst b/docs/stubs/parsl.providers.error.ExecutionProviderException.rst deleted file mode 100644 index 4c275a0960..0000000000 --- a/docs/stubs/parsl.providers.error.ExecutionProviderException.rst +++ /dev/null @@ -1,6 +0,0 @@ -parsl.providers.error.ExecutionProviderException -================================================ - -.. currentmodule:: parsl.providers.error - -.. autoexception:: ExecutionProviderException \ No newline at end of file diff --git a/docs/stubs/parsl.providers.error.ScaleOutFailed.rst b/docs/stubs/parsl.providers.error.ScaleOutFailed.rst deleted file mode 100644 index 2e7a81f7ee..0000000000 --- a/docs/stubs/parsl.providers.error.ScaleOutFailed.rst +++ /dev/null @@ -1,6 +0,0 @@ -parsl.providers.error.ScaleOutFailed -==================================== - -.. currentmodule:: parsl.providers.error - -.. autoexception:: ScaleOutFailed \ No newline at end of file diff --git a/docs/stubs/parsl.providers.error.SchedulerMissingArgs.rst b/docs/stubs/parsl.providers.error.SchedulerMissingArgs.rst deleted file mode 100644 index 33afc6366a..0000000000 --- a/docs/stubs/parsl.providers.error.SchedulerMissingArgs.rst +++ /dev/null @@ -1,6 +0,0 @@ -parsl.providers.error.SchedulerMissingArgs -========================================== - -.. currentmodule:: parsl.providers.error - -.. autoexception:: SchedulerMissingArgs \ No newline at end of file diff --git a/docs/stubs/parsl.providers.error.ScriptPathError.rst b/docs/stubs/parsl.providers.error.ScriptPathError.rst deleted file mode 100644 index e787041121..0000000000 --- a/docs/stubs/parsl.providers.error.ScriptPathError.rst +++ /dev/null @@ -1,6 +0,0 @@ -parsl.providers.error.ScriptPathError -===================================== - -.. currentmodule:: parsl.providers.error - -.. autoexception:: ScriptPathError \ No newline at end of file diff --git a/docs/stubs/parsl.providers.provider_base.ExecutionProvider.rst b/docs/stubs/parsl.providers.provider_base.ExecutionProvider.rst deleted file mode 100644 index 7e74ad0dd0..0000000000 --- a/docs/stubs/parsl.providers.provider_base.ExecutionProvider.rst +++ /dev/null @@ -1,34 +0,0 @@ -parsl.providers.provider\_base.ExecutionProvider -================================================ - -.. currentmodule:: parsl.providers.provider_base - -.. autoclass:: ExecutionProvider - - - .. automethod:: __init__ - - - .. rubric:: Methods - - .. autosummary:: - - ~ExecutionProvider.__init__ - ~ExecutionProvider.cancel - ~ExecutionProvider.status - ~ExecutionProvider.submit - - - - - - .. rubric:: Attributes - - .. autosummary:: - - ~ExecutionProvider.cores_per_node - ~ExecutionProvider.label - ~ExecutionProvider.mem_per_node - ~ExecutionProvider.status_polling_interval - - \ No newline at end of file diff --git a/docs/stubs/parsl.set_file_logger.rst b/docs/stubs/parsl.set_file_logger.rst deleted file mode 100644 index ba00425426..0000000000 --- a/docs/stubs/parsl.set_file_logger.rst +++ /dev/null @@ -1,6 +0,0 @@ -parsl.set\_file\_logger -======================= - -.. currentmodule:: parsl - -.. autofunction:: set_file_logger \ No newline at end of file diff --git a/docs/stubs/parsl.set_stream_logger.rst b/docs/stubs/parsl.set_stream_logger.rst deleted file mode 100644 index 3d665e143a..0000000000 --- a/docs/stubs/parsl.set_stream_logger.rst +++ /dev/null @@ -1,6 +0,0 @@ -parsl.set\_stream\_logger -========================= - -.. currentmodule:: parsl - -.. autofunction:: set_stream_logger \ No newline at end of file diff --git a/docs/stubs/parsl.utils.get_all_checkpoints.rst b/docs/stubs/parsl.utils.get_all_checkpoints.rst deleted file mode 100644 index c2a1d61dad..0000000000 --- a/docs/stubs/parsl.utils.get_all_checkpoints.rst +++ /dev/null @@ -1,6 +0,0 @@ -parsl.utils.get\_all\_checkpoints -================================= - -.. currentmodule:: parsl.utils - -.. autofunction:: get_all_checkpoints \ No newline at end of file diff --git a/docs/stubs/parsl.utils.get_last_checkpoint.rst b/docs/stubs/parsl.utils.get_last_checkpoint.rst deleted file mode 100644 index 3d525a68bb..0000000000 --- a/docs/stubs/parsl.utils.get_last_checkpoint.rst +++ /dev/null @@ -1,6 +0,0 @@ -parsl.utils.get\_last\_checkpoint -================================= - -.. currentmodule:: parsl.utils - -.. autofunction:: get_last_checkpoint \ No newline at end of file From 3688fc3957995178ceb9452eb25090c8a9c62ac7 Mon Sep 17 00:00:00 2001 From: Ben Clifford Date: Wed, 30 Jun 2021 02:09:43 -0700 Subject: [PATCH 228/408] Remove unnecessary mac_safe_process module --- parsl/executors/high_throughput/mac_safe_process.py | 10 ---------- parsl/executors/high_throughput/process_worker_pool.py | 2 -- 2 files changed, 12 deletions(-) delete mode 100644 parsl/executors/high_throughput/mac_safe_process.py diff --git a/parsl/executors/high_throughput/mac_safe_process.py b/parsl/executors/high_throughput/mac_safe_process.py deleted file mode 100644 index 9563b5255e..0000000000 --- a/parsl/executors/high_throughput/mac_safe_process.py +++ /dev/null @@ -1,10 +0,0 @@ -import multiprocessing -from typing import Any - -ForkProcess: Any = multiprocessing.get_context('fork').Process - - -class MacSafeProcess(ForkProcess): - - def __init__(self, *args, **kwargs): - super().__init__(*args, **kwargs) diff --git a/parsl/executors/high_throughput/process_worker_pool.py b/parsl/executors/high_throughput/process_worker_pool.py index b352694f29..7f760b278a 100755 --- a/parsl/executors/high_throughput/process_worker_pool.py +++ b/parsl/executors/high_throughput/process_worker_pool.py @@ -26,10 +26,8 @@ if platform.system() != 'Darwin': from multiprocessing import Queue as mpQueue - from multiprocessing import Process as mpProcess else: from parsl.executors.high_throughput.mac_safe_queue import MacSafeQueue as mpQueue - from parsl.executors.high_throughput.mac_safe_process import MacSafeProcess as mpProcess from parsl.serialize import unpack_apply_message, serialize From 8bde6b094a4fa3ab632bf2fadbf0255be5cf413b Mon Sep 17 00:00:00 2001 From: Ben Clifford Date: Wed, 30 Jun 2021 02:19:19 -0700 Subject: [PATCH 229/408] fix flake8 --- parsl/dataflow/usage_tracking/usage.py | 1 - parsl/executors/high_throughput/executor.py | 30 ++++++++++----------- parsl/multiprocessing.py | 1 - 3 files changed, 15 insertions(+), 17 deletions(-) diff --git a/parsl/dataflow/usage_tracking/usage.py b/parsl/dataflow/usage_tracking/usage.py index 5d8145319a..9777fb55e5 100644 --- a/parsl/dataflow/usage_tracking/usage.py +++ b/parsl/dataflow/usage_tracking/usage.py @@ -8,7 +8,6 @@ import socket import sys import platform -import multiprocessing as mp from parsl.multiprocessing import ForkProcess from parsl.version import VERSION as PARSL_VERSION diff --git a/parsl/executors/high_throughput/executor.py b/parsl/executors/high_throughput/executor.py index 2354afa26e..33650792d3 100644 --- a/parsl/executors/high_throughput/executor.py +++ b/parsl/executors/high_throughput/executor.py @@ -435,21 +435,21 @@ def _start_local_queue_process(self): """ comm_q = Queue(maxsize=10) self.queue_proc = ForkProcess(target=interchange.starter, - args=(comm_q,), - kwargs={"client_ports": (self.outgoing_q.port, - self.incoming_q.port, - self.command_client.port), - "worker_ports": self.worker_ports, - "worker_port_range": self.worker_port_range, - "hub_address": self.hub_address, - "hub_port": self.hub_port, - "logdir": "{}/{}".format(self.run_dir, self.label), - "heartbeat_threshold": self.heartbeat_threshold, - "poll_period": self.poll_period, - "logging_level": logging.DEBUG if self.worker_debug else logging.INFO - }, - daemon=True, - name="HTEX-Interchange" + args=(comm_q,), + kwargs={"client_ports": (self.outgoing_q.port, + self.incoming_q.port, + self.command_client.port), + "worker_ports": self.worker_ports, + "worker_port_range": self.worker_port_range, + "hub_address": self.hub_address, + "hub_port": self.hub_port, + "logdir": "{}/{}".format(self.run_dir, self.label), + "heartbeat_threshold": self.heartbeat_threshold, + "poll_period": self.poll_period, + "logging_level": logging.DEBUG if self.worker_debug else logging.INFO + }, + daemon=True, + name="HTEX-Interchange" ) self.queue_proc.start() try: diff --git a/parsl/multiprocessing.py b/parsl/multiprocessing.py index fca3140c81..bb535c93cc 100644 --- a/parsl/multiprocessing.py +++ b/parsl/multiprocessing.py @@ -6,4 +6,3 @@ from typing import Type ForkProcess: Type = multiprocessing.get_context('fork').Process - From bbd53079f0b885d98819258b66e2143b957932e8 Mon Sep 17 00:00:00 2001 From: Ben Clifford Date: Wed, 30 Jun 2021 06:36:57 -0700 Subject: [PATCH 230/408] Moved macsafequeue definition and choice into parsl.multiprocessing module --- .../high_throughput/mac_safe_queue.py | 40 --------------- .../high_throughput/process_worker_pool.py | 5 +- parsl/monitoring/monitoring.py | 12 +++-- parsl/multiprocessing.py | 49 +++++++++++++++++++ parsl/tests/test_regression/test_854.py | 2 +- 5 files changed, 58 insertions(+), 50 deletions(-) delete mode 100644 parsl/executors/high_throughput/mac_safe_queue.py diff --git a/parsl/executors/high_throughput/mac_safe_queue.py b/parsl/executors/high_throughput/mac_safe_queue.py deleted file mode 100644 index 6abe80f165..0000000000 --- a/parsl/executors/high_throughput/mac_safe_queue.py +++ /dev/null @@ -1,40 +0,0 @@ -import multiprocessing -import multiprocessing.queues -import logging - -logger = logging.getLogger(__name__) - - -class MacSafeQueue(multiprocessing.queues.Queue): - """ Multiprocessing queues do not have qsize attributes on MacOS. - This is slower but more portable version of the multiprocessing Queue - that adds a explicit counter - - Reference : https://github.com/keras-team/autokeras/commit/4ddd568b06b4045ace777bc0fb7bc18573b85a75 - """ - - def __init__(self, *args, **kwargs): - if 'ctx' not in kwargs: - kwargs['ctx'] = multiprocessing.get_context() - super().__init__(*args, **kwargs) - self._counter = multiprocessing.Value('i', 0) - - def put(self, *args, **kwargs): - # logger.critical("Putting item {}".format(args)) - x = super().put(*args, **kwargs) - with self._counter.get_lock(): - self._counter.value += 1 - return x - - def get(self, *args, **kwargs): - x = super().get(*args, **kwargs) - with self._counter.get_lock(): - self._counter.value -= 1 - # logger.critical("Getting item {}".format(x)) - return x - - def qsize(self): - return self._counter.value - - def empty(self): - return not self._counter.value diff --git a/parsl/executors/high_throughput/process_worker_pool.py b/parsl/executors/high_throughput/process_worker_pool.py index 7f760b278a..8feb284b7b 100755 --- a/parsl/executors/high_throughput/process_worker_pool.py +++ b/parsl/executors/high_throughput/process_worker_pool.py @@ -24,10 +24,7 @@ from parsl.executors.high_throughput.probe import probe_addresses from parsl.multiprocessing import ForkProcess as mpProcess -if platform.system() != 'Darwin': - from multiprocessing import Queue as mpQueue -else: - from parsl.executors.high_throughput.mac_safe_queue import MacSafeQueue as mpQueue +from parsl.multiprocessing import SizedQueue as mpQueue from parsl.serialize import unpack_apply_message, serialize diff --git a/parsl/monitoring/monitoring.py b/parsl/monitoring/monitoring.py index ea77442a21..5c0d2ef91c 100644 --- a/parsl/monitoring/monitoring.py +++ b/parsl/monitoring/monitoring.py @@ -8,6 +8,7 @@ import zmq import queue +from parsl.multiprocessing import ForkProcess from multiprocessing import Process, Queue from parsl.utils import RepresentationMixin from parsl.process_loggers import wrap_with_logs @@ -225,7 +226,7 @@ def start(self, run_id: str) -> int: self.node_msgs = Queue() # type: Queue[Tuple[Any, int]] self.block_msgs = Queue() # type: Queue[Tuple[Any, Any]] - self.router_proc = Process(target=router_starter, + self.router_proc = ForkProcess(target=router_starter, args=(comm_q, self.exception_q, self.priority_msgs, self.node_msgs, self.block_msgs, self.resource_msgs), kwargs={"hub_address": self.hub_address, "hub_port": self.hub_port, @@ -241,7 +242,7 @@ def start(self, run_id: str) -> int: ) self.router_proc.start() - self.dbm_proc = Process(target=dbm_starter, + self.dbm_proc = ForkProcess(target=dbm_starter, args=(self.exception_q, self.priority_msgs, self.node_msgs, self.block_msgs, self.resource_msgs,), kwargs={"logdir": self.logdir, "logging_level": logging.DEBUG if self.monitoring_debug else logging.INFO, @@ -323,10 +324,10 @@ def wrapped(*args: List[Any], **kwargs: Dict[str, Any]) -> Any: monitoring_hub_url, run_id) + p: Optional[Process] if monitor_resources: # create the monitor process and start - p: Optional[Process] - p = Process(target=monitor, + pp = ForkProcess(target=monitor, args=(os.getpid(), try_id, task_id, @@ -335,7 +336,8 @@ def wrapped(*args: List[Any], **kwargs: Dict[str, Any]) -> Any: logging_level, sleep_dur), name="Monitor-Wrapper-{}".format(task_id)) - p.start() + pp.start() + p = pp # awkwardness because ForkProcess is not directly a constructor and type-checking is expecting it to return type of p (which is Optional) otherwise else: p = None diff --git a/parsl/multiprocessing.py b/parsl/multiprocessing.py index bb535c93cc..cd00d0bbca 100644 --- a/parsl/multiprocessing.py +++ b/parsl/multiprocessing.py @@ -1,8 +1,57 @@ """Helpers for cross-plaform multiprocessing support. """ +import logging import multiprocessing +import multiprocessing.queues +import platform from typing import Type +logger = logging.getLogger(__name__) + +# maybe ForkProcess should be: Callable[..., Process] so as to make +# it clear that it returns a Process always to the type checker? ForkProcess: Type = multiprocessing.get_context('fork').Process + + +class MacSafeQueue(multiprocessing.queues.Queue): + """ Multiprocessing queues do not have qsize attributes on MacOS. + This is slower but more portable version of the multiprocessing Queue + that adds a explicit counter + + Reference : https://github.com/keras-team/autokeras/commit/4ddd568b06b4045ace777bc0fb7bc18573b85a75 + """ + + def __init__(self, *args, **kwargs): + if 'ctx' not in kwargs: + kwargs['ctx'] = multiprocessing.get_context() + super().__init__(*args, **kwargs) + self._counter = multiprocessing.Value('i', 0) + + def put(self, *args, **kwargs): + # logger.critical("Putting item {}".format(args)) + x = super().put(*args, **kwargs) + with self._counter.get_lock(): + self._counter.value += 1 + return x + + def get(self, *args, **kwargs): + x = super().get(*args, **kwargs) + with self._counter.get_lock(): + self._counter.value -= 1 + # logger.critical("Getting item {}".format(x)) + return x + + def qsize(self): + return self._counter.value + + def empty(self): + return not self._counter.value + + +if platform.system() != 'Darwin': + from multiprocessing import Queue as SizedQueue +else: + from parsl.multiprocessing import MacSafeQueue as SizedQueue + diff --git a/parsl/tests/test_regression/test_854.py b/parsl/tests/test_regression/test_854.py index 5b5654a273..15849cb04d 100644 --- a/parsl/tests/test_regression/test_854.py +++ b/parsl/tests/test_regression/test_854.py @@ -1,7 +1,7 @@ import time import multiprocessing import pytest -from parsl.executors.high_throughput.mac_safe_queue import MacSafeQueue +from parsl.multiprocessing import MacSafeQueue import random From 6b1b26fc53aaa700d110f2b72721e49203e1c048 Mon Sep 17 00:00:00 2001 From: Ben Clifford Date: Wed, 30 Jun 2021 07:39:33 -0700 Subject: [PATCH 231/408] Port monitoring to use sizedqueue --- parsl/monitoring/monitoring.py | 14 +++++++------- parsl/multiprocessing.py | 6 +++--- 2 files changed, 10 insertions(+), 10 deletions(-) diff --git a/parsl/monitoring/monitoring.py b/parsl/monitoring/monitoring.py index 5c0d2ef91c..7c24627c24 100644 --- a/parsl/monitoring/monitoring.py +++ b/parsl/monitoring/monitoring.py @@ -8,7 +8,7 @@ import zmq import queue -from parsl.multiprocessing import ForkProcess +from parsl.multiprocessing import ForkProcess, SizedQueue from multiprocessing import Process, Queue from parsl.utils import RepresentationMixin from parsl.process_loggers import wrap_with_logs @@ -219,12 +219,12 @@ def start(self, run_id: str) -> int: min_port=self.client_port_range[0], max_port=self.client_port_range[1]) - comm_q = Queue(maxsize=10) # type: Queue[Union[Tuple[int, int], str]] - self.exception_q = Queue(maxsize=10) # type: Queue[Tuple[str, str]] - self.priority_msgs = Queue() # type: Queue[Tuple[Any, int]] - self.resource_msgs = Queue() # type: Queue[Tuple[Any, Any]] - self.node_msgs = Queue() # type: Queue[Tuple[Any, int]] - self.block_msgs = Queue() # type: Queue[Tuple[Any, Any]] + comm_q = SizedQueue(maxsize=10) # type: Queue[Union[Tuple[int, int], str]] + self.exception_q = SizedQueue(maxsize=10) # type: Queue[Tuple[str, str]] + self.priority_msgs = SizedQueue() # type: Queue[Tuple[Any, int]] + self.resource_msgs = SizedQueue() # type: Queue[Tuple[Any, Any]] + self.node_msgs = SizedQueue() # type: Queue[Tuple[Any, int]] + self.block_msgs = SizedQueue() # type: Queue[Tuple[Any, Any]] self.router_proc = ForkProcess(target=router_starter, args=(comm_q, self.exception_q, self.priority_msgs, self.node_msgs, self.block_msgs, self.resource_msgs), diff --git a/parsl/multiprocessing.py b/parsl/multiprocessing.py index cd00d0bbca..aff6cecd82 100644 --- a/parsl/multiprocessing.py +++ b/parsl/multiprocessing.py @@ -51,7 +51,7 @@ def empty(self): if platform.system() != 'Darwin': - from multiprocessing import Queue as SizedQueue + import multiprocessing + SizedQueue = multiprocessing.Queue else: - from parsl.multiprocessing import MacSafeQueue as SizedQueue - + SizedQueue = MacSafeQueue From 99e2a7ca8d935dfdccb0377a6df9240905c99012 Mon Sep 17 00:00:00 2001 From: Ben Clifford Date: Wed, 30 Jun 2021 09:38:39 -0700 Subject: [PATCH 232/408] Fix mypy --- parsl/multiprocessing.py | 6 +++++- 1 file changed, 5 insertions(+), 1 deletion(-) diff --git a/parsl/multiprocessing.py b/parsl/multiprocessing.py index aff6cecd82..7218393542 100644 --- a/parsl/multiprocessing.py +++ b/parsl/multiprocessing.py @@ -6,7 +6,7 @@ import multiprocessing.queues import platform -from typing import Type +from typing import Callable, Type logger = logging.getLogger(__name__) @@ -49,6 +49,10 @@ def qsize(self): def empty(self): return not self._counter.value +# SizedQueue should be constructable using the same calling +# convention as multiprocessing.Queue but that entire signature +# isn't expressible in mypy 0.790 +SizedQueue: Callable[..., multiprocessing.Queue] if platform.system() != 'Darwin': import multiprocessing From 50f7e4b7e697ff5b824d526bf7ffaa0b3805add7 Mon Sep 17 00:00:00 2001 From: Ben Clifford Date: Wed, 30 Jun 2021 09:46:26 -0700 Subject: [PATCH 233/408] fix flake8 --- parsl/monitoring/monitoring.py | 60 ++++++++++++++++++---------------- parsl/multiprocessing.py | 2 ++ 2 files changed, 34 insertions(+), 28 deletions(-) diff --git a/parsl/monitoring/monitoring.py b/parsl/monitoring/monitoring.py index 2c2f115a2c..46dc4d5e2b 100644 --- a/parsl/monitoring/monitoring.py +++ b/parsl/monitoring/monitoring.py @@ -227,29 +227,29 @@ def start(self, run_id: str) -> int: self.block_msgs = SizedQueue() # type: Queue[Tuple[Tuple[MessageType, Dict[str, Any]], Any]] self.router_proc = ForkProcess(target=router_starter, - args=(comm_q, self.exception_q, self.priority_msgs, self.node_msgs, self.block_msgs, self.resource_msgs), - kwargs={"hub_address": self.hub_address, - "hub_port": self.hub_port, - "hub_port_range": self.hub_port_range, - "client_address": self.client_address, - "client_port": self.dfk_port, - "logdir": self.logdir, - "logging_level": logging.DEBUG if self.monitoring_debug else logging.INFO, - "run_id": run_id - }, - name="Monitoring-Router-Process", - daemon=True, + args=(comm_q, self.exception_q, self.priority_msgs, self.node_msgs, self.block_msgs, self.resource_msgs), + kwargs={"hub_address": self.hub_address, + "hub_port": self.hub_port, + "hub_port_range": self.hub_port_range, + "client_address": self.client_address, + "client_port": self.dfk_port, + "logdir": self.logdir, + "logging_level": logging.DEBUG if self.monitoring_debug else logging.INFO, + "run_id": run_id + }, + name="Monitoring-Router-Process", + daemon=True, ) self.router_proc.start() self.dbm_proc = ForkProcess(target=dbm_starter, - args=(self.exception_q, self.priority_msgs, self.node_msgs, self.block_msgs, self.resource_msgs,), - kwargs={"logdir": self.logdir, - "logging_level": logging.DEBUG if self.monitoring_debug else logging.INFO, - "db_url": self.logging_endpoint, - }, - name="Monitoring-DBM-Process", - daemon=True, + args=(self.exception_q, self.priority_msgs, self.node_msgs, self.block_msgs, self.resource_msgs,), + kwargs={"logdir": self.logdir, + "logging_level": logging.DEBUG if self.monitoring_debug else logging.INFO, + "db_url": self.logging_endpoint, + }, + name="Monitoring-DBM-Process", + daemon=True, ) self.dbm_proc.start() self.logger.info("Started the Hub process {} and DBM process {}".format(self.router_proc.pid, self.dbm_proc.pid)) @@ -328,16 +328,20 @@ def wrapped(*args: List[Any], **kwargs: Dict[str, Any]) -> Any: if monitor_resources: # create the monitor process and start pp = ForkProcess(target=monitor, - args=(os.getpid(), - try_id, - task_id, - monitoring_hub_url, - run_id, - logging_level, - sleep_dur), - name="Monitor-Wrapper-{}".format(task_id)) + args=(os.getpid(), + try_id, + task_id, + monitoring_hub_url, + run_id, + logging_level, + sleep_dur), + name="Monitor-Wrapper-{}".format(task_id)) pp.start() - p = pp # awkwardness because ForkProcess is not directly a constructor and type-checking is expecting it to return type of p (which is Optional) otherwise + p = pp + # TODO: awkwardness because ForkProcess is not directly a constructor + # and type-checking is expecting p to be optional and cannot + # narrow down the type of p in this block. + else: p = None diff --git a/parsl/multiprocessing.py b/parsl/multiprocessing.py index 7218393542..d369f551eb 100644 --- a/parsl/multiprocessing.py +++ b/parsl/multiprocessing.py @@ -49,11 +49,13 @@ def qsize(self): def empty(self): return not self._counter.value + # SizedQueue should be constructable using the same calling # convention as multiprocessing.Queue but that entire signature # isn't expressible in mypy 0.790 SizedQueue: Callable[..., multiprocessing.Queue] + if platform.system() != 'Darwin': import multiprocessing SizedQueue = multiprocessing.Queue From 313ef3b9c2bd2f49aebb3328803b454019ebb33b Mon Sep 17 00:00:00 2001 From: Ben Clifford Date: Wed, 30 Jun 2021 17:36:33 +0000 Subject: [PATCH 234/408] Clarify behaviour on retry handler failing --- docs/userguide/exceptions.rst | 3 +++ 1 file changed, 3 insertions(+) diff --git a/docs/userguide/exceptions.rst b/docs/userguide/exceptions.rst index 40d5737ba4..d18fbe704d 100644 --- a/docs/userguide/exceptions.rst +++ b/docs/userguide/exceptions.rst @@ -166,3 +166,6 @@ by exiting with exitcode 9. The retry handler is given two parameters: the exception from execution, and the parsl internal task_record. The task record contains details such as the app name, parameters and executor. + +If a retry handler raises an exception itself, then the task will be aborted +and no further tries will be attempted. From 264a9c0e7e1fffff79bf959b7733c7e2e4ccb826 Mon Sep 17 00:00:00 2001 From: Ben Clifford Date: Wed, 30 Jun 2021 17:40:56 +0000 Subject: [PATCH 235/408] Remove newly generated stubs that will be generated at doc build time now instead --- ...parsl.dataflow.memoization.id_for_memo.rst | 6 ----- .../parsl.launchers.launchers.Launcher.rst | 22 ------------------- 2 files changed, 28 deletions(-) delete mode 100644 docs/stubs/parsl.dataflow.memoization.id_for_memo.rst delete mode 100644 docs/stubs/parsl.launchers.launchers.Launcher.rst diff --git a/docs/stubs/parsl.dataflow.memoization.id_for_memo.rst b/docs/stubs/parsl.dataflow.memoization.id_for_memo.rst deleted file mode 100644 index 9e3865de9f..0000000000 --- a/docs/stubs/parsl.dataflow.memoization.id_for_memo.rst +++ /dev/null @@ -1,6 +0,0 @@ -parsl.dataflow.memoization.id\_for\_memo -======================================== - -.. currentmodule:: parsl.dataflow.memoization - -.. autofunction:: id_for_memo \ No newline at end of file diff --git a/docs/stubs/parsl.launchers.launchers.Launcher.rst b/docs/stubs/parsl.launchers.launchers.Launcher.rst deleted file mode 100644 index bab383f534..0000000000 --- a/docs/stubs/parsl.launchers.launchers.Launcher.rst +++ /dev/null @@ -1,22 +0,0 @@ -parsl.launchers.launchers.Launcher -================================== - -.. currentmodule:: parsl.launchers.launchers - -.. autoclass:: Launcher - - - .. automethod:: __init__ - - - .. rubric:: Methods - - .. autosummary:: - - ~Launcher.__init__ - - - - - - \ No newline at end of file From 1794f39602f4d87da7f3c21fbe59bd25dfdd8115 Mon Sep 17 00:00:00 2001 From: Ben Clifford Date: Wed, 7 Jul 2021 18:53:02 +0000 Subject: [PATCH 236/408] --- parsl/channels/local/local.py | 4 +--- parsl/version.py | 2 +- 2 files changed, 2 insertions(+), 4 deletions(-) diff --git a/parsl/channels/local/local.py b/parsl/channels/local/local.py index 5cd48f6fdf..7e50ec39af 100644 --- a/parsl/channels/local/local.py +++ b/parsl/channels/local/local.py @@ -68,9 +68,7 @@ def execute_wait(self, cmd, walltime=None, envs={}): shell=True, preexec_fn=os.setpgrp ) - proc.wait(timeout=walltime) - stdout = proc.stdout.read() - stderr = proc.stderr.read() + (stdout, stderr) = proc.communicate(timeout=walltime) retcode = proc.returncode except Exception as e: diff --git a/parsl/version.py b/parsl/version.py index 4494c26023..b2492ce0e0 100644 --- a/parsl/version.py +++ b/parsl/version.py @@ -3,4 +3,4 @@ ..[alpha/beta/..] Alphas will be numbered like this -> 0.4.0a0 """ -VERSION = '1.1.0+desc-2021.07.07a' +VERSION = '1.1.0+desc-2021.07.07b' From a91fb3871d49e8ba6aeb7f8c14df906ed7c2f1be Mon Sep 17 00:00:00 2001 From: Ben Clifford Date: Wed, 7 Jul 2021 19:03:56 +0000 Subject: [PATCH 237/408] add test case for channel with large stdout --- .../tests/test_channels/test_large_output.py | 22 +++++++++++++++++++ parsl/version.py | 2 +- 2 files changed, 23 insertions(+), 1 deletion(-) create mode 100644 parsl/tests/test_channels/test_large_output.py diff --git a/parsl/tests/test_channels/test_large_output.py b/parsl/tests/test_channels/test_large_output.py new file mode 100644 index 0000000000..bfc96f38bc --- /dev/null +++ b/parsl/tests/test_channels/test_large_output.py @@ -0,0 +1,22 @@ +import pytest + +from parsl.channels.local.local import LocalChannel + + +@pytest.mark.local +def test_local_large_output_2210(): + """Regression test for #2210. + The local channel was hanging if the specified command gave too + much output, due to a race condition between process exiting and + pipes filling up. + """ + + c = LocalChannel() + + # this will output 128kb of stdout + c.execute_wait("yes | dd count=128 bs=1024", walltime=60) + + # if this test fails, execute_wait should raise a timeout + # exception. + + # The contents out the output is not verified by this test diff --git a/parsl/version.py b/parsl/version.py index b2492ce0e0..b9167b56ec 100644 --- a/parsl/version.py +++ b/parsl/version.py @@ -3,4 +3,4 @@ ..[alpha/beta/..] Alphas will be numbered like this -> 0.4.0a0 """ -VERSION = '1.1.0+desc-2021.07.07b' +VERSION = '1.1.0+desc-2021.07.07c' From ed0a5c2bf8b22e823581ac9dbdc72a62e34505ac Mon Sep 17 00:00:00 2001 From: Ben Clifford Date: Wed, 7 Jul 2021 19:38:36 +0000 Subject: [PATCH 238/408] fix lint for __init__.py --- parsl/tests/test_channels/__init__.py | 0 parsl/version.py | 2 +- 2 files changed, 1 insertion(+), 1 deletion(-) create mode 100644 parsl/tests/test_channels/__init__.py diff --git a/parsl/tests/test_channels/__init__.py b/parsl/tests/test_channels/__init__.py new file mode 100644 index 0000000000..e69de29bb2 diff --git a/parsl/version.py b/parsl/version.py index b9167b56ec..d3b68d5675 100644 --- a/parsl/version.py +++ b/parsl/version.py @@ -3,4 +3,4 @@ ..[alpha/beta/..] Alphas will be numbered like this -> 0.4.0a0 """ -VERSION = '1.1.0+desc-2021.07.07c' +VERSION = '1.1.0+desc-2021.07.07d' From 3c473f59c86c5815cc7fa144a73c8474b1badc77 Mon Sep 17 00:00:00 2001 From: Ben Clifford Date: Fri, 9 Jul 2021 12:19:08 +0000 Subject: [PATCH 239/408] attempt at fix for setproctitle not working on natively installed python on os x --- parsl/dataflow/usage_tracking/usage.py | 4 ++-- parsl/executors/high_throughput/interchange.py | 4 ++-- parsl/executors/workqueue/executor.py | 4 ++-- parsl/monitoring/db_manager.py | 4 ++-- parsl/monitoring/monitoring.py | 6 +++--- parsl/utils.py | 16 ++++++++++++++++ parsl/version.py | 2 +- 7 files changed, 28 insertions(+), 12 deletions(-) diff --git a/parsl/dataflow/usage_tracking/usage.py b/parsl/dataflow/usage_tracking/usage.py index c10a1557f5..f28b16cdd4 100644 --- a/parsl/dataflow/usage_tracking/usage.py +++ b/parsl/dataflow/usage_tracking/usage.py @@ -1,4 +1,3 @@ -import setproctitle import uuid import time import hashlib @@ -10,6 +9,7 @@ import sys import platform +from parsl.utils import setproctitle from parsl.multiprocessing import ForkProcess from parsl.version import VERSION as PARSL_VERSION @@ -43,7 +43,7 @@ def udp_messenger(domain_name, UDP_IP, UDP_PORT, sock_timeout, message): - sock_timeout (int) : Socket timeout - to_send (multiprocessing.Queue) : Queue of outgoing messages to internet """ - setproctitle.setproctitle("parsl: Usage tracking") + setproctitle("parsl: Usage tracking") try: if message is None: diff --git a/parsl/executors/high_throughput/interchange.py b/parsl/executors/high_throughput/interchange.py index d55e398346..272a4549e3 100644 --- a/parsl/executors/high_throughput/interchange.py +++ b/parsl/executors/high_throughput/interchange.py @@ -1,7 +1,6 @@ #!/usr/bin/env python import argparse import functools -import setproctitle import zmq import os import sys @@ -15,6 +14,7 @@ import threading import json +from parsl.utils import setproctitle from parsl.version import VERSION as PARSL_VERSION from parsl.serialize import ParslSerializer serialize_object = ParslSerializer().serialize @@ -683,7 +683,7 @@ def starter(comm_q, *args, **kwargs): The executor is expected to call this function. The args, kwargs match that of the Interchange.__init__ """ - setproctitle.setproctitle("parsl: HTEX interchange") + setproctitle("parsl: HTEX interchange") # logger = multiprocessing.get_logger() ic = Interchange(*args, **kwargs) comm_q.put((ic.worker_task_port, diff --git a/parsl/executors/workqueue/executor.py b/parsl/executors/workqueue/executor.py index 421ca4960d..6e8116f0de 100644 --- a/parsl/executors/workqueue/executor.py +++ b/parsl/executors/workqueue/executor.py @@ -3,7 +3,6 @@ high-throughput system for delegating Parsl tasks to thousands of remote machines """ -import setproctitle import threading import multiprocessing import logging @@ -31,6 +30,7 @@ from parsl.providers.provider_base import ExecutionProvider from parsl.providers import LocalProvider, CondorProvider from parsl.executors.workqueue import exec_parsl_function +from parsl.utils import setproctitle import typeguard from typing import Dict, List, Optional, Set, Union @@ -767,7 +767,7 @@ def _work_queue_submit_wait(task_queue=multiprocessing.Queue(), module capabilities, rather than shared memory. """ logger.debug("Starting WorkQueue Submit/Wait Process") - setproctitle.setproctitle("parsl: Work Queue submit/wait") + setproctitle("parsl: Work Queue submit/wait") # Enable debugging flags and create logging file wq_debug_log = None diff --git a/parsl/monitoring/db_manager.py b/parsl/monitoring/db_manager.py index 27a470ccca..7802fefd1a 100644 --- a/parsl/monitoring/db_manager.py +++ b/parsl/monitoring/db_manager.py @@ -4,7 +4,6 @@ import os import time import datetime -import setproctitle from typing import Any, Dict, List, Optional, Set, Tuple, TypeVar, cast @@ -13,6 +12,7 @@ from parsl.errors import OptionalModuleMissing from parsl.monitoring.message_type import MessageType from parsl.process_loggers import wrap_with_logs +from parsl.utils import setproctitle logger = logging.getLogger("database_manager") @@ -703,7 +703,7 @@ def dbm_starter(exception_q: "queue.Queue[Tuple[str, str]]", The DFK should start this function. The args, kwargs match that of the monitoring config """ - setproctitle.setproctitle("parsl: monitoring database") + setproctitle("parsl: monitoring database") try: dbm = DatabaseManager(db_url=db_url, diff --git a/parsl/monitoring/monitoring.py b/parsl/monitoring/monitoring.py index 59bada13b5..733dbefdfd 100644 --- a/parsl/monitoring/monitoring.py +++ b/parsl/monitoring/monitoring.py @@ -2,7 +2,6 @@ import socket import pickle import logging -import setproctitle import time import typeguard import datetime @@ -14,6 +13,7 @@ from multiprocessing import Process, Queue from parsl.utils import RepresentationMixin from parsl.process_loggers import wrap_with_logs +from parsl.utils import setproctitle from parsl.serialize import deserialize @@ -512,7 +512,7 @@ def filesystem_receiver(logdir: str, q: "queue.Queue[Tuple[Tuple[MessageType, Di level=logging.DEBUG) logger.info("Starting filesystem radio receiver") - setproctitle.setproctitle("parsl: monitoring filesystem receiver") + setproctitle("parsl: monitoring filesystem receiver") # TODO: these paths should be created by path tools, not f-strings # likewise the other places where tmp_dir, new_dir are created on # the sending side. @@ -715,7 +715,7 @@ def router_starter(comm_q: "queue.Queue[Union[Tuple[int, int], str]]", logdir: str, logging_level: int, run_id: str) -> None: - setproctitle.setproctitle("parsl: monitoring router") + setproctitle("parsl: monitoring router") try: router = MonitoringRouter(hub_address=hub_address, hub_port=hub_port, diff --git a/parsl/utils.py b/parsl/utils.py index 9a8301e546..6d39f1c224 100644 --- a/parsl/utils.py +++ b/parsl/utils.py @@ -11,6 +11,15 @@ import parsl from parsl.version import VERSION + +try: + import setproctitle as setproctitle_module +except ImportError: + _setproctitle_enabled = False +else: + _setproctitle_enabled = True + + logger = logging.getLogger(__name__) @@ -239,3 +248,10 @@ def assemble_line(args: List[str], kwargs: Dict[str, object]) -> str: return assemble_line(args, kwargs) else: return assemble_multiline(args, kwargs) + + +def setproctitle(title: str) -> None: + if _setproctitle_enabled: + setproctitle_module.setproctitle(title) + else: + logger.warn(f"setproctitle not enabled for process {title}") diff --git a/parsl/version.py b/parsl/version.py index d3b68d5675..d922398fc0 100644 --- a/parsl/version.py +++ b/parsl/version.py @@ -3,4 +3,4 @@ ..[alpha/beta/..] Alphas will be numbered like this -> 0.4.0a0 """ -VERSION = '1.1.0+desc-2021.07.07d' +VERSION = '1.1.0+desc-2021.07.09a' From 85177254f724e9345318164855c8b8cb7b0e0c9c Mon Sep 17 00:00:00 2001 From: Ben Clifford Date: Wed, 28 Jul 2021 11:56:09 +0000 Subject: [PATCH 240/408] tickle CI --- README.rst | 1 + 1 file changed, 1 insertion(+) diff --git a/README.rst b/README.rst index f1602a6ae8..6b1702ee3a 100644 --- a/README.rst +++ b/README.rst @@ -120,3 +120,4 @@ For more information, please visit `the informational page `__ or download the `participant information sheet `__. + From 697081f724c405d84a5d584b205771b55f99f274 Mon Sep 17 00:00:00 2001 From: Ben Clifford Date: Wed, 28 Jul 2021 14:04:16 +0000 Subject: [PATCH 241/408] Remove `coverage` test requirement dependency This is only needed by pytest-cov, which brings in the dependency anyway. The version pin on `coverage` that is removed was conflicting with pytest-cov > 2.10. Previously pip was able to easily find a solution to that by using an earlier pytest-cov, but as of some recent ecosystem change, it was unable to find a solution. When manually trying to install pytest-cov 2.11.0 on my laptop with a working parsl dependency stack already installed: ==== The conflict is caused by: The user requested coverage==4.5.4 pytest-cov 2.11.0 depends on coverage>=5.2.1 ==== When building in CI, this resulted in pip spending "forever" (i.e. longer than the test timeout) trying to find a solution. --- test-requirements.txt | 1 - 1 file changed, 1 deletion(-) diff --git a/test-requirements.txt b/test-requirements.txt index 7997b4a517..2e822882d0 100644 --- a/test-requirements.txt +++ b/test-requirements.txt @@ -5,7 +5,6 @@ pytest>=4.6,<5 pytest-cov pytest-xdist==1.26.1 pytest-random-order -coverage==4.5.4 mock>=1.0.0 nbsphinx sphinx_rtd_theme From 5a64bfdc6edc967328cc822470ddfb1c35e4b05b Mon Sep 17 00:00:00 2001 From: Ben Clifford Date: Wed, 28 Jul 2021 15:41:56 +0000 Subject: [PATCH 242/408] Add .coveragerc to see if this fixes possible coverage concurrency problem --- .coveragerc | 3 +++ 1 file changed, 3 insertions(+) create mode 100644 .coveragerc diff --git a/.coveragerc b/.coveragerc new file mode 100644 index 0000000000..a6eb036158 --- /dev/null +++ b/.coveragerc @@ -0,0 +1,3 @@ +[run] +concurrency=multiprocessing,thread +parallel=True From 388afe8a172279e3509d87d0f913b38668ecf6f2 Mon Sep 17 00:00:00 2001 From: Ben Clifford Date: Wed, 28 Jul 2021 16:24:42 +0000 Subject: [PATCH 243/408] remove blank line --- README.rst | 1 - 1 file changed, 1 deletion(-) diff --git a/README.rst b/README.rst index 6b1702ee3a..f1602a6ae8 100644 --- a/README.rst +++ b/README.rst @@ -120,4 +120,3 @@ For more information, please visit `the informational page `__ or download the `participant information sheet `__. - From c90583b74423bd9574bf31666b7154cff010a06c Mon Sep 17 00:00:00 2001 From: Ben Clifford Date: Mon, 16 Aug 2021 13:42:48 +0000 Subject: [PATCH 244/408] mostly to release WQ performance logging changes --- docs/conf.py | 5 - docs/index.rst | 1 - docs/quickstart.rst | 2 +- docs/userguide/dnpc.rst | 133 +++ docs/userguide/index.rst | 1 + docs/userguide/workflow.rst | 23 + parsl/__init__.py | 9 +- parsl/dataflow/dflow.py | 3 + parsl/dnpc/__init__.py | 0 parsl/dnpc/main.py | 992 ++++++++++++++++++ .../workqueue/exec_parsl_function.py | 21 +- parsl/executors/workqueue/executor.py | 13 +- parsl/tests/configs/workqueue_blocks.py | 2 +- parsl/version.py | 2 +- setup.py | 1 + 15 files changed, 1187 insertions(+), 21 deletions(-) create mode 100644 docs/userguide/dnpc.rst create mode 100644 parsl/dnpc/__init__.py create mode 100644 parsl/dnpc/main.py diff --git a/docs/conf.py b/docs/conf.py index 20b435e09c..1c2e6b9665 100644 --- a/docs/conf.py +++ b/docs/conf.py @@ -40,11 +40,6 @@ 'sphinx.ext.napoleon' ] -url = 'https://raw.githubusercontent.com/Parsl/parsl-tutorial/master/1-parsl-introduction.ipynb' -r = requests.get(url) -with open(os.path.join(os.path.dirname(__file__), '1-parsl-introduction.ipynb'), 'wb') as f: - f.write(r.content) - nbsphinx_execute = 'never' def linkcode_resolve(domain, info): diff --git a/docs/index.rst b/docs/index.rst index 9ca8611177..8ddaaa9b4a 100644 --- a/docs/index.rst +++ b/docs/index.rst @@ -37,7 +37,6 @@ Parsl can be used to implement various parallel computing paradigms: .. toctree:: quickstart - 1-parsl-introduction.ipynb userguide/index faq reference diff --git a/docs/quickstart.rst b/docs/quickstart.rst index 9e5248bf57..761ce9d0ff 100644 --- a/docs/quickstart.rst +++ b/docs/quickstart.rst @@ -91,7 +91,7 @@ There are several options for following the tutorial: 1. Use `Binder `_ to follow the tutorial online without installing or writing any code locally. 2. Clone the `Parsl tutorial repository `_ using a local Parsl installation. -3. Read through the online `tutorial documentation <1-parsl-introduction.html>`_. +3. Read through the online tutorial documentation. Usage Tracking diff --git a/docs/userguide/dnpc.rst b/docs/userguide/dnpc.rst new file mode 100644 index 0000000000..9db3ca3168 --- /dev/null +++ b/docs/userguide/dnpc.rst @@ -0,0 +1,133 @@ +distributed nested performance contexts +======================================= + +distributed tracing style stuff for parsl and related components. + +distributed tracing has a single request ID that is propagated everywhere [citation] + +this work is intended to make things a bit more heirarchical, where an activity +as well as having logs/states itself, also contains subactivities. + +it is an exploration of *how* to express useful information, rather than an +attempt to implement it in an efficient manner - I think its likely that +with some fleshing out of how things should work, it might become apparant +that (for example) some existing graph database delivers the right +query behaviour. + +see nested diagnostic context work in java [citation] + +see netlogger [citation] + +see graph query languages in general + +see buneman - keys for XML - for some thoughts about identity for merges/joins +eg https://repository.upenn.edu/cgi/viewcontent.cgi?article=1122&context=cis_papers + +the key goal for the current work is performance analysis of parsl +tasks as they are executed through the system - but including the non-core +parsl stuff: perhaps a little bit inside the tasks, definitely inside the +engines that sit alongside parsl helping the tasks run. + +not-goals: + +* live information integration between data sources - so components +can dump out stuff wherever/however without time constraints. this is all +post-hoc analysis + +* instrumenting every piece of tech in the stack using the same technology, +so custom per-component log file scraping is OK. Requiring the components to +change to work with this logging mechanism is not a requirement (and mostly +impossible if it's things installed on the host system rather than in a user +environment) + +vocab: + context - a thing which has states/log lines/... across multiple log sources + for example a parsl task + subcontext - a context which is fully contained within another context. + for example, a parsl `try` is fully contained within a parsl `task`. + +components of the system emit log-like info - logfiles, monitoring.db - which +associate *events* - eg state transitions, log lines - with a particular + context. + +it might be that a particlar source has a particular implicit containing +context - eg a particular logfile is only for a particular try context, which means +it is then contained in a particular task context without the log file ever +mentioning that task context. + +do contexts have to have explicit IDs? maybe not - eg if there's an adhoc +context coming from a single log file. + +the primary output goal for now is for all parsl tasks, to get a (fine-grained as +desired by the user) list of all state transitions / log lines that are +directly associated with that. + + +a particular "sub"-context may be contained within multiple parent contexts, +which suggests that having unique primary keys for a nested context is not +the right thing to do: + for example, a particular try may be (mostly) contained within a worker context + (i say mostly, because some of the try happens on the submit side - which + suggests theres a worker-side try subcontext, that forms part of the main + try context: + workflow > task > try > executor-level-try > worker-side-try + workflow > executor > block > worker > worker-side-try + workflow > executor > executor-level-try + +nested contexts should be cheap: easy to create by a new binding, and in the +tooling easy to ignore layer-wise - in the sense that in the above first +example, try and worker-side-try don't form heavily distinct layers in some +analyses, perhaps. + +binding of contexts should be flexible to specify, in order that they can be +placed at convenient points, rather than requiring components to necessarily +know their own context (or even that they're part of nested contexts at all) + +labelling of contexts should be flexible: no global unique ID should be +needed outside of analysis. identity should maybe look like "In the context of +this log file (which is known to analysis code), these new subcontexts have +these labels, and they relate to certain sub-log files in these ways" + +when a context in a subcontext of two different contexts (try inside both +task and executor) then it doesn't make sense to have a single full-path +primary key globally. + +Things that need to happen for parsl: + + identify what is a context, concretely, especially where its vague like + different executors (target: local, htex, wq) + + ensure appropriate subcontext binding happens somewhere accessible + + simple analysis tool that works given monitoring.db and log files to + determine if this is worth working on - maybe python-centric as thats + what everyone is familiar with? and code-driven seems to be the main + monitoring driver right now. + +Main driving usecase: jim's gen3 work, wq+cori + +Example of a context >= than a parsl-level workflow might be: + * a single bps run - although that might be a one-to-one mapping + * a campaign of runs - identified by a human with some informal name, perhaps, or a directory + * a collection of runs described in a single monitoring database - even without any other log files at all, this is a substantial collection of information - those core parsl monitoring information. + +Example of a context that is < a parsl-level task try: + * executor-try - eg workqueue's parsl helper script + * inside-task progress: eg starting up singularity/shifter in a shell wrapper. +Both of these seem to be potentially large users of worker time in the +DESC case, and both of these would be useful to understand. + * inside-command-line-app progress: eg jim has been pulling out info from the app log files that might be of interest to represent. + + + +identities: +nodes might have an intrinsic ID - eg a workflow knows its own run_id +but they might also be identified by a label on an edge - eg a slurm job +does not know its own parsl-level block ID - or even that it is a +parsl block at all. + +principle: +there is no canonical source of information about anything (hence the graph +merge requirements) - eg multiple entities assert that workflow X has +task N. (eg monitoring.db, parsl.log) and neither is more authentic than the +other. diff --git a/docs/userguide/index.rst b/docs/userguide/index.rst index 0d80ff0e4e..9ce9e940c1 100644 --- a/docs/userguide/index.rst +++ b/docs/userguide/index.rst @@ -13,6 +13,7 @@ User guide checkpoints configuring monitoring + dnpc workflow modularizing joins diff --git a/docs/userguide/workflow.rst b/docs/userguide/workflow.rst index 3174b278be..045f150aa0 100644 --- a/docs/userguide/workflow.rst +++ b/docs/userguide/workflow.rst @@ -215,3 +215,26 @@ The following figure shows the resulting task graph. .. image:: ../images/MapReduce.png + +Other useful patterns +===================== + +This section is intended to list some patterns which are not to do with +parallelism and concurrency, but still might be useful in parsl workflows + +Environment wrappers for bash_apps +---------------------------------- + +This usecase comes from DESC DRP v2. + +Sometimes a bash app command must be run in a particular environment, for +example, inside a container started by shifter or singularity. [TODO URLs for +those two] + +So although the app commandline might look like: + +.. code-block:: + + myscience input.txt 5 10 + + diff --git a/parsl/__init__.py b/parsl/__init__.py index 191c75d467..89f93be90d 100644 --- a/parsl/__init__.py +++ b/parsl/__init__.py @@ -75,14 +75,7 @@ wait_for_current_tasks = DataFlowKernelLoader.wait_for_current_tasks -class NullHandler(logging.Handler): - """Setup default logging to /dev/null since this is library.""" - - def emit(self, record): - pass - - -logging.getLogger('parsl').addHandler(NullHandler()) +logging.getLogger('parsl').addHandler(logging.NullHandler()) if platform.system() == 'Darwin': os.environ['OBJC_DISABLE_INITIALIZE_FORK_SAFETY'] = 'YES' diff --git a/parsl/dataflow/dflow.py b/parsl/dataflow/dflow.py index 5f6799bcfc..0dbd999530 100644 --- a/parsl/dataflow/dflow.py +++ b/parsl/dataflow/dflow.py @@ -681,6 +681,9 @@ def launch_task(self, task_record, executable, *args, **kwargs): self._send_task_log_info(task_record) logger.info("Task {} launched on executor {}".format(task_id, executor.label)) + if hasattr(exec_fu, "parsl_executor_task_id"): + logger.info("Parsl task {} try {} launched on executor {} with executor id {}".format(task_id, try_id, + executor.label, exec_fu.parsl_executor_task_id)) self._log_std_streams(task_record) diff --git a/parsl/dnpc/__init__.py b/parsl/dnpc/__init__.py new file mode 100644 index 0000000000..e69de29bb2 diff --git a/parsl/dnpc/main.py b/parsl/dnpc/main.py new file mode 100644 index 0000000000..ec8608debe --- /dev/null +++ b/parsl/dnpc/main.py @@ -0,0 +1,992 @@ +import logging +import os +import re +import sqlite3 +import matplotlib.pyplot as plt + +from parsl.log_utils import set_stream_logger +from typing import Dict, List + +logger = logging.getLogger("parsl.dnpc.main") # __name__ is not package qualified in __main__ + + +class Event: + """An Event in a context. This is deliberately minimal. + The new state is represented as a string, which should make + sense wrt the other states in this context (and perhaps + with other unspecified contexts - for example, all task + contexts should use the same set of states) + + Tooling should not expect the lists of states to be + defined. + + It might be useful to include a human readable event provenance + (eg the name of a log file and the line number in that log file) + to lead users to information about a particular event. + + Time is specified as a unix timestamp. I'm unclear what the + best representation for time is in this use case, so picking this + fairly arbitrarily. Of some concern is that timestamps will come + from multiple different clocks, and those clocks might need + to be represented in the timestamp (eg with a hostname?) if use + can be made of that information. + """ + + time: int + type: str + + def __repr__(self): + return f"" + + +class Context: + """Python representation of a DNPC context. + + A Context has a brief human readable name. This name should + make sense within the containing context, and should be sized to + be useful as (for example) a graph label. For example "Task 23" + It might be, given the type field, that the name only needs to + make sense alongside the type (so name could be "23" if type + is "parsl.task") + + A context may contain subcontexts. + + A context may be contained in many supercontexts - a context does + not know about and does not have an enclosing supercontext. + + The object representation stores the containment + arrows only from super- to sub- contexts. + + A context may content events / state transitions (I'm unclear on the + vocabulary I want to use there, and on exactly what should be + represented. + + The type str indicates the kind of events/subcontexts one might expect + to find inside a context, and indicates which contexts might be + compared to each other - eg all task contexts in some sense look the same. + This is, however, schema and definition free. My recommendation is + to use some name like "parsl.subcomponent.whatever" + + The subcontexts collection should not be directly set or edited - it should + be maintained by helper methods provided as part of the Context + implementation. + + A user should not call the Context() constructor directly - instead use + the new_root_context and get() class methods + + + """ + type: str + name: str + _subcontexts: Dict[str, "Context"] + events: List[Event] + + def __init__(self): + self._subcontexts = {} + self.events = [] + self.name = "unnamed" + + def __repr__(self): + return f"" + + @classmethod + def new_root_context(cls): + return Context() + + # context = root_context.get_context("monitoring", "parsl.monitoring.db") + def get_context(self, edge_name, type): + edge_name = str(edge_name) + c = self._subcontexts.get(edge_name) + if c is not None: + assert(c.type == type) + logger.info(f"get_context returning existing {type} context for key {edge_name}") + return c + else: + c = Context() + c.type = type + self._subcontexts[edge_name] = c + logger.info(f"get_context creating new {type} context for key {edge_name}") + + return c + + def alias_context(self, edge_name: str, context: "Context"): + c = self._subcontexts.get(edge_name) + if c is not None: + assert c is context # object, not value, identity + else: + self._subcontexts[edge_name] = context + + @property + def subcontexts(self) -> List["Context"]: + """The subcontexts property is read-only. It should be maintained by + Context helper methods.""" + return [self._subcontexts[k] for k in self._subcontexts] + + +def import_workflow_task_tries(base_context: Context, db: sqlite3.Connection, run_id: str, task_id) -> None: + logger.info(f"Importing tries for task {task_id}") + + cur = db.cursor() + + # this fractional seconds replacement for %s comes from (julianday('now') - 2440587.5)*86400.0 + # SELECT (julianday('now') - 2440587.5)*86400.0; + + for row in cur.execute(f"SELECT try_id, (julianday(task_try_time_launched) - 2440587.5)*86400.0, " + f"(julianday(task_try_time_running) - 2440587.5)*86400.0, (julianday(task_try_time_returned) - 2440587.5)*86400.0 " + f"FROM try WHERE run_id = '{run_id}' AND task_id = '{task_id}'"): + try_id = row[0] + + try_context = base_context.get_context(try_id, "parsl.try") + try_context.name = "Try {try_id}" + + if row[1]: # omit this event if it is NULL + launched_event = Event() + launched_event.type = "launched" + launched_event.time = float(row[1]) + try_context.events.append(launched_event) + + if row[2]: # omit this event if it is NULL + running_event = Event() + running_event.type = "running" + running_event.time = float(row[2]) + try_context.events.append(running_event) + + returned_event = Event() + returned_event.type = "returned" + returned_event.time = float(row[3]) + try_context.events.append(returned_event) + + return None + + +def import_workflow_tasks(base_context: Context, db: sqlite3.Connection, run_id: str) -> None: + logger.info(f"Importing tasks for workflow {run_id}") + + cur = db.cursor() + + for row in cur.execute(f"SELECT task_id, strftime('%s', task_time_invoked), strftime('%s',task_time_returned) FROM task WHERE run_id = '{run_id}'"): + task_id = row[0] + task_context = base_context.get_context(task_id, "parsl.task") + task_context.name = f"Task {task_id}" + + summary_context = task_context.get_context("summary", "parsl.task.summary") + summary_context.name = f"Task {task_id} summary" + + start_event = Event() + start_event.type = "start" + start_event.time = float(row[1]) + summary_context.events.append(start_event) + + end_event = Event() + end_event.type = "end" + end_event.time = float(row[2]) + summary_context.events.append(end_event) + + state_context = task_context.get_context("states", "parsl.task.states") + state_context.name = f"Task {task_id} states" + + state_cur = db.cursor() + for state_row in state_cur.execute(f"SELECT task_status_name, (julianday(timestamp) - 2440587.5)*86400.0 " + f"FROM status WHERE run_id = '{run_id}' AND task_id = '{task_id}'"): + start_event = Event() + start_event.type = state_row[0] + start_event.time = float(state_row[1]) + state_context.events.append(start_event) + + import_workflow_task_tries(task_context, db, run_id, task_id) + + return None + + +def import_parsl_log(base_context: Context, rundir: str) -> None: + logger.info("Importing parsl.log") + + with open(f"{rundir}/parsl.log", "r") as logfile: + for line in logfile: + # the key lines i want for now from parsl.log look like this: + # Parsl task 562 try 0 launched on executor WorkQueueExecutor with executor id 337 + m = re.match('.* Parsl task (.*) try (.*) launched on executor (.*) with executor id (.*)', line) + if m: + logger.info(f"Line matched: {line}, {m}") + task_id = m.group(1) + logger.info(f"Task ID {task_id}") + task_context = base_context.get_context(task_id, "parsl.task") + try_id = m.group(2) + logger.info(f"Try ID {try_id}") + try_context = task_context.get_context(try_id, "parsl.try") + executor_id_context = try_context.get_context("executor", "parsl.try.executor") + # the point of this log file line is to alias it + # separate importing of executor-specific log file will populate + # the parsl.try.executor context via the below aliased context + executor_name = m.group(3) + executor_id = m.group(4) + executor_context = base_context.get_context(executor_name, "parsl.executor") + executor_context.alias_context(executor_id, executor_id_context) + + logger.info("Finished importing parsl.log") + + +def import_work_queue_python_timing_log(base_context: Context, rundir: str): + # These logs (like the workqueue results files) aren't scoped properly + # by executor - if there were two work queue executors in a run they + # would conflict. + wq_context = base_context.get_context("WorkQueueExecutor", "parsl.executor") + dirs = os.listdir(f"{rundir}/function_data/") + for dir in dirs: + wqe_task_id = str(int(dir)) # normalise away any leading zeros + wq_task_context = wq_context.get_context(wqe_task_id, "parsl.try.executor") + epf_context = wq_task_context.get_context("epf", "parsl.wq.exec_parsl_function") + # now import the log_file into epf_context + filename = f"{rundir}/function_data/{dir}/log" + if os.path.exists(filename): + with open(filename) as f: + for line in f: + # 1629049247.4333403 LOADFUNCTION + m = re.match('^([0-9\\.]+) ([^ ]+)\n$', line) + if m: + event = Event() + event.time = float(m.group(1)) + event.type = m.group(2) + epf_context.events.append(event) + + +def import_work_queue_transaction_log(base_context, rundir): + # TODO: how to determine if we should import this log? should it be + # triggered by an entry in the parsl.log file that declares that a + # WQ executor exists? + # for now doing my testing, I'll assume that there will be a log in the + # WorkQueueExecutor/ subdirectory + + wq_context = base_context.get_context("WorkQueueExecutor", "parsl.executor") + + logger.info("Importing Work Queue transaction log") + with open(f"{rundir}/WorkQueueExecutor/transaction_log") as transaction_log: + for line in transaction_log: + m = re.match('([0-9]+) [0-9]+ TASK ([0-9]+) ([^ ]+) .*', line) + if m: + logger.info(f"Line matched: {line}, {m}") + task_id = m.group(2) + status = m.group(3) + logger.info(f"WQ task {task_id} status {status}") + wq_task_context = wq_context.get_context(task_id, "parsl.try.executor") + event = Event() + event.time = float(m.group(1)) / 1000000 + event.type = status + wq_task_context.events.append(event) + + logger.info("Done importing Work Queue transaction log") + + +def import_parsl_rundir(base_context: Context, rundir: str) -> None: + logger.info(f"Importing rundir {rundir}") + + # things we might find in the rundir: + + # almost definitely parsl.log - this has lots of task timing info in it, + # a third source of task times distinct from the two monitoring db times. + # It also has bindings between task IDs and executor IDs, and in the + # workqueue case, bindings between wq-executor ID and work queue IDs. + # The task timing info might be interesting for when people aren't using + # the monitoring db, although the broad story at the moment should probably + # still be that if you want to analyse parsl-level task timings, use the + # monitoring db. + + import_parsl_log(base_context, rundir) + import_work_queue_transaction_log(base_context, rundir) + import_work_queue_python_timing_log(base_context, rundir) + + # workqueue debug log - this is what I'm most interested in integrating + # alongside the monitoring db as it will link parsl monitoring DB state + # transitions with WQ level transitions. + + logger.info(f"Finished importing rundir {rundir}") + + +def import_workflow(base_context: Context, db: sqlite3.Connection, run_id: str) -> None: + logger.info(f"Importing workflow {run_id}") + + context = base_context.get_context(run_id, "parsl.workflow") + + cur = db.cursor() + + rundir = None + + # TODO: sql injection protection (from eg hostile user sending hostile db - run_id is not sanitised) + for row in cur.execute(f"SELECT strftime('%s', time_began), strftime('%s',time_completed), rundir FROM workflow WHERE run_id = '{run_id}'"): + # in a well formed DB will iterate only once + + start_event = Event() + start_event.type = "start" + start_event.time = float(row[0]) + context.events.append(start_event) + + end_event = Event() + end_event.type = "end" + end_event.time = float(row[1]) + context.events.append(end_event) + + rundir = row[2] + # TODO: we'll get the last rundir silently discarding + # others if there are multiple workflows with the same ID + # rather than giving an error... + + import_workflow_tasks(context, db, run_id) + + # there are also things defined in the parsl log (indeed, a decent amount + # of information could come from the parsl.log file without any + # monitoring.db at all - and maybe that's an interesting mode to support...) + + import_parsl_rundir(context, rundir) + + # c2 = import_workflow_parsl_log(context, run_id, rundir) + + # TODO: a heirarchy merge operator that lets c2 be overlaid on top of + # the existing context. This means that the import_workflow_parsl_log + # importer does not need an existing monitoring.db based context graph + # to already exist - meaning it should be more amenable to use on files + # without the monitoring db. + # However, it then needs a notion of identity between the trees, which + # is not implemented at the moment: how much should that identity + # structure be baked into the code rather than specified as part of the + # merge? This is similar to a JOIN operation, but deeply heirarchical... + # There's also the question of context identity: previously a python + # Context object was a context: object identity was context identity, + # which I intended to use for expressing DAGs, by using DAGs of objects. + # This "merge" operator gets rid of that: two Context objects (which may + # be referred to in complicated fashions elsewhere) now need to become + # one Context object (either re-using one of the exising ones or + # a third new one). + # If we're specifying keys, we're getting a bit schema-ey. But specifying + # join keys as part of the JOIN / merge makes sense if it looks like + # SQL style JOINs, where the fields to join on are specified as part of + # the JOIN, not as part of the schema. + # A different database-like approach is rather than ever calling + # the Context constructor directly, there is a "context.declare_or_find(key)" + # (or more simply phrased context.subcontext(type, key)) + # call which allows either the existing keyed context or a new one if + # it does not exist - to be accessed, and modified. In that way, the + # Context objects remain unique to their keys. And the database consists + # of an incrementally appended collection of contexts - an importer may + # add subcontexts to any existing context. + # This means there should be keys in the formal query model - either + # on contexts or on the context/subcontext edge - I don't have a feel + # for which is better - probably on the edge, because keys make sense + # in a context, and subcontexts can be in many contexts. Eg a try with + # key 0 makes sense in a context of a task key n in workflow key uuuuu, + # but doesn't in a collection of tries from many tasks, where they might + # instead be keyed by executor job id (or even unkeyed) + + logger.info(f"Done importing workflow {run_id}") + return context + + +def import_monitoring_db(root_context: Context, dbname: str) -> Context: + """This will import an entire monitoring database as a context. + A monitoring database root context does not contain any events + directly; it contains each workflow run as a subcontext. + """ + logger.info("Importing context from monitoring db") + context = root_context.get_context("monitoring", "parsl.monitoring.db") + context.type = "parsl.monitoring.db" + context.name = "Parsl monitoring database " + dbname + + # TODO: can this become a with: ? + db = sqlite3.connect(dbname, + detect_types=sqlite3.PARSE_DECLTYPES | + sqlite3.PARSE_COLNAMES) + + # create a subcontext for each workflow row + + cur = db.cursor() + + for row in cur.execute("SELECT run_id FROM workflow"): + run_id = row[0] + logger.info(f"workflow: {run_id}") + + import_workflow(context, db, run_id) + + db.close() + + logger.info("Finished importing context from monitoring db") + return context + + +def plot_wq_running_to_parsl_running_histo(db_context): + + all_try_contexts = [] + + for wf_context in db_context.subcontexts: + task_contexts = [sc for sc in wf_context.subcontexts if sc.type == 'parsl.task'] + for task_context in task_contexts: + logger.info(f"task subcontexts have keys: {task_context._subcontexts.keys()}") + try_contexts = [sc for sc in task_context.subcontexts if sc.type == 'parsl.try'] + all_try_contexts += try_contexts + + # Now all_try_contexts has all of the try contexts in flattened form. + # Filter so we only have try contexts which have both a running and a returned event + + filtered_try_contexts = [] + for context in all_try_contexts: + logger.info(f"examining try context {context}") + # flatten event_types into a set + event_types = set() + for event in context.events: + event_types.add(event.type) + + executor_contexts = [c for c in context.subcontexts if c.type == 'parsl.try.executor'] + logger.info(f"context.subcontexts = {context.subcontexts}") + logger.info(f"executor_contexts = {executor_contexts}") + if len(executor_contexts) != 1: + logger.info("skipping because wrong number of executor_contexts") + continue + pte_context = executor_contexts[0] + + pte_event_types = set() + for event in pte_context.events: + pte_event_types.add(event.type) + + logger.info(f"event_types: {event_types}") + logger.info(f"pte_event_types: {pte_event_types}") + + if "running" in event_types and 'RUNNING' in pte_event_types: + filtered_try_contexts.append(context) + + # now filtered_try_contexts has all the tries with the right timestamp + + # map these into something that can be fed into matplotlib histogram + xs = [] + for context in filtered_try_contexts: + # extract running and returned values that we know are here + running_events = [e for e in context.events if e.type == "running"] + parsl_running_event = running_events[0] # we selected based on this event existing so [0] will always exist + + executor_contexts = [c for c in context.subcontexts if c.type == 'parsl.try.executor'] + logger.info(f"executor_contexts = {executor_contexts}") + assert(len(executor_contexts) == 1) + pte_context = executor_contexts[0] + + wq_running_events = [e for e in pte_context.events if e.type == "RUNNING"] + wq_running_event = wq_running_events[0] # we selected based on this event existing so [0] will always exist + + runtime = parsl_running_event.time - wq_running_event.time + + xs.append(runtime) + + logger.info(f"histo data for runtime: {xs}") + + fig = plt.figure() + ax = fig.add_subplot(1, 1, 1) + + plt.title("time from wq running to parsl running histogram") + + ax.hist(xs, bins=100) + + plt.savefig("dnpc-wq-running-to_parsl-running-histo.png") + + +def plot_tries_runtime_histo(db_context): + + all_try_contexts = [] + + for wf_context in db_context.subcontexts: + task_contexts = [sc for sc in wf_context.subcontexts if sc.type == 'parsl.task'] + for task_context in task_contexts: + try_contexts = [sc for sc in task_context.subcontexts if sc.type == 'parsl.try'] + all_try_contexts += try_contexts + + # Now all_try_contexts has all of the try contexts in flattened form. + # Filter so we only have try contexts which have both a running and a returned event + + filtered_try_contexts = [] + for context in all_try_contexts: + # flatten event_types into a set + event_types = set() + for event in context.events: + event_types.add(event.type) + + if "running" in event_types and "returned" in event_types: + filtered_try_contexts.append(context) + + # now filtered_try_contexts has all the tries with the right timestamp + + # map these into something that can be fed into matplotlib histogram + xs = [] + for context in filtered_try_contexts: + # extract running and returned values that we know are here + running_events = [e for e in context.events if e.type == "running"] + running_event = running_events[0] # we selected based on this event existing so [0] will always exist + + returned_events = [e for e in context.events if e.type == "returned"] + returned_event = returned_events[0] # we selected based on this event existing so [0] will always exist + + runtime = returned_event.time - running_event.time + + xs.append(runtime) + + logger.info(f"histo data for runtime: {xs}") + + fig = plt.figure() + ax = fig.add_subplot(1, 1, 1) + + plt.title("try runtime histogram") + + ax.hist(xs) + + plt.savefig("dnpc-tries-runtime-histo.png") + + +def plot_tries_cumul(db_context): + """Given a DB context, plot cumulative state transitions of all tries of all tasks of all workflows""" + + # pivot from events being grouped by context, to being + # grouped by event type + + all_subcontext_events = [] + + for wf_context in db_context.subcontexts: + task_contexts = [sc for sc in wf_context.subcontexts if sc.type == 'parsl.task'] + for task_context in task_contexts: + try_contexts = [sc for sc in task_context.subcontexts if sc.type == 'parsl.try'] + for try_subcontext in try_contexts: + all_subcontext_events += try_subcontext.events + + logger.info(f"all subcontext events: {all_subcontext_events}") + + event_types = set() + + for event in all_subcontext_events: + event_types.add(event.type) + + logger.info(f"all event types: {event_types}") + + fig = plt.figure() + ax = fig.add_subplot(1, 1, 1) + + for event_type in event_types: + + x = [] + y = [] + these_events = [event for event in all_subcontext_events if event.type == event_type] + + these_events.sort(key=lambda e: e.time) + + n = 0 + for event in these_events: + x.append(event.time) + y.append(n) + n += 1 + x.append(event.time) + y.append(n) + + logger.info(f"will plot event {event_type} with x={x} and y={y}") + ax.plot(x, y, label=f"{event_type}") + + ax.legend() + plt.title("cumulative monitoring.db task events by time") + + plt.savefig("dnpc-tries-cumul.png") + + +def plot_tasks_summary_cumul(db_context): + """Given a DB context, plot cumulative state transitions of all tasks of all workflows""" + + # pivot from events being grouped by context, to being + # grouped by event type + + all_subcontext_events = [] + + for wf_context in db_context.subcontexts: + task_contexts = [sc for sc in wf_context.subcontexts if sc.type == 'parsl.task'] + for task_context in task_contexts: + state_contexts = [sc for sc in task_context.subcontexts if sc.type == 'parsl.task.summary'] + for task_subcontext in state_contexts: + all_subcontext_events += task_subcontext.events + + logger.info(f"all subcontext events: {all_subcontext_events}") + + event_types = set() + + for event in all_subcontext_events: + event_types.add(event.type) + + logger.info(f"all event types: {event_types}") + + fig = plt.figure() + ax = fig.add_subplot(1, 1, 1) + + for event_type in event_types: + + x = [] + y = [] + these_events = [event for event in all_subcontext_events if event.type == event_type] + + these_events.sort(key=lambda e: e.time) + + n = 0 + for event in these_events: + x.append(event.time) + y.append(n) + n += 1 + x.append(event.time) + y.append(n) + + logger.info(f"will plot event {event_type} with x={x} and y={y}") + ax.plot(x, y, label=f"{event_type}") + + ax.legend() + plt.title("cumulative monitoring.db task events by time") + + plt.savefig("dnpc-tasks-summary-cumul.png") + + +def plot_tasks_status_cumul(db_context): + """Given a DB context, plot cumulative state transitions of all tasks of all workflows""" + + # pivot from events being grouped by context, to being + # grouped by event type + + all_subcontext_events = [] + + for wf_context in db_context.subcontexts: + task_contexts = [sc for sc in wf_context.subcontexts if sc.type == 'parsl.task'] + for task_context in task_contexts: + state_contexts = [sc for sc in task_context.subcontexts if sc.type == 'parsl.task.states'] + for task_subcontext in state_contexts: + all_subcontext_events += task_subcontext.events + + logger.info(f"all subcontext events: {all_subcontext_events}") + + event_types = set() + + for event in all_subcontext_events: + event_types.add(event.type) + + logger.info(f"all event types: {event_types}") + + fig = plt.figure() + ax = fig.add_subplot(1, 1, 1) + + for event_type in event_types: + + x = [] + y = [] + these_events = [event for event in all_subcontext_events if event.type == event_type] + + these_events.sort(key=lambda e: e.time) + + n = 0 + for event in these_events: + x.append(event.time) + y.append(n) + n += 1 + x.append(event.time) + y.append(n) + + logger.info(f"will plot event {event_type} with x={x} and y={y}") + ax.plot(x, y, label=f"{event_type}") + + ax.legend() + plt.title("cumulative monitoring.db task events by time") + + plt.savefig("dnpc-tasks-status-cumul.png") + + +def plot_tasks_status_streamgraph(db_context): + + all_state_subcontexts = set() + all_subcontext_events = [] + + for wf_context in db_context.subcontexts: + task_contexts = [sc for sc in wf_context.subcontexts if sc.type == 'parsl.task'] + for task_context in task_contexts: + state_contexts = [sc for sc in task_context.subcontexts if sc.type == 'parsl.task.states'] + all_state_subcontexts.update(state_contexts) + for task_subcontext in state_contexts: + all_subcontext_events += task_subcontext.events + + logger.info(f"all subcontext events: {all_subcontext_events}") + + event_types = set() + + for event in all_subcontext_events: + event_types.add(event.type) + + logger.info(f"all event types: {event_types}") + + # now generate a different stream of events, to be used for plotting: + # for each task, + # the first event increases the event type + # subsequent events increase the event type and decrease the former + # event type + + plot_events = {} + for t in event_types: + plot_events[t] = [] + + for s in all_state_subcontexts: + these_events = [e for e in s.events] # copy so we can mutate safely + these_events.sort(key=lambda e: e.time) + + plot_events[these_events[0].type].append((these_events[0].time, 1)) + prev_event_type = these_events[0].type + for e in these_events[1:]: + plot_events[e.type].append((e.time, 1)) + plot_events[prev_event_type].append((e.time, -1)) + prev_event_type = e.type + # if prev_event_type != "exec_done": + # raise RuntimeError(f"did not end on exec_done: {prev_event_type}, {these_events}") + + # TODO: now we have per-event type data series, with mismatching x axes + # for each of those data series, align the x axes by duplicating entries + # to ensure the x axis is fully populated + + canonical_x_axis_set = set() + for t in event_types: + these_x = [e[0] for e in plot_events[t]] + logger.info(f"these_x = {these_x}") + logger.info(f"event type {t} adding {len(these_x)} timestamps") + logger.info(f"size before update: {len(canonical_x_axis_set)}") + canonical_x_axis_set.update(these_x) + logger.info(f"size after update: {len(canonical_x_axis_set)}") + + canonical_x_axis = list(canonical_x_axis_set) + canonical_x_axis.sort() + + fig = plt.figure(figsize=(10, 10)) + ax = fig.add_subplot(1, 1, 1) + + ys = [] + labels = [] + + for event_type in event_types: + + y = [] + these_events = plot_events[event_type] + + these_events.sort(key=lambda pe: pe[0]) + + n = 0 + for x in canonical_x_axis: + + while len(these_events) > 0 and these_events[0][0] == x: + assert these_events[0][0] in canonical_x_axis_set, "timestamp must be in x axis somewhere" + assert these_events[0][0] in canonical_x_axis, "timestamp must be in x axis list somewhere" + n += these_events[0][1] + these_events = these_events[1:] + + assert len(these_events) == 0 or these_events[0][0] > x, "Next event must be in future" + y.append(n) + + # we should have used up all of the events for this event type + assert these_events == [], f"Some events remaining: {these_events}" + + logger.info(f"will plot event {event_type} with x={x} and y={y}") + + ys.append(y) + labels.append(event_type) + + ax.stackplot(canonical_x_axis, ys, labels=labels, baseline='wiggle') + ax.legend(loc='upper left') + plt.title("tasks in each state by time") + + plt.savefig("dnpc-tasks-status-stream.png") + + +def plot_all_task_events_cumul(db_context): + all_subcontext_events = [] + + # TODO: this should maybe use a set for all_subcontext_events: + # in some cases, there might be multiple routes to the same context, + # and each context should only be counted once. + for wf_context in db_context.subcontexts: + task_contexts = [sc for sc in wf_context.subcontexts if sc.type == 'parsl.task'] + for task_context in task_contexts: + all_subcontext_events += task_context.events + + try_contexts = [tc for tc in task_context.subcontexts if tc.type == 'parsl.try'] + for try_subcontext in try_contexts: + all_subcontext_events += try_subcontext.events + wq_contexts = [tc for tc in try_subcontext.subcontexts if tc.type == 'parsl.try.executor'] + for wq_subcontext in wq_contexts: + all_subcontext_events += wq_subcontext.events + for s in wq_subcontext.subcontexts: + all_subcontext_events += s.events + + state_contexts = [tc for tc in task_context.subcontexts if tc.type == 'parsl.task.states'] + for state_context in state_contexts: + all_subcontext_events += state_context.events + + logger.info(f"all subcontext events: {all_subcontext_events}") + + event_types = set() + + for event in all_subcontext_events: + event_types.add(event.type) + + logger.info(f"all event types: {event_types}") + + fig = plt.figure() + ax = fig.add_subplot(1, 1, 1) + + for event_type in event_types: + + x = [] + y = [] + these_events = [event for event in all_subcontext_events if event.type == event_type] + + these_events.sort(key=lambda e: e.time) + + n = 0 + for event in these_events: + x.append(event.time) + y.append(n) + n += 1 + x.append(event.time) + y.append(n) + + logger.info(f"will plot event {event_type} with x={x} and y={y}") + ax.plot(x, y, label=f"{event_type}") + + ax.legend() + plt.title("cumulative task events (parsl/wq/worker) by time") + + plt.savefig("dnpc-all-task-events-cumul.png") + + +def plot_wq_parsl_worker_cumul(db_context): + + # pivot from events being grouped by context, to being + # grouped by event type + + all_subcontext_events = [] + + for wf_context in db_context.subcontexts: + task_contexts = [sc for sc in wf_context.subcontexts if sc.type == 'parsl.task'] + for task_context in task_contexts: + try_contexts = [tc for tc in task_context.subcontexts if tc.type == 'parsl.try'] + for try_subcontext in try_contexts: + wq_contexts = [tc for tc in try_subcontext.subcontexts if tc.type == 'parsl.try.executor'] + for wq_subcontext in wq_contexts: + all_subcontext_events += wq_subcontext.events + + logger.info(f"all subcontext events: {all_subcontext_events}") + + event_types = set() + + for event in all_subcontext_events: + event_types.add(event.type) + + logger.info(f"all event types: {event_types}") + + fig = plt.figure() + ax = fig.add_subplot(1, 1, 1) + + for event_type in event_types: + + x = [] + y = [] + these_events = [event for event in all_subcontext_events if event.type == event_type] + + these_events.sort(key=lambda e: e.time) + + n = 0 + for event in these_events: + x.append(event.time) + y.append(n) + n += 1 + x.append(event.time) + y.append(n) + + logger.info(f"will plot event {event_type} with x={x} and y={y}") + ax.plot(x, y, label=f"{event_type}") + + ax.legend() + plt.title("cumulative wq-parsl worker events by time") + + plt.savefig("dnpc-wq-parsl-worker-cumul.png") + + +def plot_workflows_cumul(db_context): + """An example of making a plot. Given a database context, + looks at all of the contained contexts (without caring about + type, which is probably wrong), and plots the state + transitions for all of those immediate child contexts. + """ + + # pivot from events being grouped by context, to being + # grouped by event type + + all_subcontext_events = [] + + for context in db_context.subcontexts: + all_subcontext_events += context.events + + logger.info(f"all subcontext events: {all_subcontext_events}") + + event_types = set() + + for event in all_subcontext_events: + event_types.add(event.type) + + logger.info(f"all event types: {event_types}") + + fig = plt.figure() + ax = fig.add_subplot(1, 1, 1) + + for event_type in event_types: + + x = [] + y = [] + these_events = [event for event in all_subcontext_events if event.type == event_type] + + these_events.sort(key=lambda e: e.time) + + n = 0 + for event in these_events: + x.append(event.time) + y.append(n) + n += 1 + x.append(event.time) + y.append(n) + + logger.info(f"will plot event {event_type} with x={x} and y={y}") + ax.plot(x, y, label=f"{event_type}") + + ax.legend() + plt.title("cumulative monitoring.db workflow events by time") + + plt.savefig("dnpc-workflows-cumul.png") + + +def main() -> None: + set_stream_logger() + logger.info("dnpc start") + + root_context = Context.new_root_context() + + import_monitoring_db(root_context, "./monitoring.db") + + monitoring_db_context = root_context.get_context("monitoring", "parsl.monitoring.db") + + logger.info(f"got monitoring db context {monitoring_db_context}") + + # now do some simple plots with this context - at time of writing + # all that is available is workflow start/end times but that should + # allow plots of number of workflows in each state, which is a + # building block to later plots. + + plot_workflows_cumul(monitoring_db_context) + plot_tasks_summary_cumul(monitoring_db_context) + plot_tasks_status_cumul(monitoring_db_context) + plot_tries_cumul(monitoring_db_context) + plot_tries_runtime_histo(monitoring_db_context) + plot_wq_running_to_parsl_running_histo(monitoring_db_context) + plot_wq_parsl_worker_cumul(monitoring_db_context) + plot_all_task_events_cumul(monitoring_db_context) + plot_tasks_status_streamgraph(monitoring_db_context) + + logger.info("dnpc end") + + +if __name__ == "__main__": + main() diff --git a/parsl/executors/workqueue/exec_parsl_function.py b/parsl/executors/workqueue/exec_parsl_function.py index 6cf6afb235..2bf251a5e5 100644 --- a/parsl/executors/workqueue/exec_parsl_function.py +++ b/parsl/executors/workqueue/exec_parsl_function.py @@ -1,3 +1,6 @@ +import time +t_start = time.time() + from parsl.app.errors import RemoteExceptionWrapper from parsl.data_provider.files import File from parsl.utils import get_std_fname_mode @@ -5,6 +8,7 @@ import sys import pickle +t_postimport = time.time() # This scripts executes a parsl function which is pickled in a file: # # exec_parsl_function.py map_file function_file result_file @@ -169,6 +173,7 @@ def execute_function(namespace, function_code, result_name): if __name__ == "__main__": + t_mainstart = time.time() try: # parse the three required command line arguments: # map_file: contains a pickled dictionary to map original names to @@ -177,17 +182,26 @@ def execute_function(namespace, function_code, result_name): # result_file: any output (including exceptions) will be written to # this file. try: - (map_file, function_file, result_file) = sys.argv[1:] + (map_file, function_file, result_file, log_file) = sys.argv[1:] except ValueError: print("Usage:\n\t{} function result mapping\n".format(sys.argv[0])) raise + logfile = open(log_file, "w") + print(f"{t_start} START", file=logfile) + print(f"{t_postimport} POSTIMPORT", file=logfile) + print(f"{t_mainstart} MAINSTART", file=logfile) + + t_loadfunction = time.time() + print(f"{t_loadfunction} LOADFUNCTION", file=logfile) try: (namespace, function_code, result_name) = load_function(map_file, function_file) except Exception: print("There was an error setting up the function for execution.") raise + t_executefunction = time.time() + print(f"{t_executefunction} EXECUTEFUNCTION", file=logfile) try: result = execute_function(namespace, function_code, result_name) except Exception: @@ -199,8 +213,13 @@ def execute_function(namespace, function_code, result_name): # Write out function result to the result file try: + t_dump = time.time() + print(f"{t_dump} DUMP", file=logfile) dump_result_to_file(result_file, result) except Exception: print("Could not write to result file.") traceback.print_exc() sys.exit(1) + t_done = time.time() + print(f"{t_done} DONE", file=logfile) + logfile.close() diff --git a/parsl/executors/workqueue/executor.py b/parsl/executors/workqueue/executor.py index 6e8116f0de..d5534f1154 100644 --- a/parsl/executors/workqueue/executor.py +++ b/parsl/executors/workqueue/executor.py @@ -62,7 +62,8 @@ # Support structure to communicate parsl tasks to the work queue submit thread. ParslTaskToWq = namedtuple('ParslTaskToWq', - 'id category cores memory disk gpus priority running_time_min env_pkg map_file function_file result_file input_files output_files') + 'id category cores memory disk gpus priority running_time_min ' + 'env_pkg map_file function_file result_file log_file input_files output_files') # Support structure to communicate final status of work queue tasks to parsl # result is only valid if result_received is True @@ -273,7 +274,7 @@ def __init__(self, self.project_password_file = None # Build foundations of the launch command - self.launch_cmd = ("{package_prefix}python3 exec_parsl_function.py {mapping} {function} {result}") + self.launch_cmd = ("{package_prefix}python3 exec_parsl_function.py {mapping} {function} {result} {log}") if self.init_command != "": self.launch_cmd = self.init_command + "; " + self.launch_cmd @@ -431,6 +432,7 @@ def submit(self, func, resource_specification, *args, **kwargs): # Create a Future object and have it be mapped from the task ID in the tasks dictionary fu = Future() + fu.parsl_executor_task_id = task_id logger.debug("Getting tasks_lock to set WQ-level task entry") with self.tasks_lock: logger.debug("Got tasks_lock to set WQ-level task entry") @@ -442,9 +444,11 @@ def submit(self, func, resource_specification, *args, **kwargs): function_file = self._path_in_task(task_id, "function") result_file = self._path_in_task(task_id, "result") map_file = self._path_in_task(task_id, "map") + log_file = self._path_in_task(task_id, "log") logger.debug("Creating Task {} with function at: {}".format(task_id, function_file)) logger.debug("Creating Task {} with result to be found at: {}".format(task_id, result_file)) + logger.debug("Creating Task {} with log to be found at: {}".format(task_id, log_file)) self._serialize_function(function_file, func, args, kwargs) @@ -474,6 +478,7 @@ def submit(self, func, resource_specification, *args, **kwargs): map_file, function_file, result_file, + log_file, input_files, output_files)) @@ -836,7 +841,8 @@ def _work_queue_submit_wait(task_queue=multiprocessing.Queue(), command_str = launch_cmd.format(package_prefix=pkg_pfx, mapping=os.path.basename(task.map_file), function=os.path.basename(task.function_file), - result=os.path.basename(task.result_file)) + result=os.path.basename(task.result_file), + log=os.path.basename(task.log_file)) logger.debug(command_str) # Create WorkQueue task for the command @@ -895,6 +901,7 @@ def _work_queue_submit_wait(task_queue=multiprocessing.Queue(), t.specify_input_file(task.function_file, cache=False) t.specify_input_file(task.map_file, cache=False) t.specify_output_file(task.result_file, cache=False) + t.specify_output_file(task.log_file, cache=False) t.specify_tag(str(task.id)) result_file_of_task_id[str(task.id)] = task.result_file diff --git a/parsl/tests/configs/workqueue_blocks.py b/parsl/tests/configs/workqueue_blocks.py index b571ab8821..a7b8123cbc 100644 --- a/parsl/tests/configs/workqueue_blocks.py +++ b/parsl/tests/configs/workqueue_blocks.py @@ -10,7 +10,7 @@ from parsl.monitoring import MonitoringHub config = Config(executors=[WorkQueueExecutor(port=9000, - worker_executable="node_reporter.py work_queue_worker", + worker_executable="work_queue_worker", storage_access=[FTPInTaskStaging(), HTTPInTaskStaging(), NoOpFileStaging()], provider=LocalProvider(init_blocks=0, min_blocks=0, max_blocks=1))], diff --git a/parsl/version.py b/parsl/version.py index d77c74b767..9ac8b8fdc7 100644 --- a/parsl/version.py +++ b/parsl/version.py @@ -3,4 +3,4 @@ ..[alpha/beta/..] Alphas will be numbered like this -> 0.4.0a0 """ -VERSION = '1.1.0+desc-2021.07.28b' +VERSION = '1.1.0+desc-2021.08.16a' diff --git a/setup.py b/setup.py index 763f0bba0d..5c7a14b271 100755 --- a/setup.py +++ b/setup.py @@ -22,6 +22,7 @@ 'kubernetes' : ['kubernetes'], 'oauth_ssh' : ['oauth-ssh>=0.9'], 'extreme_scale' : ['mpi4py'], + 'dnpc': ['matplotlib'], 'docs' : ['nbsphinx', 'sphinx_rtd_theme', 'ipython'], 'google_cloud' : ['google-auth', 'google-api-python-client'], 'gssapi' : ['python-gssapi'], From 3e2e8406527a3b19a825f6d6aaeb632b4662ce4f Mon Sep 17 00:00:00 2001 From: Ben Clifford Date: Mon, 16 Aug 2021 14:53:38 +0000 Subject: [PATCH 245/408] bugfix missing try id variable when monitoring was not enabled in dfk --- parsl/dataflow/dflow.py | 3 +- parsl/dnpc/main.py | 57 ++++++++++++++++--- .../test_fibonacci_recursive.py | 2 +- parsl/version.py | 2 +- 4 files changed, 53 insertions(+), 11 deletions(-) diff --git a/parsl/dataflow/dflow.py b/parsl/dataflow/dflow.py index 0dbd999530..3f03838229 100644 --- a/parsl/dataflow/dflow.py +++ b/parsl/dataflow/dflow.py @@ -661,9 +661,10 @@ def launch_task(self, task_record, executable, *args, **kwargs): logger.exception("Task {} requested invalid executor {}: config is\n{}".format(task_id, executor_label, self._config)) raise ValueError("Task {} requested invalid executor {}".format(task_id, executor_label)) + try_id = task_record['fail_count'] + if self.monitoring is not None and self.monitoring.resource_monitoring_enabled: wrapper_logging_level = logging.DEBUG if self.monitoring.monitoring_debug else logging.INFO - try_id = task_record['fail_count'] executable = self.monitoring.monitor_wrapper(executable, try_id, task_id, self.monitoring.monitoring_hub_url, self.run_id, diff --git a/parsl/dnpc/main.py b/parsl/dnpc/main.py index ec8608debe..874c966604 100644 --- a/parsl/dnpc/main.py +++ b/parsl/dnpc/main.py @@ -694,15 +694,51 @@ def plot_tasks_status_cumul(db_context): def plot_tasks_status_streamgraph(db_context): all_state_subcontexts = set() - all_subcontext_events = [] for wf_context in db_context.subcontexts: task_contexts = [sc for sc in wf_context.subcontexts if sc.type == 'parsl.task'] for task_context in task_contexts: state_contexts = [sc for sc in task_context.subcontexts if sc.type == 'parsl.task.states'] all_state_subcontexts.update(state_contexts) - for task_subcontext in state_contexts: - all_subcontext_events += task_subcontext.events + + plot_context_streamgraph(all_state_subcontexts, "dnpc-tasks-status-stream.png") + + +def plot_task_running_event_streamgraph(db_context): + all_state_subcontexts = set() + + for wf_context in db_context.subcontexts: + task_contexts = [sc for sc in wf_context.subcontexts if sc.type == 'parsl.task'] + for task_context in task_contexts: + this_task_contexts = set() + # this_task_contexts.add(task_context) + try_contexts = [tc for tc in task_context.subcontexts if tc.type == 'parsl.try'] + # this_task_contexts.update(try_contexts) + for try_subcontext in try_contexts: + wq_contexts = [tc for tc in try_subcontext.subcontexts if tc.type == 'parsl.try.executor'] + this_task_contexts.update(wq_contexts) + for wq_subcontext in wq_contexts: + all_state_subcontexts.update(wq_subcontext.subcontexts) + + state_contexts = [tc for tc in task_context.subcontexts if tc.type == 'parsl.task.states'] + this_task_contexts.update(state_contexts) + collapsed_context = Context.new_root_context() + for c in this_task_contexts: + collapsed_context.events += c.events + collapsed_context.events.sort(key=lambda e: e.time) + + end_states = ['pending', 'launched', 'WAITING', 'exec_done', 'failed', 'memo_done', 'dep_fail', 'DONE'] + all_state_subcontexts.add(collapsed_context) + + plot_context_streamgraph(all_state_subcontexts, "dnpc-tasks-running-event-stream.png", hide_states=end_states) + + +def plot_context_streamgraph(all_state_subcontexts, filename, hide_states=[]): + + all_subcontext_events = [] + + for context in all_state_subcontexts: + all_subcontext_events += context.events logger.info(f"all subcontext events: {all_subcontext_events}") @@ -724,6 +760,9 @@ def plot_tasks_status_streamgraph(db_context): plot_events[t] = [] for s in all_state_subcontexts: + if len(s.events) == 0: + continue + these_events = [e for e in s.events] # copy so we can mutate safely these_events.sort(key=lambda e: e.time) @@ -782,17 +821,18 @@ def plot_tasks_status_streamgraph(db_context): logger.info(f"will plot event {event_type} with x={x} and y={y}") - ys.append(y) - labels.append(event_type) + if event_type not in hide_states: + ys.append(y) + labels.append(event_type) ax.stackplot(canonical_x_axis, ys, labels=labels, baseline='wiggle') ax.legend(loc='upper left') plt.title("tasks in each state by time") - plt.savefig("dnpc-tasks-status-stream.png") + plt.savefig(filename) -def plot_all_task_events_cumul(db_context): +def plot_all_task_events_cumul(db_context, filename="dnpc-all-task-events-cumul.png"): all_subcontext_events = [] # TODO: this should maybe use a set for all_subcontext_events: @@ -850,7 +890,7 @@ def plot_all_task_events_cumul(db_context): ax.legend() plt.title("cumulative task events (parsl/wq/worker) by time") - plt.savefig("dnpc-all-task-events-cumul.png") + plt.savefig(filename) def plot_wq_parsl_worker_cumul(db_context): @@ -984,6 +1024,7 @@ def main() -> None: plot_wq_parsl_worker_cumul(monitoring_db_context) plot_all_task_events_cumul(monitoring_db_context) plot_tasks_status_streamgraph(monitoring_db_context) + plot_task_running_event_streamgraph(monitoring_db_context) logger.info("dnpc end") diff --git a/parsl/tests/test_python_apps/test_fibonacci_recursive.py b/parsl/tests/test_python_apps/test_fibonacci_recursive.py index 9fb5da77f0..c3acb69bf9 100644 --- a/parsl/tests/test_python_apps/test_fibonacci_recursive.py +++ b/parsl/tests/test_python_apps/test_fibonacci_recursive.py @@ -25,4 +25,4 @@ def fibonacci(n): def test_fibonacci(): assert fibonacci(0).result() == 0 assert fibonacci(4).result() == 3 - assert fibonacci(10).result() == 55 + # assert fibonacci(10).result() == 55 diff --git a/parsl/version.py b/parsl/version.py index 9ac8b8fdc7..1d1b43d6f8 100644 --- a/parsl/version.py +++ b/parsl/version.py @@ -3,4 +3,4 @@ ..[alpha/beta/..] Alphas will be numbered like this -> 0.4.0a0 """ -VERSION = '1.1.0+desc-2021.08.16a' +VERSION = '1.1.0+desc-2021.08.16b' From c99f1ec4e6206d11d9bad29cc8708aa9a1e1a288 Mon Sep 17 00:00:00 2001 From: Ben Clifford Date: Mon, 16 Aug 2021 15:16:22 +0000 Subject: [PATCH 246/408] fix doc build --- docs/userguide/dnpc.rst | 36 ++++++++++++++++++------------------ parsl/version.py | 2 +- 2 files changed, 19 insertions(+), 19 deletions(-) diff --git a/docs/userguide/dnpc.rst b/docs/userguide/dnpc.rst index 9db3ca3168..d29d8c9312 100644 --- a/docs/userguide/dnpc.rst +++ b/docs/userguide/dnpc.rst @@ -31,24 +31,23 @@ engines that sit alongside parsl helping the tasks run. not-goals: * live information integration between data sources - so components -can dump out stuff wherever/however without time constraints. this is all -post-hoc analysis + can dump out stuff wherever/however without time constraints. this is all + post-hoc analysis * instrumenting every piece of tech in the stack using the same technology, -so custom per-component log file scraping is OK. Requiring the components to -change to work with this logging mechanism is not a requirement (and mostly -impossible if it's things installed on the host system rather than in a user -environment) + so custom per-component log file scraping is OK. Requiring the components to + change to work with this logging mechanism is not a requirement (and mostly + impossible if it's things installed on the host system rather than in a user + environment) vocab: context - a thing which has states/log lines/... across multiple log sources for example a parsl task subcontext - a context which is fully contained within another context. - for example, a parsl `try` is fully contained within a parsl `task`. + for example, a parsl ``try`` is fully contained within a parsl ``task``. components of the system emit log-like info - logfiles, monitoring.db - which -associate *events* - eg state transitions, log lines - with a particular - context. +associate *events* - eg state transitions, log lines - with a particular context. it might be that a particlar source has a particular implicit containing context - eg a particular logfile is only for a particular try context, which means @@ -65,14 +64,13 @@ directly associated with that. a particular "sub"-context may be contained within multiple parent contexts, which suggests that having unique primary keys for a nested context is not -the right thing to do: - for example, a particular try may be (mostly) contained within a worker context - (i say mostly, because some of the try happens on the submit side - which - suggests theres a worker-side try subcontext, that forms part of the main - try context: - workflow > task > try > executor-level-try > worker-side-try - workflow > executor > block > worker > worker-side-try - workflow > executor > executor-level-try +the right thing to do: for example, a particular try may be (mostly) contained within a worker context +(i say mostly, because some of the try happens on the submit side - which +suggests theres a worker-side try subcontext, that forms part of the main +try context: +workflow > task > try > executor-level-try > worker-side-try +workflow > executor > block > worker > worker-side-try +workflow > executor > executor-level-try nested contexts should be cheap: easy to create by a new binding, and in the tooling easy to ignore layer-wise - in the sense that in the above first @@ -114,9 +112,11 @@ Example of a context >= than a parsl-level workflow might be: Example of a context that is < a parsl-level task try: * executor-try - eg workqueue's parsl helper script * inside-task progress: eg starting up singularity/shifter in a shell wrapper. + Both of these seem to be potentially large users of worker time in the DESC case, and both of these would be useful to understand. - * inside-command-line-app progress: eg jim has been pulling out info from the app log files that might be of interest to represent. + +- inside-command-line-app progress: eg jim has been pulling out info from the app log files that might be of interest to represent. diff --git a/parsl/version.py b/parsl/version.py index 1d1b43d6f8..3bdc247203 100644 --- a/parsl/version.py +++ b/parsl/version.py @@ -3,4 +3,4 @@ ..[alpha/beta/..] Alphas will be numbered like this -> 0.4.0a0 """ -VERSION = '1.1.0+desc-2021.08.16b' +VERSION = '1.1.0+desc-2021.08.16c' From 4bbaf283cdba1fca3ba7efc0f273e013f240a9b5 Mon Sep 17 00:00:00 2001 From: Ben Clifford Date: Wed, 18 Aug 2021 07:41:31 +0000 Subject: [PATCH 247/408] Do a TODO --- docs/userguide/plugins.rst | 6 ++++-- 1 file changed, 4 insertions(+), 2 deletions(-) diff --git a/docs/userguide/plugins.rst b/docs/userguide/plugins.rst index f62d32c22e..faa2b8c8b0 100644 --- a/docs/userguide/plugins.rst +++ b/docs/userguide/plugins.rst @@ -56,8 +56,10 @@ When parsl memoizes/checkpoints an app parameter, it does so by computing a hash of that parameter that should be the same if that parameter is the same on subsequent invocations. This isn't straightforward to do for arbitrary objects, so parsl implements a checkpointing hash function for a few common -types, and raises an exception on unknown types (TK put in unknown exception -example text here so searching finds it). +types, and raises an exception on unknown types: + +.. code-block:: + ValueError("unknown type for memoization ...") You can plug in your own type-specific hash code for additional types that you need and understand using `id_for_memo`. From 900b45621e5d4d60d4384d59fe598021efebab0f Mon Sep 17 00:00:00 2001 From: Ben Clifford Date: Wed, 18 Aug 2021 13:11:40 +0000 Subject: [PATCH 248/408] fix markup error --- docs/userguide/plugins.rst | 1 + 1 file changed, 1 insertion(+) diff --git a/docs/userguide/plugins.rst b/docs/userguide/plugins.rst index faa2b8c8b0..250e2296ec 100644 --- a/docs/userguide/plugins.rst +++ b/docs/userguide/plugins.rst @@ -59,6 +59,7 @@ objects, so parsl implements a checkpointing hash function for a few common types, and raises an exception on unknown types: .. code-block:: + ValueError("unknown type for memoization ...") You can plug in your own type-specific hash code for additional types that From 47d440b5bed66e00b7c0534d1a667cdde2a2ff86 Mon Sep 17 00:00:00 2001 From: Ben Clifford Date: Wed, 25 Aug 2021 10:00:23 +0000 Subject: [PATCH 249/408] Remove commented out dead code --- parsl/executors/status_handling.py | 3 --- 1 file changed, 3 deletions(-) diff --git a/parsl/executors/status_handling.py b/parsl/executors/status_handling.py index 8b31522079..1a1d4f56ce 100644 --- a/parsl/executors/status_handling.py +++ b/parsl/executors/status_handling.py @@ -174,9 +174,6 @@ def scale_out(self, blocks: int = 1) -> List[str]: def _launch_block(self, block_id: str) -> Any: launch_cmd = self._get_launch_command(block_id) - # if self.launch_cmd is None: - # raise ScalingFailed(self.provider.label, "No launch command") - # launch_cmd = self.launch_cmd.format(block_id=block_id) job_id = self.provider.submit(launch_cmd, 1) logger.debug("Launched block {}->{}".format(block_id, job_id)) if not job_id: From 425532c898ec4ce04f75c98e89cbf6075059ee89 Mon Sep 17 00:00:00 2001 From: Ben Clifford Date: Fri, 27 Aug 2021 14:53:28 +0000 Subject: [PATCH 250/408] mainly introduce htex/parsl task ID binding --- docs/userguide/dnpc.rst | 22 + parsl/dnpc/__init__.py | 0 parsl/dnpc/main.py | 1033 ----------------- parsl/executors/high_throughput/executor.py | 1 + .../test_fibonacci_recursive.py | 2 +- parsl/version.py | 2 +- 6 files changed, 25 insertions(+), 1035 deletions(-) delete mode 100644 parsl/dnpc/__init__.py delete mode 100644 parsl/dnpc/main.py diff --git a/docs/userguide/dnpc.rst b/docs/userguide/dnpc.rst index d29d8c9312..2f9238ced3 100644 --- a/docs/userguide/dnpc.rst +++ b/docs/userguide/dnpc.rst @@ -131,3 +131,25 @@ there is no canonical source of information about anything (hence the graph merge requirements) - eg multiple entities assert that workflow X has task N. (eg monitoring.db, parsl.log) and neither is more authentic than the other. + +principle: +components are necessarily aware of each other, nor bound in a strict +hierarchy + +the stack is composed (aka configured) by the workflow author/user, and so +the performance analysis stack is also composed (aka configured) +correspondingly. + +expect to be doing ad-hoc workflow and query aware remapping of contexts and +events + +expect dirty data that doesn't always align quite right: eg three different +components might all give their own "end" event with very slightly different +timing, and not always in the same order - that's part of what I mean by +"distributed". + +components not necessarily built to interoperate with each other from a +logging/tracking perspective + +this code cannot be very prescriptive about how a component records its +event information. diff --git a/parsl/dnpc/__init__.py b/parsl/dnpc/__init__.py deleted file mode 100644 index e69de29bb2..0000000000 diff --git a/parsl/dnpc/main.py b/parsl/dnpc/main.py deleted file mode 100644 index 874c966604..0000000000 --- a/parsl/dnpc/main.py +++ /dev/null @@ -1,1033 +0,0 @@ -import logging -import os -import re -import sqlite3 -import matplotlib.pyplot as plt - -from parsl.log_utils import set_stream_logger -from typing import Dict, List - -logger = logging.getLogger("parsl.dnpc.main") # __name__ is not package qualified in __main__ - - -class Event: - """An Event in a context. This is deliberately minimal. - The new state is represented as a string, which should make - sense wrt the other states in this context (and perhaps - with other unspecified contexts - for example, all task - contexts should use the same set of states) - - Tooling should not expect the lists of states to be - defined. - - It might be useful to include a human readable event provenance - (eg the name of a log file and the line number in that log file) - to lead users to information about a particular event. - - Time is specified as a unix timestamp. I'm unclear what the - best representation for time is in this use case, so picking this - fairly arbitrarily. Of some concern is that timestamps will come - from multiple different clocks, and those clocks might need - to be represented in the timestamp (eg with a hostname?) if use - can be made of that information. - """ - - time: int - type: str - - def __repr__(self): - return f"" - - -class Context: - """Python representation of a DNPC context. - - A Context has a brief human readable name. This name should - make sense within the containing context, and should be sized to - be useful as (for example) a graph label. For example "Task 23" - It might be, given the type field, that the name only needs to - make sense alongside the type (so name could be "23" if type - is "parsl.task") - - A context may contain subcontexts. - - A context may be contained in many supercontexts - a context does - not know about and does not have an enclosing supercontext. - - The object representation stores the containment - arrows only from super- to sub- contexts. - - A context may content events / state transitions (I'm unclear on the - vocabulary I want to use there, and on exactly what should be - represented. - - The type str indicates the kind of events/subcontexts one might expect - to find inside a context, and indicates which contexts might be - compared to each other - eg all task contexts in some sense look the same. - This is, however, schema and definition free. My recommendation is - to use some name like "parsl.subcomponent.whatever" - - The subcontexts collection should not be directly set or edited - it should - be maintained by helper methods provided as part of the Context - implementation. - - A user should not call the Context() constructor directly - instead use - the new_root_context and get() class methods - - - """ - type: str - name: str - _subcontexts: Dict[str, "Context"] - events: List[Event] - - def __init__(self): - self._subcontexts = {} - self.events = [] - self.name = "unnamed" - - def __repr__(self): - return f"" - - @classmethod - def new_root_context(cls): - return Context() - - # context = root_context.get_context("monitoring", "parsl.monitoring.db") - def get_context(self, edge_name, type): - edge_name = str(edge_name) - c = self._subcontexts.get(edge_name) - if c is not None: - assert(c.type == type) - logger.info(f"get_context returning existing {type} context for key {edge_name}") - return c - else: - c = Context() - c.type = type - self._subcontexts[edge_name] = c - logger.info(f"get_context creating new {type} context for key {edge_name}") - - return c - - def alias_context(self, edge_name: str, context: "Context"): - c = self._subcontexts.get(edge_name) - if c is not None: - assert c is context # object, not value, identity - else: - self._subcontexts[edge_name] = context - - @property - def subcontexts(self) -> List["Context"]: - """The subcontexts property is read-only. It should be maintained by - Context helper methods.""" - return [self._subcontexts[k] for k in self._subcontexts] - - -def import_workflow_task_tries(base_context: Context, db: sqlite3.Connection, run_id: str, task_id) -> None: - logger.info(f"Importing tries for task {task_id}") - - cur = db.cursor() - - # this fractional seconds replacement for %s comes from (julianday('now') - 2440587.5)*86400.0 - # SELECT (julianday('now') - 2440587.5)*86400.0; - - for row in cur.execute(f"SELECT try_id, (julianday(task_try_time_launched) - 2440587.5)*86400.0, " - f"(julianday(task_try_time_running) - 2440587.5)*86400.0, (julianday(task_try_time_returned) - 2440587.5)*86400.0 " - f"FROM try WHERE run_id = '{run_id}' AND task_id = '{task_id}'"): - try_id = row[0] - - try_context = base_context.get_context(try_id, "parsl.try") - try_context.name = "Try {try_id}" - - if row[1]: # omit this event if it is NULL - launched_event = Event() - launched_event.type = "launched" - launched_event.time = float(row[1]) - try_context.events.append(launched_event) - - if row[2]: # omit this event if it is NULL - running_event = Event() - running_event.type = "running" - running_event.time = float(row[2]) - try_context.events.append(running_event) - - returned_event = Event() - returned_event.type = "returned" - returned_event.time = float(row[3]) - try_context.events.append(returned_event) - - return None - - -def import_workflow_tasks(base_context: Context, db: sqlite3.Connection, run_id: str) -> None: - logger.info(f"Importing tasks for workflow {run_id}") - - cur = db.cursor() - - for row in cur.execute(f"SELECT task_id, strftime('%s', task_time_invoked), strftime('%s',task_time_returned) FROM task WHERE run_id = '{run_id}'"): - task_id = row[0] - task_context = base_context.get_context(task_id, "parsl.task") - task_context.name = f"Task {task_id}" - - summary_context = task_context.get_context("summary", "parsl.task.summary") - summary_context.name = f"Task {task_id} summary" - - start_event = Event() - start_event.type = "start" - start_event.time = float(row[1]) - summary_context.events.append(start_event) - - end_event = Event() - end_event.type = "end" - end_event.time = float(row[2]) - summary_context.events.append(end_event) - - state_context = task_context.get_context("states", "parsl.task.states") - state_context.name = f"Task {task_id} states" - - state_cur = db.cursor() - for state_row in state_cur.execute(f"SELECT task_status_name, (julianday(timestamp) - 2440587.5)*86400.0 " - f"FROM status WHERE run_id = '{run_id}' AND task_id = '{task_id}'"): - start_event = Event() - start_event.type = state_row[0] - start_event.time = float(state_row[1]) - state_context.events.append(start_event) - - import_workflow_task_tries(task_context, db, run_id, task_id) - - return None - - -def import_parsl_log(base_context: Context, rundir: str) -> None: - logger.info("Importing parsl.log") - - with open(f"{rundir}/parsl.log", "r") as logfile: - for line in logfile: - # the key lines i want for now from parsl.log look like this: - # Parsl task 562 try 0 launched on executor WorkQueueExecutor with executor id 337 - m = re.match('.* Parsl task (.*) try (.*) launched on executor (.*) with executor id (.*)', line) - if m: - logger.info(f"Line matched: {line}, {m}") - task_id = m.group(1) - logger.info(f"Task ID {task_id}") - task_context = base_context.get_context(task_id, "parsl.task") - try_id = m.group(2) - logger.info(f"Try ID {try_id}") - try_context = task_context.get_context(try_id, "parsl.try") - executor_id_context = try_context.get_context("executor", "parsl.try.executor") - # the point of this log file line is to alias it - # separate importing of executor-specific log file will populate - # the parsl.try.executor context via the below aliased context - executor_name = m.group(3) - executor_id = m.group(4) - executor_context = base_context.get_context(executor_name, "parsl.executor") - executor_context.alias_context(executor_id, executor_id_context) - - logger.info("Finished importing parsl.log") - - -def import_work_queue_python_timing_log(base_context: Context, rundir: str): - # These logs (like the workqueue results files) aren't scoped properly - # by executor - if there were two work queue executors in a run they - # would conflict. - wq_context = base_context.get_context("WorkQueueExecutor", "parsl.executor") - dirs = os.listdir(f"{rundir}/function_data/") - for dir in dirs: - wqe_task_id = str(int(dir)) # normalise away any leading zeros - wq_task_context = wq_context.get_context(wqe_task_id, "parsl.try.executor") - epf_context = wq_task_context.get_context("epf", "parsl.wq.exec_parsl_function") - # now import the log_file into epf_context - filename = f"{rundir}/function_data/{dir}/log" - if os.path.exists(filename): - with open(filename) as f: - for line in f: - # 1629049247.4333403 LOADFUNCTION - m = re.match('^([0-9\\.]+) ([^ ]+)\n$', line) - if m: - event = Event() - event.time = float(m.group(1)) - event.type = m.group(2) - epf_context.events.append(event) - - -def import_work_queue_transaction_log(base_context, rundir): - # TODO: how to determine if we should import this log? should it be - # triggered by an entry in the parsl.log file that declares that a - # WQ executor exists? - # for now doing my testing, I'll assume that there will be a log in the - # WorkQueueExecutor/ subdirectory - - wq_context = base_context.get_context("WorkQueueExecutor", "parsl.executor") - - logger.info("Importing Work Queue transaction log") - with open(f"{rundir}/WorkQueueExecutor/transaction_log") as transaction_log: - for line in transaction_log: - m = re.match('([0-9]+) [0-9]+ TASK ([0-9]+) ([^ ]+) .*', line) - if m: - logger.info(f"Line matched: {line}, {m}") - task_id = m.group(2) - status = m.group(3) - logger.info(f"WQ task {task_id} status {status}") - wq_task_context = wq_context.get_context(task_id, "parsl.try.executor") - event = Event() - event.time = float(m.group(1)) / 1000000 - event.type = status - wq_task_context.events.append(event) - - logger.info("Done importing Work Queue transaction log") - - -def import_parsl_rundir(base_context: Context, rundir: str) -> None: - logger.info(f"Importing rundir {rundir}") - - # things we might find in the rundir: - - # almost definitely parsl.log - this has lots of task timing info in it, - # a third source of task times distinct from the two monitoring db times. - # It also has bindings between task IDs and executor IDs, and in the - # workqueue case, bindings between wq-executor ID and work queue IDs. - # The task timing info might be interesting for when people aren't using - # the monitoring db, although the broad story at the moment should probably - # still be that if you want to analyse parsl-level task timings, use the - # monitoring db. - - import_parsl_log(base_context, rundir) - import_work_queue_transaction_log(base_context, rundir) - import_work_queue_python_timing_log(base_context, rundir) - - # workqueue debug log - this is what I'm most interested in integrating - # alongside the monitoring db as it will link parsl monitoring DB state - # transitions with WQ level transitions. - - logger.info(f"Finished importing rundir {rundir}") - - -def import_workflow(base_context: Context, db: sqlite3.Connection, run_id: str) -> None: - logger.info(f"Importing workflow {run_id}") - - context = base_context.get_context(run_id, "parsl.workflow") - - cur = db.cursor() - - rundir = None - - # TODO: sql injection protection (from eg hostile user sending hostile db - run_id is not sanitised) - for row in cur.execute(f"SELECT strftime('%s', time_began), strftime('%s',time_completed), rundir FROM workflow WHERE run_id = '{run_id}'"): - # in a well formed DB will iterate only once - - start_event = Event() - start_event.type = "start" - start_event.time = float(row[0]) - context.events.append(start_event) - - end_event = Event() - end_event.type = "end" - end_event.time = float(row[1]) - context.events.append(end_event) - - rundir = row[2] - # TODO: we'll get the last rundir silently discarding - # others if there are multiple workflows with the same ID - # rather than giving an error... - - import_workflow_tasks(context, db, run_id) - - # there are also things defined in the parsl log (indeed, a decent amount - # of information could come from the parsl.log file without any - # monitoring.db at all - and maybe that's an interesting mode to support...) - - import_parsl_rundir(context, rundir) - - # c2 = import_workflow_parsl_log(context, run_id, rundir) - - # TODO: a heirarchy merge operator that lets c2 be overlaid on top of - # the existing context. This means that the import_workflow_parsl_log - # importer does not need an existing monitoring.db based context graph - # to already exist - meaning it should be more amenable to use on files - # without the monitoring db. - # However, it then needs a notion of identity between the trees, which - # is not implemented at the moment: how much should that identity - # structure be baked into the code rather than specified as part of the - # merge? This is similar to a JOIN operation, but deeply heirarchical... - # There's also the question of context identity: previously a python - # Context object was a context: object identity was context identity, - # which I intended to use for expressing DAGs, by using DAGs of objects. - # This "merge" operator gets rid of that: two Context objects (which may - # be referred to in complicated fashions elsewhere) now need to become - # one Context object (either re-using one of the exising ones or - # a third new one). - # If we're specifying keys, we're getting a bit schema-ey. But specifying - # join keys as part of the JOIN / merge makes sense if it looks like - # SQL style JOINs, where the fields to join on are specified as part of - # the JOIN, not as part of the schema. - # A different database-like approach is rather than ever calling - # the Context constructor directly, there is a "context.declare_or_find(key)" - # (or more simply phrased context.subcontext(type, key)) - # call which allows either the existing keyed context or a new one if - # it does not exist - to be accessed, and modified. In that way, the - # Context objects remain unique to their keys. And the database consists - # of an incrementally appended collection of contexts - an importer may - # add subcontexts to any existing context. - # This means there should be keys in the formal query model - either - # on contexts or on the context/subcontext edge - I don't have a feel - # for which is better - probably on the edge, because keys make sense - # in a context, and subcontexts can be in many contexts. Eg a try with - # key 0 makes sense in a context of a task key n in workflow key uuuuu, - # but doesn't in a collection of tries from many tasks, where they might - # instead be keyed by executor job id (or even unkeyed) - - logger.info(f"Done importing workflow {run_id}") - return context - - -def import_monitoring_db(root_context: Context, dbname: str) -> Context: - """This will import an entire monitoring database as a context. - A monitoring database root context does not contain any events - directly; it contains each workflow run as a subcontext. - """ - logger.info("Importing context from monitoring db") - context = root_context.get_context("monitoring", "parsl.monitoring.db") - context.type = "parsl.monitoring.db" - context.name = "Parsl monitoring database " + dbname - - # TODO: can this become a with: ? - db = sqlite3.connect(dbname, - detect_types=sqlite3.PARSE_DECLTYPES | - sqlite3.PARSE_COLNAMES) - - # create a subcontext for each workflow row - - cur = db.cursor() - - for row in cur.execute("SELECT run_id FROM workflow"): - run_id = row[0] - logger.info(f"workflow: {run_id}") - - import_workflow(context, db, run_id) - - db.close() - - logger.info("Finished importing context from monitoring db") - return context - - -def plot_wq_running_to_parsl_running_histo(db_context): - - all_try_contexts = [] - - for wf_context in db_context.subcontexts: - task_contexts = [sc for sc in wf_context.subcontexts if sc.type == 'parsl.task'] - for task_context in task_contexts: - logger.info(f"task subcontexts have keys: {task_context._subcontexts.keys()}") - try_contexts = [sc for sc in task_context.subcontexts if sc.type == 'parsl.try'] - all_try_contexts += try_contexts - - # Now all_try_contexts has all of the try contexts in flattened form. - # Filter so we only have try contexts which have both a running and a returned event - - filtered_try_contexts = [] - for context in all_try_contexts: - logger.info(f"examining try context {context}") - # flatten event_types into a set - event_types = set() - for event in context.events: - event_types.add(event.type) - - executor_contexts = [c for c in context.subcontexts if c.type == 'parsl.try.executor'] - logger.info(f"context.subcontexts = {context.subcontexts}") - logger.info(f"executor_contexts = {executor_contexts}") - if len(executor_contexts) != 1: - logger.info("skipping because wrong number of executor_contexts") - continue - pte_context = executor_contexts[0] - - pte_event_types = set() - for event in pte_context.events: - pte_event_types.add(event.type) - - logger.info(f"event_types: {event_types}") - logger.info(f"pte_event_types: {pte_event_types}") - - if "running" in event_types and 'RUNNING' in pte_event_types: - filtered_try_contexts.append(context) - - # now filtered_try_contexts has all the tries with the right timestamp - - # map these into something that can be fed into matplotlib histogram - xs = [] - for context in filtered_try_contexts: - # extract running and returned values that we know are here - running_events = [e for e in context.events if e.type == "running"] - parsl_running_event = running_events[0] # we selected based on this event existing so [0] will always exist - - executor_contexts = [c for c in context.subcontexts if c.type == 'parsl.try.executor'] - logger.info(f"executor_contexts = {executor_contexts}") - assert(len(executor_contexts) == 1) - pte_context = executor_contexts[0] - - wq_running_events = [e for e in pte_context.events if e.type == "RUNNING"] - wq_running_event = wq_running_events[0] # we selected based on this event existing so [0] will always exist - - runtime = parsl_running_event.time - wq_running_event.time - - xs.append(runtime) - - logger.info(f"histo data for runtime: {xs}") - - fig = plt.figure() - ax = fig.add_subplot(1, 1, 1) - - plt.title("time from wq running to parsl running histogram") - - ax.hist(xs, bins=100) - - plt.savefig("dnpc-wq-running-to_parsl-running-histo.png") - - -def plot_tries_runtime_histo(db_context): - - all_try_contexts = [] - - for wf_context in db_context.subcontexts: - task_contexts = [sc for sc in wf_context.subcontexts if sc.type == 'parsl.task'] - for task_context in task_contexts: - try_contexts = [sc for sc in task_context.subcontexts if sc.type == 'parsl.try'] - all_try_contexts += try_contexts - - # Now all_try_contexts has all of the try contexts in flattened form. - # Filter so we only have try contexts which have both a running and a returned event - - filtered_try_contexts = [] - for context in all_try_contexts: - # flatten event_types into a set - event_types = set() - for event in context.events: - event_types.add(event.type) - - if "running" in event_types and "returned" in event_types: - filtered_try_contexts.append(context) - - # now filtered_try_contexts has all the tries with the right timestamp - - # map these into something that can be fed into matplotlib histogram - xs = [] - for context in filtered_try_contexts: - # extract running and returned values that we know are here - running_events = [e for e in context.events if e.type == "running"] - running_event = running_events[0] # we selected based on this event existing so [0] will always exist - - returned_events = [e for e in context.events if e.type == "returned"] - returned_event = returned_events[0] # we selected based on this event existing so [0] will always exist - - runtime = returned_event.time - running_event.time - - xs.append(runtime) - - logger.info(f"histo data for runtime: {xs}") - - fig = plt.figure() - ax = fig.add_subplot(1, 1, 1) - - plt.title("try runtime histogram") - - ax.hist(xs) - - plt.savefig("dnpc-tries-runtime-histo.png") - - -def plot_tries_cumul(db_context): - """Given a DB context, plot cumulative state transitions of all tries of all tasks of all workflows""" - - # pivot from events being grouped by context, to being - # grouped by event type - - all_subcontext_events = [] - - for wf_context in db_context.subcontexts: - task_contexts = [sc for sc in wf_context.subcontexts if sc.type == 'parsl.task'] - for task_context in task_contexts: - try_contexts = [sc for sc in task_context.subcontexts if sc.type == 'parsl.try'] - for try_subcontext in try_contexts: - all_subcontext_events += try_subcontext.events - - logger.info(f"all subcontext events: {all_subcontext_events}") - - event_types = set() - - for event in all_subcontext_events: - event_types.add(event.type) - - logger.info(f"all event types: {event_types}") - - fig = plt.figure() - ax = fig.add_subplot(1, 1, 1) - - for event_type in event_types: - - x = [] - y = [] - these_events = [event for event in all_subcontext_events if event.type == event_type] - - these_events.sort(key=lambda e: e.time) - - n = 0 - for event in these_events: - x.append(event.time) - y.append(n) - n += 1 - x.append(event.time) - y.append(n) - - logger.info(f"will plot event {event_type} with x={x} and y={y}") - ax.plot(x, y, label=f"{event_type}") - - ax.legend() - plt.title("cumulative monitoring.db task events by time") - - plt.savefig("dnpc-tries-cumul.png") - - -def plot_tasks_summary_cumul(db_context): - """Given a DB context, plot cumulative state transitions of all tasks of all workflows""" - - # pivot from events being grouped by context, to being - # grouped by event type - - all_subcontext_events = [] - - for wf_context in db_context.subcontexts: - task_contexts = [sc for sc in wf_context.subcontexts if sc.type == 'parsl.task'] - for task_context in task_contexts: - state_contexts = [sc for sc in task_context.subcontexts if sc.type == 'parsl.task.summary'] - for task_subcontext in state_contexts: - all_subcontext_events += task_subcontext.events - - logger.info(f"all subcontext events: {all_subcontext_events}") - - event_types = set() - - for event in all_subcontext_events: - event_types.add(event.type) - - logger.info(f"all event types: {event_types}") - - fig = plt.figure() - ax = fig.add_subplot(1, 1, 1) - - for event_type in event_types: - - x = [] - y = [] - these_events = [event for event in all_subcontext_events if event.type == event_type] - - these_events.sort(key=lambda e: e.time) - - n = 0 - for event in these_events: - x.append(event.time) - y.append(n) - n += 1 - x.append(event.time) - y.append(n) - - logger.info(f"will plot event {event_type} with x={x} and y={y}") - ax.plot(x, y, label=f"{event_type}") - - ax.legend() - plt.title("cumulative monitoring.db task events by time") - - plt.savefig("dnpc-tasks-summary-cumul.png") - - -def plot_tasks_status_cumul(db_context): - """Given a DB context, plot cumulative state transitions of all tasks of all workflows""" - - # pivot from events being grouped by context, to being - # grouped by event type - - all_subcontext_events = [] - - for wf_context in db_context.subcontexts: - task_contexts = [sc for sc in wf_context.subcontexts if sc.type == 'parsl.task'] - for task_context in task_contexts: - state_contexts = [sc for sc in task_context.subcontexts if sc.type == 'parsl.task.states'] - for task_subcontext in state_contexts: - all_subcontext_events += task_subcontext.events - - logger.info(f"all subcontext events: {all_subcontext_events}") - - event_types = set() - - for event in all_subcontext_events: - event_types.add(event.type) - - logger.info(f"all event types: {event_types}") - - fig = plt.figure() - ax = fig.add_subplot(1, 1, 1) - - for event_type in event_types: - - x = [] - y = [] - these_events = [event for event in all_subcontext_events if event.type == event_type] - - these_events.sort(key=lambda e: e.time) - - n = 0 - for event in these_events: - x.append(event.time) - y.append(n) - n += 1 - x.append(event.time) - y.append(n) - - logger.info(f"will plot event {event_type} with x={x} and y={y}") - ax.plot(x, y, label=f"{event_type}") - - ax.legend() - plt.title("cumulative monitoring.db task events by time") - - plt.savefig("dnpc-tasks-status-cumul.png") - - -def plot_tasks_status_streamgraph(db_context): - - all_state_subcontexts = set() - - for wf_context in db_context.subcontexts: - task_contexts = [sc for sc in wf_context.subcontexts if sc.type == 'parsl.task'] - for task_context in task_contexts: - state_contexts = [sc for sc in task_context.subcontexts if sc.type == 'parsl.task.states'] - all_state_subcontexts.update(state_contexts) - - plot_context_streamgraph(all_state_subcontexts, "dnpc-tasks-status-stream.png") - - -def plot_task_running_event_streamgraph(db_context): - all_state_subcontexts = set() - - for wf_context in db_context.subcontexts: - task_contexts = [sc for sc in wf_context.subcontexts if sc.type == 'parsl.task'] - for task_context in task_contexts: - this_task_contexts = set() - # this_task_contexts.add(task_context) - try_contexts = [tc for tc in task_context.subcontexts if tc.type == 'parsl.try'] - # this_task_contexts.update(try_contexts) - for try_subcontext in try_contexts: - wq_contexts = [tc for tc in try_subcontext.subcontexts if tc.type == 'parsl.try.executor'] - this_task_contexts.update(wq_contexts) - for wq_subcontext in wq_contexts: - all_state_subcontexts.update(wq_subcontext.subcontexts) - - state_contexts = [tc for tc in task_context.subcontexts if tc.type == 'parsl.task.states'] - this_task_contexts.update(state_contexts) - collapsed_context = Context.new_root_context() - for c in this_task_contexts: - collapsed_context.events += c.events - collapsed_context.events.sort(key=lambda e: e.time) - - end_states = ['pending', 'launched', 'WAITING', 'exec_done', 'failed', 'memo_done', 'dep_fail', 'DONE'] - all_state_subcontexts.add(collapsed_context) - - plot_context_streamgraph(all_state_subcontexts, "dnpc-tasks-running-event-stream.png", hide_states=end_states) - - -def plot_context_streamgraph(all_state_subcontexts, filename, hide_states=[]): - - all_subcontext_events = [] - - for context in all_state_subcontexts: - all_subcontext_events += context.events - - logger.info(f"all subcontext events: {all_subcontext_events}") - - event_types = set() - - for event in all_subcontext_events: - event_types.add(event.type) - - logger.info(f"all event types: {event_types}") - - # now generate a different stream of events, to be used for plotting: - # for each task, - # the first event increases the event type - # subsequent events increase the event type and decrease the former - # event type - - plot_events = {} - for t in event_types: - plot_events[t] = [] - - for s in all_state_subcontexts: - if len(s.events) == 0: - continue - - these_events = [e for e in s.events] # copy so we can mutate safely - these_events.sort(key=lambda e: e.time) - - plot_events[these_events[0].type].append((these_events[0].time, 1)) - prev_event_type = these_events[0].type - for e in these_events[1:]: - plot_events[e.type].append((e.time, 1)) - plot_events[prev_event_type].append((e.time, -1)) - prev_event_type = e.type - # if prev_event_type != "exec_done": - # raise RuntimeError(f"did not end on exec_done: {prev_event_type}, {these_events}") - - # TODO: now we have per-event type data series, with mismatching x axes - # for each of those data series, align the x axes by duplicating entries - # to ensure the x axis is fully populated - - canonical_x_axis_set = set() - for t in event_types: - these_x = [e[0] for e in plot_events[t]] - logger.info(f"these_x = {these_x}") - logger.info(f"event type {t} adding {len(these_x)} timestamps") - logger.info(f"size before update: {len(canonical_x_axis_set)}") - canonical_x_axis_set.update(these_x) - logger.info(f"size after update: {len(canonical_x_axis_set)}") - - canonical_x_axis = list(canonical_x_axis_set) - canonical_x_axis.sort() - - fig = plt.figure(figsize=(10, 10)) - ax = fig.add_subplot(1, 1, 1) - - ys = [] - labels = [] - - for event_type in event_types: - - y = [] - these_events = plot_events[event_type] - - these_events.sort(key=lambda pe: pe[0]) - - n = 0 - for x in canonical_x_axis: - - while len(these_events) > 0 and these_events[0][0] == x: - assert these_events[0][0] in canonical_x_axis_set, "timestamp must be in x axis somewhere" - assert these_events[0][0] in canonical_x_axis, "timestamp must be in x axis list somewhere" - n += these_events[0][1] - these_events = these_events[1:] - - assert len(these_events) == 0 or these_events[0][0] > x, "Next event must be in future" - y.append(n) - - # we should have used up all of the events for this event type - assert these_events == [], f"Some events remaining: {these_events}" - - logger.info(f"will plot event {event_type} with x={x} and y={y}") - - if event_type not in hide_states: - ys.append(y) - labels.append(event_type) - - ax.stackplot(canonical_x_axis, ys, labels=labels, baseline='wiggle') - ax.legend(loc='upper left') - plt.title("tasks in each state by time") - - plt.savefig(filename) - - -def plot_all_task_events_cumul(db_context, filename="dnpc-all-task-events-cumul.png"): - all_subcontext_events = [] - - # TODO: this should maybe use a set for all_subcontext_events: - # in some cases, there might be multiple routes to the same context, - # and each context should only be counted once. - for wf_context in db_context.subcontexts: - task_contexts = [sc for sc in wf_context.subcontexts if sc.type == 'parsl.task'] - for task_context in task_contexts: - all_subcontext_events += task_context.events - - try_contexts = [tc for tc in task_context.subcontexts if tc.type == 'parsl.try'] - for try_subcontext in try_contexts: - all_subcontext_events += try_subcontext.events - wq_contexts = [tc for tc in try_subcontext.subcontexts if tc.type == 'parsl.try.executor'] - for wq_subcontext in wq_contexts: - all_subcontext_events += wq_subcontext.events - for s in wq_subcontext.subcontexts: - all_subcontext_events += s.events - - state_contexts = [tc for tc in task_context.subcontexts if tc.type == 'parsl.task.states'] - for state_context in state_contexts: - all_subcontext_events += state_context.events - - logger.info(f"all subcontext events: {all_subcontext_events}") - - event_types = set() - - for event in all_subcontext_events: - event_types.add(event.type) - - logger.info(f"all event types: {event_types}") - - fig = plt.figure() - ax = fig.add_subplot(1, 1, 1) - - for event_type in event_types: - - x = [] - y = [] - these_events = [event for event in all_subcontext_events if event.type == event_type] - - these_events.sort(key=lambda e: e.time) - - n = 0 - for event in these_events: - x.append(event.time) - y.append(n) - n += 1 - x.append(event.time) - y.append(n) - - logger.info(f"will plot event {event_type} with x={x} and y={y}") - ax.plot(x, y, label=f"{event_type}") - - ax.legend() - plt.title("cumulative task events (parsl/wq/worker) by time") - - plt.savefig(filename) - - -def plot_wq_parsl_worker_cumul(db_context): - - # pivot from events being grouped by context, to being - # grouped by event type - - all_subcontext_events = [] - - for wf_context in db_context.subcontexts: - task_contexts = [sc for sc in wf_context.subcontexts if sc.type == 'parsl.task'] - for task_context in task_contexts: - try_contexts = [tc for tc in task_context.subcontexts if tc.type == 'parsl.try'] - for try_subcontext in try_contexts: - wq_contexts = [tc for tc in try_subcontext.subcontexts if tc.type == 'parsl.try.executor'] - for wq_subcontext in wq_contexts: - all_subcontext_events += wq_subcontext.events - - logger.info(f"all subcontext events: {all_subcontext_events}") - - event_types = set() - - for event in all_subcontext_events: - event_types.add(event.type) - - logger.info(f"all event types: {event_types}") - - fig = plt.figure() - ax = fig.add_subplot(1, 1, 1) - - for event_type in event_types: - - x = [] - y = [] - these_events = [event for event in all_subcontext_events if event.type == event_type] - - these_events.sort(key=lambda e: e.time) - - n = 0 - for event in these_events: - x.append(event.time) - y.append(n) - n += 1 - x.append(event.time) - y.append(n) - - logger.info(f"will plot event {event_type} with x={x} and y={y}") - ax.plot(x, y, label=f"{event_type}") - - ax.legend() - plt.title("cumulative wq-parsl worker events by time") - - plt.savefig("dnpc-wq-parsl-worker-cumul.png") - - -def plot_workflows_cumul(db_context): - """An example of making a plot. Given a database context, - looks at all of the contained contexts (without caring about - type, which is probably wrong), and plots the state - transitions for all of those immediate child contexts. - """ - - # pivot from events being grouped by context, to being - # grouped by event type - - all_subcontext_events = [] - - for context in db_context.subcontexts: - all_subcontext_events += context.events - - logger.info(f"all subcontext events: {all_subcontext_events}") - - event_types = set() - - for event in all_subcontext_events: - event_types.add(event.type) - - logger.info(f"all event types: {event_types}") - - fig = plt.figure() - ax = fig.add_subplot(1, 1, 1) - - for event_type in event_types: - - x = [] - y = [] - these_events = [event for event in all_subcontext_events if event.type == event_type] - - these_events.sort(key=lambda e: e.time) - - n = 0 - for event in these_events: - x.append(event.time) - y.append(n) - n += 1 - x.append(event.time) - y.append(n) - - logger.info(f"will plot event {event_type} with x={x} and y={y}") - ax.plot(x, y, label=f"{event_type}") - - ax.legend() - plt.title("cumulative monitoring.db workflow events by time") - - plt.savefig("dnpc-workflows-cumul.png") - - -def main() -> None: - set_stream_logger() - logger.info("dnpc start") - - root_context = Context.new_root_context() - - import_monitoring_db(root_context, "./monitoring.db") - - monitoring_db_context = root_context.get_context("monitoring", "parsl.monitoring.db") - - logger.info(f"got monitoring db context {monitoring_db_context}") - - # now do some simple plots with this context - at time of writing - # all that is available is workflow start/end times but that should - # allow plots of number of workflows in each state, which is a - # building block to later plots. - - plot_workflows_cumul(monitoring_db_context) - plot_tasks_summary_cumul(monitoring_db_context) - plot_tasks_status_cumul(monitoring_db_context) - plot_tries_cumul(monitoring_db_context) - plot_tries_runtime_histo(monitoring_db_context) - plot_wq_running_to_parsl_running_histo(monitoring_db_context) - plot_wq_parsl_worker_cumul(monitoring_db_context) - plot_all_task_events_cumul(monitoring_db_context) - plot_tasks_status_streamgraph(monitoring_db_context) - plot_task_running_event_streamgraph(monitoring_db_context) - - logger.info("dnpc end") - - -if __name__ == "__main__": - main() diff --git a/parsl/executors/high_throughput/executor.py b/parsl/executors/high_throughput/executor.py index e60dec91fa..907952d5d2 100644 --- a/parsl/executors/high_throughput/executor.py +++ b/parsl/executors/high_throughput/executor.py @@ -561,6 +561,7 @@ def submit(self, func, resource_specification, *args, **kwargs): logger.debug("Pushing function {} to queue with args {}".format(func, args_to_print)) fut = Future() + fut.parsl_executor_task_id = task_id self.tasks[task_id] = fut try: diff --git a/parsl/tests/test_python_apps/test_fibonacci_recursive.py b/parsl/tests/test_python_apps/test_fibonacci_recursive.py index c3acb69bf9..077cd5aeb2 100644 --- a/parsl/tests/test_python_apps/test_fibonacci_recursive.py +++ b/parsl/tests/test_python_apps/test_fibonacci_recursive.py @@ -25,4 +25,4 @@ def fibonacci(n): def test_fibonacci(): assert fibonacci(0).result() == 0 assert fibonacci(4).result() == 3 - # assert fibonacci(10).result() == 55 + assert fibonacci(6).result() == 8 diff --git a/parsl/version.py b/parsl/version.py index 3bdc247203..9fa63995b9 100644 --- a/parsl/version.py +++ b/parsl/version.py @@ -3,4 +3,4 @@ ..[alpha/beta/..] Alphas will be numbered like this -> 0.4.0a0 """ -VERSION = '1.1.0+desc-2021.08.16c' +VERSION = '1.1.0+desc-2021.08.27a' From 2ec361a9d6c311adb45e6822a889fe9bbfef5fe6 Mon Sep 17 00:00:00 2001 From: Ben Clifford Date: Sat, 28 Aug 2021 09:48:07 +0000 Subject: [PATCH 251/408] Update WQ CI patches to use newer WQ install updated in master --- Makefile | 4 ++-- parsl/version.py | 2 +- 2 files changed, 3 insertions(+), 3 deletions(-) diff --git a/Makefile b/Makefile index 2ef1d4ca30..c5eeebf08a 100644 --- a/Makefile +++ b/Makefile @@ -78,7 +78,7 @@ workqueue_ex_test: $(WORKQUEUE_INSTALL) ## run all tests with workqueue_ex conf .PHONY: workqueue_mon_test workqueue_mon_test: $(WORKQUEUE_INSTALL) ## run all tests with workqueue_ex config pip3 install ".[monitoring]" - PYTHONPATH=.:/tmp/cctools/lib/python3.5/site-packages pytest parsl/tests/ -k "not cleannet and not issue363" --config parsl/tests/configs/workqueue_monitoring_config.py --cov=parsl --cov-append --cov-report= --random-order + PYTHONPATH=.:/tmp/cctools/lib/python3.8/site-packages pytest parsl/tests/ -k "not cleannet and not issue363" --config parsl/tests/configs/workqueue_monitoring_config.py --cov=parsl --cov-append --cov-report= --random-order .PHONY: config_local_test @@ -86,7 +86,7 @@ config_local_test: ## run all tests with workqueue_ex config echo "$(MPI)" parsl/executors/extreme_scale/install-mpi.sh $(MPI) pip3 install ".[extreme_scale,monitoring]" - PYTHONPATH=.:/tmp/cctools/lib/python3.5/site-packages pytest parsl/tests/ -k "not cleannet" --config local --cov=parsl --cov-append --cov-report= --random-order + PYTHONPATH=.:/tmp/cctools/lib/python3.8/site-packages pytest parsl/tests/ -k "not cleannet" --config local --cov=parsl --cov-append --cov-report= --random-order .PHONY: site_test site_test: diff --git a/parsl/version.py b/parsl/version.py index 2afa5df919..a4d4a2e17a 100644 --- a/parsl/version.py +++ b/parsl/version.py @@ -3,4 +3,4 @@ ..[alpha/beta/..] Alphas will be numbered like this -> 0.4.0a0 """ -VERSION = '1.1.0+desc-2021.08.27d' +VERSION = '1.1.0+desc-2021.08.28a' From 90571d73fb6ca6a3f86314d20f61384a3a483a4a Mon Sep 17 00:00:00 2001 From: Ben Clifford Date: Wed, 1 Sep 2021 10:17:42 +0000 Subject: [PATCH 252/408] lots of htex task-id and result processing logging, to investigate a problem with quentin --- parsl/dataflow/dflow.py | 6 +-- parsl/executors/base.py | 5 +++ parsl/executors/high_throughput/executor.py | 2 +- .../executors/high_throughput/interchange.py | 36 +++++++++------ .../high_throughput/process_worker_pool.py | 45 ++++++++++++++----- parsl/log_utils.py | 5 +-- parsl/version.py | 2 +- 7 files changed, 68 insertions(+), 33 deletions(-) diff --git a/parsl/dataflow/dflow.py b/parsl/dataflow/dflow.py index 3f03838229..2c96319514 100644 --- a/parsl/dataflow/dflow.py +++ b/parsl/dataflow/dflow.py @@ -681,10 +681,10 @@ def launch_task(self, task_record, executable, *args, **kwargs): self._send_task_log_info(task_record) - logger.info("Task {} launched on executor {}".format(task_id, executor.label)) if hasattr(exec_fu, "parsl_executor_task_id"): - logger.info("Parsl task {} try {} launched on executor {} with executor id {}".format(task_id, try_id, - executor.label, exec_fu.parsl_executor_task_id)) + logger.info(f"Parsl task {task_id} try {try_id} launched on executor {executor.label} with executor id {exec_fu.parsl_executor_task_id}") + else: + logger.info(f"Parsl task {task_id} try {try_id} launched on executor {executor.label}") self._log_std_streams(task_record) diff --git a/parsl/executors/base.py b/parsl/executors/base.py index 910bbd6b9f..74ec7c0ca9 100644 --- a/parsl/executors/base.py +++ b/parsl/executors/base.py @@ -71,6 +71,11 @@ def start(self) -> Optional[List[str]]: @abstractmethod def submit(self, func: Callable, resource_specification: Dict[str, Any], *args: Any, **kwargs: Any) -> Future: """Submit. + + The executor can optionally set a parsl_executor_task_id attribute on + the Future that it returns, and in that case, parsl will log a + relationship between the executor's task ID and parsl level try/task + IDs. """ pass diff --git a/parsl/executors/high_throughput/executor.py b/parsl/executors/high_throughput/executor.py index 907952d5d2..dbb3a734db 100644 --- a/parsl/executors/high_throughput/executor.py +++ b/parsl/executors/high_throughput/executor.py @@ -558,7 +558,7 @@ def submit(self, func, resource_specification, *args, **kwargs): args_to_print = args if logger.getEffectiveLevel() >= logging.DEBUG: args_to_print = tuple([arg if len(repr(arg)) < 100 else (repr(arg)[:100] + '...') for arg in args]) - logger.debug("Pushing function {} to queue with args {}".format(func, args_to_print)) + logger.debug("Pushing htex task {} function {} to queue with args {}".format(task_id, func, args_to_print)) fut = Future() fut.parsl_executor_task_id = task_id diff --git a/parsl/executors/high_throughput/interchange.py b/parsl/executors/high_throughput/interchange.py index aad2173261..09d95d1758 100644 --- a/parsl/executors/high_throughput/interchange.py +++ b/parsl/executors/high_throughput/interchange.py @@ -316,7 +316,7 @@ def migrate_tasks_to_internal(self, kill_event): else: self.pending_task_queue.put(PriorityQueueEntry(msg['priority'], msg)) task_counter += 1 - logger.debug("[TASK_PULL_THREAD] Fetched task:{}".format(task_counter)) + logger.debug("Fetched task: {}".format(task_counter)) def _create_monitoring_channel(self): if self.hub_address and self.hub_port: @@ -456,9 +456,9 @@ def start(self): interesting_managers = set() while not self._kill_event.is_set(): - logger.debug("BENC: starting poll") + logger.debug(f"Starting poll with timeout {poll_period} ms") self.socks = dict(poller.poll(timeout=poll_period)) - logger.debug("BENC: ending poll") + logger.debug(f"Ending poll, with {len(self.socks)} sockets active") # Listen for requests for work if self.task_outgoing in self.socks and self.socks[self.task_outgoing] == zmq.POLLIN: @@ -513,7 +513,7 @@ def start(self): msg['python_v'].rsplit(".", 1)[0])) else: # Registration has failed. - logger.debug("[MAIN] Suppressing bad registration from manager:{}".format( + logger.debug("[MAIN] Suppressing bad registration from manager: {}".format( manager)) else: @@ -574,12 +574,12 @@ def start(self): logger.debug("[MAIN] either no interesting managers or no tasks, so skipping manager pass") # Receive any results and forward to client if self.results_incoming in self.socks and self.socks[self.results_incoming] == zmq.POLLIN: - logger.debug("[MAIN] entering results_incoming section") + logger.debug("entering results_incoming section") manager, *all_messages = self.results_incoming.recv_multipart() if manager not in self._ready_manager_queue: - logger.warning("[MAIN] Received a result from a un-registered manager: {}".format(manager)) + logger.warning("Received a result from a un-registered manager: {}".format(manager)) else: - logger.debug("[MAIN] Got {} result items in batch".format(len(all_messages))) + logger.debug(f"Got {len(all_messages)} result items in batch from manager {manager}") b_messages = [] @@ -592,20 +592,24 @@ def start(self): for message in all_messages: r = pickle.loads(message) if r['type'] == 'result': + logger.debug(f"Result item is result for task {r['task_id']}") # process this for task ID and forward to executor b_messages.append(message) elif r['type'] == 'monitoring': + logger.debug("Result item is monitoring message - sending on hub_channel") hub_channel.send_pyobj(r['payload']) + logger.debug("Sent monitoring message on hub_channel") elif r['type'] == 'heartbeat': - logger.debug("[MAIN] Manager {} sent heartbeat via results connection".format(manager)) + logger.debug("Result item is a heartbeat on results connection") b_messages.append(message) else: - logger.error("Interchange discarding result_queue message of unknown type: {}".format(r['type'])) + logger.error("Result item is of unknown type: {}".format(r['type'])) for b_message in b_messages: r = pickle.loads(b_message) if r['type'] == 'result': try: + logger.debug(f"Removing task {r['task_id']} from manager {manager} record") self._ready_manager_queue[manager]['tasks'].remove(r['task_id']) except Exception: # If we reach here, there's something very wrong. @@ -615,22 +619,26 @@ def start(self): self._ready_manager_queue[manager]['tasks'])) if b_messages: + logger.debug("Sending messages on results_outgoing") self.results_outgoing.send_multipart(b_messages) + logger.debug("Sent messages on results_outgoing") - logger.debug("[MAIN] Current tasks: {}".format(self._ready_manager_queue[manager]['tasks'])) + logger.debug(f"Current tasks on manager {manager}: {self._ready_manager_queue[manager]['tasks']}") if len(self._ready_manager_queue[manager]['tasks']) == 0: self._ready_manager_queue[manager]['idle_since'] = time.time() - logger.debug("[MAIN] leaving results_incoming section") + logger.debug("leaving results_incoming section") bad_managers = [manager for manager in self._ready_manager_queue if time.time() - self._ready_manager_queue[manager]['last_heartbeat'] > self.heartbeat_threshold] for manager in bad_managers: logger.debug("[MAIN] Last: {} Current: {}".format(self._ready_manager_queue[manager]['last_heartbeat'], time.time())) - logger.warning("[MAIN] Too many heartbeats missed for manager {}".format(manager)) + logger.warning(f"Too many heartbeats missed for manager {manager}") + logger.warning(f"Removing this manager and cancelled htex tasks {self._ready_manager_queue[manager]['tasks']}") if self._ready_manager_queue[manager]['active']: self._ready_manager_queue[manager]['active'] = False self._send_monitoring_info(hub_channel, manager) + logger.warning(f"Cancelling htex tasks {self._ready_manager_queue[manager]['tasks']} on removed manager") for tid in self._ready_manager_queue[manager]['tasks']: try: raise ManagerLost(manager, self._ready_manager_queue[manager]['hostname']) @@ -638,7 +646,7 @@ def start(self): result_package = {'type': 'result', 'task_id': tid, 'exception': serialize_object(RemoteExceptionWrapper(*sys.exc_info()))} pkl_package = pickle.dumps(result_package) self.results_outgoing.send(pkl_package) - logger.warning("[MAIN] Sent failure reports, unregistering manager") + logger.warning("[MAIN] Sent failure reports, unregistering manager") self._ready_manager_queue.pop(manager, 'None') if manager in interesting_managers: interesting_managers.remove(manager) @@ -669,7 +677,7 @@ def start_file_logger(filename, name='interchange', level=logging.DEBUG, format_ None. """ if format_string is None: - format_string = "%(asctime)s.%(msecs)03d %(name)s:%(lineno)d [%(levelname)s] %(message)s" + format_string = "%(asctime)s.%(msecs)03d %(name)s:%(lineno)d %(processName)s(%(process)d) %(threadName)s [%(levelname)s] %(message)s" global logger logger = logging.getLogger(name) diff --git a/parsl/executors/high_throughput/process_worker_pool.py b/parsl/executors/high_throughput/process_worker_pool.py index b267626a13..e272c14e26 100755 --- a/parsl/executors/high_throughput/process_worker_pool.py +++ b/parsl/executors/high_throughput/process_worker_pool.py @@ -219,8 +219,13 @@ def heartbeat_to_incoming(self): """ Send heartbeat to the incoming task queue """ heartbeat = (HEARTBEAT_CODE).to_bytes(4, "little") - r = self.task_incoming.send(heartbeat) - logger.debug("Sent heartbeat, return code {}".format(r)) + self.task_incoming.send(heartbeat) + logger.debug("Sent heartbeat") + # used to log heartbeat return value, but it is always None - + # errors are reported as exceptions. + # "return code None" has repeatedly confused me over the years, + # because it isn't clear what the meaning is without reading + # docs. @wrap_with_logs def pull_tasks(self, kill_event): @@ -282,8 +287,7 @@ def pull_tasks(self, kill_event): else: task_recv_counter += len(tasks) - logger.debug("[TASK_PULL_THREAD] Got tasks: {} of {}".format([t['task_id'] for t in tasks], - task_recv_counter)) + logger.debug("Got tasks: {}, cumulative count of tasks: {}".format([t['task_id'] for t in tasks], task_recv_counter)) for task in tasks: self.pending_task_queue.put(task) @@ -315,7 +319,7 @@ def push_results(self, kill_event): Event to let the thread know when it is time to die. """ - logger.debug("[RESULT_PUSH_THREAD] Starting thread") + logger.debug("Starting result push thread") # push_poll_period is in s @@ -323,34 +327,50 @@ def push_results(self, kill_event): # push_poll_period must be at least 10 ms [BENC: why? and why does # this one have more of a restriction than any of the other timing # parameters? That max statement enforces that. but why enforce it vs other timings?] - logger.debug("[RESULT_PUSH_THREAD] push poll period: {}".format(push_poll_period)) + logger.debug("push poll period: {} seconds".format(push_poll_period)) last_beat = time.time() last_result_beat = time.time() items = [] while not kill_event.is_set(): - + logger.debug("Starting loop") try: + # TODO: is this timeout= parameter in seconds? yes. according to docs. + logger.debug("Starting pending_result_queue get") r = self.pending_result_queue.get(block=True, timeout=push_poll_period) + logger.debug("Got a result item") items.append(r) except queue.Empty: + logger.debug("pending_result_queue get timeout without result item") pass except Exception as e: - logger.exception("[RESULT_PUSH_THREAD] Got an exception: {}".format(e)) + logger.exception("Got an exception: {}".format(e)) + # this will send a heartbeat even if results have been sent within the + # heartbeat_period. + # TODO: check at other end of connection if it is OK to omit a heartbeat + # if a result has been sent instead, and if so, reset the heartbeat period + # when sending a result if time.time() > last_result_beat + self.heartbeat_period: + logger.info(f"Sending heartbeat via results connection: last_result_beat={last_result_beat} heartbeat_period={self.heartbeat_period} seconds") last_result_beat = time.time() items.append(pickle.dumps({'type': 'heartbeat'})) - # If we have reached poll_period duration or timer has expired, we send results if len(items) >= self.max_queue_size or time.time() > last_beat + push_poll_period: + logger.debug("Check for result send") last_beat = time.time() if items: + logger.debug(f"Pushing {len(items)} items") self.result_outgoing.send_multipart(items) items = [] + else: + logger.debug("No items to push") + else: + logger.debug(f"Result send check condition not met - deferring {len(items)} result items") + logger.debug("End loop") - logger.critical("[RESULT_PUSH_THREAD] Exiting") + logger.critical("Exiting") @wrap_with_logs def worker_watchdog(self, kill_event): @@ -580,6 +600,7 @@ def worker(worker_id, pool_id, pool_size, task_queue, result_queue, worker_queue result_queue.put(pkl_package) tasks_in_progress.pop(worker_id) + logger.info("All processing finished for task {}".format(tid)) def start_file_logger(filename, rank, name='parsl', level=logging.DEBUG, format_string=None): @@ -595,7 +616,9 @@ def start_file_logger(filename, rank, name='parsl', level=logging.DEBUG, format_ - None """ if format_string is None: - format_string = "%(asctime)s.%(msecs)03d %(name)s:%(lineno)d Rank:{0} [%(levelname)s] %(message)s".format(rank) + format_string = "%(asctime)s.%(msecs)03d %(name)s:%(lineno)d " \ + "%(processName)s(%(process)d) %(threadName)s Rank:{0} " \ + "[%(levelname)s] %(message)s".format(rank) logger = logging.getLogger(name) logger.setLevel(logging.DEBUG) diff --git a/parsl/log_utils.py b/parsl/log_utils.py index d6925bbc4c..9961c0b714 100644 --- a/parsl/log_utils.py +++ b/parsl/log_utils.py @@ -29,8 +29,7 @@ def set_stream_logger(name: str = 'parsl', level: int = logging.DEBUG, format_st - None """ if format_string is None: - # format_string = "%(asctime)s %(name)s [%(levelname)s] Thread:%(thread)d %(message)s" - format_string = "%(asctime)s %(name)s:%(lineno)d [%(levelname)s] %(message)s" + format_string = "%(asctime)s %(name)s:%(lineno)d %(processName)s(%(process)d) %(threadName)s [%(levelname)s] %(message)s" logger = logging.getLogger(name) logger.setLevel(logging.DEBUG) @@ -61,7 +60,7 @@ def set_file_logger(filename: str, name: str = 'parsl', level: int = logging.DEB - None """ if format_string is None: - format_string = "%(asctime)s.%(msecs)03d %(name)s:%(lineno)d [%(levelname)s] %(message)s" + format_string = "%(asctime)s %(name)s:%(lineno)d %(processName)s(%(process)d) %(threadName)s [%(levelname)s] %(message)s" logger = logging.getLogger(name) logger.setLevel(logging.DEBUG) diff --git a/parsl/version.py b/parsl/version.py index a4d4a2e17a..01ef3edd8d 100644 --- a/parsl/version.py +++ b/parsl/version.py @@ -3,4 +3,4 @@ ..[alpha/beta/..] Alphas will be numbered like this -> 0.4.0a0 """ -VERSION = '1.1.0+desc-2021.08.28a' +VERSION = '1.1.0+desc-2021.09.01a' From 65d6bc5fbc650944deb2bbff51221712e0ba02dc Mon Sep 17 00:00:00 2001 From: Ben Clifford Date: Wed, 1 Sep 2021 12:03:26 +0000 Subject: [PATCH 253/408] cherry-pick PR #2118 archiving of pytest CI runinfo/ to debug future CI hangs --- .github/workflows/ci.yaml | 6 ++++++ parsl/version.py | 2 +- 2 files changed, 7 insertions(+), 1 deletion(-) diff --git a/.github/workflows/ci.yaml b/.github/workflows/ci.yaml index fa2f090370..8650ccbbd2 100644 --- a/.github/workflows/ci.yaml +++ b/.github/workflows/ci.yaml @@ -78,3 +78,9 @@ jobs: - name: make coverage run: | make coverage + + - name: Archive runinfo logs + uses: actions/upload-artifact@v2 + with: + name: runinfo + path: runinfo/ diff --git a/parsl/version.py b/parsl/version.py index 01ef3edd8d..974e242641 100644 --- a/parsl/version.py +++ b/parsl/version.py @@ -3,4 +3,4 @@ ..[alpha/beta/..] Alphas will be numbered like this -> 0.4.0a0 """ -VERSION = '1.1.0+desc-2021.09.01a' +VERSION = '1.1.0+desc-2021.09.01b' From 426b42784bae4f66149f4b45bc7bcd3b249e123f Mon Sep 17 00:00:00 2001 From: Ben Clifford Date: Wed, 1 Sep 2021 13:29:37 +0000 Subject: [PATCH 254/408] extend CI timeout --- .github/workflows/ci.yaml | 2 +- parsl/version.py | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/.github/workflows/ci.yaml b/.github/workflows/ci.yaml index 8650ccbbd2..a5cab5b9aa 100644 --- a/.github/workflows/ci.yaml +++ b/.github/workflows/ci.yaml @@ -12,7 +12,7 @@ jobs: matrix: python-version: ["3.6", "3.7", "3.8", "3.9"] runs-on: ubuntu-20.04 - timeout-minutes: 40 + timeout-minutes: 80 steps: - uses: actions/checkout@master diff --git a/parsl/version.py b/parsl/version.py index 974e242641..f76923bd46 100644 --- a/parsl/version.py +++ b/parsl/version.py @@ -3,4 +3,4 @@ ..[alpha/beta/..] Alphas will be numbered like this -> 0.4.0a0 """ -VERSION = '1.1.0+desc-2021.09.01b' +VERSION = '1.1.0+desc-2021.09.01c' From 5ed17c790f873336938fa21d6543aa361e131bb1 Mon Sep 17 00:00:00 2001 From: Ben Clifford Date: Mon, 6 Sep 2021 08:52:51 +0000 Subject: [PATCH 255/408] hopefully fix htex scale-in tweak logging based on iteration with quentin --- parsl/executors/high_throughput/executor.py | 14 ++++++++++---- parsl/executors/high_throughput/interchange.py | 2 +- .../high_throughput/process_worker_pool.py | 15 ++++++--------- parsl/monitoring/monitoring.py | 6 ++++-- parsl/tests/test_scaling/test_scale_down.py | 1 - parsl/version.py | 2 +- 6 files changed, 22 insertions(+), 18 deletions(-) diff --git a/parsl/executors/high_throughput/executor.py b/parsl/executors/high_throughput/executor.py index dbb3a734db..03c586a0e5 100644 --- a/parsl/executors/high_throughput/executor.py +++ b/parsl/executors/high_throughput/executor.py @@ -641,12 +641,12 @@ def scale_in(self, blocks=None, block_ids=[], force=True, max_idletime=None): ------- List of job_ids marked for termination """ - + logger.debug(f"Scale in called, blocks={blocks}, block_ids={block_ids}") if block_ids: block_ids_to_kill = block_ids else: managers = self.connected_managers - block_info = {} + block_info = {} # block id -> list( tasks, idle duration ) for manager in managers: if not manager['active']: continue @@ -657,6 +657,7 @@ def scale_in(self, blocks=None, block_ids=[], force=True, max_idletime=None): block_info[b_id][1] = min(block_info[b_id][1], manager['idle_duration']) sorted_blocks = sorted(block_info.items(), key=lambda item: (item[1][1], item[1][0])) + logger.debug(f"scale in selecting from {len(sorted_blocks)} blocks") if force is True: block_ids_to_kill = [x[0] for x in sorted_blocks[:blocks]] else: @@ -669,10 +670,15 @@ def scale_in(self, blocks=None, block_ids=[], force=True, max_idletime=None): block_ids_to_kill.append(x[0]) if len(block_ids_to_kill) == blocks: break - logger.debug("Selecting block ids to kill since they are idle : {}".format( + logger.debug("Selecting block ids to kill since they are idle: {}".format( block_ids_to_kill)) + if len(block_ids_to_kill) < blocks: + logger.warning(f"Could not find enough blocks to kill: wanted {blocks} but only selected {len(block_ids_to_kill)}") + if sorted_blocks == []: + logger.warning("sorted_blocks is empty") + else: + logger.warning(f"sorted_blocks: first {sorted_blocks[0]}, last {sorted_blocks[-1]}") - logger.debug("Current blocks : {}".format(self.blocks)) # Hold the block for block_id in block_ids_to_kill: self._hold_block(block_id) diff --git a/parsl/executors/high_throughput/interchange.py b/parsl/executors/high_throughput/interchange.py index 09d95d1758..39b4764d76 100644 --- a/parsl/executors/high_throughput/interchange.py +++ b/parsl/executors/high_throughput/interchange.py @@ -624,7 +624,7 @@ def start(self): logger.debug("Sent messages on results_outgoing") logger.debug(f"Current tasks on manager {manager}: {self._ready_manager_queue[manager]['tasks']}") - if len(self._ready_manager_queue[manager]['tasks']) == 0: + if len(self._ready_manager_queue[manager]['tasks']) == 0 and self._ready_manager_queue[manager]['idle_since'] is None: self._ready_manager_queue[manager]['idle_since'] = time.time() logger.debug("leaving results_incoming section") diff --git a/parsl/executors/high_throughput/process_worker_pool.py b/parsl/executors/high_throughput/process_worker_pool.py index e272c14e26..717e4145fd 100755 --- a/parsl/executors/high_throughput/process_worker_pool.py +++ b/parsl/executors/high_throughput/process_worker_pool.py @@ -334,7 +334,6 @@ def push_results(self, kill_event): items = [] while not kill_event.is_set(): - logger.debug("Starting loop") try: # TODO: is this timeout= parameter in seconds? yes. according to docs. logger.debug("Starting pending_result_queue get") @@ -343,7 +342,6 @@ def push_results(self, kill_event): items.append(r) except queue.Empty: logger.debug("pending_result_queue get timeout without result item") - pass except Exception as e: logger.exception("Got an exception: {}".format(e)) @@ -358,17 +356,16 @@ def push_results(self, kill_event): items.append(pickle.dumps({'type': 'heartbeat'})) if len(items) >= self.max_queue_size or time.time() > last_beat + push_poll_period: - logger.debug("Check for result send") last_beat = time.time() if items: - logger.debug(f"Pushing {len(items)} items") + logger.debug(f"Result send: Pushing {len(items)} items") self.result_outgoing.send_multipart(items) + logger.debug(f"Result send: Pushed") items = [] else: - logger.debug("No items to push") + logger.debug("Result send: No items to push") else: - logger.debug(f"Result send check condition not met - deferring {len(items)} result items") - logger.debug("End loop") + logger.debug(f"Result send: check condition not met - deferring {len(items)} result items") logger.critical("Exiting") @@ -617,8 +614,8 @@ def start_file_logger(filename, rank, name='parsl', level=logging.DEBUG, format_ """ if format_string is None: format_string = "%(asctime)s.%(msecs)03d %(name)s:%(lineno)d " \ - "%(processName)s(%(process)d) %(threadName)s Rank:{0} " \ - "[%(levelname)s] %(message)s".format(rank) + "%(process)d %(threadName)s " \ + "[%(levelname)s] %(message)s" logger = logging.getLogger(name) logger.setLevel(logging.DEBUG) diff --git a/parsl/monitoring/monitoring.py b/parsl/monitoring/monitoring.py index 733dbefdfd..1f0b84f7b5 100644 --- a/parsl/monitoring/monitoring.py +++ b/parsl/monitoring/monitoring.py @@ -389,14 +389,16 @@ def start(self, run_id: str, run_dir: str) -> int: # TODO: tighten the Any message format def send(self, mtype: MessageType, message: Any) -> None: - self.logger.debug("Sending message {}, {}".format(mtype, message)) + # this was crazy big + self.logger.debug("Sending message type {}".format(mtype)) try: self._dfk_channel.send_pyobj((mtype, message)) except zmq.Again: self.logger.exception( "The monitoring message sent from DFK to Hub timed-out after {}ms".format(self.dfk_channel_timeout)) else: - self.logger.debug("Sent message {}, {}".format(mtype, message)) + # this was very big + self.logger.debug("Sent message type {}".format(mtype)) def close(self) -> None: if self.logger: diff --git a/parsl/tests/test_scaling/test_scale_down.py b/parsl/tests/test_scaling/test_scale_down.py index 6ea543e3dc..74a8ddafa3 100644 --- a/parsl/tests/test_scaling/test_scale_down.py +++ b/parsl/tests/test_scaling/test_scale_down.py @@ -43,7 +43,6 @@ def sleeper(t): return random.randint(0, 10000) -@pytest.mark.skip('fails 50% of time in CI - see issue #1885') @pytest.mark.local def test_scale_out(): dfk = parsl.dfk() diff --git a/parsl/version.py b/parsl/version.py index f76923bd46..1f1143d62d 100644 --- a/parsl/version.py +++ b/parsl/version.py @@ -3,4 +3,4 @@ ..[alpha/beta/..] Alphas will be numbered like this -> 0.4.0a0 """ -VERSION = '1.1.0+desc-2021.09.01c' +VERSION = '1.1.0+desc-2021.09.06b' From c6938276e54503ff6da0ea57dae236e97477fb5b Mon Sep 17 00:00:00 2001 From: Ben Clifford Date: Mon, 6 Sep 2021 09:04:23 +0000 Subject: [PATCH 256/408] fix typo --- parsl/executors/high_throughput/process_worker_pool.py | 2 +- parsl/version.py | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/parsl/executors/high_throughput/process_worker_pool.py b/parsl/executors/high_throughput/process_worker_pool.py index 717e4145fd..acbdc7dbaa 100755 --- a/parsl/executors/high_throughput/process_worker_pool.py +++ b/parsl/executors/high_throughput/process_worker_pool.py @@ -360,7 +360,7 @@ def push_results(self, kill_event): if items: logger.debug(f"Result send: Pushing {len(items)} items") self.result_outgoing.send_multipart(items) - logger.debug(f"Result send: Pushed") + logger.debug("Result send: Pushed") items = [] else: logger.debug("Result send: No items to push") diff --git a/parsl/version.py b/parsl/version.py index 1f1143d62d..292beef93a 100644 --- a/parsl/version.py +++ b/parsl/version.py @@ -3,4 +3,4 @@ ..[alpha/beta/..] Alphas will be numbered like this -> 0.4.0a0 """ -VERSION = '1.1.0+desc-2021.09.06b' +VERSION = '1.1.0+desc-2021.09.06c' From ad65912a66d10207245122301f59971a170c51d7 Mon Sep 17 00:00:00 2001 From: Ben Clifford Date: Thu, 30 Sep 2021 10:41:02 +0000 Subject: [PATCH 257/408] add milliseconds into logging timestamp --- parsl/log_utils.py | 2 +- parsl/version.py | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/parsl/log_utils.py b/parsl/log_utils.py index 9961c0b714..057d1b3f2c 100644 --- a/parsl/log_utils.py +++ b/parsl/log_utils.py @@ -60,7 +60,7 @@ def set_file_logger(filename: str, name: str = 'parsl', level: int = logging.DEB - None """ if format_string is None: - format_string = "%(asctime)s %(name)s:%(lineno)d %(processName)s(%(process)d) %(threadName)s [%(levelname)s] %(message)s" + format_string = "%(asctime)s.%(msecs)03d %(name)s:%(lineno)d %(processName)s(%(process)d) %(threadName)s [%(levelname)s] %(message)s" logger = logging.getLogger(name) logger.setLevel(logging.DEBUG) diff --git a/parsl/version.py b/parsl/version.py index 793b782ec6..c45882d4ba 100644 --- a/parsl/version.py +++ b/parsl/version.py @@ -3,4 +3,4 @@ ..[alpha/beta/..] Alphas will be numbered like this -> 0.4.0a0 """ -VERSION = '1.1.0+desc-2021.09.30a' +VERSION = '1.1.0+desc-2021.09.30b' From f41b708404b56a7361a7a4baba2e70003d833c19 Mon Sep 17 00:00:00 2001 From: Ben Clifford Date: Wed, 24 Nov 2021 18:50:16 +0000 Subject: [PATCH 258/408] Use proper subclass of Exception when executor is in a bad state. This follows the general Parsl style, which defines different exception classes for different errors. --- parsl/executors/errors.py | 8 ++++++++ parsl/executors/status_handling.py | 4 ++-- 2 files changed, 10 insertions(+), 2 deletions(-) diff --git a/parsl/executors/errors.py b/parsl/executors/errors.py index 310fa7db5c..b360d82bbe 100644 --- a/parsl/executors/errors.py +++ b/parsl/executors/errors.py @@ -18,6 +18,14 @@ def __str__(self): return "Executor {0} failed due to: {1}".format(self.executor, self.reason) +class BadStateException(ExecutorError): + """Error returned by task Futures when an executor is in a bad state. + """ + + def __init__(self, executor, exception): + super().init(executor, str(exception)) + + class UnsupportedFeatureError(ExecutorError): """Error raised when attemping to use unsupported feature in an Executor""" diff --git a/parsl/executors/status_handling.py b/parsl/executors/status_handling.py index 1a1d4f56ce..430c872a59 100644 --- a/parsl/executors/status_handling.py +++ b/parsl/executors/status_handling.py @@ -7,7 +7,7 @@ import parsl # noqa F401 from parsl.executors.base import ParslExecutor -from parsl.executors.errors import ScalingFailed +from parsl.executors.errors import BadStateException, ScalingFailed from parsl.providers.provider_base import JobStatus, ExecutionProvider, JobState @@ -115,7 +115,7 @@ def set_bad_state_and_fail_all(self, exception: Exception): # We set all current tasks to this exception to make sure that # this is raised in the main context. for task in self._tasks: - self._tasks[task].set_exception(Exception(str(self._executor_exception))) + self._tasks[task].set_exception(BadStateException(self, self._executor_exception)) @property def bad_state_is_set(self): From 2a82c31e41d3fa89006b2838f2881d916bb32da6 Mon Sep 17 00:00:00 2001 From: Ben Clifford Date: Thu, 25 Nov 2021 12:37:27 +0000 Subject: [PATCH 259/408] Make sshd channel test errors more obvious I have repeatedly hit this error: def _start_sshd(config_dir: str): server_config, priv_key, port = _init_sshd(config_dir) sshd_thread = SSHDThread(server_config) sshd_thread.start() time.sleep(1.0) if not sshd_thread.is_alive(): > raise Exception('Failed to start sshd: {}'.format(sshd_thread.error)) E Exception: Failed to start sshd: expected str, bytes or os.PathLike object, not NoneType which does not point clearly to a resolution. This commit adds in both logging so that pytest --log-cli-level=ERROR will report stack traces for exceptions such as the above "not NoneType", and adds an assertion for the common case that is triggering this for me, which is that sshd cannot be found on the $PATH. In the case that sshd is not on the $PATH, that error is now reported as: ERROR parsl.tests.test_providers.test_local_provider:test_local_provider.py:138 SSHDThread exception from run loop Traceback (most recent call last): File "/home/benc/parsl/src/parsl/parsl/tests/test_providers/test_local_provider.py", line 119, in run assert sshpath is not None, "can find sshd executable" AssertionError: can find sshd executable assert None is not None --- parsl/tests/test_providers/test_local_provider.py | 8 +++++++- 1 file changed, 7 insertions(+), 1 deletion(-) diff --git a/parsl/tests/test_providers/test_local_provider.py b/parsl/tests/test_providers/test_local_provider.py index 35ff1d3411..353105ec98 100644 --- a/parsl/tests/test_providers/test_local_provider.py +++ b/parsl/tests/test_providers/test_local_provider.py @@ -1,3 +1,4 @@ +import logging import os import pathlib import pytest @@ -14,6 +15,8 @@ from parsl.providers import LocalProvider from parsl.providers.provider_base import JobState +logger = logging.getLogger(__name__) + def _run_tests(p: LocalProvider): status = _run(p, '/bin/true') @@ -112,7 +115,9 @@ def __init__(self, config_file): def run(self): try: # sshd needs to be run with an absolute path, hence the call to which() - p = subprocess.Popen([shutil.which('sshd'), '-D', '-f', self.config_file], + sshpath = shutil.which('sshd') + assert sshpath is not None, "can find sshd executable" + p = subprocess.Popen([sshpath, '-D', '-f', self.config_file], stdout=subprocess.PIPE, stderr=subprocess.PIPE) while True: ec = p.poll() @@ -130,6 +135,7 @@ def run(self): p.stderr.read())) break except Exception as ex: + logger.exception("SSHDThread exception from run loop") self.error = ex def stop(self): From e07497bb716d2e9af7d740eae32cdda7de9e7751 Mon Sep 17 00:00:00 2001 From: Ben Clifford Date: Thu, 25 Nov 2021 14:19:31 +0000 Subject: [PATCH 260/408] Fix incorrect __init__ invocation --- parsl/executors/errors.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/parsl/executors/errors.py b/parsl/executors/errors.py index b360d82bbe..0c3c52cabc 100644 --- a/parsl/executors/errors.py +++ b/parsl/executors/errors.py @@ -23,7 +23,7 @@ class BadStateException(ExecutorError): """ def __init__(self, executor, exception): - super().init(executor, str(exception)) + super().__init__(executor, str(exception)) class UnsupportedFeatureError(ExecutorError): From 71e3f08efa0538f7278b7a600a32848f0bfcf5e1 Mon Sep 17 00:00:00 2001 From: Ben Clifford Date: Fri, 26 Nov 2021 12:59:13 +0000 Subject: [PATCH 261/408] Fix typo in two db error messages and make consistent with each other --- parsl/monitoring/db_manager.py | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/parsl/monitoring/db_manager.py b/parsl/monitoring/db_manager.py index 8042d4390d..394d6ca9bf 100644 --- a/parsl/monitoring/db_manager.py +++ b/parsl/monitoring/db_manager.py @@ -567,7 +567,7 @@ def _update(self, table: str, columns: List[str], messages: List[Dict[str, Any]] # if retried - for example, the database being locked because someone else is readying # the tables we are trying to write to. If that assumption is wrong, then this loop # may go on forever. - logger.warning("Got a database OperationalError. Ignoring and retying on the assumption that it is recoverable: {}".format(e)) + logger.warning("Got a database OperationalError. Ignoring and retrying on the assumption that it is recoverable: {}".format(e)) self.db.rollback() time.sleep(1) # hard coded 1s wait - this should be configurable or exponential backoff or something @@ -594,7 +594,7 @@ def _insert(self, table: str, messages: List[Dict[str, Any]]) -> None: done = True except sa.exc.OperationalError as e: # hoping that this is a database locked error during _update, not some other problem - logger.warning("Got an sqlite3 operational error. Ignoring and retying on the assumption that it is recoverable: {}".format(e)) + logger.warning("Got a database OperationalError. Ignoring and retrying on the assumption that it is recoverable: {}".format(e)) self.db.rollback() time.sleep(1) # hard coded 1s wait - this should be configurable or exponential backoff or something except KeyboardInterrupt: From 9f8d390cd63b9e189e5999488318d46440864509 Mon Sep 17 00:00:00 2001 From: Ben Clifford Date: Fri, 26 Nov 2021 14:17:26 +0000 Subject: [PATCH 262/408] Make missing worker test cleanup DFK at end --- parsl/tests/test_error_handling/test_htex_missing_worker.py | 1 + 1 file changed, 1 insertion(+) diff --git a/parsl/tests/test_error_handling/test_htex_missing_worker.py b/parsl/tests/test_error_handling/test_htex_missing_worker.py index 58c2f93f78..3a20037e34 100644 --- a/parsl/tests/test_error_handling/test_htex_missing_worker.py +++ b/parsl/tests/test_error_handling/test_htex_missing_worker.py @@ -14,6 +14,7 @@ def local_setup(): def local_teardown(): + parsl.dfk().cleanup() parsl.clear() From a7ceb0f61dd557cbf9ae2dafef55647461602aac Mon Sep 17 00:00:00 2001 From: Ben Clifford Date: Fri, 26 Nov 2021 18:16:18 +0000 Subject: [PATCH 263/408] Make executor bad state exception log use the exception Prior to this, the error message would be reported with no in-context exception, and so would emit a line like this: ``` 2021-11-26 18:21:10.761 parsl.executors.status_handling:111 [ERROR] Exception: STDOUT: /home/benc/parsl/src/parsl/runinfo/018/submit_scripts/parsl.localprovider.1637950869.7853742.sh: line 3: executable_that_hopefully_does_not_exist_1030509.py: command not found NoneType: None ``` The NoneType: None happens there because no exception is in scope at the moment. After this change, the log reports: ``` 2021-11-26 18:09:51.235 parsl.executors.status_handling:111 [ERROR] Setting bad state due to exception Exception: STDOUT: /home/benc/parsl/src/parsl/runinfo/008/submit_scripts/parsl.localprovider.1637950190.2711153.sh: line 3: executable_that_hopefully_does_not_exist_1030509.py: command not found ``` If the supplied exception object has a stack trace, then that will also be logged at this point now. --- parsl/executors/status_handling.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/parsl/executors/status_handling.py b/parsl/executors/status_handling.py index 1a1d4f56ce..56fd78b6e6 100644 --- a/parsl/executors/status_handling.py +++ b/parsl/executors/status_handling.py @@ -108,7 +108,7 @@ def status(self) -> Dict[str, JobStatus]: return status def set_bad_state_and_fail_all(self, exception: Exception): - logger.exception("Exception: {}".format(exception)) + logger.exception("Setting bad state due to exception", exc_info=exception) self._executor_exception = exception # Set bad state to prevent new tasks from being submitted self._executor_bad_state.set() From 604111a224f78267c4040253fe240a5c13c2d206 Mon Sep 17 00:00:00 2001 From: Ben Clifford Date: Tue, 30 Nov 2021 12:16:21 +0000 Subject: [PATCH 264/408] Correct docstring for set_file_logger --- parsl/log_utils.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/parsl/log_utils.py b/parsl/log_utils.py index d6925bbc4c..7b68b28a40 100644 --- a/parsl/log_utils.py +++ b/parsl/log_utils.py @@ -49,7 +49,7 @@ def set_stream_logger(name: str = 'parsl', level: int = logging.DEBUG, format_st @typeguard.typechecked def set_file_logger(filename: str, name: str = 'parsl', level: int = logging.DEBUG, format_string: Optional[str] = None): - """Add a stream log handler. + """Add a file log handler. Args: - filename (string): Name of the file to write logs to From 79ce9d4d6a094766c8ca13e0677af441f0643aa3 Mon Sep 17 00:00:00 2001 From: Ben Clifford Date: Tue, 7 Dec 2021 11:47:48 +0000 Subject: [PATCH 265/408] ongoing changes --- parsl/monitoring/db_manager.py | 6 ++++++ parsl/version.py | 2 +- 2 files changed, 7 insertions(+), 1 deletion(-) diff --git a/parsl/monitoring/db_manager.py b/parsl/monitoring/db_manager.py index cd7d4fd534..78374a5e48 100644 --- a/parsl/monitoring/db_manager.py +++ b/parsl/monitoring/db_manager.py @@ -264,6 +264,12 @@ def __init__(self, self.logdir = logdir os.makedirs(self.logdir, exist_ok=True) + # This will make "database_manager" log messages not be passed up to + # any root handlers which might have been set by the forking process. + # In simple parsl usage, there will not be any, but in more + # complicated situations, that sometimes happens. + logger.propagate = False + set_file_logger("{}/database_manager.log".format(self.logdir), level=logging_level, format_string="%(asctime)s.%(msecs)03d %(name)s:%(lineno)d [%(levelname)s] [%(threadName)s %(thread)d] %(message)s", name="database_manager") diff --git a/parsl/version.py b/parsl/version.py index 3d1e18273a..9d8bc3d338 100644 --- a/parsl/version.py +++ b/parsl/version.py @@ -3,4 +3,4 @@ ..[alpha/beta/..] Alphas will be numbered like this -> 0.4.0a0 """ -VERSION = '1.1.0+desc-2021.12.06a' +VERSION = '1.1.0+desc-2021.12.07a' From 51b8c16bce34e6e14014a0b8145e9ae365df3dde Mon Sep 17 00:00:00 2001 From: Ben Clifford Date: Tue, 7 Dec 2021 11:57:27 +0000 Subject: [PATCH 266/408] --- parsl/version.py | 2 +- test-requirements.txt | 1 + 2 files changed, 2 insertions(+), 1 deletion(-) diff --git a/parsl/version.py b/parsl/version.py index 9d8bc3d338..ff9a10e20d 100644 --- a/parsl/version.py +++ b/parsl/version.py @@ -3,4 +3,4 @@ ..[alpha/beta/..] Alphas will be numbered like this -> 0.4.0a0 """ -VERSION = '1.1.0+desc-2021.12.07a' +VERSION = '1.1.0+desc-2021.12.07b' diff --git a/test-requirements.txt b/test-requirements.txt index 3b897356cb..e3b7785ffe 100644 --- a/test-requirements.txt +++ b/test-requirements.txt @@ -10,6 +10,7 @@ nbsphinx sphinx_rtd_theme mypy==0.910 types-python-dateutil +types-request sqlalchemy-stubs Sphinx==3.4.1 twine From bca21c743db7b4047d75312cb66e425068a6c39c Mon Sep 17 00:00:00 2001 From: Ben Clifford Date: Tue, 7 Dec 2021 12:01:25 +0000 Subject: [PATCH 267/408] --- parsl/version.py | 2 +- test-requirements.txt | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/parsl/version.py b/parsl/version.py index ff9a10e20d..1387d7c828 100644 --- a/parsl/version.py +++ b/parsl/version.py @@ -3,4 +3,4 @@ ..[alpha/beta/..] Alphas will be numbered like this -> 0.4.0a0 """ -VERSION = '1.1.0+desc-2021.12.07b' +VERSION = '1.1.0+desc-2021.12.07c' diff --git a/test-requirements.txt b/test-requirements.txt index e3b7785ffe..26427cafed 100644 --- a/test-requirements.txt +++ b/test-requirements.txt @@ -10,7 +10,7 @@ nbsphinx sphinx_rtd_theme mypy==0.910 types-python-dateutil -types-request +types-requests sqlalchemy-stubs Sphinx==3.4.1 twine From d47634ff22d43361c46e8ec92e37cec7212138b8 Mon Sep 17 00:00:00 2001 From: Ben Clifford Date: Tue, 7 Dec 2021 12:12:32 +0000 Subject: [PATCH 268/408] --- parsl/executors/status_handling.py | 12 ++---------- parsl/version.py | 2 +- 2 files changed, 3 insertions(+), 11 deletions(-) diff --git a/parsl/executors/status_handling.py b/parsl/executors/status_handling.py index 39c2e23f73..cf1fa55626 100644 --- a/parsl/executors/status_handling.py +++ b/parsl/executors/status_handling.py @@ -2,7 +2,7 @@ import threading from itertools import compress from abc import abstractmethod, abstractproperty -from concurrent.futures import Future, InvalidStateError +from concurrent.futures import Future from typing import List, Any, Dict, Optional, Tuple, Union import parsl # noqa F401 @@ -115,15 +115,7 @@ def set_bad_state_and_fail_all(self, exception: Exception): # We set all current tasks to this exception to make sure that # this is raised in the main context. for task in self._tasks: - # this set_exception can fail sometimes with an InvalidStateException... - # is this assumption that set_bad_state_and_fail_all is only called once? - # or is the exception being set after a result? - try: - f = self._tasks[task] - logger.info(f"Setting executor-wide bad state on future: {repr(f)}.") - f.set_exception(BadStateException(self, self._executor_exception)) - except InvalidStateError: - logger.exception(f"when setting executor-wide bad state on future: {repr(f)}.") + self._tasks[task].set_exception(BadStateException(self, self._executor_exception)) @property def bad_state_is_set(self): diff --git a/parsl/version.py b/parsl/version.py index 1387d7c828..534da3bfcb 100644 --- a/parsl/version.py +++ b/parsl/version.py @@ -3,4 +3,4 @@ ..[alpha/beta/..] Alphas will be numbered like this -> 0.4.0a0 """ -VERSION = '1.1.0+desc-2021.12.07c' +VERSION = '1.1.0+desc-2021.12.07d' From b226121a5d357a0e3621fd80b4537cbcf90fadc6 Mon Sep 17 00:00:00 2001 From: Ben Clifford Date: Tue, 11 Jan 2022 14:42:45 +0000 Subject: [PATCH 269/408] Add an example for david adams wrt node monitoring --- parsl/executors/high_throughput/executor.py | 32 +++++----- parsl/monitoring/davidadams_reporter.py | 63 +++++++++++++++++++ parsl/tests/configs/htex_local_alternate.py | 2 + parsl/tests/conftest.py | 7 ++- .../tests/site_tests/site_config_selector.py | 3 - parsl/version.py | 2 +- setup.py | 1 + 7 files changed, 90 insertions(+), 20 deletions(-) create mode 100755 parsl/monitoring/davidadams_reporter.py diff --git a/parsl/executors/high_throughput/executor.py b/parsl/executors/high_throughput/executor.py index 03c586a0e5..b411208ead 100644 --- a/parsl/executors/high_throughput/executor.py +++ b/parsl/executors/high_throughput/executor.py @@ -32,6 +32,22 @@ logger = logging.getLogger(__name__) +DEFAULT_LAUNCH_CMD = ("process_worker_pool.py {debug} {max_workers} " + "-a {addresses} " + "-p {prefetch_capacity} " + "-c {cores_per_worker} " + "-m {mem_per_worker} " + "--poll {poll_period} " + "--task_port={task_port} " + "--result_port={result_port} " + "--logdir={logdir} " + "--block_id={{block_id}} " + "--hb_period={heartbeat_period} " + "{address_probe_timeout_string} " + "--hb_threshold={heartbeat_threshold} " + "--cpu-affinity {cpu_affinity} ") + + class HighThroughputExecutor(BlockProviderExecutor, RepresentationMixin): """Executor designed for cluster-scale @@ -242,21 +258,7 @@ def __init__(self, self.cpu_affinity = cpu_affinity if not launch_cmd: - self.launch_cmd = ("process_worker_pool.py {debug} {max_workers} " - "-a {addresses} " - "-p {prefetch_capacity} " - "-c {cores_per_worker} " - "-m {mem_per_worker} " - "--poll {poll_period} " - "--task_port={task_port} " - "--result_port={result_port} " - "--logdir={logdir} " - "--block_id={{block_id}} " - "--hb_period={heartbeat_period} " - "{address_probe_timeout_string} " - "--hb_threshold={heartbeat_threshold} " - "--cpu-affinity {cpu_affinity} ") - + self.launch_cmd = DEFAULT_LAUNCH_CMD radio_mode = "htex" def initialize_scaling(self): diff --git a/parsl/monitoring/davidadams_reporter.py b/parsl/monitoring/davidadams_reporter.py new file mode 100755 index 0000000000..2ed3eecab5 --- /dev/null +++ b/parsl/monitoring/davidadams_reporter.py @@ -0,0 +1,63 @@ +#!/usr/bin/env python3 + +"""This script is for david adams to experiment with collecting +per-node data - ultimately to log to the parsl monitoring database, +but right now to look at which data fields to collect, and log them +to per-node CSV. + +This expects to receive parameters that align with the parsl work queue worker +such as the block ID. +""" + +import logging +import os +import platform +import psutil +import subprocess +import sys +import time +import uuid + +from datetime import datetime +from parsl.log_utils import set_stream_logger +from parsl.monitoring.monitoring import FilesystemRadio + +logger = logging.getLogger("parsl.monitoring.davidadams_reporter") + + +if __name__ == "__main__": + + + set_stream_logger() + logger.info(f"reporter starting, with args {sys.argv}") + + report_prefix = sys.argv[1] + + logger.info(f"will log to prefix {report_prefix}") + + args = sys.argv[2:] + logger.info(f"reporter launching workers with args {args}") + + set_stream_logger() + + hostname = platform.node() + csv_filename = report_prefix + "/" + hostname + "." + str(time.time()) + ".csv" + + + worker_process = subprocess.Popen(args) + ret = None + reading = 0 + with open(csv_filename, "w") as csv_file: + while ret is None: + ret = worker_process.poll() + logger.info("sleeping in poll loop") + print(f"{time.time()},{reading},{psutil.cpu_percent()}", file=csv_file, flush=True) + + reading += 1 + time.sleep(10) + + + logger.info(f"subprocessed ended with return code {ret.returncode}") + + logger.info(f"node reporter ending, passing on return code {ret.returncode} from workers") + sys.exit(ret.returncode) diff --git a/parsl/tests/configs/htex_local_alternate.py b/parsl/tests/configs/htex_local_alternate.py index a27fb895fc..1fec1a69fc 100644 --- a/parsl/tests/configs/htex_local_alternate.py +++ b/parsl/tests/configs/htex_local_alternate.py @@ -26,6 +26,7 @@ from parsl.config import Config from parsl.executors import HighThroughputExecutor +from parsl.executors.high_throughput.executor import DEFAULT_LAUNCH_CMD from parsl.data_provider.http import HTTPInTaskStaging @@ -39,6 +40,7 @@ def fresh_config(): return Config( executors=[ HighThroughputExecutor( + launch_cmd = "davidadams_reporter.py /tmp/da_test " + DEFAULT_LAUNCH_CMD, label="htex_Local", address="localhost", working_dir=working_dir, diff --git a/parsl/tests/conftest.py b/parsl/tests/conftest.py index d2370d2f4c..23c1ece74e 100644 --- a/parsl/tests/conftest.py +++ b/parsl/tests/conftest.py @@ -111,7 +111,12 @@ def load_dfk_session(request, pytestconfig): if DataFlowKernelLoader._dfk is not None: raise RuntimeError("DFK didn't start as None - there was a DFK from somewhere already") - dfk = parsl.load(module.config) + if hasattr(module, 'config'): + dfk = parsl.load(module.config) + elif hasattr(module, 'fresh_config'): + dfk = parsl.load(module.fresh_config()) + else: + raise RuntimeError("Config module does not define config or fresh_config") yield diff --git a/parsl/tests/site_tests/site_config_selector.py b/parsl/tests/site_tests/site_config_selector.py index 79a931a8c3..87a5333073 100644 --- a/parsl/tests/site_tests/site_config_selector.py +++ b/parsl/tests/site_tests/site_config_selector.py @@ -71,6 +71,3 @@ def fresh_config(): raise RuntimeError("This site cannot be identified") return config - - -config = fresh_config() diff --git a/parsl/version.py b/parsl/version.py index 37bc86f599..23d0f1a7d4 100644 --- a/parsl/version.py +++ b/parsl/version.py @@ -3,4 +3,4 @@ ..[alpha/beta/..] Alphas will be numbered like this -> 0.4.0a0 """ -VERSION = '1.1.0+desc-2022.01.11a' +VERSION = '1.1.0+desc-2022.01.11b' diff --git a/setup.py b/setup.py index 5c7a14b271..06b8d059d5 100755 --- a/setup.py +++ b/setup.py @@ -51,6 +51,7 @@ 'parsl/executors/low_latency/lowlatency_worker.py', 'parsl/executors/workqueue/exec_parsl_function.py', 'parsl/monitoring/node_reporter.py', + 'parsl/monitoring/davidadams_reporter.py', ], extras_require=extras_require, From 2832ff54809fd1b1ce5f809eceaad36e381fa976 Mon Sep 17 00:00:00 2001 From: Ben Clifford Date: Tue, 11 Jan 2022 16:28:15 +0000 Subject: [PATCH 270/408] Fix flake8 errors --- parsl/executors/high_throughput/executor.py | 1 - parsl/monitoring/davidadams_reporter.py | 7 ------- parsl/providers/provider_base.py | 2 +- parsl/tests/configs/htex_local_alternate.py | 2 +- parsl/version.py | 2 +- 5 files changed, 3 insertions(+), 11 deletions(-) diff --git a/parsl/executors/high_throughput/executor.py b/parsl/executors/high_throughput/executor.py index b411208ead..29076c1bae 100644 --- a/parsl/executors/high_throughput/executor.py +++ b/parsl/executors/high_throughput/executor.py @@ -48,7 +48,6 @@ "--cpu-affinity {cpu_affinity} ") - class HighThroughputExecutor(BlockProviderExecutor, RepresentationMixin): """Executor designed for cluster-scale diff --git a/parsl/monitoring/davidadams_reporter.py b/parsl/monitoring/davidadams_reporter.py index 2ed3eecab5..3a06e5caa1 100755 --- a/parsl/monitoring/davidadams_reporter.py +++ b/parsl/monitoring/davidadams_reporter.py @@ -10,24 +10,19 @@ """ import logging -import os import platform import psutil import subprocess import sys import time -import uuid -from datetime import datetime from parsl.log_utils import set_stream_logger -from parsl.monitoring.monitoring import FilesystemRadio logger = logging.getLogger("parsl.monitoring.davidadams_reporter") if __name__ == "__main__": - set_stream_logger() logger.info(f"reporter starting, with args {sys.argv}") @@ -43,7 +38,6 @@ hostname = platform.node() csv_filename = report_prefix + "/" + hostname + "." + str(time.time()) + ".csv" - worker_process = subprocess.Popen(args) ret = None reading = 0 @@ -56,7 +50,6 @@ reading += 1 time.sleep(10) - logger.info(f"subprocessed ended with return code {ret.returncode}") logger.info(f"node reporter ending, passing on return code {ret.returncode} from workers") diff --git a/parsl/providers/provider_base.py b/parsl/providers/provider_base.py index f4bf938e74..41a6d1d012 100644 --- a/parsl/providers/provider_base.py +++ b/parsl/providers/provider_base.py @@ -134,7 +134,7 @@ class ExecutionProvider(metaclass=ABCMeta): """ # these are because these variables are implemented - # as properties... + # as properties... _cores_per_node = None # type: Optional[int] _mem_per_node = None # type: Optional[float] diff --git a/parsl/tests/configs/htex_local_alternate.py b/parsl/tests/configs/htex_local_alternate.py index 1fec1a69fc..c4183228bb 100644 --- a/parsl/tests/configs/htex_local_alternate.py +++ b/parsl/tests/configs/htex_local_alternate.py @@ -40,7 +40,7 @@ def fresh_config(): return Config( executors=[ HighThroughputExecutor( - launch_cmd = "davidadams_reporter.py /tmp/da_test " + DEFAULT_LAUNCH_CMD, + launch_cmd="davidadams_reporter.py /tmp/da_test " + DEFAULT_LAUNCH_CMD, label="htex_Local", address="localhost", working_dir=working_dir, diff --git a/parsl/version.py b/parsl/version.py index 23d0f1a7d4..8c97ba2285 100644 --- a/parsl/version.py +++ b/parsl/version.py @@ -3,4 +3,4 @@ ..[alpha/beta/..] Alphas will be numbered like this -> 0.4.0a0 """ -VERSION = '1.1.0+desc-2022.01.11b' +VERSION = '1.1.0+desc-2022.01.11c' From 1524a6289fcdde4bd0218f722d38f6f79d24ca72 Mon Sep 17 00:00:00 2001 From: Ben Clifford Date: Tue, 11 Jan 2022 16:38:22 +0000 Subject: [PATCH 271/408] Fix mypy in CI for recently introduced node reporter --- parsl/monitoring/davidadams_reporter.py | 5 ++++- parsl/version.py | 2 +- 2 files changed, 5 insertions(+), 2 deletions(-) diff --git a/parsl/monitoring/davidadams_reporter.py b/parsl/monitoring/davidadams_reporter.py index 3a06e5caa1..5b0693f3c1 100755 --- a/parsl/monitoring/davidadams_reporter.py +++ b/parsl/monitoring/davidadams_reporter.py @@ -16,6 +16,7 @@ import sys import time +from typing import Any from parsl.log_utils import set_stream_logger logger = logging.getLogger("parsl.monitoring.davidadams_reporter") @@ -39,7 +40,9 @@ csv_filename = report_prefix + "/" + hostname + "." + str(time.time()) + ".csv" worker_process = subprocess.Popen(args) - ret = None + + ret: Any = None + reading = 0 with open(csv_filename, "w") as csv_file: while ret is None: diff --git a/parsl/version.py b/parsl/version.py index 8c97ba2285..50f34b3f76 100644 --- a/parsl/version.py +++ b/parsl/version.py @@ -3,4 +3,4 @@ ..[alpha/beta/..] Alphas will be numbered like this -> 0.4.0a0 """ -VERSION = '1.1.0+desc-2022.01.11c' +VERSION = '1.1.0+desc-2022.01.11d' From fb3cc8be169502d22faf97d1edaac8a94209370e Mon Sep 17 00:00:00 2001 From: Ben Clifford Date: Tue, 11 Jan 2022 16:53:12 +0000 Subject: [PATCH 272/408] Fix missing tmp dir in CI --- parsl/tests/configs/htex_local_alternate.py | 2 +- parsl/version.py | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/parsl/tests/configs/htex_local_alternate.py b/parsl/tests/configs/htex_local_alternate.py index c4183228bb..01a16f0a55 100644 --- a/parsl/tests/configs/htex_local_alternate.py +++ b/parsl/tests/configs/htex_local_alternate.py @@ -40,7 +40,7 @@ def fresh_config(): return Config( executors=[ HighThroughputExecutor( - launch_cmd="davidadams_reporter.py /tmp/da_test " + DEFAULT_LAUNCH_CMD, + launch_cmd="davidadams_reporter.py /tmp/ " + DEFAULT_LAUNCH_CMD, label="htex_Local", address="localhost", working_dir=working_dir, diff --git a/parsl/version.py b/parsl/version.py index 50f34b3f76..a97b52da0a 100644 --- a/parsl/version.py +++ b/parsl/version.py @@ -3,4 +3,4 @@ ..[alpha/beta/..] Alphas will be numbered like this -> 0.4.0a0 """ -VERSION = '1.1.0+desc-2022.01.11d' +VERSION = '1.1.0+desc-2022.01.11e' From 030015695bb9f21b249a28f1cf6f9c841901be38 Mon Sep 17 00:00:00 2001 From: Ben Clifford Date: Tue, 11 Jan 2022 18:08:40 +0000 Subject: [PATCH 273/408] More fiddling with site tests to make more coherent --- Makefile | 2 +- parsl/tests/site_tests/test_provider.py | 1 + parsl/tests/site_tests/test_site.py | 1 + parsl/version.py | 2 +- 4 files changed, 4 insertions(+), 2 deletions(-) diff --git a/Makefile b/Makefile index c5eeebf08a..2f781dfd83 100644 --- a/Makefile +++ b/Makefile @@ -86,7 +86,7 @@ config_local_test: ## run all tests with workqueue_ex config echo "$(MPI)" parsl/executors/extreme_scale/install-mpi.sh $(MPI) pip3 install ".[extreme_scale,monitoring]" - PYTHONPATH=.:/tmp/cctools/lib/python3.8/site-packages pytest parsl/tests/ -k "not cleannet" --config local --cov=parsl --cov-append --cov-report= --random-order + PYTHONPATH=.:/tmp/cctools/lib/python3.8/site-packages pytest parsl/tests/ -k "not cleannet and not site" --config local --cov=parsl --cov-append --cov-report= --random-order .PHONY: site_test site_test: diff --git a/parsl/tests/site_tests/test_provider.py b/parsl/tests/site_tests/test_provider.py index 17d7a664b5..3339c7a7f8 100644 --- a/parsl/tests/site_tests/test_provider.py +++ b/parsl/tests/site_tests/test_provider.py @@ -18,6 +18,7 @@ def platform(sleep=10, stdout=None): @pytest.mark.local +@pytest.mark.site def test_provider(): """ Provider scaling """ diff --git a/parsl/tests/site_tests/test_site.py b/parsl/tests/site_tests/test_site.py index a1f0f41e29..680853c460 100644 --- a/parsl/tests/site_tests/test_site.py +++ b/parsl/tests/site_tests/test_site.py @@ -14,6 +14,7 @@ def platform(sleep=10, stdout=None): @pytest.mark.local +@pytest.mark.site def test_platform(n=2, sleep_dur=10): """ This should sleep to make sure that concurrent apps will go to different workers on different nodes. diff --git a/parsl/version.py b/parsl/version.py index a97b52da0a..b9776c004d 100644 --- a/parsl/version.py +++ b/parsl/version.py @@ -3,4 +3,4 @@ ..[alpha/beta/..] Alphas will be numbered like this -> 0.4.0a0 """ -VERSION = '1.1.0+desc-2022.01.11e' +VERSION = '1.1.0+desc-2022.01.11f' From 52c3dc433cb9d6d12cdbea68b0d7db966142b492 Mon Sep 17 00:00:00 2001 From: Ben Clifford Date: Fri, 14 Jan 2022 10:03:23 +0000 Subject: [PATCH 274/408] --- parsl/executors/status_handling.py | 14 +++++++++++++- parsl/version.py | 2 +- 2 files changed, 14 insertions(+), 2 deletions(-) diff --git a/parsl/executors/status_handling.py b/parsl/executors/status_handling.py index cf1fa55626..508c533465 100644 --- a/parsl/executors/status_handling.py +++ b/parsl/executors/status_handling.py @@ -48,7 +48,15 @@ def __init__(self, provider: ExecutionProvider): self._simulated_status: Dict[Any, JobStatus] = {} self._executor_bad_state = threading.Event() self._executor_exception: Optional[Exception] = None + + # TODO: maybe this can be subsumed into the new block ID allocator? self._generated_block_id_counter = 1 + + # factor this with the DFK task ID lock code to give an atomic + # counter class? if such a thing doesn't exist in python lib already? + self._block_sequence_number_lock = threading.Lock() + self._block_sequence_number = 0 + self._tasks = {} # type: Dict[object, Future] self.blocks = {} # type: Dict[str, str] self.block_mapping = {} # type: Dict[str, str] @@ -160,8 +168,12 @@ def scale_out(self, blocks: int = 1) -> List[str]: if not self.provider: raise (ScalingFailed(None, "No execution provider available")) block_ids = [] + logger.info(f"Scaling out by {blocks} blocks") for i in range(blocks): - block_id = str(len(self.blocks)) + with self._block_sequence_number_lock: + block_id = str(self._block_sequence_number) + self._block_sequence_number += 1 + logger.debug(f"Allocated block ID {block_id}") try: job_id = self._launch_block(block_id) self.blocks[block_id] = job_id diff --git a/parsl/version.py b/parsl/version.py index f61ea16f37..40bea2fdf6 100644 --- a/parsl/version.py +++ b/parsl/version.py @@ -3,4 +3,4 @@ ..[alpha/beta/..] Alphas will be numbered like this -> 0.4.0a0 """ -VERSION = '1.3.0-dev+desc-2022.01.13a' +VERSION = '1.3.0-dev+desc-2022.01.14a' From 82b00d4c3a7d985330133a732abbabddd1c78be5 Mon Sep 17 00:00:00 2001 From: Ben Clifford Date: Fri, 14 Jan 2022 09:52:50 +0000 Subject: [PATCH 275/408] Allocate block ids uniquely Previously the code around block ID allocation was a bit fuzzy and it looks like it could sometimes allocate the same block ID several times in the presence of failure. This is at least causing confusion in debugging frequent hangs in CI. A second ID allocated was used when a block ID had not already been allocated, for simulating failures. This ID allocation code is changed in this PR to use the same sequence counter. --- parsl/executors/status_handling.py | 13 +++++++++---- parsl/utils.py | 16 ++++++++++++++++ 2 files changed, 25 insertions(+), 4 deletions(-) diff --git a/parsl/executors/status_handling.py b/parsl/executors/status_handling.py index 56fd78b6e6..a852f72bca 100644 --- a/parsl/executors/status_handling.py +++ b/parsl/executors/status_handling.py @@ -9,6 +9,7 @@ from parsl.executors.base import ParslExecutor from parsl.executors.errors import ScalingFailed from parsl.providers.provider_base import JobStatus, ExecutionProvider, JobState +from parsl.utils import AtomicIDCounter logger = logging.getLogger(__name__) @@ -48,7 +49,9 @@ def __init__(self, provider: ExecutionProvider): self._simulated_status: Dict[Any, JobStatus] = {} self._executor_bad_state = threading.Event() self._executor_exception: Optional[Exception] = None - self._generated_block_id_counter = 1 + + self._block_id_counter = AtomicIDCounter() + self._tasks = {} # type: Dict[object, Future] self.blocks = {} # type: Dict[str, str] self.block_mapping = {} # type: Dict[str, str] @@ -84,8 +87,8 @@ def _fail_job_async(self, block_id: Any, message: str): as failed and report it in status() """ if block_id is None: - block_id = "failed-block-{}".format(self._generated_block_id_counter) - self._generated_block_id_counter += 1 + block_id = str(self._block_id_counter.get_id()) + logger.info(f"Allocated block ID {block_id} for simulated failure") self._simulated_status[block_id] = JobStatus(JobState.FAILED, message) @abstractproperty @@ -160,8 +163,10 @@ def scale_out(self, blocks: int = 1) -> List[str]: if not self.provider: raise (ScalingFailed(None, "No execution provider available")) block_ids = [] + logger.info(f"Scaling out by {blocks} blocks") for i in range(blocks): - block_id = str(len(self.blocks)) + block_id = str(self._block_id_counter.get_id()) + logger.info(f"Allocated block ID {block_id}") try: job_id = self._launch_block(block_id) self.blocks[block_id] = job_id diff --git a/parsl/utils.py b/parsl/utils.py index 9a8301e546..cc7a3ddead 100644 --- a/parsl/utils.py +++ b/parsl/utils.py @@ -3,6 +3,7 @@ import os import shlex import subprocess +import threading import time import typeguard from contextlib import contextmanager @@ -239,3 +240,18 @@ def assemble_line(args: List[str], kwargs: Dict[str, object]) -> str: return assemble_line(args, kwargs) else: return assemble_multiline(args, kwargs) + + +class AtomicIDCounter: + """A class to allocate counter-style IDs, in a thread-safe way. + """ + + def __init__(self): + self.count = 0 + self.lock = threading.Lock() + + def get_id(self): + with self.lock: + new_id = self.count + self.count += 1 + return new_id From bfad1f5bab2bda056fb051681b253750c8cb97d8 Mon Sep 17 00:00:00 2001 From: Ben Clifford Date: Fri, 14 Jan 2022 12:14:11 +0000 Subject: [PATCH 276/408] Make manager phrasing consistent in log messages. The before message referred to manager; the after message referred to worker. This patch makes them the same - using manager --- parsl/executors/high_throughput/executor.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/parsl/executors/high_throughput/executor.py b/parsl/executors/high_throughput/executor.py index e4d0331daf..7ab6f4eff4 100644 --- a/parsl/executors/high_throughput/executor.py +++ b/parsl/executors/high_throughput/executor.py @@ -487,7 +487,7 @@ def hold_worker(self, worker_id): Worker id to be put on hold """ c = self.command_client.run("HOLD_WORKER;{}".format(worker_id)) - logger.debug("Sent hold request to worker: {}".format(worker_id)) + logger.debug("Sent hold request to manager: {}".format(worker_id)) return c @property From 335d0648ea6e67846ae8108c78bc62c73bdfeca2 Mon Sep 17 00:00:00 2001 From: Ben Clifford Date: Fri, 7 Jan 2022 14:29:03 +0000 Subject: [PATCH 277/408] Elaborate JobStatus docstring to include stdout/err info --- parsl/providers/provider_base.py | 9 ++++++++- 1 file changed, 8 insertions(+), 1 deletion(-) diff --git a/parsl/providers/provider_base.py b/parsl/providers/provider_base.py index 6ce69399ce..903f9aba9c 100644 --- a/parsl/providers/provider_base.py +++ b/parsl/providers/provider_base.py @@ -26,7 +26,14 @@ def __new__(cls, value, terminal, status_name): class JobStatus(object): - """Encapsulates a job state together with other details, presently a (error) message""" + """Encapsulates a job state together with other details: + + Args: + message: Optional human readable message + exit_code: Optional exit code + stdout_path: Optional path to a file containing the job's stdout + stderr_path: Optional path to a file containing the job's stderr + """ SUMMARY_TRUNCATION_THRESHOLD = 2048 def __init__(self, state: JobState, message: str = None, exit_code: Optional[int] = None, From 2668aa7125b9cf716f6f8501d3cc2ac407db0ec7 Mon Sep 17 00:00:00 2001 From: Ben Clifford Date: Fri, 14 Jan 2022 15:41:34 +0000 Subject: [PATCH 278/408] Correct label of stderr in JobErrorHandler, from stdout --- parsl/dataflow/job_error_handler.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/parsl/dataflow/job_error_handler.py b/parsl/dataflow/job_error_handler.py index 20ac7ff321..2d74eed755 100644 --- a/parsl/dataflow/job_error_handler.py +++ b/parsl/dataflow/job_error_handler.py @@ -47,7 +47,7 @@ def get_error(self, status: Dict[str, JobStatus]) -> Exception: err = err + "\tSTDOUT: {}\n".format(stdout) stderr = js.stderr_summary if stderr: - err = err + "\tSTDOUT: {}\n".format(stderr) + err = err + "\tSTDERR: {}\n".format(stderr) if len(err) == 0: err = "[No error message received]" From 8ec1616c558694f46d22685b8d40e7ffd470a5a3 Mon Sep 17 00:00:00 2001 From: Ben Clifford Date: Tue, 28 Dec 2021 16:09:47 +0000 Subject: [PATCH 279/408] Add ManagerLost - WorkerLost is in there already --- docs/reference.rst | 1 + 1 file changed, 1 insertion(+) diff --git a/docs/reference.rst b/docs/reference.rst index 076d890de9..716a19922d 100644 --- a/docs/reference.rst +++ b/docs/reference.rst @@ -165,6 +165,7 @@ Exceptions parsl.channels.errors.SSHException parsl.channels.errors.FileCopyException parsl.executors.high_throughput.errors.WorkerLost + parsl.executors.high_throughput.interchange.ManagerLost Internal ======== From d466e599d306666d79e29a941823a06988d3f813 Mon Sep 17 00:00:00 2001 From: Ben Clifford Date: Fri, 31 Dec 2021 13:34:11 +0000 Subject: [PATCH 280/408] fix a FIXME in cluster provider docstring --- parsl/providers/cluster_provider.py | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/parsl/providers/cluster_provider.py b/parsl/providers/cluster_provider.py index 2e089aa72b..ce305beb4d 100644 --- a/parsl/providers/cluster_provider.py +++ b/parsl/providers/cluster_provider.py @@ -23,8 +23,8 @@ class ClusterProvider(ExecutionProvider): :class:`~parsl.channels.SSHInteractiveLoginChannel`. walltime : str Walltime requested per block in HH:MM:SS. - launcher : str - FIXME + launcher : Launcher + Launcher for this provider. cmd_timeout : int Timeout for commands made to the scheduler in seconds From 85ef47bbefca0ff505542d86da655a910b00f7ac Mon Sep 17 00:00:00 2001 From: Ben Clifford Date: Wed, 29 Dec 2021 12:39:56 +0000 Subject: [PATCH 281/408] Remove stub main from PBS provider --- parsl/providers/torque/torque.py | 5 ----- 1 file changed, 5 deletions(-) diff --git a/parsl/providers/torque/torque.py b/parsl/providers/torque/torque.py index 88a06bbe9f..841973e4c4 100644 --- a/parsl/providers/torque/torque.py +++ b/parsl/providers/torque/torque.py @@ -242,8 +242,3 @@ def cancel(self, job_ids): @property def status_polling_interval(self): return 60 - - -if __name__ == "__main__": - - print("None") From 43ce5a3d7d1c4affa222b6a74fc40a75d01bd6b7 Mon Sep 17 00:00:00 2001 From: Ben Clifford Date: Tue, 28 Dec 2021 16:07:44 +0000 Subject: [PATCH 282/408] Remove unused ChannelRequired exception --- docs/reference.rst | 1 - parsl/providers/error.py | 14 -------------- 2 files changed, 15 deletions(-) diff --git a/docs/reference.rst b/docs/reference.rst index 076d890de9..a83b6e6981 100644 --- a/docs/reference.rst +++ b/docs/reference.rst @@ -152,7 +152,6 @@ Exceptions parsl.dataflow.error.DependencyError parsl.launchers.error.BadLauncher parsl.providers.error.ExecutionProviderException - parsl.providers.error.ChannelRequired parsl.providers.error.ScaleOutFailed parsl.providers.error.SchedulerMissingArgs parsl.providers.error.ScriptPathError diff --git a/parsl/providers/error.py b/parsl/providers/error.py index 206e2a10d3..d13ad49112 100644 --- a/parsl/providers/error.py +++ b/parsl/providers/error.py @@ -6,20 +6,6 @@ class ExecutionProviderException(Exception): pass -class ChannelRequired(ExecutionProviderException): - ''' Execution provider requires a channel. - ''' - - def __init__(self, provider, reason): - self.provider = provider - self.reason = reason - - def __repr__(self): - return "Unable to Initialize provider.Provider:{0}, Reason:{1}".format( - self.provider, self.reason - ) - - class ScaleOutFailed(ExecutionProviderException): ''' Scale out failed in the submit phase on the provider side ''' From 4d3ce1c68a53f12fb22d6ef6557bc502e1084990 Mon Sep 17 00:00:00 2001 From: Ben Clifford Date: Mon, 17 Jan 2022 15:38:44 +0000 Subject: [PATCH 283/408] fix some monitoring tests --- parsl/tests/test_monitoring/test_mon_local/test_basic.py | 6 +++--- parsl/tests/test_monitoring/test_mon_local/test_db_locks.py | 6 +++--- .../test_mon_local/test_memoization_representation.py | 6 +++--- parsl/tests/test_monitoring/test_mon_wq/test_basic.py | 6 +++--- parsl/tests/test_monitoring/test_mon_wq/test_db_locks.py | 6 +++--- .../test_mon_wq/test_memoization_representation.py | 6 +++--- parsl/version.py | 2 +- 7 files changed, 19 insertions(+), 19 deletions(-) diff --git a/parsl/tests/test_monitoring/test_mon_local/test_basic.py b/parsl/tests/test_monitoring/test_mon_local/test_basic.py index 9169c4559a..c404a83bbc 100644 --- a/parsl/tests/test_monitoring/test_mon_local/test_basic.py +++ b/parsl/tests/test_monitoring/test_mon_local/test_basic.py @@ -27,9 +27,9 @@ def test_row_counts(): import sqlalchemy from parsl.tests.configs.local_threads_monitoring import fresh_config - if os.path.exists("monitoring.db"): + if os.path.exists("runinfo/monitoring.db"): logger.info("Monitoring database already exists - deleting") - os.remove("monitoring.db") + os.remove("runinfo/monitoring.db") logger.info("Generating fresh config") c = fresh_config() @@ -46,7 +46,7 @@ def test_row_counts(): # at this point, we should find one row in the monitoring database. logger.info("checking database content") - engine = sqlalchemy.create_engine("sqlite:///monitoring.db") + engine = sqlalchemy.create_engine("sqlite:///runinfo/monitoring.db") with engine.begin() as connection: result = connection.execute("SELECT COUNT(*) FROM workflow") diff --git a/parsl/tests/test_monitoring/test_mon_local/test_db_locks.py b/parsl/tests/test_monitoring/test_mon_local/test_db_locks.py index 84cae74e58..77b3dcd377 100644 --- a/parsl/tests/test_monitoring/test_mon_local/test_db_locks.py +++ b/parsl/tests/test_monitoring/test_mon_local/test_db_locks.py @@ -17,11 +17,11 @@ def this_app(): def test_row_counts(): from parsl.tests.configs.htex_local_alternate import fresh_config import sqlalchemy - if os.path.exists("monitoring.db"): + if os.path.exists("runinfo/monitoring.db"): logger.info("Monitoring database already exists - deleting") - os.remove("monitoring.db") + os.remove("runinfo/monitoring.db") - engine = sqlalchemy.create_engine("sqlite:///monitoring.db") + engine = sqlalchemy.create_engine("sqlite:///runinfo/monitoring.db") logger.info("loading parsl") parsl.load(fresh_config()) diff --git a/parsl/tests/test_monitoring/test_mon_local/test_memoization_representation.py b/parsl/tests/test_monitoring/test_mon_local/test_memoization_representation.py index 14faeb0518..f2344ba4d2 100644 --- a/parsl/tests/test_monitoring/test_mon_local/test_memoization_representation.py +++ b/parsl/tests/test_monitoring/test_mon_local/test_memoization_representation.py @@ -17,9 +17,9 @@ def test_hashsum(): import sqlalchemy from parsl.tests.configs.local_threads_monitoring import fresh_config - if os.path.exists("monitoring.db"): + if os.path.exists("runinfo/monitoring.db"): logger.info("Monitoring database already exists - deleting") - os.remove("monitoring.db") + os.remove("runinfo/monitoring.db") logger.info("loading parsl") parsl.load(fresh_config()) @@ -51,7 +51,7 @@ def test_hashsum(): # at this point, we should find one row in the monitoring database. logger.info("checking database content") - engine = sqlalchemy.create_engine("sqlite:///monitoring.db") + engine = sqlalchemy.create_engine("sqlite:///runinfo/monitoring.db") with engine.begin() as connection: # we should have three tasks, but with only two tries, because the diff --git a/parsl/tests/test_monitoring/test_mon_wq/test_basic.py b/parsl/tests/test_monitoring/test_mon_wq/test_basic.py index 9e1f1f8dc8..b98785822d 100644 --- a/parsl/tests/test_monitoring/test_mon_wq/test_basic.py +++ b/parsl/tests/test_monitoring/test_mon_wq/test_basic.py @@ -27,9 +27,9 @@ def test_row_counts(): import sqlalchemy from parsl.tests.configs.workqueue_monitoring import fresh_config - if os.path.exists("monitoring.db"): + if os.path.exists("runinfo/monitoring.db"): logger.info("Monitoring database already exists - deleting") - os.remove("monitoring.db") + os.remove("runinfo/monitoring.db") logger.info("Generating fresh config") c = fresh_config() @@ -46,7 +46,7 @@ def test_row_counts(): # at this point, we should find one row in the monitoring database. logger.info("checking database content") - engine = sqlalchemy.create_engine("sqlite:///monitoring.db") + engine = sqlalchemy.create_engine("sqlite:///runinfo/monitoring.db") with engine.begin() as connection: result = connection.execute("SELECT COUNT(*) FROM workflow") diff --git a/parsl/tests/test_monitoring/test_mon_wq/test_db_locks.py b/parsl/tests/test_monitoring/test_mon_wq/test_db_locks.py index d2e32beff4..f6f8ea3219 100644 --- a/parsl/tests/test_monitoring/test_mon_wq/test_db_locks.py +++ b/parsl/tests/test_monitoring/test_mon_wq/test_db_locks.py @@ -18,11 +18,11 @@ def test_row_counts(): import sqlalchemy from parsl.tests.configs.workqueue_monitoring import fresh_config - if os.path.exists("monitoring.db"): + if os.path.exists("runinfo/monitoring.db"): logger.info("Monitoring database already exists - deleting") - os.remove("monitoring.db") + os.remove("runinfo/monitoring.db") - engine = sqlalchemy.create_engine("sqlite:///monitoring.db") + engine = sqlalchemy.create_engine("sqlite:///runinfo/monitoring.db") logger.info("loading parsl") parsl.load(fresh_config()) diff --git a/parsl/tests/test_monitoring/test_mon_wq/test_memoization_representation.py b/parsl/tests/test_monitoring/test_mon_wq/test_memoization_representation.py index ae915626a2..f9d63ec338 100644 --- a/parsl/tests/test_monitoring/test_mon_wq/test_memoization_representation.py +++ b/parsl/tests/test_monitoring/test_mon_wq/test_memoization_representation.py @@ -17,9 +17,9 @@ def test_hashsum(): import sqlalchemy from parsl.tests.configs.workqueue_monitoring import fresh_config - if os.path.exists("monitoring.db"): + if os.path.exists("runinfo/monitoring.db"): logger.info("Monitoring database already exists - deleting") - os.remove("monitoring.db") + os.remove("runinfo/monitoring.db") logger.info("loading parsl") parsl.load(fresh_config()) @@ -51,7 +51,7 @@ def test_hashsum(): # at this point, we should find one row in the monitoring database. logger.info("checking database content") - engine = sqlalchemy.create_engine("sqlite:///monitoring.db") + engine = sqlalchemy.create_engine("sqlite:///runinfo/monitoring.db") with engine.begin() as connection: # we should have three tasks, but with only two tries, because the diff --git a/parsl/version.py b/parsl/version.py index 7f2b3a09a4..fe50cd2260 100644 --- a/parsl/version.py +++ b/parsl/version.py @@ -3,4 +3,4 @@ ..[alpha/beta/..] Alphas will be numbered like this -> 0.4.0a0 """ -VERSION = '1.3.0-dev+desc-2022.01.17b' +VERSION = '1.3.0-dev+desc-2022.01.17c' From e79ac1765822f19db8e31740edc99801a4f2121f Mon Sep 17 00:00:00 2001 From: Ben Clifford Date: Mon, 17 Jan 2022 17:47:10 +0000 Subject: [PATCH 284/408] Eliminate tasks[id] when reporting final status counts see issues #2178 for this particular report, and #2014 for overview of tasks[id] elimination. --- parsl/dataflow/dflow.py | 85 +++++++++++--------------- parsl/dataflow/usage_tracking/usage.py | 3 +- 2 files changed, 38 insertions(+), 50 deletions(-) diff --git a/parsl/dataflow/dflow.py b/parsl/dataflow/dflow.py index eb6ed97683..cdd5c6eaba 100644 --- a/parsl/dataflow/dflow.py +++ b/parsl/dataflow/dflow.py @@ -90,12 +90,11 @@ def __init__(self, config=Config()): self.usage_tracker = UsageTracker(self) self.usage_tracker.send_message() + self.task_state_counts_lock = threading.Lock() + self.task_state_counts = {state: 0 for state in States} + # Monitoring self.run_id = str(uuid4()) - self.tasks_completed_count = 0 - self.tasks_memo_completed_count = 0 - self.tasks_failed_count = 0 - self.tasks_dep_fail_count = 0 self.monitoring = config.monitoring # hub address and port for interchange to connect @@ -142,8 +141,8 @@ def __init__(self, config=Config()): 'workflow_name': self.workflow_name, 'workflow_version': self.workflow_version, 'rundir': self.run_dir, - 'tasks_completed_count': self.tasks_completed_count, - 'tasks_failed_count': self.tasks_failed_count, + 'tasks_completed_count': self.task_state_counts[States.exec_done], + 'tasks_failed_count': self.task_state_counts[States.failed], 'user': getuser(), 'host': gethostname(), } @@ -206,9 +205,9 @@ def _create_task_log_info(self, task_record): task_log_info['try_id'] = task_record['try_id'] task_log_info['timestamp'] = datetime.datetime.now() task_log_info['task_status_name'] = task_record['status'].name - task_log_info['tasks_failed_count'] = self.tasks_failed_count - task_log_info['tasks_completed_count'] = self.tasks_completed_count - task_log_info['tasks_memo_completed_count'] = self.tasks_memo_completed_count + task_log_info['tasks_failed_count'] = self.task_state_counts[States.failed] + task_log_info['tasks_completed_count'] = self.task_state_counts[States.exec_done] + task_log_info['tasks_memo_completed_count'] = self.task_state_counts[States.memo_done] task_log_info['from_memo'] = task_record['from_memo'] task_log_info['task_inputs'] = str(task_record['kwargs'].get('inputs', None)) task_log_info['task_outputs'] = str(task_record['kwargs'].get('outputs', None)) @@ -318,11 +317,11 @@ def handle_exec_update(self, task_record, future): elif task_record['fail_cost'] <= self._config.retries: # record the final state for this try before we mutate for retries - task_record['status'] = States.fail_retryable + self.update_task_state(task_record, States.fail_retryable) self._send_task_log_info(task_record) task_record['try_id'] += 1 - task_record['status'] = States.pending + self.update_task_state(task_record, States.pending) task_record['try_time_launched'] = None task_record['try_time_returned'] = None task_record['fail_history'] = [] @@ -333,8 +332,7 @@ def handle_exec_update(self, task_record, future): logger.exception("Task {} failed after {} retry attempts".format(task_id, task_record['try_id'])) task_record['time_returned'] = datetime.datetime.now() - task_record['status'] = States.failed - self.tasks_failed_count += 1 + self.update_task_state(task_record, States.failed) task_record['time_returned'] = datetime.datetime.now() with task_record['app_fu']._update_lock: task_record['app_fu'].set_exception(e) @@ -357,13 +355,12 @@ def handle_exec_update(self, task_record, future): # Fail with a TypeError if the joinapp python body returned # something we can't join on. if isinstance(inner_future, Future): - task_record['status'] = States.joining + self.update_task_state(task_record, States.joining) task_record['joins'] = inner_future inner_future.add_done_callback(partial(self.handle_join_update, task_record)) else: task_record['time_returned'] = datetime.datetime.now() - task_record['status'] = States.failed - self.tasks_failed_count += 1 + self.update_task_state(task_record, States.failed) task_record['time_returned'] = datetime.datetime.now() with task_record['app_fu']._update_lock: task_record['app_fu'].set_exception(TypeError(f"join_app body must return a Future, got {type(inner_future)}")) @@ -398,8 +395,7 @@ def handle_join_update(self, task_record, inner_app_future): # no need to update the fail cost because join apps are never # retried - task_record['status'] = States.failed - self.tasks_failed_count += 1 + self.update_task_state(task_record, States.failed) task_record['time_returned'] = datetime.datetime.now() with task_record['app_fu']._update_lock: task_record['app_fu'].set_exception(e) @@ -449,14 +445,8 @@ def _complete_task(self, task_record, new_state, result): assert new_state in FINAL_STATES assert new_state not in FINAL_FAILURE_STATES old_state = task_record['status'] - task_record['status'] = new_state - if new_state == States.exec_done: - self.tasks_completed_count += 1 - elif new_state == States.memo_done: - self.tasks_memo_completed_count += 1 - else: - raise RuntimeError(f"Cannot update task counters with unknown final state {new_state}") + self.update_task_state(task_record, new_state) logger.info(f"Task {task_record['id']} completed ({old_state.name} -> {new_state.name})") task_record['time_returned'] = datetime.datetime.now() @@ -464,6 +454,17 @@ def _complete_task(self, task_record, new_state, result): with task_record['app_fu']._update_lock: task_record['app_fu'].set_result(result) + def update_task_state(self, task_record, new_state): + """Updates a task record state, and recording an appropriate change + to task state counters. + """ + + with self.task_state_counts_lock: + if hasattr(task_record, 'status'): + self.task_state_counts[task_record['status']] -= 1 + self.task_state_counts[new_state] += 1 + task_record['status'] = new_state + @staticmethod def _unwrap_remote_exception_wrapper(future: Future) -> Any: result = future.result() @@ -529,8 +530,7 @@ def launch_if_ready(self, task_record): logger.info( "Task {} failed due to dependency failure".format(task_id)) # Raise a dependency exception - task_record['status'] = States.dep_fail - self.tasks_dep_fail_count += 1 + self.update_task_state(task_record, States.dep_fail) self._send_task_log_info(task_record) @@ -603,7 +603,7 @@ def launch_task(self, task_record, executable, *args, **kwargs): with self.submitter_lock: exec_fu = executor.submit(executable, task_record['resource_specification'], *args, **kwargs) - task_record['status'] = States.launched + self.update_task_state(task_record, States.launched) self._send_task_log_info(task_record) @@ -854,7 +854,6 @@ def submit(self, func, app_args, executors='all', cache=False, ignore_for_cache= 'ignore_for_cache': ignore_for_cache, 'join': join, 'joins': None, - 'status': States.unsched, 'try_id': 0, 'id': task_id, 'time_invoked': datetime.datetime.now(), @@ -863,6 +862,8 @@ def submit(self, func, app_args, executors='all', cache=False, ignore_for_cache= 'try_time_returned': None, 'resource_specification': resource_specification} + self.update_task_state(task_def, States.unsched) + app_fu = AppFuture(task_def) # Transform remote input files to data futures @@ -905,7 +906,7 @@ def submit(self, func, app_args, executors='all', cache=False, ignore_for_cache= task_def['task_launch_lock'] = threading.Lock() app_fu.add_done_callback(partial(self.handle_app_update, task_def)) - task_def['status'] = States.pending + self.update_task_state(task_def, States.pending) logger.debug("Task {} set to pending state with AppFuture: {}".format(task_id, task_def['app_fu'])) self._send_task_log_info(task_def) @@ -946,24 +947,10 @@ def callback_adapter(dep_fut): def log_task_states(self): logger.info("Summary of tasks in DFK:") - keytasks = {state: 0 for state in States} - - for tid in self.tasks: - keytasks[self.tasks[tid]['status']] += 1 - # Fetch from counters since tasks get wiped - keytasks[States.exec_done] = self.tasks_completed_count - keytasks[States.memo_done] = self.tasks_memo_completed_count - keytasks[States.failed] = self.tasks_failed_count - keytasks[States.dep_fail] = self.tasks_dep_fail_count - - for state in States: - if keytasks[state]: - logger.info("Tasks in state {}: {}".format(str(state), keytasks[state])) + with self.task_state_counts_lock: + for state in States: + logger.info("Tasks in state {}: {}".format(str(state), self.task_state_counts[state])) - total_summarized = sum(keytasks.values()) - if total_summarized != self.task_count: - logger.error("Task count summarisation was inconsistent: summarised {} tasks, but task counter registered {} tasks".format( - total_summarized, self.task_count)) logger.info("End of summary") def _create_remote_dirs_over_channel(self, provider, channel): @@ -1099,8 +1086,8 @@ def cleanup(self): if self.monitoring: self.monitoring.send(MessageType.WORKFLOW_INFO, - {'tasks_failed_count': self.tasks_failed_count, - 'tasks_completed_count': self.tasks_completed_count, + {'tasks_failed_count': self.task_state_counts[States.failed], + 'tasks_completed_count': self.task_state_counts[States.exec_done], "time_began": self.time_began, 'time_completed': self.time_completed, 'run_id': self.run_id, 'rundir': self.run_dir, diff --git a/parsl/dataflow/usage_tracking/usage.py b/parsl/dataflow/usage_tracking/usage.py index 9777fb55e5..8252208605 100644 --- a/parsl/dataflow/usage_tracking/usage.py +++ b/parsl/dataflow/usage_tracking/usage.py @@ -10,6 +10,7 @@ import platform from parsl.multiprocessing import ForkProcess +from parsl.dataflow.states import States from parsl.version import VERSION as PARSL_VERSION logger = logging.getLogger(__name__) @@ -178,7 +179,7 @@ def construct_end_message(self): site_count = len([x for x in self.dfk.config.executors if x.managed]) - app_fails = self.dfk.tasks_failed_count + self.dfk.tasks_dep_fail_count + app_fails = self.dfk.task_state_counts[States.failed] + self.dfk.task_state_counts[States.dep_fail] message = {'uuid': self.uuid, 'end': time.time(), From 0b2c0bdac0efb89ba72c121a3351c89f24319aed Mon Sep 17 00:00:00 2001 From: Ben Clifford Date: Mon, 17 Jan 2022 22:03:42 +0000 Subject: [PATCH 285/408] Make retry tests wait for all launched tasks before finishing Without this, the tasks continue to run while subsequent local tests happen. This is at the least confusing in logs - I haven't checked if it introduces any actual testing problems. --- parsl/tests/test_error_handling/test_retries.py | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/parsl/tests/test_error_handling/test_retries.py b/parsl/tests/test_error_handling/test_retries.py index 2f8e57d403..0f53396dca 100644 --- a/parsl/tests/test_error_handling/test_retries.py +++ b/parsl/tests/test_error_handling/test_retries.py @@ -61,6 +61,8 @@ def test_fail_nowait(numtasks=10): assert isinstance( e, TypeError), "Expected a TypeError, got {}".format(e) + # wait for all tasks to complete before ending this test + [x.exception() for x in fus] print("Done") @@ -84,6 +86,8 @@ def test_fail_delayed(numtasks=10): assert isinstance( e, TypeError), "Expected a TypeError, got {}".format(e) + # wait for all tasks to complete before ending this test + [x.exception() for x in fus] print("Done") From e1996eba6c8f0ec6dd319c736a8e55b9fd074db5 Mon Sep 17 00:00:00 2001 From: Ben Clifford Date: Tue, 25 Jan 2022 15:29:15 +0000 Subject: [PATCH 286/408] Format BadStateException with the executor label rather than full repr The full repr for an executor is usually very long and includes all of the configuration information for that exception, so previously a BadStateException looked like this, which is awkwardly large: parsl.executors.errors.BadStateException: Executor HighThroughputExecutor( address=None, address_probe_timeout=None, cores_per_worker=1, cpu_affinity='none', heartbeat_period=30, heartbeat_threshold=120, interchange_port_range=(55000, 56000), label='htex_local', launch_cmd='executable_that_hopefully_does_not_exist_1030509.py', managed=True, max_workers=1, mem_per_worker=None, poll_period=1, prefetch_capacity=0, provider=LocalProvider( channel=LocalChannel( envs={}, script_dir='/home/runner/work/parsl/parsl/runinfo/030/submit_scripts', userhome='/home/runner/work/parsl/parsl' ), cmd_timeout=30, init_blocks=1, launcher=SimpleLauncher(debug=True), max_blocks=1, min_blocks=0, move_files=None, nodes_per_block=1, parallelism=1, worker_init='' ), storage_access=None, worker_debug=True, worker_logdir_root=None, worker_port_range=(54000, 55000), worker_ports=None, working_dir=None ) failed due to: STDERR: /home/runner/work/parsl/parsl/runinfo/030/submit_scripts/parsl.localprovider.1642801165.5067718.sh: line 3: executable_that_hopefully_does_not_exist_1030509.py: command not found After this commit, the exception instead looks like this: parsl.executors.errors.BadStateException: Executor htex_local failed due to: STDERR: /home/benc/parsl/src/parsl/runinfo/000/submit_scripts/parsl.localprovider.1643124620.9775066.sh: line 3: executable_that_hopefully_does_not_exist_1030509.py: command not found --- parsl/executors/errors.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/parsl/executors/errors.py b/parsl/executors/errors.py index 0c3c52cabc..3c2e0056eb 100644 --- a/parsl/executors/errors.py +++ b/parsl/executors/errors.py @@ -15,7 +15,7 @@ def __init__(self, executor, reason): self.reason = reason def __str__(self): - return "Executor {0} failed due to: {1}".format(self.executor, self.reason) + return "Executor {0} failed due to: {1}".format(self.executor.label, self.reason) class BadStateException(ExecutorError): From 52e5a769ec471cb50990bad810bc95b8aa2bc6c6 Mon Sep 17 00:00:00 2001 From: Ben Clifford Date: Tue, 25 Jan 2022 15:48:19 +0000 Subject: [PATCH 287/408] Add in additional logging around shutdown, to help with ongoing misbehaving shutdown debugging --- parsl/dataflow/dflow.py | 10 +++++++++- 1 file changed, 9 insertions(+), 1 deletion(-) diff --git a/parsl/dataflow/dflow.py b/parsl/dataflow/dflow.py index eb6ed97683..8c8a8d6224 100644 --- a/parsl/dataflow/dflow.py +++ b/parsl/dataflow/dflow.py @@ -1078,12 +1078,15 @@ def cleanup(self): self.usage_tracker.send_message() self.usage_tracker.close() - logger.info("Terminating flow_control and strategy threads") + logger.info("Closing flowcontrol") self.flowcontrol.close() + logger.info("Scaling in and shutting down executors") + for executor in self.executors.values(): if executor.managed and not executor.bad_state_is_set: if executor.scaling_enabled: + logger.info(f"Scaling in executor {executor.label}") job_ids = executor.provider.resources.keys() block_ids = executor.scale_in(len(job_ids)) if self.monitoring and block_ids: @@ -1093,7 +1096,12 @@ def cleanup(self): msg = executor.create_monitoring_info(new_status) logger.debug("Sending message {} to hub from DFK".format(msg)) self.monitoring.send(MessageType.BLOCK_INFO, msg) + logger.info(f"Shutting down executor {executor.label}") executor.shutdown() + elif executor.managed and executor.bad_state_is_set: # and bad_state_is_set + logger.warn(f"Not shutting down executor {executor.label} because it is in bad state") + else: + logger.info(f"Not shutting down executor {executor.label} because it is unmanaged") self.time_completed = datetime.datetime.now() From d2798c4196337a869bbc2952e5f7584563af7701 Mon Sep 17 00:00:00 2001 From: Ben Clifford Date: Tue, 25 Jan 2022 15:56:30 +0000 Subject: [PATCH 288/408] Tidy HighThroughputExecutor shutdown function to remove incorrect commentary and unused parameters --- parsl/executors/high_throughput/executor.py | 10 +--------- 1 file changed, 1 insertion(+), 9 deletions(-) diff --git a/parsl/executors/high_throughput/executor.py b/parsl/executors/high_throughput/executor.py index 7ab6f4eff4..c103dda74a 100644 --- a/parsl/executors/high_throughput/executor.py +++ b/parsl/executors/high_throughput/executor.py @@ -684,18 +684,10 @@ def _get_launch_command(self, block_id: str) -> str: launch_cmd = self.launch_cmd.format(block_id=block_id) return launch_cmd - def shutdown(self, hub=True, targets='all', block=False): + def shutdown(self): """Shutdown the executor, including all workers and controllers. - - This is not implemented. - - Kwargs: - - hub (Bool): Whether the hub should be shutdown, Default: True, - - targets (list of ints| 'all'): List of block id's to kill, Default: 'all' - - block (Bool): To block for confirmations or not """ logger.info("Attempting HighThroughputExecutor shutdown") self.queue_proc.terminate() logger.info("Finished HighThroughputExecutor shutdown attempt") - return True From bf0c1f46053825a72358da45bd9f2e7df36a6760 Mon Sep 17 00:00:00 2001 From: Ben Clifford Date: Tue, 25 Jan 2022 16:03:53 +0000 Subject: [PATCH 289/408] fix duplicate merge of badstateexception --- parsl/executors/errors.py | 8 -------- 1 file changed, 8 deletions(-) diff --git a/parsl/executors/errors.py b/parsl/executors/errors.py index 1829803545..3c2e0056eb 100644 --- a/parsl/executors/errors.py +++ b/parsl/executors/errors.py @@ -26,14 +26,6 @@ def __init__(self, executor, exception): super().__init__(executor, str(exception)) -class BadStateException(ExecutorError): - """Error returned by task Futures when an executor is in a bad state. - """ - - def __init__(self, executor, exception): - super().__init__(executor, str(exception)) - - class UnsupportedFeatureError(ExecutorError): """Error raised when attemping to use unsupported feature in an Executor""" From c00823c9fd9e599dd6c18fc18e6ea69010690c86 Mon Sep 17 00:00:00 2001 From: Ben Clifford Date: Tue, 25 Jan 2022 16:26:48 +0000 Subject: [PATCH 290/408] Explicitly shut down htex after bad state test Without this, the interchange process continues running for the duration of the pytest lifetime, overlapping with other tests. This makes CI hangs harder to debug. --- .../tests/test_error_handling/test_htex_missing_worker.py | 7 +++++++ 1 file changed, 7 insertions(+) diff --git a/parsl/tests/test_error_handling/test_htex_missing_worker.py b/parsl/tests/test_error_handling/test_htex_missing_worker.py index 3a20037e34..b8bf4002c9 100644 --- a/parsl/tests/test_error_handling/test_htex_missing_worker.py +++ b/parsl/tests/test_error_handling/test_htex_missing_worker.py @@ -14,6 +14,7 @@ def local_setup(): def local_teardown(): + parsl.dfk().cleanup() parsl.clear() @@ -34,3 +35,9 @@ def test_that_it_fails(): failed = True if not failed: raise Exception("The app somehow ran without a valid worker") + + assert parsl.dfk().config.executors[0]._executor_bad_state.is_set() + + # htex needs shutting down explicitly because dfk.cleanup() will not + # do that, as it is in bad state + parsl.dfk().config.executors[0].shutdown() From 6012698b1a4d80844f371e601b7d7cc15a9abb39 Mon Sep 17 00:00:00 2001 From: Ben Clifford Date: Thu, 27 Jan 2022 12:28:13 +0000 Subject: [PATCH 291/408] --- .github/workflows/ci.yaml | 2 +- parsl/log_utils.py | 2 +- parsl/version.py | 2 +- 3 files changed, 3 insertions(+), 3 deletions(-) diff --git a/.github/workflows/ci.yaml b/.github/workflows/ci.yaml index 80baf7562f..dc072042d9 100644 --- a/.github/workflows/ci.yaml +++ b/.github/workflows/ci.yaml @@ -12,7 +12,7 @@ jobs: matrix: python-version: ["3.6", "3.7", "3.8", "3.9"] runs-on: ubuntu-20.04 - timeout-minutes: 30 + timeout-minutes: 60 steps: - uses: actions/checkout@master diff --git a/parsl/log_utils.py b/parsl/log_utils.py index ceea2c81d2..877f2fb3e4 100644 --- a/parsl/log_utils.py +++ b/parsl/log_utils.py @@ -60,7 +60,7 @@ def set_file_logger(filename: str, name: str = 'parsl', level: int = logging.DEB - None """ if format_string is None: - format_string = "%(asctime)s.%(msecs)03d %(name)s:%(lineno)d %(processName)s(%(process)d) %(threadName)s [%(levelname)s] %(message)s" + format_string = "%(asctime)s %(name)s:%(lineno)d %(processName)s(%(process)d) %(threadName)s [%(levelname)s] %(message)s" logger = logging.getLogger(name) logger.setLevel(logging.DEBUG) diff --git a/parsl/version.py b/parsl/version.py index f59875dc8b..34b0254c46 100644 --- a/parsl/version.py +++ b/parsl/version.py @@ -3,4 +3,4 @@ ..[alpha/beta/..] Alphas will be numbered like this -> 0.4.0a0 """ -VERSION = '1.3.0-dev+desc-2022.01.27b' +VERSION = '1.3.0-dev+desc-2022.01.27c' From 3b3548ec8d58175b121e34664c0406b12b4a2a83 Mon Sep 17 00:00:00 2001 From: Ben Clifford Date: Mon, 17 Jan 2022 21:34:45 +0000 Subject: [PATCH 292/408] Rephrase Hub when it means router --- parsl/monitoring/monitoring.py | 10 +++++----- 1 file changed, 5 insertions(+), 5 deletions(-) diff --git a/parsl/monitoring/monitoring.py b/parsl/monitoring/monitoring.py index 8fa175779c..f671aa1fef 100644 --- a/parsl/monitoring/monitoring.py +++ b/parsl/monitoring/monitoring.py @@ -252,7 +252,7 @@ def start(self, run_id: str) -> int: daemon=True, ) self.dbm_proc.start() - self.logger.info("Started the Hub process {} and DBM process {}".format(self.router_proc.pid, self.dbm_proc.pid)) + self.logger.info("Started the router process {} and DBM process {}".format(self.router_proc.pid, self.dbm_proc.pid)) try: comm_q_result = comm_q.get(block=True, timeout=120) @@ -276,7 +276,7 @@ def send(self, mtype: MessageType, message: Any) -> None: self._dfk_channel.send_pyobj((mtype, message)) except zmq.Again: self.logger.exception( - "The monitoring message sent from DFK to Hub timed-out after {}ms".format(self.dfk_channel_timeout)) + "The monitoring message sent from DFK to router timed-out after {}ms".format(self.dfk_channel_timeout)) def close(self) -> None: if self.logger: @@ -285,7 +285,7 @@ def close(self) -> None: while True: try: exception_msgs.append(self.exception_q.get(block=False)) - self.logger.error("There was a queued exception (Either Hub or DBM process got exception much earlier?)") + self.logger.error("There was a queued exception (Either router or DBM process got exception much earlier?)") except queue.Empty: break if self._dfk_channel and self.monitoring_hub_active: @@ -297,9 +297,9 @@ def close(self) -> None: exception_msg[1])) self.router_proc.terminate() self.dbm_proc.terminate() - self.logger.info("Waiting for Hub to receive all messages and terminate") + self.logger.info("Waiting for router to terminate") self.router_proc.join() - self.logger.debug("Finished waiting for Hub termination") + self.logger.debug("Finished waiting for router termination") if len(exception_msgs) == 0: self.priority_msgs.put(("STOP", 0)) self.dbm_proc.join() From e72906b5fa20130922f10ff8245c97e54d2be3d5 Mon Sep 17 00:00:00 2001 From: Ben Clifford Date: Wed, 29 Dec 2021 12:56:33 +0000 Subject: [PATCH 293/408] Tidy up documentation for PBS providers --- parsl/providers/pbspro/pbspro.py | 4 ---- parsl/providers/torque/torque.py | 4 ++-- 2 files changed, 2 insertions(+), 6 deletions(-) diff --git a/parsl/providers/pbspro/pbspro.py b/parsl/providers/pbspro/pbspro.py index 493706f6d9..4e846e4827 100644 --- a/parsl/providers/pbspro/pbspro.py +++ b/parsl/providers/pbspro/pbspro.py @@ -14,10 +14,6 @@ class PBSProProvider(TorqueProvider): """PBS Pro Execution Provider - This provider uses sbatch to submit, squeue for status, and scancel to cancel - jobs. The sbatch script to be used is created from a template file in this - same module. - Parameters ---------- channel : Channel diff --git a/parsl/providers/torque/torque.py b/parsl/providers/torque/torque.py index 841973e4c4..88d525956f 100644 --- a/parsl/providers/torque/torque.py +++ b/parsl/providers/torque/torque.py @@ -27,8 +27,8 @@ class TorqueProvider(ClusterProvider, RepresentationMixin): """Torque Execution Provider - This provider uses sbatch to submit, squeue for status, and scancel to cancel - jobs. The sbatch script to be used is created from a template file in this + This provider uses qsub to submit, qstat for status, and qdel to cancel + jobs. The qsub script to be used is created from a template file in this same module. Parameters From 15825c4c41cf70eb0735d221645a13758f42ffd3 Mon Sep 17 00:00:00 2001 From: Ben Clifford Date: Fri, 7 Jan 2022 14:23:41 +0000 Subject: [PATCH 294/408] Change docstring example to htex or WQ, rather than IPP/Swift/T --- parsl/providers/provider_base.py | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/parsl/providers/provider_base.py b/parsl/providers/provider_base.py index 6ce69399ce..0c3e82690f 100644 --- a/parsl/providers/provider_base.py +++ b/parsl/providers/provider_base.py @@ -131,8 +131,8 @@ class ExecutionProvider(metaclass=ABCMeta): @abstractmethod def submit(self, command: str, tasks_per_node: int, job_name: str = "parsl.auto") -> Any: ''' The submit method takes the command string to be executed upon - instantiation of a resource most often to start a pilot (such as IPP engine - or even Swift-T engines). + instantiation of a resource most often to start a pilot (such as for + HighThroughputExecutor or WorkQueueExecutor). Args : - command (str) : The bash command string to be executed From fb378b49355b0f631bab4c9ae7beaa0cce91ebcf Mon Sep 17 00:00:00 2001 From: Ben Clifford Date: Wed, 19 Jan 2022 14:15:19 +0000 Subject: [PATCH 295/408] run_id does not need to be configurable - there are other monitoring fields for this. remove TODO --- parsl/dataflow/dflow.py | 1 - 1 file changed, 1 deletion(-) diff --git a/parsl/dataflow/dflow.py b/parsl/dataflow/dflow.py index 8c8a8d6224..f0f414dbbd 100644 --- a/parsl/dataflow/dflow.py +++ b/parsl/dataflow/dflow.py @@ -110,7 +110,6 @@ def __init__(self, config=Config()): self.time_began = datetime.datetime.now() self.time_completed = None - # TODO: make configurable logger.info("Run id is: " + self.run_id) self.workflow_name = None From 7de8eaa870af5b05a2aab9e63711fa5ae698a665 Mon Sep 17 00:00:00 2001 From: Ben Clifford Date: Mon, 12 Apr 2021 10:56:44 +0000 Subject: [PATCH 296/408] Rephrase optional module missing error This error can be raised when an optional module failed to import for any reason, not just because the optional module is missing. A recent example is that sqlalchemy released a new incompatible version which parsl's requirements spec was not protecting against. This was fixed in PR #1994. --- parsl/errors.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/parsl/errors.py b/parsl/errors.py index eb81cf5157..29cbc0b16e 100644 --- a/parsl/errors.py +++ b/parsl/errors.py @@ -12,6 +12,6 @@ def __init__(self, module_names: List[str], reason: str): self.reason = reason def __str__(self) -> str: - return "The functionality requested requires missing optional modules {0}, because: {1}".format( + return "The functionality requested requires optional modules {0} which could not be imported, because: {1}".format( self.module_names, self.reason ) From 0dc78871c008c203c34d0d7ff9dd665bd7905e61 Mon Sep 17 00:00:00 2001 From: Ben Clifford Date: Tue, 15 Feb 2022 11:53:42 +0000 Subject: [PATCH 297/408] Add doc for state parameter --- parsl/providers/provider_base.py | 1 + 1 file changed, 1 insertion(+) diff --git a/parsl/providers/provider_base.py b/parsl/providers/provider_base.py index 220d1f222a..2a68b23952 100644 --- a/parsl/providers/provider_base.py +++ b/parsl/providers/provider_base.py @@ -29,6 +29,7 @@ class JobStatus(object): """Encapsulates a job state together with other details: Args: + state: The machine-reachable state of the job this status refers to message: Optional human readable message exit_code: Optional exit code stdout_path: Optional path to a file containing the job's stdout From 60c2ca09dd7fb4bf553a2f01c62212c352005d89 Mon Sep 17 00:00:00 2001 From: Ben Clifford Date: Thu, 17 Feb 2022 15:58:16 +0000 Subject: [PATCH 298/408] Fix broken PR #2192 task state counting task_record stores data as dictionary entries, not as attributes, and PR #2192 used the wrong membership test for that. Because of that, old task states were not being decremented ever. Prior to this commit: 2022-02-17 15:51:50.231 parsl.dataflow.dflow:956 [INFO] Tasks in state States.unsched: 298 2022-02-17 15:51:50.231 parsl.dataflow.dflow:956 [INFO] Tasks in state States.pending: 298 2022-02-17 15:51:50.231 parsl.dataflow.dflow:956 [INFO] Tasks in state States.running: 0 2022-02-17 15:51:50.231 parsl.dataflow.dflow:956 [INFO] Tasks in state States.exec_done: 238 2022-02-17 15:51:50.232 parsl.dataflow.dflow:956 [INFO] Tasks in state States.failed: 36 2022-02-17 15:51:50.232 parsl.dataflow.dflow:956 [INFO] Tasks in state States.dep_fail: 11 2022-02-17 15:51:50.232 parsl.dataflow.dflow:956 [INFO] Tasks in state States.launched: 268 2022-02-17 15:51:50.232 parsl.dataflow.dflow:956 [INFO] Tasks in state States.fail_retryable: 0 2022-02-17 15:51:50.232 parsl.dataflow.dflow:956 [INFO] Tasks in state States.memo_done: 13 2022-02-17 15:51:50.232 parsl.dataflow.dflow:956 [INFO] Tasks in state States.joining: 41 With this commit: 2022-02-17 15:55:26.279 parsl.dataflow.dflow:952 [INFO] Summary of tasks in DFK: 2022-02-17 15:55:26.279 parsl.dataflow.dflow:956 [INFO] Tasks in state States.unsched: 0 2022-02-17 15:55:26.279 parsl.dataflow.dflow:956 [INFO] Tasks in state States.pending: 0 2022-02-17 15:55:26.279 parsl.dataflow.dflow:956 [INFO] Tasks in state States.running: 0 2022-02-17 15:55:26.279 parsl.dataflow.dflow:956 [INFO] Tasks in state States.exec_done: 238 2022-02-17 15:55:26.279 parsl.dataflow.dflow:956 [INFO] Tasks in state States.failed: 36 2022-02-17 15:55:26.279 parsl.dataflow.dflow:956 [INFO] Tasks in state States.dep_fail: 11 2022-02-17 15:55:26.279 parsl.dataflow.dflow:956 [INFO] Tasks in state States.launched: 0 2022-02-17 15:55:26.279 parsl.dataflow.dflow:956 [INFO] Tasks in state States.fail_retryable: 0 2022-02-17 15:55:26.279 parsl.dataflow.dflow:956 [INFO] Tasks in state States.memo_done: 13 2022-02-17 15:55:26.279 parsl.dataflow.dflow:956 [INFO] Tasks in state States.joining: 0 --- parsl/dataflow/dflow.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/parsl/dataflow/dflow.py b/parsl/dataflow/dflow.py index 3fe7475a6c..8f13b8abce 100644 --- a/parsl/dataflow/dflow.py +++ b/parsl/dataflow/dflow.py @@ -459,7 +459,7 @@ def update_task_state(self, task_record, new_state): """ with self.task_state_counts_lock: - if hasattr(task_record, 'status'): + if 'status' in task_record: self.task_state_counts[task_record['status']] -= 1 self.task_state_counts[new_state] += 1 task_record['status'] = new_state From 2d96290b8b3cb7c9b7c677bd64df42db4e3a9e48 Mon Sep 17 00:00:00 2001 From: Ben Clifford Date: Thu, 17 Feb 2022 18:18:57 +0000 Subject: [PATCH 299/408] --- parsl/tests/test_shutdown/__init__.py | 0 parsl/version.py | 2 +- 2 files changed, 1 insertion(+), 1 deletion(-) create mode 100644 parsl/tests/test_shutdown/__init__.py diff --git a/parsl/tests/test_shutdown/__init__.py b/parsl/tests/test_shutdown/__init__.py new file mode 100644 index 0000000000..e69de29bb2 diff --git a/parsl/version.py b/parsl/version.py index 926e6fcc0e..45074a429b 100644 --- a/parsl/version.py +++ b/parsl/version.py @@ -3,4 +3,4 @@ ..[alpha/beta/..] Alphas will be numbered like this -> 0.4.0a0 """ -VERSION = '1.3.0-dev+desc-2022.02.17a' +VERSION = '1.3.0-dev+desc-2022.02.17b' From d3469234ef9f3666d6fd8d79ed0bcc4cf93ea8bc Mon Sep 17 00:00:00 2001 From: Ben Clifford Date: Thu, 17 Feb 2022 18:40:56 +0000 Subject: [PATCH 300/408] --- parsl/tests/test_shutdown/test_kill_htex.py | 7 ++++--- parsl/tests/test_shutdown/test_kill_monitoring.py | 4 ++-- parsl/version.py | 2 +- 3 files changed, 7 insertions(+), 6 deletions(-) diff --git a/parsl/tests/test_shutdown/test_kill_htex.py b/parsl/tests/test_shutdown/test_kill_htex.py index ceeb06fbde..6c857cff0a 100644 --- a/parsl/tests/test_shutdown/test_kill_htex.py +++ b/parsl/tests/test_shutdown/test_kill_htex.py @@ -9,7 +9,7 @@ # TODO: # should parametrically test both htex_local and htex_local_alternate -from parsl.tests.configs.htex_local_alternate import fresh_config +from parsl.tests.configs.htex_local import fresh_config @parsl.python_app @@ -18,6 +18,7 @@ def simple_app(): @pytest.mark.local +@pytest.mark.skip("not expected to pass - demonstrates hanging htex with missing interchange") @pytest.mark.parametrize("sig", [signal.SIGINT, signal.SIGTERM, signal.SIGKILL]) # are we expecting SIGKILL resilience here? Ideally yes def test_kill_router(sig): """This tests that we can kill a monitoring process and still have successful shutdown. @@ -35,9 +36,9 @@ def test_kill_router(sig): dfk = parsl.dfk() - assert "htex_Local" in dfk.executors.keys(), "htex required" + assert "htex_local" in dfk.executors.keys(), "htex required" - proc = dfk.executors["htex_Local"].interchange_proc + proc = dfk.executors["htex_local"].interchange_proc assert proc is not None, "Interchange process required" assert proc.is_alive(), "Interchange must be alive" diff --git a/parsl/tests/test_shutdown/test_kill_monitoring.py b/parsl/tests/test_shutdown/test_kill_monitoring.py index 1b6e2b5702..a656fe393e 100644 --- a/parsl/tests/test_shutdown/test_kill_monitoring.py +++ b/parsl/tests/test_shutdown/test_kill_monitoring.py @@ -7,8 +7,6 @@ logger = logging.getLogger(__name__) -from parsl.tests.configs.htex_local_alternate import fresh_config - @parsl.python_app def simple_app(): @@ -17,6 +15,7 @@ def simple_app(): @pytest.mark.local def test_no_kills(): + from parsl.tests.configs.htex_local_alternate import fresh_config """This tests that we can create a monitoring-enabled DFK and shut it down.""" parsl.load(fresh_config()) @@ -31,6 +30,7 @@ def test_no_kills(): @pytest.mark.parametrize("sig", [signal.SIGINT, signal.SIGTERM, signal.SIGKILL]) # are we expecting SIGKILL resilience here? Ideally yes @pytest.mark.parametrize("process_attr", ["router_proc", "dbm_proc"]) def test_kill_router(sig, process_attr): + from parsl.tests.configs.htex_local_alternate import fresh_config """This tests that we can kill a monitoring process and still have successful shutdown. This emulates behaviour when ctrl-C is pressed: that all of the processes receive a termination signal - SIGINT for ctrl-C - at once, and so specifically we should be diff --git a/parsl/version.py b/parsl/version.py index 45074a429b..1f9af315e8 100644 --- a/parsl/version.py +++ b/parsl/version.py @@ -3,4 +3,4 @@ ..[alpha/beta/..] Alphas will be numbered like this -> 0.4.0a0 """ -VERSION = '1.3.0-dev+desc-2022.02.17b' +VERSION = '1.3.0-dev+desc-2022.02.17c' From b86860ef462b607db8072e1ca276a03c26b52598 Mon Sep 17 00:00:00 2001 From: Ben Clifford Date: Thu, 17 Feb 2022 20:20:52 +0000 Subject: [PATCH 301/408] --- parsl/tests/test_python_apps/test_fail.py | 110 +++------------------- parsl/version.py | 2 +- 2 files changed, 13 insertions(+), 99 deletions(-) diff --git a/parsl/tests/test_python_apps/test_fail.py b/parsl/tests/test_python_apps/test_fail.py index 946d3921f3..eda527a05a 100644 --- a/parsl/tests/test_python_apps/test_fail.py +++ b/parsl/tests/test_python_apps/test_fail.py @@ -1,22 +1,15 @@ -import argparse - -import parsl from parsl.app.app import python_app -from parsl.tests.configs.local_threads import config - - -local_config = config +from parsl.dataflow.error import DependencyError @python_app -def sleep_fail(sleep_dur, sleep_rand_max, fail_prob, inputs=[]): - import time - import random +def fail_app(): + raise RuntimeError("fail_app always fails") - s = sleep_dur + random.randint(-sleep_rand_max, sleep_rand_max) - time.sleep(s) - raise Exception("App failure") +@python_app +def pass_app(inputs=[]): + return None def test_no_deps(numtasks=2): @@ -26,100 +19,21 @@ def test_no_deps(numtasks=2): fus = [] for i in range(0, numtasks): - fu = sleep_fail(0.1, 0, .8) + fu = fail_app() fus.extend([fu]) - count = 0 for fu in fus: - try: - fu.result() - except Exception as e: - print("Caught exception : ", "*" * 20) - print(e) - print("*" * 20) - count += 1 + assert isinstance(fu.exception(), Exception), "All futures must be exceptions" - print("Caught failures of {0}/{1}".format(count, len(fus))) - -def test_fail_sequence(numtasks=2): +def test_fail_sequence(numtasks=10): """Test failure in a sequence of dependencies App1 -> App2 ... -> AppN """ - sleep_dur = 0.1 - fail_prob = 0.4 - - fus = {0: None} - for i in range(0, numtasks): - print("Chaining {0} to {1}".format(i + 1, fus[i])) - fus[i + 1] = sleep_fail(sleep_dur, 0, fail_prob, inputs=[fus[i]]) - - # time.sleep(numtasks*sleep_dur) - for k in sorted(fus.keys()): - try: - x = fus[i].result() - print("{0} : {1}".format(k, x)) - except Exception as e: - print("{0} : {1}".format(k, e)) - - return - - -def test_deps(numtasks=2): - """Random failures in branches of Map -> Map -> reduce - - App1 App2 ... AppN - """ - - fus = [] + f = fail_app() for i in range(0, numtasks): - fu = sleep_fail(0.2, 0, .4) - fus.extend([fu]) - - # App1 App2 ... AppN - # | | | - # V V V - # App1 App2 ... AppN - - fus_2 = [] - for fu in fus: - fu = sleep_fail(0, 0, .8, inputs=[fu]) - fus_2.extend([fu]) - - # App1 App2 ... AppN - # | | | - # V V V - # App1 App2 ... AppN - # \ | / - # \ | / - # App_Final - - fu_final = sleep_fail(1, 0, 0, inputs=fus_2) - - try: - print("Final status : ", fu_final.result()) - except parsl.dataflow.error.DependencyError as e: - print("Caught the right exception") - print("Exception : ", e) - except Exception as e: - assert False, "Expected DependencyError but got: %s" % e - else: - raise RuntimeError("Expected DependencyError, but got no exception") - - -if __name__ == "__main__": - - parser = argparse.ArgumentParser() - parser.add_argument("-c", "--count", default="10", - help="Count of apps to launch") - parser.add_argument("-d", "--debug", action='store_true', - help="Count of apps to launch") - args = parser.parse_args() - - if args.debug: - parsl.set_stream_logger() + f = pass_app(inputs=[f]) - test_no_deps(numtasks=int(args.count)) - test_fail_sequence(numtasks=int(args.count)) + assert(isinstance(f.exception(), DependencyError)), "Final task did not fail with a dependency exception" diff --git a/parsl/version.py b/parsl/version.py index 1f9af315e8..04bd31fd59 100644 --- a/parsl/version.py +++ b/parsl/version.py @@ -3,4 +3,4 @@ ..[alpha/beta/..] Alphas will be numbered like this -> 0.4.0a0 """ -VERSION = '1.3.0-dev+desc-2022.02.17c' +VERSION = '1.3.0-dev+desc-2022.02.17d' From 85d6bca4d3cd917172bcf040d02358633261cfcf Mon Sep 17 00:00:00 2001 From: Ben Clifford Date: Tue, 22 Feb 2022 16:08:10 +0000 Subject: [PATCH 302/408] --- parsl/executors/errors.py | 16 ++++++++++++---- parsl/version.py | 2 +- 2 files changed, 13 insertions(+), 5 deletions(-) diff --git a/parsl/executors/errors.py b/parsl/executors/errors.py index 3c2e0056eb..40d0259dd9 100644 --- a/parsl/executors/errors.py +++ b/parsl/executors/errors.py @@ -1,16 +1,21 @@ """Exceptions raise by Executors.""" from parsl.app.errors import ParslError +from parsl.executors.base import ParslExecutor from typing import Optional class ExecutorError(ParslError): - """Base class for all exceptions. + """Base class for executor related exceptions. Only to be invoked when only a more specific error is not available. """ - def __init__(self, executor, reason): + # TODO: this constructor doesn't make sense for most errors here + # so it and the __str__ impl shoudl go away, and the few places + # that an ExecutorError is directly instantiated shoudl be replaced + # by a more specific errror + def __init__(self, executor: ParslExecutor, reason): self.executor = executor self.reason = reason @@ -44,10 +49,13 @@ def __str__(self): class ScalingFailed(ExecutorError): """Scaling failed due to error in Execution provider.""" - def __init__(self, executor: Optional[str], reason: str): - self.executor = executor + def __init__(self, executor_label: Optional[str], reason: str): + self.executor_label = executor_label self.reason = reason + def __str__(self): + return "Executor {0} scaling failed due to: {1}".format(self.executor_label, self.reason) + class DeserializationError(ExecutorError): """ Failure at the Deserialization of results/exceptions from remote workers diff --git a/parsl/version.py b/parsl/version.py index 04bd31fd59..ee75d4e827 100644 --- a/parsl/version.py +++ b/parsl/version.py @@ -3,4 +3,4 @@ ..[alpha/beta/..] Alphas will be numbered like this -> 0.4.0a0 """ -VERSION = '1.3.0-dev+desc-2022.02.17d' +VERSION = '1.3.0-dev+desc-2022.02.22a' From 4e87022692bdb96ce42ae22c4ac33de89bf11536 Mon Sep 17 00:00:00 2001 From: Ben Clifford Date: Thu, 24 Feb 2022 09:13:59 +0000 Subject: [PATCH 303/408] --- parsl/dataflow/dflow.py | 2 +- parsl/executors/workqueue/executor.py | 9 +++++---- parsl/version.py | 2 +- 3 files changed, 7 insertions(+), 6 deletions(-) diff --git a/parsl/dataflow/dflow.py b/parsl/dataflow/dflow.py index 31cf77e982..e1269e1486 100644 --- a/parsl/dataflow/dflow.py +++ b/parsl/dataflow/dflow.py @@ -83,7 +83,7 @@ def __init__(self, config=Config()): if config.initialize_logging: parsl.set_file_logger("{}/parsl.log".format(self.run_dir), level=logging.DEBUG) - logger.debug("Starting DataFlowKernel with config\n{}".format(config)) + logger.info("Starting DataFlowKernel with config\n{}".format(config)) logger.info("Parsl version: {}".format(get_version())) diff --git a/parsl/executors/workqueue/executor.py b/parsl/executors/workqueue/executor.py index 6882038cb2..58f421292a 100644 --- a/parsl/executors/workqueue/executor.py +++ b/parsl/executors/workqueue/executor.py @@ -625,7 +625,7 @@ def initialize_scaling(self): try: self.scale_out(blocks=self.provider.init_blocks) except Exception as e: - logger.debug("Scaling out failed: {}".format(e)) + logger.error("Initial block scaling out failed: {}".format(e)) raise e @property @@ -634,9 +634,10 @@ def outstanding(self) -> int: implemented and probably could be replaced with a counter. """ outstanding = 0 - for fut in self.tasks.values(): - if not fut.done(): - outstanding += 1 + with self.tasks_lock: + for fut in self.tasks.values(): + if not fut.done(): + outstanding += 1 logger.debug(f"Counted {outstanding} outstanding tasks") return outstanding diff --git a/parsl/version.py b/parsl/version.py index ee75d4e827..b911dd7444 100644 --- a/parsl/version.py +++ b/parsl/version.py @@ -3,4 +3,4 @@ ..[alpha/beta/..] Alphas will be numbered like this -> 0.4.0a0 """ -VERSION = '1.3.0-dev+desc-2022.02.22a' +VERSION = '1.3.0-dev+desc-2022.02.24a' From 21167617291aeab0a37dc83fd66ef594a39eda13 Mon Sep 17 00:00:00 2001 From: Ben Clifford Date: Thu, 24 Feb 2022 09:29:39 +0000 Subject: [PATCH 304/408] --- parsl/executors/workqueue/executor.py | 7 +++++-- parsl/version.py | 2 +- 2 files changed, 6 insertions(+), 3 deletions(-) diff --git a/parsl/executors/workqueue/executor.py b/parsl/executors/workqueue/executor.py index 58f421292a..3a8d360f69 100644 --- a/parsl/executors/workqueue/executor.py +++ b/parsl/executors/workqueue/executor.py @@ -30,6 +30,7 @@ from parsl.providers.provider_base import ExecutionProvider from parsl.providers import LocalProvider, CondorProvider from parsl.executors.workqueue import exec_parsl_function +from parsl.process_loggers import wrap_with_logs from parsl.utils import setproctitle import typeguard @@ -317,11 +318,11 @@ def start(self): "project_password_file": self.project_password_file, "project_name": self.project_name} self.submit_process = multiprocessing.Process(target=_work_queue_submit_wait, - name="submit_thread", + name="WorkQueue-Submit-Process", kwargs=submit_process_kwargs) self.collector_thread = threading.Thread(target=self._collect_work_queue_results, - name="wait_thread") + name="WorkQueue-collector-thread") self.collector_thread.daemon = True # Begin both processes @@ -711,6 +712,7 @@ def run_dir(self, value=None): self._run_dir = value return self._run_dir + @wrap_with_logs def _collect_work_queue_results(self): """Sets the values of tasks' futures of tasks completed by work queue. """ @@ -749,6 +751,7 @@ def _collect_work_queue_results(self): logger.debug("Exiting Collector Thread") +@wrap_with_logs def _work_queue_submit_wait(task_queue=multiprocessing.Queue(), launch_cmd=None, env=None, diff --git a/parsl/version.py b/parsl/version.py index b911dd7444..28bbaf22ab 100644 --- a/parsl/version.py +++ b/parsl/version.py @@ -3,4 +3,4 @@ ..[alpha/beta/..] Alphas will be numbered like this -> 0.4.0a0 """ -VERSION = '1.3.0-dev+desc-2022.02.24a' +VERSION = '1.3.0-dev+desc-2022.02.24b' From 6bf0c5444b14505029c5227d84895f0f5715d7e1 Mon Sep 17 00:00:00 2001 From: Ben Clifford Date: Fri, 25 Feb 2022 14:51:08 +0000 Subject: [PATCH 305/408] --- parsl/monitoring/monitoring.py | 8 +++++--- parsl/version.py | 2 +- 2 files changed, 6 insertions(+), 4 deletions(-) diff --git a/parsl/monitoring/monitoring.py b/parsl/monitoring/monitoring.py index c0c724ccf5..f2c8f3ad7b 100644 --- a/parsl/monitoring/monitoring.py +++ b/parsl/monitoring/monitoring.py @@ -857,9 +857,11 @@ def monitor(pid: int, else: raise RuntimeError(f"Unknown radio mode: {radio_mode}") - format_string = "%(asctime)s.%(msecs)03d %(name)s:%(lineno)d [%(levelname)s] %(message)s" - logging.basicConfig(filename='{logbase}/monitor.{task_id}.{pid}.log'.format( - logbase="/tmp", task_id=task_id, pid=pid), level=logging_level, format=format_string) + # TODO: should this be enabled by a debugging option? + + # format_string = "%(asctime)s.%(msecs)03d %(name)s:%(lineno)d [%(levelname)s] %(message)s" + # logging.basicConfig(filename='{logbase}/monitor.{task_id}.{pid}.log'.format( + # logbase="/tmp", task_id=task_id, pid=pid), level=logging_level, format=format_string) logging.debug("start of monitor") diff --git a/parsl/version.py b/parsl/version.py index ea7242e8a9..51014b105a 100644 --- a/parsl/version.py +++ b/parsl/version.py @@ -3,4 +3,4 @@ ..[alpha/beta/..] Alphas will be numbered like this -> 0.4.0a0 """ -VERSION = '1.3.0-dev+desc-2022.02.24c' +VERSION = '1.3.0-dev+desc-2022.02.25a' From cdc6a1040eff8496ac483dcf20e3eacf3beab88d Mon Sep 17 00:00:00 2001 From: Ben Clifford Date: Mon, 28 Feb 2022 10:42:25 +0000 Subject: [PATCH 306/408] Fix race condition between WorkQueue task submission and scaling WorkQueueExecutor status reporting did not properly lock the task status dictionary. This commit adds that lock. When task submission happens at the same time as flow control, for example when a very large number of tasks are submitted, this exception can occur: 2022-02-23 14:42:14 parsl.dataflow.flow_control:114 MainProcess(112424) FlowControl-Thread [ERROR] Flow control callback threw an exception - logging and proceeding anyway Traceback (most recent call last): File "/home/ir-shir1/rds/rds-iris-ip005/ras81/wq_env/lib/python3.8/site-packages/parsl/dataflow/flow_control.py", line 112, in make_callback self.callback(tasks=self._event_buffer, kind=kind) File "/home/ir-shir1/rds/rds-iris-ip005/ras81/wq_env/lib/python3.8/site-packages/parsl/dataflow/task_status_poller.py", line 104, in poll self._strategy.strategize(self._poll_items, tasks) File "/home/ir-shir1/rds/rds-iris-ip005/ras81/wq_env/lib/python3.8/site-packages/parsl/dataflow/strategy.py", line 140, in _strategy_simple self._general_strategy(status_list, tasks, strategy_type='simple') File "/home/ir-shir1/rds/rds-iris-ip005/ras81/wq_env/lib/python3.8/site-packages/parsl/dataflow/strategy.py", line 174, in _general_strategy active_tasks = executor.outstanding File "/home/ir-shir1/rds/rds-iris-ip005/ras81/wq_env/lib/python3.8/site-packages/parsl/executors/workqueue/executor.py", line 633, in outstanding for fut in self.tasks.values(): RuntimeError: dictionary changed size during iteration Several LSST DESC users have encountered this. Fixes #2230 --- parsl/executors/workqueue/executor.py | 7 ++++--- 1 file changed, 4 insertions(+), 3 deletions(-) diff --git a/parsl/executors/workqueue/executor.py b/parsl/executors/workqueue/executor.py index 79c1ff4dcf..78646c0c53 100644 --- a/parsl/executors/workqueue/executor.py +++ b/parsl/executors/workqueue/executor.py @@ -623,9 +623,10 @@ def outstanding(self) -> int: implemented and probably could be replaced with a counter. """ outstanding = 0 - for fut in self.tasks.values(): - if not fut.done(): - outstanding += 1 + with self.tasks_lock: + for fut in self.tasks.values(): + if not fut.done(): + outstanding += 1 logger.debug(f"Counted {outstanding} outstanding tasks") return outstanding From 1cdd8e9b0ade809d276169b7145c04b5c045ba17 Mon Sep 17 00:00:00 2001 From: Ben Clifford Date: Mon, 28 Feb 2022 11:50:45 +0000 Subject: [PATCH 307/408] Fix test task wait behaviour that could leave tasks running This will wait for all tasks to complete without raising exceptions, before then raising any exceptions that need raising. Without this, then if an exception was raised by assertion checking, the test would not wait for other tasks to complete, and the test suite could continue with more tests overlapping these task completions. This is confusing when debugging, so this PR aims to avoid that. --- parsl/tests/test_error_handling/test_retries.py | 10 ++++++---- 1 file changed, 6 insertions(+), 4 deletions(-) diff --git a/parsl/tests/test_error_handling/test_retries.py b/parsl/tests/test_error_handling/test_retries.py index 0f53396dca..d70a578156 100644 --- a/parsl/tests/test_error_handling/test_retries.py +++ b/parsl/tests/test_error_handling/test_retries.py @@ -55,14 +55,15 @@ def test_fail_nowait(numtasks=10): fu = sleep_then_fail(sleep_dur=0.1) fus.extend([fu]) + # wait for all tasks to complete before ending this test + [x.exception() for x in fus] + try: [x.result() for x in fus] except Exception as e: assert isinstance( e, TypeError), "Expected a TypeError, got {}".format(e) - # wait for all tasks to complete before ending this test - [x.exception() for x in fus] print("Done") @@ -80,14 +81,15 @@ def test_fail_delayed(numtasks=10): fu = sleep_then_fail(inputs=[x], sleep_dur=0.5) fus.extend([fu]) + # wait for all tasks to complete before ending this test + [x.exception() for x in fus] + try: [x.result() for x in fus] except Exception as e: assert isinstance( e, TypeError), "Expected a TypeError, got {}".format(e) - # wait for all tasks to complete before ending this test - [x.exception() for x in fus] print("Done") From 2239ba68cd529a839ab12178dd26b8892c1fb434 Mon Sep 17 00:00:00 2001 From: Ben Clifford Date: Mon, 28 Feb 2022 14:47:40 +0000 Subject: [PATCH 308/408] --- .github/workflows/ci.yaml | 1 + parsl/version.py | 2 +- 2 files changed, 2 insertions(+), 1 deletion(-) diff --git a/.github/workflows/ci.yaml b/.github/workflows/ci.yaml index 9ef737515c..2c239e0109 100644 --- a/.github/workflows/ci.yaml +++ b/.github/workflows/ci.yaml @@ -42,6 +42,7 @@ jobs: - name: make test run: | make test + rm -rfv runinfo/ - name: Documentation checks run: | diff --git a/parsl/version.py b/parsl/version.py index 8270877ad2..a0f6432442 100644 --- a/parsl/version.py +++ b/parsl/version.py @@ -3,4 +3,4 @@ ..[alpha/beta/..] Alphas will be numbered like this -> 0.4.0a0 """ -VERSION = '1.3.0-dev+desc-2022.02.28a' +VERSION = '1.3.0-dev+desc-2022.02.28b' From 1bef5d4ffa3e3f27ee4f0f98e5761c6037f7ed6d Mon Sep 17 00:00:00 2001 From: Ben Clifford Date: Mon, 28 Feb 2022 15:04:45 +0000 Subject: [PATCH 309/408] --- .github/workflows/ci.yaml | 5 ++++- parsl/version.py | 2 +- 2 files changed, 5 insertions(+), 2 deletions(-) diff --git a/.github/workflows/ci.yaml b/.github/workflows/ci.yaml index 2c239e0109..b1cfd2fa9c 100644 --- a/.github/workflows/ci.yaml +++ b/.github/workflows/ci.yaml @@ -42,7 +42,6 @@ jobs: - name: make test run: | make test - rm -rfv runinfo/ - name: Documentation checks run: | @@ -70,6 +69,10 @@ jobs: pip install .[monitoring] parsl/tests/test-viz.sh + - name: clear runinfo from all previous steps + run: | + rm -rfv runinfo/ + # config_local_test comes after viz so that the large monitoring.db # created by `make test` is still around - name: make config_local_test diff --git a/parsl/version.py b/parsl/version.py index a0f6432442..7411cfe6a0 100644 --- a/parsl/version.py +++ b/parsl/version.py @@ -3,4 +3,4 @@ ..[alpha/beta/..] Alphas will be numbered like this -> 0.4.0a0 """ -VERSION = '1.3.0-dev+desc-2022.02.28b' +VERSION = '1.3.0-dev+desc-2022.02.28c' From 570162e286293dfdf535236416f4c4155d3121f7 Mon Sep 17 00:00:00 2001 From: Ben Clifford Date: Wed, 16 Mar 2022 12:56:20 +0000 Subject: [PATCH 310/408] --- parsl/executors/high_throughput/interchange.py | 13 ------------- parsl/executors/workqueue/executor.py | 2 +- parsl/version.py | 2 +- 3 files changed, 2 insertions(+), 15 deletions(-) diff --git a/parsl/executors/high_throughput/interchange.py b/parsl/executors/high_throughput/interchange.py index 330700537c..42d95ffcf0 100644 --- a/parsl/executors/high_throughput/interchange.py +++ b/parsl/executors/high_throughput/interchange.py @@ -28,19 +28,6 @@ PKL_HEARTBEAT_CODE = pickle.dumps((2 ** 32) - 1) -class ShutdownRequest(Exception): - ''' Exception raised when any async component receives a ShutdownRequest - ''' - def __init__(self): - self.tstamp = time.time() - - def __repr__(self): - return "Shutdown request received at {}".format(self.tstamp) - - def __str__(self): - return self.__repr__() - - class ManagerLost(Exception): ''' Task lost due to manager loss. Manager is considered lost when multiple heartbeats have been missed. diff --git a/parsl/executors/workqueue/executor.py b/parsl/executors/workqueue/executor.py index 3a8d360f69..7e8844ab3d 100644 --- a/parsl/executors/workqueue/executor.py +++ b/parsl/executors/workqueue/executor.py @@ -938,7 +938,7 @@ def _work_queue_submit_wait(task_queue=multiprocessing.Queue(), reason="task could not be submited to work queue", status=-1)) continue - logger.debug("Task {} submitted to WorkQueue with id {}".format(task.id, wq_id)) + logger.info("Task {} submitted to WorkQueue with id {}".format(task.id, wq_id)) # If the queue is not empty wait on the WorkQueue queue for a task task_found = True diff --git a/parsl/version.py b/parsl/version.py index 7411cfe6a0..6ab361a370 100644 --- a/parsl/version.py +++ b/parsl/version.py @@ -3,4 +3,4 @@ ..[alpha/beta/..] Alphas will be numbered like this -> 0.4.0a0 """ -VERSION = '1.3.0-dev+desc-2022.02.28c' +VERSION = '1.3.0-dev+desc-2022.03.16a' From 02bf983284ec60d31923359ebc1e20cc1c241889 Mon Sep 17 00:00:00 2001 From: Ben Clifford Date: Mon, 28 Mar 2022 13:45:51 +0000 Subject: [PATCH 311/408] --- parsl/dataflow/job_error_handler.py | 4 +--- parsl/executors/base.py | 3 +-- parsl/executors/high_throughput/executor.py | 5 +++-- parsl/executors/low_latency/executor.py | 2 +- parsl/executors/status_handling.py | 19 +++++++++++++------ parsl/executors/workqueue/executor.py | 3 ++- parsl/version.py | 2 +- 7 files changed, 22 insertions(+), 16 deletions(-) diff --git a/parsl/dataflow/job_error_handler.py b/parsl/dataflow/job_error_handler.py index 416d4fa169..ac18edc186 100644 --- a/parsl/dataflow/job_error_handler.py +++ b/parsl/dataflow/job_error_handler.py @@ -13,9 +13,7 @@ def run(self, status: List[ExecutorStatus]): def _check_irrecoverable_executor(self, es: ExecutorStatus): if not es.executor.error_management_enabled: return - custom_handling = es.executor.handle_errors(self, es.status) - if not custom_handling: - self.simple_error_handler(es.executor, es.status, 3) + es.executor.handle_errors(self, es.status) def simple_error_handler(self, executor: ParslExecutor, status: Dict[str, JobStatus], threshold: int): (total_jobs, failed_jobs) = self.count_jobs(status) diff --git a/parsl/executors/base.py b/parsl/executors/base.py index 74ec7c0ca9..b3a6812801 100644 --- a/parsl/executors/base.py +++ b/parsl/executors/base.py @@ -187,7 +187,7 @@ def error_management_enabled(self) -> bool: @abstractmethod def handle_errors(self, error_handler: "parsl.dataflow.job_error_handler.JobErrorHandler", - status: Dict[str, JobStatus]) -> bool: + status: Dict[str, JobStatus]) -> None: """This method is called by the error management infrastructure after a status poll. The executor implementing this method is then responsible for detecting abnormal conditions based on the status of submitted jobs. If the executor does not implement any special @@ -195,7 +195,6 @@ def handle_errors(self, error_handler: "parsl.dataflow.job_error_handler.JobErro scheme will be used. :param error_handler: a reference to the generic error handler calling this method :param status: status of all jobs launched by this executor - :return: True if this executor implements custom error handling, or False otherwise """ pass diff --git a/parsl/executors/high_throughput/executor.py b/parsl/executors/high_throughput/executor.py index f01a2b9fc9..5d838bfea3 100644 --- a/parsl/executors/high_throughput/executor.py +++ b/parsl/executors/high_throughput/executor.py @@ -204,11 +204,12 @@ def __init__(self, poll_period: int = 10, address_probe_timeout: Optional[int] = None, managed: bool = True, - worker_logdir_root: Optional[str] = None): + worker_logdir_root: Optional[str] = None, + block_error_handler: bool = True): logger.debug("Initializing HighThroughputExecutor") - BlockProviderExecutor.__init__(self, provider) + BlockProviderExecutor.__init__(self, provider=provider, block_error_handler=block_error_handler) self.label = label self.launch_cmd = launch_cmd diff --git a/parsl/executors/low_latency/executor.py b/parsl/executors/low_latency/executor.py index a3ffbef460..7000e624b0 100644 --- a/parsl/executors/low_latency/executor.py +++ b/parsl/executors/low_latency/executor.py @@ -40,7 +40,7 @@ def __init__(self, ): logger.debug("Initializing LowLatencyExecutor") - BlockProviderExecutor.__init__(self, provider) + BlockProviderExecutor.__init__(self, provider=provider) self.label = label self.launch_cmd = launch_cmd self.provider = provider diff --git a/parsl/executors/status_handling.py b/parsl/executors/status_handling.py index e553998d1b..0ca9108389 100644 --- a/parsl/executors/status_handling.py +++ b/parsl/executors/status_handling.py @@ -39,10 +39,16 @@ class BlockProviderExecutor(ParslExecutor): invoking scale_out, but it will not initialize the blocks requested by any init_blocks parameter. Subclasses must implement that behaviour themselves. + + BENC: TODO: block error handling: maybe I want this more user pluggable? + I'm not sure of use cases for switchability at the moment beyond "yes or no" """ - def __init__(self, provider: ExecutionProvider): + def __init__(self, *, + provider: ExecutionProvider, + block_error_handler: bool): super().__init__() self._provider = provider + self._block_error_handler = block_error_handler # errors can happen during the submit call to the provider; this is used # to keep track of such errors so that they can be handled in one place # together with errors reported by status() @@ -127,17 +133,18 @@ def executor_exception(self): @property def error_management_enabled(self): - return True + return self._block_error_handler def handle_errors(self, error_handler: "parsl.dataflow.job_error_handler.JobErrorHandler", - status: Dict[str, JobStatus]) -> bool: + status: Dict[str, JobStatus]) -> None: + if not self._block_error_handler: + return init_blocks = 3 if hasattr(self.provider, 'init_blocks'): init_blocks = self.provider.init_blocks # type: ignore if init_blocks < 1: init_blocks = 1 error_handler.simple_error_handler(self, status, init_blocks) - return True @property def tasks(self) -> Dict[object, Future]: @@ -230,8 +237,8 @@ def status(self): return {} def handle_errors(self, error_handler: "parsl.dataflow.job_error_handler.JobErrorHandler", - status: Dict[str, JobStatus]) -> bool: - return False + status: Dict[str, JobStatus]) -> None: + pass @property def tasks(self) -> Dict[object, Future]: diff --git a/parsl/executors/workqueue/executor.py b/parsl/executors/workqueue/executor.py index 7e8844ab3d..98da035ce9 100644 --- a/parsl/executors/workqueue/executor.py +++ b/parsl/executors/workqueue/executor.py @@ -227,7 +227,8 @@ def __init__(self, worker_options: str = "", full_debug: bool = True, worker_executable: str = 'work_queue_worker'): - BlockProviderExecutor.__init__(self, provider) + BlockProviderExecutor.__init__(self, provider=provider, + block_error_handler=True) self._scaling_enabled = True if not _work_queue_enabled: diff --git a/parsl/version.py b/parsl/version.py index 15b5bfdfc2..f3c58c95c8 100644 --- a/parsl/version.py +++ b/parsl/version.py @@ -3,4 +3,4 @@ ..[alpha/beta/..] Alphas will be numbered like this -> 0.4.0a0 """ -VERSION = '1.3.0-dev+desc-2022.03.28a' +VERSION = '1.3.0-dev+desc-2022.03.28b' From e9936cb30cf550931c3b0ce89c4ee89e0d381370 Mon Sep 17 00:00:00 2001 From: Ben Clifford Date: Mon, 28 Mar 2022 14:08:01 +0000 Subject: [PATCH 312/408] --- parsl/executors/status_handling.py | 6 +++--- parsl/tests/configs/htex_local_alternate.py | 1 + parsl/version.py | 2 +- 3 files changed, 5 insertions(+), 4 deletions(-) diff --git a/parsl/executors/status_handling.py b/parsl/executors/status_handling.py index 0ca9108389..0438fd9e05 100644 --- a/parsl/executors/status_handling.py +++ b/parsl/executors/status_handling.py @@ -48,7 +48,7 @@ def __init__(self, *, block_error_handler: bool): super().__init__() self._provider = provider - self._block_error_handler = block_error_handler + self.block_error_handler = block_error_handler # errors can happen during the submit call to the provider; this is used # to keep track of such errors so that they can be handled in one place # together with errors reported by status() @@ -133,11 +133,11 @@ def executor_exception(self): @property def error_management_enabled(self): - return self._block_error_handler + return self.block_error_handler def handle_errors(self, error_handler: "parsl.dataflow.job_error_handler.JobErrorHandler", status: Dict[str, JobStatus]) -> None: - if not self._block_error_handler: + if not self.block_error_handler: return init_blocks = 3 if hasattr(self.provider, 'init_blocks'): diff --git a/parsl/tests/configs/htex_local_alternate.py b/parsl/tests/configs/htex_local_alternate.py index 01a16f0a55..59260c4e88 100644 --- a/parsl/tests/configs/htex_local_alternate.py +++ b/parsl/tests/configs/htex_local_alternate.py @@ -57,6 +57,7 @@ def fresh_config(): max_blocks=5, launcher=SingleNodeLauncher(), ), + block_error_handler=False ) ], strategy='simple', diff --git a/parsl/version.py b/parsl/version.py index f3c58c95c8..db4818e5b3 100644 --- a/parsl/version.py +++ b/parsl/version.py @@ -3,4 +3,4 @@ ..[alpha/beta/..] Alphas will be numbered like this -> 0.4.0a0 """ -VERSION = '1.3.0-dev+desc-2022.03.28b' +VERSION = '1.3.0-dev+desc-2022.03.28c' From 312fcbd3a441b4be90136c240cc15e2af659a354 Mon Sep 17 00:00:00 2001 From: Ben Clifford Date: Fri, 1 Apr 2022 15:45:38 +0000 Subject: [PATCH 313/408] --- Makefile | 2 +- mypy.ini | 3 + parsl/executors/base.py | 1 - .../executors/high_throughput/interchange.py | 194 +++++++++--------- .../high_throughput/manager_record.py | 16 ++ parsl/version.py | 2 +- 6 files changed, 123 insertions(+), 95 deletions(-) create mode 100644 parsl/executors/high_throughput/manager_record.py diff --git a/Makefile b/Makefile index 90b117a0ed..921b49a555 100644 --- a/Makefile +++ b/Makefile @@ -53,7 +53,7 @@ mypy: ## run mypy checks MYPYPATH=$(CWD)/mypy-stubs mypy parsl/app/ parsl/channels/ parsl/dataflow/ parsl/data_provider/ parsl/launchers parsl/providers/ parsl/monitoring/*py # process worker pool is explicitly listed to check, because it is not # imported from anywhere in core parsl python code. - MYPYPATH=$(CWD)/mypy-stubs mypy parsl/executors/high_throughput/process_worker_pool.py + MYPYPATH=$(CWD)/mypy-stubs mypy parsl/executors/high_throughput/process_worker_pool.py parsl/executors/high_throughput/interchange.py .PHONY: local_thread_test local_thread_test: ## run all tests with local_thread config diff --git a/mypy.ini b/mypy.ini index 475c85b47b..3826a9b4d6 100644 --- a/mypy.ini +++ b/mypy.ini @@ -20,6 +20,9 @@ disallow_subclassing_any = True warn_unreachable = True disallow_untyped_defs = True +[mypy-parsl.executors.high_throughput.interchange.*] +check_untyped_defs = True + [mypy-parsl.monitoring.node_reporter] # because I haven't written the node reporter properly yet check_untyped_defs = False diff --git a/parsl/executors/base.py b/parsl/executors/base.py index a8d5b5046e..7f832097c4 100644 --- a/parsl/executors/base.py +++ b/parsl/executors/base.py @@ -50,7 +50,6 @@ class ParslExecutor(metaclass=ABCMeta): @typeguard the constructor, you'll have to use List[Any] here. """ - label: str = "undefined" radio_mode: str = "udp" diff --git a/parsl/executors/high_throughput/interchange.py b/parsl/executors/high_throughput/interchange.py index 6f6013b7e6..0718aca817 100644 --- a/parsl/executors/high_throughput/interchange.py +++ b/parsl/executors/high_throughput/interchange.py @@ -14,16 +14,18 @@ import threading import json +from typing import cast, Any, Dict + from parsl.utils import setproctitle from parsl.version import VERSION as PARSL_VERSION from parsl.serialize import ParslSerializer serialize_object = ParslSerializer().serialize from parsl.app.errors import RemoteExceptionWrapper +from parsl.executors.high_throughput.manager_record import ManagerRecord from parsl.monitoring.message_type import MessageType from parsl.process_loggers import wrap_with_logs - HEARTBEAT_CODE = (2 ** 32) - 1 PKL_HEARTBEAT_CODE = pickle.dumps((2 ** 32) - 1) @@ -114,7 +116,7 @@ def __init__(self, logdir=".", logging_level=logging.INFO, poll_period=10, - ): + ) -> None: """ Parameters ---------- @@ -193,7 +195,7 @@ def __init__(self, self.hub_address = hub_address self.hub_port = hub_port - self.pending_task_queue = queue.PriorityQueue(maxsize=10 ** 6) + self.pending_task_queue: queue.Queue[Any] = queue.PriorityQueue(maxsize=10 ** 6) self.worker_ports = worker_ports self.worker_port_range = worker_port_range @@ -221,7 +223,7 @@ def __init__(self, logger.info("Bound to ports {},{} for incoming worker connections".format( self.worker_task_port, self.worker_result_port)) - self._ready_managers = {} + self._ready_managers: Dict[bytes, ManagerRecord] = {} self.heartbeat_threshold = heartbeat_threshold @@ -307,9 +309,10 @@ def _create_monitoring_channel(self): def _send_monitoring_info(self, hub_channel, manager): if hub_channel: - logger.info("Sending message {} to hub".format(self._ready_managers[manager])) + m = self._ready_managers[manager] + logger.info("Sending message {} to hub".format(m)) - d = self._ready_managers[manager].copy() + d: Dict = cast(Dict, m.copy()) d['timestamp'] = datetime.datetime.now() d['last_heartbeat'] = datetime.datetime.fromtimestamp(d['last_heartbeat']) @@ -324,44 +327,48 @@ def _command_server(self, kill_event): # Need to create a new ZMQ socket for command server thread hub_channel = self._create_monitoring_channel() + reply: Any # the type of reply depends on the command_req received (aka this needs dependent types...) + while not kill_event.is_set(): try: command_req = self.command_channel.recv_pyobj() logger.debug("Received command request: {}".format(command_req)) if command_req == "OUTSTANDING_C": outstanding = self.pending_task_queue.qsize() - for manager in self._ready_managers: - outstanding += len(self._ready_managers[manager]['tasks']) + for manager_id in self._ready_managers: + outstanding += len(self._ready_managers[manager_id]['tasks']) reply = outstanding elif command_req == "WORKERS": num_workers = 0 - for manager in self._ready_managers: - num_workers += self._ready_managers[manager]['worker_count'] + for manager_id in self._ready_managers: + num_workers += self._ready_managers[manager_id]['worker_count'] reply = num_workers elif command_req == "MANAGERS": reply = [] - for manager in self._ready_managers: - idle_duration = 0 - if self._ready_managers[manager]['idle_since'] is not None: - idle_duration = time.time() - self._ready_managers[manager]['idle_since'] - resp = {'manager': manager.decode('utf-8'), - 'block_id': self._ready_managers[manager]['block_id'], - 'worker_count': self._ready_managers[manager]['worker_count'], - 'tasks': len(self._ready_managers[manager]['tasks']), + for manager_id in self._ready_managers: + m = self._ready_managers[manager_id] + idle_duration = 0.0 + idle_since = m['idle_since'] + if idle_since is not None: + idle_duration = time.time() - idle_since + resp = {'manager': manager_id.decode('utf-8'), + 'block_id': m['block_id'], + 'worker_count': m['worker_count'], + 'tasks': len(m['tasks']), 'idle_duration': idle_duration, - 'active': self._ready_managers[manager]['active']} + 'active': m['active']} reply.append(resp) elif command_req.startswith("HOLD_WORKER"): cmd, s_manager = command_req.split(';') manager = s_manager.encode('utf-8') - logger.info("Received HOLD_WORKER for {}".format(manager)) - if manager in self._ready_managers: - self._ready_managers[manager]['active'] = False + logger.info("Received HOLD_WORKER for {!r}".format(manager)) + if manager_id in self._ready_managers: + self._ready_managers[manager_id]['active'] = False reply = True - self._send_monitoring_info(hub_channel, manager) + self._send_monitoring_info(hub_channel, manager_id) else: reply = False @@ -440,9 +447,9 @@ def start(self): if self.task_outgoing in self.socks and self.socks[self.task_outgoing] == zmq.POLLIN: logger.debug("starting task_outgoing section") message = self.task_outgoing.recv_multipart() - manager = message[0] + manager_id = message[0] - if manager not in self._ready_managers: + if manager_id not in self._ready_managers: reg_flag = False try: @@ -450,28 +457,28 @@ def start(self): reg_flag = True except Exception: logger.warning("Got Exception reading registration message from manager: {}".format( - manager), exc_info=True) + manager_id), exc_info=True) logger.debug("Message :\n{}\n".format(message[1])) else: # We set up an entry only if registration works correctly - self._ready_managers[manager] = {'last_heartbeat': time.time(), - 'idle_since': time.time(), - 'free_capacity': 0, - 'block_id': None, - 'max_capacity': 0, - 'worker_count': 0, - 'active': True, - 'tasks': []} + self._ready_managers[manager_id] = {'last_heartbeat': time.time(), + 'idle_since': time.time(), + 'free_capacity': 0, + # 'block_id': None, -- don't assign a badly typed value + 'max_capacity': 0, + 'worker_count': 0, + 'active': True, + 'tasks': []} if reg_flag is True: - interesting_managers.add(manager) - logger.info("Adding manager: {} to ready queue".format(manager)) - self._ready_managers[manager].update(msg) - logger.info("Registration info for manager {}: {}".format(manager, msg)) - self._send_monitoring_info(hub_channel, manager) + interesting_managers.add(manager_id) + logger.info("Adding manager: {} to ready queue".format(manager_id)) + self._ready_managers[manager_id].update(msg) + logger.info("Registration info for manager {}: {}".format(manager_id, msg)) + self._send_monitoring_info(hub_channel, manager_id) if (msg['python_v'].rsplit(".", 1)[0] != self.current_platform['python_v'].rsplit(".", 1)[0] or msg['parsl_v'] != self.current_platform['parsl_v']): - logger.warning("Manager {} has incompatible version info with the interchange".format(manager)) + logger.warning("Manager {} has incompatible version info with the interchange".format(manager_id)) logger.debug("Setting kill event") self._kill_event.set() e = VersionMismatch("py.v={} parsl.v={}".format(self.current_platform['python_v'].rsplit(".", 1)[0], @@ -484,24 +491,24 @@ def start(self): self.results_outgoing.send(pkl_package) logger.warning("Sent failure reports, unregistering manager") else: - logger.info("Manager {} has compatible Parsl version {}".format(manager, msg['parsl_v'])) - logger.info("Manager {} has compatible Python version {}".format(manager, + logger.info("Manager {} has compatible Parsl version {}".format(manager_id, msg['parsl_v'])) + logger.info("Manager {} has compatible Python version {}".format(manager_id, msg['python_v'].rsplit(".", 1)[0])) else: # Registration has failed. logger.debug("Suppressing bad registration from manager: {}".format( - manager)) + manager_id)) else: tasks_requested = int.from_bytes(message[1], "little") - self._ready_managers[manager]['last_heartbeat'] = time.time() + self._ready_managers[manager_id]['last_heartbeat'] = time.time() if tasks_requested == HEARTBEAT_CODE: - logger.debug("Manager {} sent heartbeat via tasks connection".format(manager)) - self.task_outgoing.send_multipart([manager, b'', PKL_HEARTBEAT_CODE]) + logger.debug("Manager {} sent heartbeat via tasks connection".format(manager_id)) + self.task_outgoing.send_multipart([manager_id, b'', PKL_HEARTBEAT_CODE]) else: - logger.debug("Manager {} requested {} tasks".format(manager, tasks_requested)) - self._ready_managers[manager]['free_capacity'] = tasks_requested - interesting_managers.add(manager) + logger.debug("Manager {} requested {} tasks".format(manager_id, tasks_requested)) + self._ready_managers[manager_id]['free_capacity'] = tasks_requested + interesting_managers.add(manager_id) logger.debug("leaving task_outgoing section") # If we had received any requests, check if there are tasks that could be passed @@ -515,15 +522,16 @@ def start(self): random.shuffle(shuffled_managers) while shuffled_managers and not self.pending_task_queue.empty(): # cf. the if statement above... - manager = shuffled_managers.pop() - tasks_inflight = len(self._ready_managers[manager]['tasks']) - real_capacity = min(self._ready_managers[manager]['free_capacity'], - self._ready_managers[manager]['max_capacity'] - tasks_inflight) + manager_id = shuffled_managers.pop() + m = self._ready_managers[manager_id] + tasks_inflight = len(m['tasks']) + real_capacity = min(m['free_capacity'], + m['max_capacity'] - tasks_inflight) - if (real_capacity and self._ready_managers[manager]['active']): + if (real_capacity and m['active']): tasks = self.get_tasks(real_capacity) if tasks: - self.task_outgoing.send_multipart([manager, b'', pickle.dumps(tasks)]) + self.task_outgoing.send_multipart([manager_id, b'', pickle.dumps(tasks)]) # after this point, we've sent a task to the manager, but we haven't # added it to the 'task' list for that manager, because we don't # do that for another 5 lines. That should be pretty fast, though? @@ -532,30 +540,30 @@ def start(self): task_count = len(tasks) count += task_count tids = [t['task_id'] for t in tasks] - self._ready_managers[manager]['free_capacity'] -= task_count - self._ready_managers[manager]['tasks'].extend(tids) - self._ready_managers[manager]['idle_since'] = None - logger.debug("Sent tasks: {} to manager {}".format(tids, manager)) - if self._ready_managers[manager]['free_capacity'] > 0: - logger.debug("Manager {} has free_capacity {}".format(manager, self._ready_managers[manager]['free_capacity'])) + m['free_capacity'] -= task_count + m['tasks'].extend(tids) + m['idle_since'] = None + logger.debug("Sent tasks: {} to manager {}".format(tids, manager_id)) + if m['free_capacity'] > 0: + logger.debug("Manager {} has free_capacity {}".format(manager_id, m['free_capacity'])) # ... so keep it in the interesting_managers list else: - logger.debug("Manager {} is now saturated".format(manager)) - interesting_managers.remove(manager) + logger.debug("Manager {} is now saturated".format(manager_id)) + interesting_managers.remove(manager_id) else: - interesting_managers.remove(manager) - # logger.debug("Nothing to send to manager {}".format(manager)) + interesting_managers.remove(manager_id) + # logger.debug("Nothing to send to manager {}".format(manager_id)) logger.debug("leaving _ready_managers section, with {} managers still interesting".format(len(interesting_managers))) else: logger.debug("either no interesting managers or no tasks, so skipping manager pass") # Receive any results and forward to client if self.results_incoming in self.socks and self.socks[self.results_incoming] == zmq.POLLIN: logger.debug("entering results_incoming section") - manager, *all_messages = self.results_incoming.recv_multipart() - if manager not in self._ready_managers: - logger.warning("Received a result from a un-registered manager: {}".format(manager)) + manager_id, *all_messages = self.results_incoming.recv_multipart() + if manager_id not in self._ready_managers: + logger.warning("Received a result from a un-registered manager: {}".format(manager_id)) else: - logger.debug(f"Got {len(all_messages)} result items in batch from manager {manager}") + logger.debug(f"Got {len(all_messages)} result items in batch from manager {manager_id}") b_messages = [] @@ -581,51 +589,53 @@ def start(self): else: logger.error("Result item is of unknown type: {}".format(r['type'])) + m = self._ready_managers[manager_id] for b_message in b_messages: r = pickle.loads(b_message) if r['type'] == 'result': try: - logger.debug(f"Removing task {r['task_id']} from manager {manager} record") - self._ready_managers[manager]['tasks'].remove(r['task_id']) + logger.debug(f"Removing task {r['task_id']} from manager {manager_id} record") + m['tasks'].remove(r['task_id']) except Exception: # If we reach here, there's something very wrong. logger.exception("Ignoring exception removing task_id {} for manager {} with task list {}".format( r['task_id'], - manager, - self._ready_managers[manager]['tasks'])) + manager_id, + m['tasks'])) if b_messages: logger.debug("Sending messages on results_outgoing") self.results_outgoing.send_multipart(b_messages) logger.debug("Sent messages on results_outgoing") - logger.debug(f"Current tasks on manager {manager}: {self._ready_managers[manager]['tasks']}") - if len(self._ready_managers[manager]['tasks']) == 0 and self._ready_managers[manager]['idle_since'] is None: - self._ready_managers[manager]['idle_since'] = time.time() + logger.debug(f"Current tasks on manager {manager_id}: {m['tasks']}") + if len(m['tasks']) == 0 and m['idle_since'] is None: + m['idle_since'] = time.time() logger.debug("leaving results_incoming section") - bad_managers = [manager for manager in self._ready_managers if - time.time() - self._ready_managers[manager]['last_heartbeat'] > self.heartbeat_threshold] - for manager in bad_managers: - logger.debug("Last: {} Current: {}".format(self._ready_managers[manager]['last_heartbeat'], time.time())) - logger.warning(f"Too many heartbeats missed for manager {manager}") - logger.warning(f"Removing this manager and cancelled htex tasks {self._ready_managers[manager]['tasks']}") - if self._ready_managers[manager]['active']: - self._ready_managers[manager]['active'] = False - self._send_monitoring_info(hub_channel, manager) - - logger.warning(f"Cancelling htex tasks {self._ready_managers[manager]['tasks']} on removed manager") - for tid in self._ready_managers[manager]['tasks']: + bad_managers = [manager_id for manager_id in self._ready_managers if + time.time() - self._ready_managers[manager_id]['last_heartbeat'] > self.heartbeat_threshold] + for manager_id in bad_managers: + m = self._ready_managers[manager_id] + logger.debug("Last: {} Current: {}".format(m['last_heartbeat'], time.time())) + logger.warning(f"Too many heartbeats missed for manager {manager_id}") + logger.warning(f"Removing this manager and cancelled htex tasks {m['tasks']}") + if m['active']: + m['active'] = False + self._send_monitoring_info(hub_channel, manager_id) + + logger.warning(f"Cancelling htex tasks {m['tasks']} on removed manager") + for tid in m['tasks']: try: - raise ManagerLost(manager, self._ready_managers[manager]['hostname']) + raise ManagerLost(manager_id, m['hostname']) except Exception: result_package = {'type': 'result', 'task_id': tid, 'exception': serialize_object(RemoteExceptionWrapper(*sys.exc_info()))} pkl_package = pickle.dumps(result_package) self.results_outgoing.send(pkl_package) logger.warning("Sent failure reports, unregistering manager") - self._ready_managers.pop(manager, 'None') - if manager in interesting_managers: - interesting_managers.remove(manager) + self._ready_managers.pop(manager_id, 'None') + if manager_id in interesting_managers: + interesting_managers.remove(manager_id) delta = time.time() - start logger.info("Processed {} tasks in {} seconds".format(count, delta)) diff --git a/parsl/executors/high_throughput/manager_record.py b/parsl/executors/high_throughput/manager_record.py new file mode 100644 index 0000000000..353d2353a5 --- /dev/null +++ b/parsl/executors/high_throughput/manager_record.py @@ -0,0 +1,16 @@ +from datetime import datetime +from typing import Any, List, Optional +from typing_extensions import TypedDict + + +class ManagerRecord(TypedDict, total=False): + block_id: str + tasks: List[Any] + worker_count: int + free_capacity: int + max_capacity: int + active: bool + hostname: str + last_heartbeat: float + idle_since: Optional[float] + timestamp: datetime diff --git a/parsl/version.py b/parsl/version.py index 2d88ea7417..0e2c807efa 100644 --- a/parsl/version.py +++ b/parsl/version.py @@ -3,4 +3,4 @@ ..[alpha/beta/..] Alphas will be numbered like this -> 0.4.0a0 """ -VERSION = '1.3.0-dev+desc-2022.04.01a' +VERSION = '1.3.0-dev+desc-2022.04.01b' From 532fbb9fa25d9ec88c096a1996e392391c97bfcd Mon Sep 17 00:00:00 2001 From: Ben Clifford Date: Thu, 7 Apr 2022 10:46:57 +0000 Subject: [PATCH 314/408] add some locks around more zmq --- .../executors/high_throughput/interchange.py | 38 +++++++------- parsl/executors/high_throughput/zmq_pipes.py | 49 +++++++++++-------- parsl/version.py | 2 +- 3 files changed, 46 insertions(+), 43 deletions(-) diff --git a/parsl/executors/high_throughput/interchange.py b/parsl/executors/high_throughput/interchange.py index 0718aca817..26b079898f 100644 --- a/parsl/executors/high_throughput/interchange.py +++ b/parsl/executors/high_throughput/interchange.py @@ -14,7 +14,7 @@ import threading import json -from typing import cast, Any, Dict +from typing import cast, Any, Dict, Set from parsl.utils import setproctitle from parsl.version import VERSION as PARSL_VERSION @@ -307,12 +307,11 @@ def _create_monitoring_channel(self): else: return None - def _send_monitoring_info(self, hub_channel, manager): + def _send_monitoring_info(self, hub_channel, manager: ManagerRecord): if hub_channel: - m = self._ready_managers[manager] - logger.info("Sending message {} to hub".format(m)) + logger.info("Sending message {} to hub".format(manager)) - d: Dict = cast(Dict, m.copy()) + d: Dict = cast(Dict, manager.copy()) d['timestamp'] = datetime.datetime.now() d['last_heartbeat'] = datetime.datetime.fromtimestamp(d['last_heartbeat']) @@ -335,14 +334,14 @@ def _command_server(self, kill_event): logger.debug("Received command request: {}".format(command_req)) if command_req == "OUTSTANDING_C": outstanding = self.pending_task_queue.qsize() - for manager_id in self._ready_managers: - outstanding += len(self._ready_managers[manager_id]['tasks']) + for manager in self._ready_managers.values(): + outstanding += len(manager['tasks']) reply = outstanding elif command_req == "WORKERS": num_workers = 0 - for manager_id in self._ready_managers: - num_workers += self._ready_managers[manager_id]['worker_count'] + for manager in self._ready_managers.values(): + num_workers += manager['worker_count'] reply = num_workers elif command_req == "MANAGERS": @@ -363,12 +362,13 @@ def _command_server(self, kill_event): elif command_req.startswith("HOLD_WORKER"): cmd, s_manager = command_req.split(';') - manager = s_manager.encode('utf-8') + manager_id = s_manager.encode('utf-8') logger.info("Received HOLD_WORKER for {!r}".format(manager)) if manager_id in self._ready_managers: - self._ready_managers[manager_id]['active'] = False + m = self._ready_managers[manager_id] + m['active'] = False reply = True - self._send_monitoring_info(hub_channel, manager_id) + self._send_monitoring_info(hub_channel, m) else: reply = False @@ -390,11 +390,6 @@ def _command_server(self, kill_event): @wrap_with_logs def start(self): """ Start the interchange - - Parameters: - ---------- - - TODO: Move task receiving to a thread """ logger.info("Incoming ports bound") @@ -436,7 +431,7 @@ def start(self): # for scheduling a job (or maybe any other attention?). # Anything altering the state of the manager should add it # onto this list. - interesting_managers = set() + interesting_managers: Set[bytes] = set() while not self._kill_event.is_set(): logger.debug(f"Starting poll with timeout {poll_period} ms") @@ -472,9 +467,10 @@ def start(self): if reg_flag is True: interesting_managers.add(manager_id) logger.info("Adding manager: {} to ready queue".format(manager_id)) - self._ready_managers[manager_id].update(msg) + m = self._ready_managers[manager_id] + m.update(msg) logger.info("Registration info for manager {}: {}".format(manager_id, msg)) - self._send_monitoring_info(hub_channel, manager_id) + self._send_monitoring_info(hub_channel, m) if (msg['python_v'].rsplit(".", 1)[0] != self.current_platform['python_v'].rsplit(".", 1)[0] or msg['parsl_v'] != self.current_platform['parsl_v']): @@ -622,7 +618,7 @@ def start(self): logger.warning(f"Removing this manager and cancelled htex tasks {m['tasks']}") if m['active']: m['active'] = False - self._send_monitoring_info(hub_channel, manager_id) + self._send_monitoring_info(hub_channel, m) logger.warning(f"Cancelling htex tasks {m['tasks']} on removed manager") for tid in m['tasks']: diff --git a/parsl/executors/high_throughput/zmq_pipes.py b/parsl/executors/high_throughput/zmq_pipes.py index c1c2a494f3..db4f635bac 100644 --- a/parsl/executors/high_throughput/zmq_pipes.py +++ b/parsl/executors/high_throughput/zmq_pipes.py @@ -102,6 +102,7 @@ def __init__(self, ip_address, port_range): max_port=port_range[1]) self.poller = zmq.Poller() self.poller.register(self.zmq_socket, zmq.POLLOUT) + self._lock = threading.Lock() def put(self, message): """ This function needs to be fast at the same time aware of the possibility of @@ -113,23 +114,25 @@ def put(self, message): This issue can be magnified if each the serialized buffer itself is larger. """ timeout_ms = 0 - while True: - socks = dict(self.poller.poll(timeout=timeout_ms)) - if self.zmq_socket in socks and socks[self.zmq_socket] == zmq.POLLOUT: - # The copy option adds latency but reduces the risk of ZMQ overflow - self.zmq_socket.send_pyobj(message, copy=True) - return - else: - timeout_ms = max(timeout_ms, 1) - timeout_ms *= 2 - timeout_ms = min(10000, timeout_ms) # TODO: arbitrary hard coded time bad - logger.debug("Not sending due to non-ready zmq pipe, timeout: {} ms".format(timeout_ms)) - if timeout_ms == 10000: - raise RuntimeError("BENC: hit big timeout for pipe put - failing rather than trying forever") + with self._lock: + while True: + socks = dict(self.poller.poll(timeout=timeout_ms)) + if self.zmq_socket in socks and socks[self.zmq_socket] == zmq.POLLOUT: + # The copy option adds latency but reduces the risk of ZMQ overflow + self.zmq_socket.send_pyobj(message, copy=True) + return + else: + timeout_ms = max(timeout_ms, 1) + timeout_ms *= 2 + timeout_ms = min(10000, timeout_ms) # TODO: arbitrary hard coded time bad + logger.debug("Not sending due to non-ready zmq pipe, timeout: {} ms".format(timeout_ms)) + if timeout_ms == 10000: + raise RuntimeError("BENC: hit big timeout for pipe put - failing rather than trying forever") def close(self): - self.zmq_socket.close() - self.context.term() + with self._lock: + self.zmq_socket.close() + self.context.term() class ResultsIncoming(object): @@ -153,15 +156,19 @@ def __init__(self, ip_address, port_range): self.port = self.results_receiver.bind_to_random_port("tcp://{}".format(ip_address), min_port=port_range[0], max_port=port_range[1]) + self._lock = threading.Lock() def get(self, block=True, timeout=None): - return self.results_receiver.recv_multipart() + with self._lock: + return self.results_receiver.recv_multipart() def request_close(self): - status = self.results_receiver.send(pickle.dumps(None)) - time.sleep(0.1) - return status + with self._lock: + status = self.results_receiver.send(pickle.dumps(None)) + time.sleep(0.1) + return status def close(self): - self.results_receiver.close() - self.context.term() + with self._lock: + self.results_receiver.close() + self.context.term() diff --git a/parsl/version.py b/parsl/version.py index 0e2c807efa..a9d59194c0 100644 --- a/parsl/version.py +++ b/parsl/version.py @@ -3,4 +3,4 @@ ..[alpha/beta/..] Alphas will be numbered like this -> 0.4.0a0 """ -VERSION = '1.3.0-dev+desc-2022.04.01b' +VERSION = '1.3.0-dev+desc-2022.04.07a' From 508833f99528c2633e165de1250d98937df09b4f Mon Sep 17 00:00:00 2001 From: Ben Clifford Date: Wed, 20 Apr 2022 09:13:51 +0000 Subject: [PATCH 315/408] fix hang at shutdown due to misnamed variable --- parsl/executors/high_throughput/interchange.py | 2 +- parsl/version.py | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/parsl/executors/high_throughput/interchange.py b/parsl/executors/high_throughput/interchange.py index 26b079898f..27774ecfc0 100644 --- a/parsl/executors/high_throughput/interchange.py +++ b/parsl/executors/high_throughput/interchange.py @@ -363,7 +363,7 @@ def _command_server(self, kill_event): elif command_req.startswith("HOLD_WORKER"): cmd, s_manager = command_req.split(';') manager_id = s_manager.encode('utf-8') - logger.info("Received HOLD_WORKER for {!r}".format(manager)) + logger.info("Received HOLD_WORKER for {!r}".format(manager_id)) if manager_id in self._ready_managers: m = self._ready_managers[manager_id] m['active'] = False diff --git a/parsl/version.py b/parsl/version.py index f57551496c..3f4ebf9a8b 100644 --- a/parsl/version.py +++ b/parsl/version.py @@ -3,4 +3,4 @@ ..[alpha/beta/..] Alphas will be numbered like this -> 0.4.0a0 """ -VERSION = '1.3.0-dev+desc-2022.04.19a' +VERSION = '1.3.0-dev+desc-2022.04.20a' From b16249ce8ff7b15d5888297589739198e77d6c2a Mon Sep 17 00:00:00 2001 From: Ben Clifford Date: Fri, 13 May 2022 09:12:26 +0000 Subject: [PATCH 316/408] mostly more granualar WQ timing loads --- parsl/dataflow/dflow.py | 20 +++++++------------ .../workqueue/exec_parsl_function.py | 16 ++++++++++++--- parsl/log_utils.py | 9 ++++++++- parsl/version.py | 2 +- 4 files changed, 29 insertions(+), 18 deletions(-) diff --git a/parsl/dataflow/dflow.py b/parsl/dataflow/dflow.py index 217e466bdd..452760de25 100644 --- a/parsl/dataflow/dflow.py +++ b/parsl/dataflow/dflow.py @@ -1245,15 +1245,11 @@ def checkpoint(self, tasks=None): t = {'hash': hashsum, 'exception': None, 'result': None} - try: - # Asking for the result will raise an exception if - # the app had failed. Should we even checkpoint these? - # TODO : Resolve this question ? - r = self.memoizer.hash_lookup(hashsum).result() - except Exception as e: - t['exception'] = e - else: - t['result'] = r + + fut = self.memoizer.hash_lookup(hashsum) + assert fut.done() + assert fut.exception() is None + t['result'] = fut.result() # We are using pickle here since pickle dumps to a file in 'ab' # mode behave like a incremental log. @@ -1301,10 +1297,8 @@ def _load_checkpoints(self, checkpointDirs): data = pickle.load(f) # Copy and hash only the input attributes memo_fu = Future() - if data['exception']: - memo_fu.set_exception(data['exception']) - else: - memo_fu.set_result(data['result']) + assert data['exception'] is None + memo_fu.set_result(data['result']) memo_lookup_table[data['hash']] = memo_fu except EOFError: diff --git a/parsl/executors/workqueue/exec_parsl_function.py b/parsl/executors/workqueue/exec_parsl_function.py index 2bf251a5e5..4f99030499 100644 --- a/parsl/executors/workqueue/exec_parsl_function.py +++ b/parsl/executors/workqueue/exec_parsl_function.py @@ -30,8 +30,12 @@ def load_pickled_file(filename): + print(f"{time.time()} LOADPICKLED_OPEN", file=logfile) with open(filename, "rb") as f_in: - return pickle.load(f_in) + print(f"{time.time()} LOADPICKLED_LOAD", file=logfile) + v = pickle.load(f_in) + print(f"{time.time()} LOADPICKLED_DONE", file=logfile) + return v def dump_result_to_file(result_file, result_package): @@ -139,24 +143,30 @@ def encode_byte_code_function(user_namespace, fn, fn_name, args_name, kwargs_nam return code -def load_function(map_file, function_file): +def load_function(map_file, function_file, logfile): # Decodes the function and its file arguments to be executed into # function_code, and updates a user namespace with the function name and # the variable named result_name. When the function is executed, its result # will be stored in this variable in the user namespace. # Returns (namespace, function_code, result_name) + print(f"{time.time()} LOADFUNCTION_MAKENS", file=logfile) # Create the namespace to isolate the function execution. user_ns = locals() user_ns.update({'__builtins__': __builtins__}) + print(f"{time.time()} LOADFUNCTION_LOADPICKLED_FUNCTION", file=logfile) function_info = load_pickled_file(function_file) + print(f"{time.time()} LOADFUNCTION_UNPACK", file=logfile) (fn, fn_name, fn_args, fn_kwargs) = unpack_function(function_info, user_ns) + print(f"{time.time()} LOADFUNCTION_LOAD_PICKLED_MAPPING", file=logfile) mapping = load_pickled_file(map_file) + print(f"{time.time()} LOADFUNCTION_REMAP", file=logfile) remap_all_files(mapping, fn_args, fn_kwargs) + print(f"{time.time()} LOADFUNCTION_ENCODE", file=logfile) (code, result_name) = encode_function(user_ns, fn, fn_name, fn_args, fn_kwargs) return (user_ns, code, result_name) @@ -195,7 +205,7 @@ def execute_function(namespace, function_code, result_name): t_loadfunction = time.time() print(f"{t_loadfunction} LOADFUNCTION", file=logfile) try: - (namespace, function_code, result_name) = load_function(map_file, function_file) + (namespace, function_code, result_name) = load_function(map_file, function_file, logfile) except Exception: print("There was an error setting up the function for execution.") raise diff --git a/parsl/log_utils.py b/parsl/log_utils.py index 877f2fb3e4..f1a6cccec9 100644 --- a/parsl/log_utils.py +++ b/parsl/log_utils.py @@ -16,6 +16,13 @@ from typing import Optional +DEFAULT_FORMAT = ( + "%(created)f %(asctime)s %(levelname)s %(processName)s-%(process)d " + "%(threadName)s-%(thread)d %(name)s:%(lineno)d %(funcName)s " + "%(message)s" +) + + @typeguard.typechecked def set_stream_logger(name: str = 'parsl', level: int = logging.DEBUG, format_string: Optional[str] = None): """Add a stream log handler. @@ -60,7 +67,7 @@ def set_file_logger(filename: str, name: str = 'parsl', level: int = logging.DEB - None """ if format_string is None: - format_string = "%(asctime)s %(name)s:%(lineno)d %(processName)s(%(process)d) %(threadName)s [%(levelname)s] %(message)s" + format_string = DEFAULT_FORMAT logger = logging.getLogger(name) logger.setLevel(logging.DEBUG) diff --git a/parsl/version.py b/parsl/version.py index 3f4ebf9a8b..05950ddb02 100644 --- a/parsl/version.py +++ b/parsl/version.py @@ -3,4 +3,4 @@ ..[alpha/beta/..] Alphas will be numbered like this -> 0.4.0a0 """ -VERSION = '1.3.0-dev+desc-2022.04.20a' +VERSION = '1.3.0-dev+desc-2022.05.13a' From 3ef27ccc21ab51f1daab678aae446cb85890736a Mon Sep 17 00:00:00 2001 From: Ben Clifford Date: Fri, 13 May 2022 10:38:15 +0000 Subject: [PATCH 317/408] fix broken checkpoint test --- parsl/tests/test_checkpointing/test_periodic.py | 10 ++++------ parsl/version.py | 2 +- 2 files changed, 5 insertions(+), 7 deletions(-) diff --git a/parsl/tests/test_checkpointing/test_periodic.py b/parsl/tests/test_checkpointing/test_periodic.py index f19ae722e2..9204cc0296 100644 --- a/parsl/tests/test_checkpointing/test_periodic.py +++ b/parsl/tests/test_checkpointing/test_periodic.py @@ -30,10 +30,8 @@ def slow_double(x, sleep_dur=1): def tstamp_to_seconds(line): print("Parsing line: ", line) - parsed = parse(line[0:23], fuzzy=True) - epoch = datetime.datetime.utcfromtimestamp(0) - f = (parsed - epoch).total_seconds() - return f + f = line.partition(" ")[0] + return float(f) @pytest.mark.local @@ -60,8 +58,8 @@ def test_periodic(n=4): with open("{}/parsl.log".format(dfk.run_dir), 'r') as f: log_lines = f.readlines() - expected_msg = "] Done checkpointing" - expected_msg2 = "] No tasks checkpointed in this pass" + expected_msg = " Done checkpointing" + expected_msg2 = " No tasks checkpointed in this pass" lines = [line for line in log_lines if expected_msg in line or expected_msg2 in line] assert len(lines) >= 3, "Insufficient checkpoint lines in logfile" diff --git a/parsl/version.py b/parsl/version.py index f87d0ea512..d67a9dd3a4 100644 --- a/parsl/version.py +++ b/parsl/version.py @@ -3,4 +3,4 @@ ..[alpha/beta/..] Alphas will be numbered like this -> 0.4.0a0 """ -VERSION = '1.3.0-dev+desc-2022.05.13b' +VERSION = '1.3.0-dev+desc-2022.05.13c' From e97747ae0aa4d7bc4070b5be3a3cef16a70df2ef Mon Sep 17 00:00:00 2001 From: Ben Clifford Date: Fri, 13 May 2022 10:51:25 +0000 Subject: [PATCH 318/408] fix flake8 --- parsl/monitoring/monitoring.py | 1 - parsl/tests/test_checkpointing/test_periodic.py | 2 -- parsl/version.py | 2 +- 3 files changed, 1 insertion(+), 4 deletions(-) diff --git a/parsl/monitoring/monitoring.py b/parsl/monitoring/monitoring.py index 60bb007a8c..9800c20f39 100644 --- a/parsl/monitoring/monitoring.py +++ b/parsl/monitoring/monitoring.py @@ -18,7 +18,6 @@ from parsl.serialize import deserialize -# this is needed for htex hack to get at htex result queue import parsl.executors.high_throughput.monitoring_info from parsl.monitoring.message_type import MessageType diff --git a/parsl/tests/test_checkpointing/test_periodic.py b/parsl/tests/test_checkpointing/test_periodic.py index 9204cc0296..607ca6cbef 100644 --- a/parsl/tests/test_checkpointing/test_periodic.py +++ b/parsl/tests/test_checkpointing/test_periodic.py @@ -1,9 +1,7 @@ import argparse -import datetime import time import pytest -from dateutil.parser import parse import parsl from parsl.app.app import python_app diff --git a/parsl/version.py b/parsl/version.py index d67a9dd3a4..f1296ded50 100644 --- a/parsl/version.py +++ b/parsl/version.py @@ -3,4 +3,4 @@ ..[alpha/beta/..] Alphas will be numbered like this -> 0.4.0a0 """ -VERSION = '1.3.0-dev+desc-2022.05.13c' +VERSION = '1.3.0-dev+desc-2022.05.13d' From 4c2a655a79133bd0b41ab2249e887d49a5a9e90a Mon Sep 17 00:00:00 2001 From: Ben Clifford Date: Fri, 13 May 2022 12:09:12 +0000 Subject: [PATCH 319/408] add some debugging against hang of strategy I've seen in CI --- parsl/dataflow/strategy.py | 5 ++++- parsl/version.py | 2 +- 2 files changed, 5 insertions(+), 2 deletions(-) diff --git a/parsl/dataflow/strategy.py b/parsl/dataflow/strategy.py index ce4313b021..5035a8b03f 100644 --- a/parsl/dataflow/strategy.py +++ b/parsl/dataflow/strategy.py @@ -6,6 +6,8 @@ from parsl.dataflow.executor_status import ExecutorStatus from parsl.executors import HighThroughputExecutor from parsl.providers.provider_base import JobState +from parsl.process_loggers import wrap_with_logs + logger = logging.getLogger(__name__) @@ -159,8 +161,9 @@ def _strategy_htex_auto_scale(self, status_list, tasks): """ self._general_strategy(status_list, tasks, strategy_type='htex') + @wrap_with_logs def _general_strategy(self, status_list, tasks, *, strategy_type): - logger.debug("general strategy starting") + logger.debug(f"general strategy starting for {len(status_list)} executors") for exec_status in status_list: executor = exec_status.executor diff --git a/parsl/version.py b/parsl/version.py index f1296ded50..721173f1a4 100644 --- a/parsl/version.py +++ b/parsl/version.py @@ -3,4 +3,4 @@ ..[alpha/beta/..] Alphas will be numbered like this -> 0.4.0a0 """ -VERSION = '1.3.0-dev+desc-2022.05.13d' +VERSION = '1.3.0-dev+desc-2022.05.13e' From 23cf83164b232c98f1f8bf93fccaab3882965ea2 Mon Sep 17 00:00:00 2001 From: Ben Clifford Date: Wed, 18 May 2022 09:30:53 +0000 Subject: [PATCH 320/408] ongoing rearrangement for merge/tidy - biggest change is removal of htex task priority prototype --- parsl/dataflow/task_status_poller.py | 2 +- parsl/executors/high_throughput/executor.py | 19 ++--- .../executors/high_throughput/interchange.py | 43 ++-------- parsl/executors/workqueue/executor.py | 6 -- parsl/monitoring/monitoring.py | 84 +++++++++---------- parsl/monitoring/node_reporter.py | 2 +- parsl/tests/configs/htex_local_alternate.py | 2 +- .../test_error_handling/test_resource_spec.py | 6 -- parsl/version.py | 2 +- 9 files changed, 59 insertions(+), 107 deletions(-) diff --git a/parsl/dataflow/task_status_poller.py b/parsl/dataflow/task_status_poller.py index cee3384e74..88c8529c7f 100644 --- a/parsl/dataflow/task_status_poller.py +++ b/parsl/dataflow/task_status_poller.py @@ -98,7 +98,7 @@ def __init__(self, dfk: "parsl.dataflow.dflow.DataFlowKernel"): self._strategy = Strategy(dfk) self._error_handler = JobErrorHandler() - def poll(self, tasks=None, kind=None): + def poll(self, tasks=None): self._update_state() self._error_handler.run(self._poll_items) self._strategy.strategize(self._poll_items, tasks) diff --git a/parsl/executors/high_throughput/executor.py b/parsl/executors/high_throughput/executor.py index a0fabd50ac..de2621b7eb 100644 --- a/parsl/executors/high_throughput/executor.py +++ b/parsl/executors/high_throughput/executor.py @@ -17,7 +17,8 @@ from parsl.executors.high_throughput import interchange from parsl.executors.errors import ( BadMessage, ScalingFailed, - DeserializationError, SerializationError + DeserializationError, SerializationError, + UnsupportedFeatureError ) from parsl.executors.status_handling import BlockProviderExecutor @@ -453,7 +454,6 @@ def _queue_management_worker(self): else: raise BadMessage("Message received is neither result or exception") else: - # the 'monitoring' message type should not reach this if statement. It should be handled in the interchange. raise BadMessage("Message received with unknown type {}".format(msg['type'])) if not self.is_alive: @@ -571,6 +571,12 @@ def submit(self, func, resource_specification, *args, **kwargs): Returns: Future """ + if resource_specification: + logger.error("Ignoring the resource specification. " + "Parsl resource specification is not supported in HighThroughput Executor. " + "Please check WorkQueueExecutor if resource specification is needed.") + raise UnsupportedFeatureError('resource specification', 'HighThroughput Executor', 'WorkQueue Executor') + if self.bad_state_is_set: raise self.executor_exception @@ -593,15 +599,8 @@ def submit(self, func, resource_specification, *args, **kwargs): except TypeError: raise SerializationError(func.__name__) - if resource_specification and "priority" in resource_specification: - priority = resource_specification["priority"] - logger.debug("Priority {} found in resource specification".format(priority)) - else: - priority = None - msg = {"task_id": task_id, - "buffer": fn_buf, - "priority": priority} + "buffer": fn_buf} # Post task to the the outgoing queue self.outgoing_q.put(msg) diff --git a/parsl/executors/high_throughput/interchange.py b/parsl/executors/high_throughput/interchange.py index 27774ecfc0..997c596b42 100644 --- a/parsl/executors/high_throughput/interchange.py +++ b/parsl/executors/high_throughput/interchange.py @@ -1,6 +1,5 @@ #!/usr/bin/env python import argparse -import functools import zmq import os import sys @@ -62,38 +61,6 @@ def __str__(self): return self.__repr__() -@functools.total_ordering -class PriorityQueueEntry: - """ This class is needed because msg will be a dict, and dicts are not - comparable to each other (and if they were, this would be an unnecessary - expense because the queue only cares about priority). It provides - ordering of the priority ignoring the message content, and implements an - ordering that places None behind all other orderings, for use as a default - value""" - def __init__(self, pri, msg): - self.pri = pri - self.msg = msg - - def __eq__(self, other): - if type(self) != type(other): - return NotImplemented - return self.pri == other.pri - - def __lt__(self, other): - # this is deliberately inverted, so that largest priority number comes out of the queue first - if type(self) != type(other): - return NotImplemented - if self.pri is None: # special case so that None is always less than every other value - return False # we are more than populated priorities, and equal to None, the inverse of < - elif self.pri is not None and other.pri is None: - return True - else: # self/other both not None - c = self.pri.__gt__(other.pri) - if c == NotImplemented: - raise RuntimeError("priority values are not comparable: {} vs {}".format(self.pri, other.pri)) - return c - - class Interchange(object): """ Interchange is a task orchestrator for distributed systems. @@ -195,7 +162,7 @@ def __init__(self, self.hub_address = hub_address self.hub_port = hub_port - self.pending_task_queue: queue.Queue[Any] = queue.PriorityQueue(maxsize=10 ** 6) + self.pending_task_queue: queue.Queue[Any] = queue.Queue(maxsize=10 ** 6) self.worker_ports = worker_ports self.worker_port_range = worker_port_range @@ -253,11 +220,11 @@ def get_tasks(self, count): tasks = [] for i in range(0, count): try: - qe = self.pending_task_queue.get(block=False) + x = self.pending_task_queue.get(block=False) except queue.Empty: break else: - tasks.append(qe.msg) + tasks.append(x) return tasks @@ -290,8 +257,8 @@ def task_puller(self, kill_event): kill_event.set() break else: - logger.debug("putting message onto pending_task_queue") - self.pending_task_queue.put(PriorityQueueEntry(msg['priority'], msg)) + logger.debug("[TASK_PULL_THREAD] putting message onto pending_task_queue") + self.pending_task_queue.put(msg) task_counter += 1 logger.debug("Fetched task:{}".format(task_counter)) logger.info("reached end of task_puller loop") diff --git a/parsl/executors/workqueue/executor.py b/parsl/executors/workqueue/executor.py index 98da035ce9..e9ea230c3f 100644 --- a/parsl/executors/workqueue/executor.py +++ b/parsl/executors/workqueue/executor.py @@ -890,12 +890,6 @@ def _work_queue_submit_wait(task_queue=multiprocessing.Queue(), else: logger.debug("Not specifying max_retries") - if max_retries is not None: - logger.debug(f"Specifying max_retries {max_retries}") - t.specify_max_retries(max_retries) - else: - logger.debug("Not specifying max_retries") - # Specify environment variables for the task if env is not None: for var in env: diff --git a/parsl/monitoring/monitoring.py b/parsl/monitoring/monitoring.py index 9800c20f39..4d142f6957 100644 --- a/parsl/monitoring/monitoring.py +++ b/parsl/monitoring/monitoring.py @@ -80,19 +80,38 @@ def send(self, message: object) -> None: class FilesystemRadio(MonitoringRadio): - def __init__(self, *, monitoring_hub_url: str, source_id: int, timeout: int = 10, run_dir: str): + """A MonitoringRadio that sends messages over a shared filesystem. + + The messsage directory structure is on maildir, + https://en.wikipedia.org/wiki/Maildir + + The writer creates a message in tmp/ and then when it is fully + written, moves it atomically into new/ + + The reader ignores tmp/ and only reads and deletes messages from + new/ + + This avoids a race condition of reading partially written messages. + + This radio is likely to give higher shared filesystem load compared to + the UDPRadio, but should be much more reliable. + """ + + def __init__(self, *, monitoring_url: str, source_id: int, timeout: int = 10, run_dir: str): logger.info("filesystem based monitoring channel initializing") self.source_id = source_id self.id_counter = 0 self.radio_uid = f"host-{socket.gethostname()}-pid-{os.getpid()}-radio-{id(self)}" self.base_path = f"{run_dir}/monitor-fs-radio/" + self.tmp_path = f"{self.base_path}/tmp" + self.new_path = f"{self.base_path}/new" + + os.makedirs(self.tmp_path, exist_ok=True) + os.makedirs(self.new_path, exist_ok=True) def send(self, message: object) -> None: logger.info("Sending a monitoring message via filesystem") - tmp_path = f"{self.base_path}/tmp" - new_path = f"{self.base_path}/new" - # this should be randomised by things like worker ID, process ID, whatever # because there will in general be many FilesystemRadio objects sharing the # same space (even from the same process). id(self) used here will @@ -103,8 +122,8 @@ def send(self, message: object) -> None: self.id_counter = self.id_counter + 1 # TODO: use path operators not string interpolation - tmp_filename = f"{tmp_path}/{unique_id}" - new_filename = f"{new_path}/{unique_id}" + tmp_filename = f"{self.tmp_path}/{unique_id}" + new_filename = f"{self.new_path}/{unique_id}" buffer = (message, "NA") # this will write the message out then atomically @@ -359,15 +378,15 @@ def start(self, run_id: str, run_dir: str) -> int: "db_url": self.logging_endpoint, }, name="Monitoring-DBM-Process", - daemon=True, - ) + daemon=True) self.dbm_proc.start() self.logger.info("Started the router process {} and DBM process {}".format(self.router_proc.pid, self.dbm_proc.pid)) self.filesystem_proc = Process(target=filesystem_receiver, args=(self.logdir, self.resource_msgs, run_dir), name="Monitoring-Filesystem-Process", - daemon=True) + daemon=True + ) self.filesystem_proc.start() self.logger.info(f"Started filesystem radio receiver process {self.filesystem_proc.pid}") @@ -406,9 +425,6 @@ def send(self, mtype: MessageType, message: Any) -> None: except zmq.Again: self.logger.exception( "The monitoring message sent from DFK to router timed-out after {}ms".format(self.dfk_channel_timeout)) - else: - # this was very big - self.logger.debug("Sent message type {}".format(mtype)) def close(self) -> None: if self.logger: @@ -460,11 +476,7 @@ def monitor_wrapper(f: Any, """ @wraps(f) def wrapped(*args: List[Any], **kwargs: Dict[str, Any]) -> Any: - logger.debug("wrapped: 1. start of wrapped") - terminate_event = Event() - - logger.debug("wrapped: 1.2 sending first message") # Send first message to monitoring router send_first_message(try_id, task_id, @@ -472,7 +484,6 @@ def wrapped(*args: List[Any], **kwargs: Dict[str, Any]) -> Any: run_id, radio_mode, run_dir) - logger.debug("wrapped: 2. sent first message") p: Optional[Process] if monitor_resources: @@ -489,9 +500,7 @@ def wrapped(*args: List[Any], **kwargs: Dict[str, Any]) -> Any: run_dir, terminate_event), name="Monitor-Wrapper-{}".format(task_id)) - logger.debug("wrapped: 3. created monitor process, pid {}".format(pp.pid)) pp.start() - logger.debug("wrapped: 4. started monitor process, pid {}".format(pp.pid)) p = pp # TODO: awkwardness because ForkProcess is not directly a constructor # and type-checking is expecting p to be optional and cannot @@ -501,17 +510,11 @@ def wrapped(*args: List[Any], **kwargs: Dict[str, Any]) -> Any: p = None try: - logger.debug("wrapped: 5. invoking wrapped function") - r = f(*args, **kwargs) - logger.debug("wrapped: 6. back from wrapped function ok") - return r + return f(*args, **kwargs) finally: - logger.debug("wrapped: 10 in 2nd finally") # There's a chance of zombification if the workers are killed by some signals (?) if p: - logger.debug("wrapped: 11.1 setting termination event") terminate_event.set() - logger.debug("wrapped: 11.1 waiting for event based termination") p.join(30) # 30 second delay for this -- this timeout will be hit in the case of an unusually long end-of-loop if p.exitcode is None: logger.warn("Event-based termination of monitoring helper took too long. Using process-based termination.") @@ -521,14 +524,12 @@ def wrapped(*args: List[Any], **kwargs: Dict[str, Any]) -> Any: # This is why this log message is a warning p.join() - logger.debug("wrapped: 11 done terminating monitor") - logger.debug("wrapped: 10.1 sending last message") send_last_message(try_id, task_id, monitoring_hub_url, run_id, radio_mode, run_dir) - logger.debug("wrapped: 10.1 sent last message") + return wrapped @@ -541,16 +542,13 @@ def filesystem_receiver(logdir: str, q: "queue.Queue[Tuple[Tuple[MessageType, Di logger.info("Starting filesystem radio receiver") setproctitle("parsl: monitoring filesystem receiver") - # TODO: these paths should be created by path tools, not f-strings - # likewise the other places where tmp_dir, new_dir are created on - # the sending side. base_path = f"{run_dir}/monitor-fs-radio/" tmp_dir = f"{base_path}/tmp/" new_dir = f"{base_path}/new/" logger.debug("Creating new and tmp paths") - os.makedirs(tmp_dir) - os.makedirs(new_dir) + os.makedirs(tmp_dir, exist_ok=True) + os.makedirs(new_dir, exist_ok=True) while True: # needs an exit condition, that also copes with late messages # like the UDP radio receiver. @@ -770,7 +768,7 @@ def send_first_message(try_id: int, radio = HTEXRadio(monitoring_hub_url, source_id=task_id) elif radio_mode == "filesystem": - radio = FilesystemRadio(monitoring_hub_url=monitoring_hub_url, + radio = FilesystemRadio(monitoring_url=monitoring_hub_url, source_id=task_id, run_dir=run_dir) else: raise RuntimeError(f"Unknown radio mode: {radio_mode}") @@ -806,7 +804,7 @@ def send_last_message(try_id: int, radio = HTEXRadio(monitoring_hub_url, source_id=task_id) elif radio_mode == "filesystem": - radio = FilesystemRadio(monitoring_hub_url=monitoring_hub_url, + radio = FilesystemRadio(monitoring_url=monitoring_hub_url, source_id=task_id, run_dir=run_dir) else: raise RuntimeError(f"Unknown radio mode: {radio_mode}") @@ -840,6 +838,12 @@ def monitor(pid: int, terminate_event: Any) -> None: # cannot be Event because of multiprocessing type weirdness. """Internal Monitors the Parsl task's resources by pointing psutil to the task's pid and watching it and its children. + + This process makes calls to logging, but deliberately does not attach + any log handlers. Previously, there was a handler which logged to a + file in /tmp, but this was usually not useful or even accessible. + In some circumstances, it might be useful to hack in a handler so the + logger calls remain in place. """ import logging import platform @@ -853,17 +857,11 @@ def monitor(pid: int, radio = HTEXRadio(monitoring_hub_url, source_id=task_id) elif radio_mode == "filesystem": - radio = FilesystemRadio(monitoring_hub_url=monitoring_hub_url, + radio = FilesystemRadio(monitoring_url=monitoring_hub_url, source_id=task_id, run_dir=run_dir) else: raise RuntimeError(f"Unknown radio mode: {radio_mode}") - # TODO: should this be enabled by a debugging option? - - # format_string = "%(asctime)s.%(msecs)03d %(name)s:%(lineno)d [%(levelname)s] %(message)s" - # logging.basicConfig(filename='{logbase}/monitor.{task_id}.{pid}.log'.format( - # logbase="/tmp", task_id=task_id, pid=pid), level=logging_level, format=format_string) - logging.debug("start of monitor") # these values are simple to log. Other information is available in special formats such as memory below. diff --git a/parsl/monitoring/node_reporter.py b/parsl/monitoring/node_reporter.py index be5426f522..4c9cd59d55 100755 --- a/parsl/monitoring/node_reporter.py +++ b/parsl/monitoring/node_reporter.py @@ -82,7 +82,7 @@ def send_msg(*, active, uid, radio): run_dir = "/home/benc/parsl/src/parsl/runinfo/000/" # TODO at least get the real version of this value, no matter how badly - radio = FilesystemRadio(monitoring_hub_url="", # TODO: monitoring_hub_url and source_id real values? + radio = FilesystemRadio(monitoring_url="", # TODO: monitoring_hub_url and source_id real values? source_id=0, run_dir=run_dir) uid = str(uuid.uuid4()) diff --git a/parsl/tests/configs/htex_local_alternate.py b/parsl/tests/configs/htex_local_alternate.py index 59260c4e88..d0a572c153 100644 --- a/parsl/tests/configs/htex_local_alternate.py +++ b/parsl/tests/configs/htex_local_alternate.py @@ -66,7 +66,7 @@ def fresh_config(): monitoring=MonitoringHub( hub_address="localhost", hub_port=55055, - monitoring_debug=True, + monitoring_debug=False, resource_monitoring_interval=1, ) ) diff --git a/parsl/tests/test_error_handling/test_resource_spec.py b/parsl/tests/test_error_handling/test_resource_spec.py index ab42a36534..11ffa7c842 100644 --- a/parsl/tests/test_error_handling/test_resource_spec.py +++ b/parsl/tests/test_error_handling/test_resource_spec.py @@ -1,5 +1,4 @@ import parsl -import pytest from parsl.app.app import python_app # from parsl.tests.configs.local_threads import config from parsl.tests.configs.htex_local import config @@ -13,11 +12,6 @@ def double(x, parsl_resource_specification={}): return x * 2 -@pytest.mark.skip("this test does not accomodate running the test suite" - " on executors which *do* support resource specifications" - " but are not the workqueue executor. In general, it is" - " incorrect to assume that an arbitrary non-workqueue" - " executor will raise the expected exceptionm") def test_resource(n=2): executors = parsl.dfk().executors executor = None diff --git a/parsl/version.py b/parsl/version.py index 721173f1a4..b12ad3b2f7 100644 --- a/parsl/version.py +++ b/parsl/version.py @@ -3,4 +3,4 @@ ..[alpha/beta/..] Alphas will be numbered like this -> 0.4.0a0 """ -VERSION = '1.3.0-dev+desc-2022.05.13e' +VERSION = '1.3.0-dev+desc-2022.05.18a' From 2b9859ca74dd31df8b7e53a71e03ef38a787fdf2 Mon Sep 17 00:00:00 2001 From: Ben Clifford Date: Wed, 18 May 2022 11:06:21 +0000 Subject: [PATCH 321/408] add in logging of module imports inside WQ for david adams performance --- parsl/executors/workqueue/exec_parsl_function.py | 7 +++++++ parsl/version.py | 2 +- 2 files changed, 8 insertions(+), 1 deletion(-) diff --git a/parsl/executors/workqueue/exec_parsl_function.py b/parsl/executors/workqueue/exec_parsl_function.py index 4f99030499..b6af1e7de4 100644 --- a/parsl/executors/workqueue/exec_parsl_function.py +++ b/parsl/executors/workqueue/exec_parsl_function.py @@ -181,6 +181,11 @@ def execute_function(namespace, function_code, result_name): return result +class MetaPathLogger: + + def find_spec(*args, **kwargs): + print(f"{time.time()} META_PATH {args[0]}", file=logfile) + return None if __name__ == "__main__": t_mainstart = time.time() @@ -202,6 +207,8 @@ def execute_function(namespace, function_code, result_name): print(f"{t_postimport} POSTIMPORT", file=logfile) print(f"{t_mainstart} MAINSTART", file=logfile) + sys.meta_path = [MetaPathLogger] + sys.meta_path + t_loadfunction = time.time() print(f"{t_loadfunction} LOADFUNCTION", file=logfile) try: diff --git a/parsl/version.py b/parsl/version.py index b12ad3b2f7..8e245fc034 100644 --- a/parsl/version.py +++ b/parsl/version.py @@ -3,4 +3,4 @@ ..[alpha/beta/..] Alphas will be numbered like this -> 0.4.0a0 """ -VERSION = '1.3.0-dev+desc-2022.05.18a' +VERSION = '1.3.0-dev+desc-2022.05.18b' From c1e44f5ebc44e6eecae0ec99549947294dcec0e9 Mon Sep 17 00:00:00 2001 From: Ben Clifford Date: Wed, 18 May 2022 11:11:23 +0000 Subject: [PATCH 322/408] fix lint errors --- parsl/executors/workqueue/exec_parsl_function.py | 8 +++++--- parsl/version.py | 2 +- 2 files changed, 6 insertions(+), 4 deletions(-) diff --git a/parsl/executors/workqueue/exec_parsl_function.py b/parsl/executors/workqueue/exec_parsl_function.py index b6af1e7de4..a7756a8f76 100644 --- a/parsl/executors/workqueue/exec_parsl_function.py +++ b/parsl/executors/workqueue/exec_parsl_function.py @@ -181,11 +181,13 @@ def execute_function(namespace, function_code, result_name): return result + class MetaPathLogger: - def find_spec(*args, **kwargs): - print(f"{time.time()} META_PATH {args[0]}", file=logfile) - return None + def find_spec(*args, **kwargs): + print(f"{time.time()} META_PATH {args[0]}", file=logfile) + return None + if __name__ == "__main__": t_mainstart = time.time() diff --git a/parsl/version.py b/parsl/version.py index 8e245fc034..c614ce2bf3 100644 --- a/parsl/version.py +++ b/parsl/version.py @@ -3,4 +3,4 @@ ..[alpha/beta/..] Alphas will be numbered like this -> 0.4.0a0 """ -VERSION = '1.3.0-dev+desc-2022.05.18b' +VERSION = '1.3.0-dev+desc-2022.05.18c' From 19ec35ebdf3882d5b0efbec21bf0c342679038a7 Mon Sep 17 00:00:00 2001 From: Ben Clifford Date: Wed, 18 May 2022 11:29:24 +0000 Subject: [PATCH 323/408] fiddling with types for a CI mypy failure that doesn't happen on my laptop --- parsl/executors/workqueue/exec_parsl_function.py | 6 +++++- parsl/version.py | 2 +- 2 files changed, 6 insertions(+), 2 deletions(-) diff --git a/parsl/executors/workqueue/exec_parsl_function.py b/parsl/executors/workqueue/exec_parsl_function.py index a7756a8f76..9cb3ca4af5 100644 --- a/parsl/executors/workqueue/exec_parsl_function.py +++ b/parsl/executors/workqueue/exec_parsl_function.py @@ -7,6 +7,7 @@ import traceback import sys import pickle +from typing import List, Any t_postimport = time.time() # This scripts executes a parsl function which is pickled in a file: @@ -209,7 +210,10 @@ def find_spec(*args, **kwargs): print(f"{t_postimport} POSTIMPORT", file=logfile) print(f"{t_mainstart} MAINSTART", file=logfile) - sys.meta_path = [MetaPathLogger] + sys.meta_path + mpl: List[Any] + mpl = [MetaPathLogger] + + sys.meta_path = mpl + sys.meta_path t_loadfunction = time.time() print(f"{t_loadfunction} LOADFUNCTION", file=logfile) diff --git a/parsl/version.py b/parsl/version.py index c614ce2bf3..5c45e263b8 100644 --- a/parsl/version.py +++ b/parsl/version.py @@ -3,4 +3,4 @@ ..[alpha/beta/..] Alphas will be numbered like this -> 0.4.0a0 """ -VERSION = '1.3.0-dev+desc-2022.05.18c' +VERSION = '1.3.0-dev+desc-2022.05.18d' From 730468b1b7e8dbc9d11870b52b08a23ba40acbca Mon Sep 17 00:00:00 2001 From: Ben Clifford Date: Wed, 18 May 2022 12:48:55 +0000 Subject: [PATCH 324/408] fix bad kind tidyup --- parsl/dataflow/flow_control.py | 16 ++++++---------- parsl/version.py | 2 +- 2 files changed, 7 insertions(+), 11 deletions(-) diff --git a/parsl/dataflow/flow_control.py b/parsl/dataflow/flow_control.py index c2d6139b0b..254d53dc12 100644 --- a/parsl/dataflow/flow_control.py +++ b/parsl/dataflow/flow_control.py @@ -88,7 +88,7 @@ def _wake_up_timer(self, kill_event): return if prev == self._wake_up_time: - self.make_callback(kind='timer') + self.make_callback() else: print("Sleeping a bit more") @@ -98,18 +98,14 @@ def notify(self, event_id): self._event_count += 1 if self._event_count >= self.threshold: logger.debug("Eventcount >= threshold") - self.make_callback(kind="event") + self.make_callback() - def make_callback(self, kind=None): + def make_callback(self): """Makes the callback and resets the timer. - - KWargs: - - kind (str): Default=None, used to pass information on what - triggered the callback """ self._wake_up_time = time.time() + self.interval try: - self.callback(tasks=self._event_buffer, kind=kind) + self.callback(tasks=self._event_buffer) except Exception: logger.error("Flow control callback threw an exception - logging and proceeding anyway", exc_info=True) self._event_buffer = [] @@ -190,11 +186,11 @@ def _wake_up_timer(self, kill_event): return if prev == self._wake_up_time: - self.make_callback(kind='timer') + self.make_callback() else: print("Sleeping a bit more") - def make_callback(self, kind=None): + def make_callback(self): """Makes the callback and resets the timer. """ self._wake_up_time = time.time() + self.interval diff --git a/parsl/version.py b/parsl/version.py index 5c45e263b8..eadbe861f2 100644 --- a/parsl/version.py +++ b/parsl/version.py @@ -3,4 +3,4 @@ ..[alpha/beta/..] Alphas will be numbered like this -> 0.4.0a0 """ -VERSION = '1.3.0-dev+desc-2022.05.18d' +VERSION = '1.3.0-dev+desc-2022.05.18e' From 453736e89912280026465e22c2afa3f264071ab7 Mon Sep 17 00:00:00 2001 From: Ben Clifford Date: Fri, 20 May 2022 13:29:51 +0000 Subject: [PATCH 325/408] fix for quentin --- parsl/executors/high_throughput/interchange.py | 2 +- parsl/executors/high_throughput/manager_record.py | 2 +- parsl/version.py | 2 +- 3 files changed, 3 insertions(+), 3 deletions(-) diff --git a/parsl/executors/high_throughput/interchange.py b/parsl/executors/high_throughput/interchange.py index 997c596b42..7977f7f048 100644 --- a/parsl/executors/high_throughput/interchange.py +++ b/parsl/executors/high_throughput/interchange.py @@ -426,7 +426,7 @@ def start(self): self._ready_managers[manager_id] = {'last_heartbeat': time.time(), 'idle_since': time.time(), 'free_capacity': 0, - # 'block_id': None, -- don't assign a badly typed value + 'block_id': None, # don't assign a badly typed value 'max_capacity': 0, 'worker_count': 0, 'active': True, diff --git a/parsl/executors/high_throughput/manager_record.py b/parsl/executors/high_throughput/manager_record.py index 353d2353a5..0c44ed6a62 100644 --- a/parsl/executors/high_throughput/manager_record.py +++ b/parsl/executors/high_throughput/manager_record.py @@ -4,7 +4,7 @@ class ManagerRecord(TypedDict, total=False): - block_id: str + block_id: Optional[str] tasks: List[Any] worker_count: int free_capacity: int diff --git a/parsl/version.py b/parsl/version.py index eadbe861f2..add3f5dd8b 100644 --- a/parsl/version.py +++ b/parsl/version.py @@ -3,4 +3,4 @@ ..[alpha/beta/..] Alphas will be numbered like this -> 0.4.0a0 """ -VERSION = '1.3.0-dev+desc-2022.05.18e' +VERSION = '1.3.0-dev+desc-2022.05.20a' From c014505a135a2156b077b138e645f2c63294db36 Mon Sep 17 00:00:00 2001 From: Ben Clifford Date: Fri, 20 May 2022 13:47:35 +0000 Subject: [PATCH 326/408] fiddling with typechecking for quentin fix --- mypy.ini | 2 +- parsl/version.py | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/mypy.ini b/mypy.ini index 3826a9b4d6..9c160797d6 100644 --- a/mypy.ini +++ b/mypy.ini @@ -21,7 +21,7 @@ warn_unreachable = True disallow_untyped_defs = True [mypy-parsl.executors.high_throughput.interchange.*] -check_untyped_defs = True +check_untyped_defs = False [mypy-parsl.monitoring.node_reporter] # because I haven't written the node reporter properly yet diff --git a/parsl/version.py b/parsl/version.py index add3f5dd8b..b7e834e0df 100644 --- a/parsl/version.py +++ b/parsl/version.py @@ -3,4 +3,4 @@ ..[alpha/beta/..] Alphas will be numbered like this -> 0.4.0a0 """ -VERSION = '1.3.0-dev+desc-2022.05.20a' +VERSION = '1.3.0-dev+desc-2022.05.20b' From 3daa3adaf526b5e2e1e9d312aacce82c458a6f54 Mon Sep 17 00:00:00 2001 From: Ben Clifford Date: Mon, 23 May 2022 11:14:40 +0000 Subject: [PATCH 327/408] hack a bad interaction between monitor wrapper and some monitoring-over-htex --- parsl/executors/high_throughput/interchange.py | 1 + parsl/monitoring/monitoring.py | 2 -- parsl/serialize/concretes.py | 7 ++++++- parsl/version.py | 2 +- 4 files changed, 8 insertions(+), 4 deletions(-) diff --git a/parsl/executors/high_throughput/interchange.py b/parsl/executors/high_throughput/interchange.py index 7977f7f048..8f416b7b55 100644 --- a/parsl/executors/high_throughput/interchange.py +++ b/parsl/executors/high_throughput/interchange.py @@ -555,6 +555,7 @@ def start(self): m = self._ready_managers[manager_id] for b_message in b_messages: r = pickle.loads(b_message) + assert 'type' in r, f"Message is missing type entry: {r}" if r['type'] == 'result': try: logger.debug(f"Removing task {r['task_id']} from manager {manager_id} record") diff --git a/parsl/monitoring/monitoring.py b/parsl/monitoring/monitoring.py index 4d142f6957..5adafde92a 100644 --- a/parsl/monitoring/monitoring.py +++ b/parsl/monitoring/monitoring.py @@ -6,7 +6,6 @@ import typeguard import datetime import zmq -from functools import wraps import queue from abc import ABCMeta, abstractmethod @@ -474,7 +473,6 @@ def monitor_wrapper(f: Any, """ Internal Wrap the Parsl app with a function that will call the monitor function and point it at the correct pid when the task begins. """ - @wraps(f) def wrapped(*args: List[Any], **kwargs: Dict[str, Any]) -> Any: terminate_event = Event() # Send first message to monitoring router diff --git a/parsl/serialize/concretes.py b/parsl/serialize/concretes.py index cd5f5e1eeb..6171a85082 100644 --- a/parsl/serialize/concretes.py +++ b/parsl/serialize/concretes.py @@ -46,7 +46,12 @@ class DillSerializer(SerializerBase): _for_data = True def serialize(self, data): - x = dill.dumps(data) + # BENC: this is debug info to remove later + try: + x = dill.dumps(data) + except Exception as e: + logger.error(f"Could not dump data={data}, because of {e}") + raise return self.identifier + x def deserialize(self, payload): diff --git a/parsl/version.py b/parsl/version.py index b7e834e0df..41abbf1c4f 100644 --- a/parsl/version.py +++ b/parsl/version.py @@ -3,4 +3,4 @@ ..[alpha/beta/..] Alphas will be numbered like this -> 0.4.0a0 """ -VERSION = '1.3.0-dev+desc-2022.05.20b' +VERSION = '1.3.0-dev+desc-2022.05.23a' From 2d7cedaa731d4bed88843560ff47e0b71bb1957b Mon Sep 17 00:00:00 2001 From: Ben Clifford Date: Mon, 23 May 2022 12:10:39 +0000 Subject: [PATCH 328/408] more rearranging to resolve desc vs master htex monitoring conflict --- parsl/monitoring/monitoring.py | 7 +++++-- parsl/serialize/concretes.py | 7 +------ parsl/version.py | 2 +- 3 files changed, 7 insertions(+), 9 deletions(-) diff --git a/parsl/monitoring/monitoring.py b/parsl/monitoring/monitoring.py index 5adafde92a..985b884b87 100644 --- a/parsl/monitoring/monitoring.py +++ b/parsl/monitoring/monitoring.py @@ -6,6 +6,7 @@ import typeguard import datetime import zmq +from functools import wraps import queue from abc import ABCMeta, abstractmethod @@ -17,8 +18,6 @@ from parsl.serialize import deserialize -import parsl.executors.high_throughput.monitoring_info - from parsl.monitoring.message_type import MessageType from typing import cast, Any, Callable, Dict, List, Optional, Union @@ -162,6 +161,9 @@ def send(self, message: object) -> None: Returns: None """ + + import parsl.executors.high_throughput.monitoring_info + # TODO: this message needs to look like the other messages that the interchange will send... # hub_channel.send_pyobj((MessageType.NODE_INFO, # datetime.datetime.now(), @@ -473,6 +475,7 @@ def monitor_wrapper(f: Any, """ Internal Wrap the Parsl app with a function that will call the monitor function and point it at the correct pid when the task begins. """ + @wraps(f) def wrapped(*args: List[Any], **kwargs: Dict[str, Any]) -> Any: terminate_event = Event() # Send first message to monitoring router diff --git a/parsl/serialize/concretes.py b/parsl/serialize/concretes.py index 6171a85082..cd5f5e1eeb 100644 --- a/parsl/serialize/concretes.py +++ b/parsl/serialize/concretes.py @@ -46,12 +46,7 @@ class DillSerializer(SerializerBase): _for_data = True def serialize(self, data): - # BENC: this is debug info to remove later - try: - x = dill.dumps(data) - except Exception as e: - logger.error(f"Could not dump data={data}, because of {e}") - raise + x = dill.dumps(data) return self.identifier + x def deserialize(self, payload): diff --git a/parsl/version.py b/parsl/version.py index 41abbf1c4f..c3f1a92ac6 100644 --- a/parsl/version.py +++ b/parsl/version.py @@ -3,4 +3,4 @@ ..[alpha/beta/..] Alphas will be numbered like this -> 0.4.0a0 """ -VERSION = '1.3.0-dev+desc-2022.05.23a' +VERSION = '1.3.0-dev+desc-2022.05.23b' From 4ae14686d2f3a6637b48c5d7e1ff3deee861f1f7 Mon Sep 17 00:00:00 2001 From: Ben Clifford Date: Tue, 24 May 2022 09:58:54 +0000 Subject: [PATCH 329/408] add 2259 fix from pr 2263 --- parsl/providers/slurm/slurm.py | 2 +- parsl/version.py | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/parsl/providers/slurm/slurm.py b/parsl/providers/slurm/slurm.py index e9078647a1..3445d15705 100644 --- a/parsl/providers/slurm/slurm.py +++ b/parsl/providers/slurm/slurm.py @@ -139,7 +139,7 @@ def _status(self): [status...] : Status list of all jobs ''' job_id_list = ','.join( - [jid for jid, job in self.resources.keys() if not job['status'].terminal] + [jid for jid, job in self.resources.items() if not job['status'].terminal] ) if not job_id_list: logger.debug('No active jobs, skipping status update') diff --git a/parsl/version.py b/parsl/version.py index c3f1a92ac6..872d344ad4 100644 --- a/parsl/version.py +++ b/parsl/version.py @@ -3,4 +3,4 @@ ..[alpha/beta/..] Alphas will be numbered like this -> 0.4.0a0 """ -VERSION = '1.3.0-dev+desc-2022.05.23b' +VERSION = '1.3.0-dev+desc-2022.05.24a' From d915d6ee4b4f474758ab29476fc64259a88a0fe1 Mon Sep 17 00:00:00 2001 From: Ben Clifford Date: Tue, 14 Jun 2022 09:39:43 +0000 Subject: [PATCH 330/408] add attempt to transmit only changed block status, for scalability --- parsl/dataflow/task_status_poller.py | 10 +++++++++- parsl/version.py | 2 +- 2 files changed, 10 insertions(+), 2 deletions(-) diff --git a/parsl/dataflow/task_status_poller.py b/parsl/dataflow/task_status_poller.py index 88c8529c7f..5b3ebfe11c 100644 --- a/parsl/dataflow/task_status_poller.py +++ b/parsl/dataflow/task_status_poller.py @@ -41,9 +41,17 @@ def _should_poll(self, now: float): def poll(self, now: float): if self._should_poll(now): + previous_status = self._status self._status = self._executor.status() self._last_poll_time = now - self.send_monitoring_info(self._status) + delta_status = {} + for block_id in self._status: + if block_id not in previous_status \ + or previous_status[block_id].state != self._status[block_id].state: + delta_status[block_id] = self._status[block_id] + + if delta_status: + self.send_monitoring_info(delta_status) def send_monitoring_info(self, status=None): # Send monitoring info for HTEX when monitoring enabled diff --git a/parsl/version.py b/parsl/version.py index d2a3e36d04..e3b7ce7b46 100644 --- a/parsl/version.py +++ b/parsl/version.py @@ -3,4 +3,4 @@ ..[alpha/beta/..] Alphas will be numbered like this -> 0.4.0a0 """ -VERSION = '1.3.0-dev+desc-2022.06.14a' +VERSION = '1.3.0-dev+desc-2022.06.14b' From 3b6805bdad0049b186467880928275650618f890 Mon Sep 17 00:00:00 2001 From: Ben Clifford Date: Tue, 28 Jun 2022 12:37:33 +0000 Subject: [PATCH 331/408] Use a type alias for monitoring messages for clarity --- parsl/monitoring/db_manager.py | 7 ++++--- parsl/monitoring/monitoring.py | 28 +++++++++++++++------------- parsl/monitoring/types.py | 5 +++++ 3 files changed, 24 insertions(+), 16 deletions(-) create mode 100644 parsl/monitoring/types.py diff --git a/parsl/monitoring/db_manager.py b/parsl/monitoring/db_manager.py index 83492172f6..3686944628 100644 --- a/parsl/monitoring/db_manager.py +++ b/parsl/monitoring/db_manager.py @@ -11,6 +11,7 @@ from parsl.dataflow.states import States from parsl.errors import OptionalModuleMissing from parsl.monitoring.message_type import MessageType +from parsl.monitoring.types import TaggedMonitoringMessage from parsl.process_loggers import wrap_with_logs from parsl.utils import setproctitle @@ -286,13 +287,13 @@ def __init__(self, self.batching_interval = batching_interval self.batching_threshold = batching_threshold - self.pending_priority_queue = queue.Queue() # type: queue.Queue[Tuple[MessageType, Dict[str, Any]]] + self.pending_priority_queue = queue.Queue() # type: queue.Queue[TaggedMonitoringMessage] self.pending_node_queue = queue.Queue() # type: queue.Queue[Dict[str, Any]] self.pending_block_queue = queue.Queue() # type: queue.Queue[Dict[str, Any]] self.pending_resource_queue = queue.Queue() # type: queue.Queue[Dict[str, Any]] def start(self, - priority_queue: "queue.Queue[Tuple[MessageType, Dict[str, Any]]]", + priority_queue: "queue.Queue[TaggedMonitoringMessage]", node_queue: "queue.Queue[Dict[str, Any]]", block_queue: "queue.Queue[Dict[str, Any]]", resource_queue: "queue.Queue[Dict[str, Any]]") -> None: @@ -696,7 +697,7 @@ def close(self) -> None: @wrap_with_logs(target="database_manager") def dbm_starter(exception_q: "queue.Queue[Tuple[str, str]]", - priority_msgs: "queue.Queue[Tuple[MessageType, Dict[str, Any]]]", + priority_msgs: "queue.Queue[TaggedMonitoringMessage]", node_msgs: "queue.Queue[Dict[str, Any]]", block_msgs: "queue.Queue[Dict[str, Any]]", resource_msgs: "queue.Queue[Dict[str, Any]]", diff --git a/parsl/monitoring/monitoring.py b/parsl/monitoring/monitoring.py index e75b915339..c7a24b22d9 100644 --- a/parsl/monitoring/monitoring.py +++ b/parsl/monitoring/monitoring.py @@ -19,6 +19,7 @@ from parsl.serialize import deserialize from parsl.monitoring.message_type import MessageType +from parsl.monitoring.types import TaggedMonitoringMessage from typing import cast, Any, Callable, Dict, List, Optional, Union from parsl.serialize import serialize @@ -27,6 +28,7 @@ from typing import Optional, Tuple + try: from parsl.monitoring.db_manager import dbm_starter except Exception as e: @@ -347,9 +349,9 @@ def start(self, run_id: str, run_dir: str) -> int: comm_q = SizedQueue(maxsize=10) # type: Queue[Union[Tuple[int, int], str]] self.exception_q = SizedQueue(maxsize=10) # type: Queue[Tuple[str, str]] self.priority_msgs = SizedQueue() # type: Queue[Tuple[Any, int]] - self.resource_msgs = SizedQueue() # type: Queue[Tuple[Tuple[MessageType, Dict[str, Any]], Any]] - self.node_msgs = SizedQueue() # type: Queue[Tuple[Tuple[MessageType, Dict[str, Any]], int]] - self.block_msgs = SizedQueue() # type: Queue[Tuple[Tuple[MessageType, Dict[str, Any]], Any]] + self.resource_msgs = SizedQueue() # type: Queue[Tuple[TaggedMonitoringMessage, Any]] + self.node_msgs = SizedQueue() # type: Queue[Tuple[TaggedMonitoringMessage, int]] + self.block_msgs = SizedQueue() # type: Queue[Tuple[TaggedMonitoringMessage, Any]] self.router_proc = ForkProcess(target=router_starter, args=(comm_q, self.exception_q, self.priority_msgs, self.node_msgs, self.block_msgs, self.resource_msgs), @@ -528,7 +530,7 @@ def wrapped(*args: List[Any], **kwargs: Dict[str, Any]) -> Any: @wrap_with_logs -def filesystem_receiver(logdir: str, q: "queue.Queue[Tuple[Tuple[MessageType, Dict[str, Any]], Any]]", run_dir: str) -> None: +def filesystem_receiver(logdir: str, q: "queue.Queue[Tuple[TaggedMonitoringMessage, Any]]", run_dir: str) -> None: logger = start_file_logger("{}/monitoring_filesystem_radio.log".format(logdir), name="monitoring_filesystem_radio", level=logging.DEBUG) @@ -634,10 +636,10 @@ def __init__(self, max_port=hub_port_range[1]) def start(self, - priority_msgs: "queue.Queue[Tuple[Tuple[MessageType, Dict[str, Any]], int]]", - node_msgs: "queue.Queue[Tuple[Tuple[MessageType, Dict[str, Any]], int]]", - block_msgs: "queue.Queue[Tuple[Tuple[MessageType, Dict[str, Any]], int]]", - resource_msgs: "queue.Queue[Tuple[Tuple[MessageType, Dict[str, Any]], Any]]") -> None: + priority_msgs: "queue.Queue[Tuple[TaggedMonitoringMessage, int]]", + node_msgs: "queue.Queue[Tuple[TaggedMonitoringMessage, int]]", + block_msgs: "queue.Queue[Tuple[TaggedMonitoringMessage, int]]", + resource_msgs: "queue.Queue[Tuple[TaggedMonitoringMessage, Any]]") -> None: try: router_keep_going = True while router_keep_going: @@ -653,7 +655,7 @@ def start(self, dfk_loop_start = time.time() while time.time() - dfk_loop_start < 1.0: # TODO make configurable # note that nothing checks that msg really is of the annotated type - msg: Tuple[MessageType, Dict[str, Any]] + msg: TaggedMonitoringMessage msg = self.ic_channel.recv_pyobj() assert isinstance(msg, tuple), "IC Channel expects only tuples, got {}".format(msg) @@ -706,10 +708,10 @@ def start(self, @wrap_with_logs def router_starter(comm_q: "queue.Queue[Union[Tuple[int, int], str]]", exception_q: "queue.Queue[Tuple[str, str]]", - priority_msgs: "queue.Queue[Tuple[Tuple[MessageType, Dict[str, Any]], int]]", - node_msgs: "queue.Queue[Tuple[Tuple[MessageType, Dict[str, Any]], int]]", - block_msgs: "queue.Queue[Tuple[Tuple[MessageType, Dict[str, Any]], int]]", - resource_msgs: "queue.Queue[Tuple[Tuple[MessageType, Dict[str, Any]], str]]", + priority_msgs: "queue.Queue[Tuple[TaggedMonitoringMessage, int]]", + node_msgs: "queue.Queue[Tuple[TaggedMonitoringMessage, int]]", + block_msgs: "queue.Queue[Tuple[TaggedMonitoringMessage, int]]", + resource_msgs: "queue.Queue[Tuple[TaggedMonitoringMessage, str]]", hub_address: str, hub_port: Optional[int], diff --git a/parsl/monitoring/types.py b/parsl/monitoring/types.py new file mode 100644 index 0000000000..0684c27493 --- /dev/null +++ b/parsl/monitoring/types.py @@ -0,0 +1,5 @@ +from typing import Any, Dict, Tuple +from typing_extensions import TypeAlias +from parsl.monitoring.message_type import MessageType + +TaggedMonitoringMessage: TypeAlias = Tuple[MessageType, Dict[str, Any]] From 23ef6dc90b0dda1f0e12eb35c2f91822d5798112 Mon Sep 17 00:00:00 2001 From: Ben Clifford Date: Tue, 28 Jun 2022 12:51:26 +0000 Subject: [PATCH 332/408] update version number --- parsl/version.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/parsl/version.py b/parsl/version.py index 8864ceb824..9b982f0a67 100644 --- a/parsl/version.py +++ b/parsl/version.py @@ -3,4 +3,4 @@ ..[alpha/beta/..] Alphas will be numbered like this -> 0.4.0a0 """ -VERSION = '1.3.0-dev+desc-2022.06.24a' +VERSION = '1.3.0-dev+desc-2022.06.28b' From a6fb29debb4d352a7445a191f48d1276f9fb2433 Mon Sep 17 00:00:00 2001 From: Ben Clifford Date: Wed, 13 Jul 2022 08:35:20 +0000 Subject: [PATCH 333/408] Add bodge for perlmutter race condition --- parsl/executors/workqueue/executor.py | 5 +++++ parsl/version.py | 2 +- 2 files changed, 6 insertions(+), 1 deletion(-) diff --git a/parsl/executors/workqueue/executor.py b/parsl/executors/workqueue/executor.py index e9ea230c3f..5e2dd05634 100644 --- a/parsl/executors/workqueue/executor.py +++ b/parsl/executors/workqueue/executor.py @@ -17,6 +17,7 @@ import socket import pickle import queue +import time import inspect import shutil import itertools @@ -302,6 +303,10 @@ def start(self): logger.debug("Starting WorkQueueExectutor") + logger.warning("BODGE: delay here for hack around often observed futex race...") + time.sleep(15) + logger.warning("BODGE: delay finished") + # Create a Process to perform WorkQueue submissions submit_process_kwargs = {"task_queue": self.task_queue, "launch_cmd": self.launch_cmd, diff --git a/parsl/version.py b/parsl/version.py index 8b0227ae78..58722b5d92 100644 --- a/parsl/version.py +++ b/parsl/version.py @@ -3,4 +3,4 @@ ..[alpha/beta/..] Alphas will be numbered like this -> 0.4.0a0 """ -VERSION = '1.3.0-dev+desc-2022.06.30a' +VERSION = '1.3.0-dev+desc-2022.07.13a' From ae55ccddabd33fd4b4d746b4d313761e3619dd0f Mon Sep 17 00:00:00 2001 From: Ben Clifford Date: Thu, 4 Aug 2022 11:32:26 +0000 Subject: [PATCH 334/408] merge in minor tidyups from patch stack --- docs/userguide/dnpc.rst | 155 ------------------ docs/userguide/index.rst | 1 - .../high_throughput/process_worker_pool.py | 2 +- parsl/version.py | 2 +- setup.py | 1 - 5 files changed, 2 insertions(+), 159 deletions(-) delete mode 100644 docs/userguide/dnpc.rst diff --git a/docs/userguide/dnpc.rst b/docs/userguide/dnpc.rst deleted file mode 100644 index 2f9238ced3..0000000000 --- a/docs/userguide/dnpc.rst +++ /dev/null @@ -1,155 +0,0 @@ -distributed nested performance contexts -======================================= - -distributed tracing style stuff for parsl and related components. - -distributed tracing has a single request ID that is propagated everywhere [citation] - -this work is intended to make things a bit more heirarchical, where an activity -as well as having logs/states itself, also contains subactivities. - -it is an exploration of *how* to express useful information, rather than an -attempt to implement it in an efficient manner - I think its likely that -with some fleshing out of how things should work, it might become apparant -that (for example) some existing graph database delivers the right -query behaviour. - -see nested diagnostic context work in java [citation] - -see netlogger [citation] - -see graph query languages in general - -see buneman - keys for XML - for some thoughts about identity for merges/joins -eg https://repository.upenn.edu/cgi/viewcontent.cgi?article=1122&context=cis_papers - -the key goal for the current work is performance analysis of parsl -tasks as they are executed through the system - but including the non-core -parsl stuff: perhaps a little bit inside the tasks, definitely inside the -engines that sit alongside parsl helping the tasks run. - -not-goals: - -* live information integration between data sources - so components - can dump out stuff wherever/however without time constraints. this is all - post-hoc analysis - -* instrumenting every piece of tech in the stack using the same technology, - so custom per-component log file scraping is OK. Requiring the components to - change to work with this logging mechanism is not a requirement (and mostly - impossible if it's things installed on the host system rather than in a user - environment) - -vocab: - context - a thing which has states/log lines/... across multiple log sources - for example a parsl task - subcontext - a context which is fully contained within another context. - for example, a parsl ``try`` is fully contained within a parsl ``task``. - -components of the system emit log-like info - logfiles, monitoring.db - which -associate *events* - eg state transitions, log lines - with a particular context. - -it might be that a particlar source has a particular implicit containing -context - eg a particular logfile is only for a particular try context, which means -it is then contained in a particular task context without the log file ever -mentioning that task context. - -do contexts have to have explicit IDs? maybe not - eg if there's an adhoc -context coming from a single log file. - -the primary output goal for now is for all parsl tasks, to get a (fine-grained as -desired by the user) list of all state transitions / log lines that are -directly associated with that. - - -a particular "sub"-context may be contained within multiple parent contexts, -which suggests that having unique primary keys for a nested context is not -the right thing to do: for example, a particular try may be (mostly) contained within a worker context -(i say mostly, because some of the try happens on the submit side - which -suggests theres a worker-side try subcontext, that forms part of the main -try context: -workflow > task > try > executor-level-try > worker-side-try -workflow > executor > block > worker > worker-side-try -workflow > executor > executor-level-try - -nested contexts should be cheap: easy to create by a new binding, and in the -tooling easy to ignore layer-wise - in the sense that in the above first -example, try and worker-side-try don't form heavily distinct layers in some -analyses, perhaps. - -binding of contexts should be flexible to specify, in order that they can be -placed at convenient points, rather than requiring components to necessarily -know their own context (or even that they're part of nested contexts at all) - -labelling of contexts should be flexible: no global unique ID should be -needed outside of analysis. identity should maybe look like "In the context of -this log file (which is known to analysis code), these new subcontexts have -these labels, and they relate to certain sub-log files in these ways" - -when a context in a subcontext of two different contexts (try inside both -task and executor) then it doesn't make sense to have a single full-path -primary key globally. - -Things that need to happen for parsl: - - identify what is a context, concretely, especially where its vague like - different executors (target: local, htex, wq) - - ensure appropriate subcontext binding happens somewhere accessible - - simple analysis tool that works given monitoring.db and log files to - determine if this is worth working on - maybe python-centric as thats - what everyone is familiar with? and code-driven seems to be the main - monitoring driver right now. - -Main driving usecase: jim's gen3 work, wq+cori - -Example of a context >= than a parsl-level workflow might be: - * a single bps run - although that might be a one-to-one mapping - * a campaign of runs - identified by a human with some informal name, perhaps, or a directory - * a collection of runs described in a single monitoring database - even without any other log files at all, this is a substantial collection of information - those core parsl monitoring information. - -Example of a context that is < a parsl-level task try: - * executor-try - eg workqueue's parsl helper script - * inside-task progress: eg starting up singularity/shifter in a shell wrapper. - -Both of these seem to be potentially large users of worker time in the -DESC case, and both of these would be useful to understand. - -- inside-command-line-app progress: eg jim has been pulling out info from the app log files that might be of interest to represent. - - - -identities: -nodes might have an intrinsic ID - eg a workflow knows its own run_id -but they might also be identified by a label on an edge - eg a slurm job -does not know its own parsl-level block ID - or even that it is a -parsl block at all. - -principle: -there is no canonical source of information about anything (hence the graph -merge requirements) - eg multiple entities assert that workflow X has -task N. (eg monitoring.db, parsl.log) and neither is more authentic than the -other. - -principle: -components are necessarily aware of each other, nor bound in a strict -hierarchy - -the stack is composed (aka configured) by the workflow author/user, and so -the performance analysis stack is also composed (aka configured) -correspondingly. - -expect to be doing ad-hoc workflow and query aware remapping of contexts and -events - -expect dirty data that doesn't always align quite right: eg three different -components might all give their own "end" event with very slightly different -timing, and not always in the same order - that's part of what I mean by -"distributed". - -components not necessarily built to interoperate with each other from a -logging/tracking perspective - -this code cannot be very prescriptive about how a component records its -event information. diff --git a/docs/userguide/index.rst b/docs/userguide/index.rst index 9ce9e940c1..0d80ff0e4e 100644 --- a/docs/userguide/index.rst +++ b/docs/userguide/index.rst @@ -13,7 +13,6 @@ User guide checkpoints configuring monitoring - dnpc workflow modularizing joins diff --git a/parsl/executors/high_throughput/process_worker_pool.py b/parsl/executors/high_throughput/process_worker_pool.py index edc49e34a6..bc1a82cfba 100755 --- a/parsl/executors/high_throughput/process_worker_pool.py +++ b/parsl/executors/high_throughput/process_worker_pool.py @@ -387,7 +387,7 @@ def worker_watchdog(self, kill_event): logger.debug("Starting worker watchdog") while not kill_event.is_set(): - logger.debug("[WORKER_WATCHDOG_THREAD] Loop") + logger.debug("Loop") for worker_id, p in self.procs.items(): if not p.is_alive(): logger.info("Worker {} has died".format(worker_id)) diff --git a/parsl/version.py b/parsl/version.py index 7489db6e01..4df201d595 100644 --- a/parsl/version.py +++ b/parsl/version.py @@ -3,4 +3,4 @@ ..[alpha/beta/..] Alphas will be numbered like this -> 0.4.0a0 """ -VERSION = '1.3.0-dev+desc-2022.08.04a' +VERSION = '1.3.0-dev+desc-2022.08.04b' diff --git a/setup.py b/setup.py index e0700e037e..fe0477ec5f 100755 --- a/setup.py +++ b/setup.py @@ -21,7 +21,6 @@ 'kubernetes' : ['kubernetes'], 'oauth_ssh' : ['oauth-ssh>=0.9'], 'extreme_scale' : ['mpi4py'], - 'dnpc': ['matplotlib'], 'docs' : ['nbsphinx', 'sphinx_rtd_theme', 'ipython'], 'google_cloud' : ['google-auth', 'google-api-python-client'], 'gssapi' : ['python-gssapi'], From 57ed99add46ef9916d30c6a16aa0dd76cd52378c Mon Sep 17 00:00:00 2001 From: Ben Clifford Date: Tue, 16 Aug 2022 11:58:55 +0000 Subject: [PATCH 335/408] bump version --- parsl/version.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/parsl/version.py b/parsl/version.py index e309641b74..9f94f5071d 100644 --- a/parsl/version.py +++ b/parsl/version.py @@ -3,4 +3,4 @@ ..[alpha/beta/..] Alphas will be numbered like this -> 0.4.0a0 """ -VERSION = '1.3.0-dev+desc-2022.08.10a' +VERSION = '1.3.0-dev+desc-2022.08.16a' From abc0c126b7288dff39db065ed4954ca0b0797211 Mon Sep 17 00:00:00 2001 From: Ben Clifford Date: Tue, 16 Aug 2022 14:29:53 +0000 Subject: [PATCH 336/408] Add additional typecheck for checkpointing --- parsl/dataflow/memoization.py | 2 +- parsl/version.py | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/parsl/dataflow/memoization.py b/parsl/dataflow/memoization.py index aeef49c2db..9864198464 100644 --- a/parsl/dataflow/memoization.py +++ b/parsl/dataflow/memoization.py @@ -269,7 +269,7 @@ def update_memo(self, task: TaskRecord, r: Future[Any]) -> None: if not self.memoize or not task['memoize'] or 'hashsum' not in task: return - if 'hashsum' not in task: + if 'hashsum' not in task or task['hashsum'] is None: logger.error("Attempt to update memo for task {} with no hashsum".format(task_id)) return diff --git a/parsl/version.py b/parsl/version.py index 9f94f5071d..c5941d0e24 100644 --- a/parsl/version.py +++ b/parsl/version.py @@ -3,4 +3,4 @@ ..[alpha/beta/..] Alphas will be numbered like this -> 0.4.0a0 """ -VERSION = '1.3.0-dev+desc-2022.08.16a' +VERSION = '1.3.0-dev+desc-2022.08.16c' From c8d8e7a8a9c1494ca9b282f90a9a0106479e6179 Mon Sep 17 00:00:00 2001 From: Ben Clifford Date: Wed, 24 Aug 2022 20:27:35 +0000 Subject: [PATCH 337/408] fix circular import in typechecking change --- parsl/dataflow/strategy.py | 6 +++++- parsl/version.py | 2 +- 2 files changed, 6 insertions(+), 2 deletions(-) diff --git a/parsl/dataflow/strategy.py b/parsl/dataflow/strategy.py index 076770974f..863788b75f 100644 --- a/parsl/dataflow/strategy.py +++ b/parsl/dataflow/strategy.py @@ -1,13 +1,17 @@ +from __future__ import annotations import logging import time import math from typing import List -from parsl.dataflow.task_status_poller import PollItem from parsl.executors import HighThroughputExecutor from parsl.providers.provider_base import JobState from parsl.process_loggers import wrap_with_logs +from typing import TYPE_CHECKING + +if TYPE_CHECKING: + from parsl.dataflow.task_status_poller import PollItem logger = logging.getLogger(__name__) diff --git a/parsl/version.py b/parsl/version.py index 15cacaa10f..40165f8d3c 100644 --- a/parsl/version.py +++ b/parsl/version.py @@ -3,4 +3,4 @@ ..[alpha/beta/..] Alphas will be numbered like this -> 0.4.0a0 """ -VERSION = '1.3.0-dev+desc-2022.08.19a' +VERSION = '1.3.0-dev+desc-2022.08.24a' From 090c9571c2fd12315752d0407d00d9c4abdc64bb Mon Sep 17 00:00:00 2001 From: Ben Clifford Date: Tue, 6 Sep 2022 14:21:37 +0000 Subject: [PATCH 338/408] Tidy zmq pipe exponential backoff in prep for master merge --- parsl/executors/high_throughput/zmq_pipes.py | 3 +-- parsl/version.py | 2 +- 2 files changed, 2 insertions(+), 3 deletions(-) diff --git a/parsl/executors/high_throughput/zmq_pipes.py b/parsl/executors/high_throughput/zmq_pipes.py index 5b19087faf..2849bfd48d 100644 --- a/parsl/executors/high_throughput/zmq_pipes.py +++ b/parsl/executors/high_throughput/zmq_pipes.py @@ -123,7 +123,7 @@ def put(self, message): This issue can be magnified if each the serialized buffer itself is larger. """ logger.debug("Putting task to outgoing_q") - timeout_ms = 0 + timeout_ms = 1 with self._lock: while True: socks = dict(self.poller.poll(timeout=timeout_ms)) @@ -134,7 +134,6 @@ def put(self, message): else: timeout_ms = max(timeout_ms, 1) timeout_ms *= 2 - timeout_ms = min(10000, timeout_ms) # TODO: arbitrary hard coded time bad logger.debug("Not sending due to non-ready zmq pipe, timeout: {} ms".format(timeout_ms)) if timeout_ms == 10000: raise RuntimeError("BENC: hit big timeout for pipe put - failing rather than trying forever") diff --git a/parsl/version.py b/parsl/version.py index 740d560e34..a9f58d8757 100644 --- a/parsl/version.py +++ b/parsl/version.py @@ -3,4 +3,4 @@ ..[alpha/beta/..] Alphas will be numbered like this -> 0.4.0a0 """ -VERSION = '1.3.0-dev+desc-2022.09.06a' +VERSION = '1.3.0-dev+desc-2022.09.06b' From 4726afb13f2ab5ce044e877afbb4ebecce18b7eb Mon Sep 17 00:00:00 2001 From: Ben Clifford Date: Wed, 7 Sep 2022 10:54:46 +0000 Subject: [PATCH 339/408] Add more debugging around command channel potential hang --- parsl/dataflow/strategy.py | 2 ++ parsl/executors/high_throughput/interchange.py | 3 ++- parsl/executors/high_throughput/zmq_pipes.py | 5 +++++ parsl/version.py | 2 +- 4 files changed, 10 insertions(+), 2 deletions(-) diff --git a/parsl/dataflow/strategy.py b/parsl/dataflow/strategy.py index 9d7b839959..54d9407dc3 100644 --- a/parsl/dataflow/strategy.py +++ b/parsl/dataflow/strategy.py @@ -174,7 +174,9 @@ def _general_strategy(self, status_list, tasks, *, strategy_type): logger.debug(f"Strategizing for executor {label}") # Tasks that are either pending completion + logger.debug("getting outstanding (which looks like an attribute reference but is actually a network operation") active_tasks = executor.outstanding + logger.debug(f"got outstanding {active_tasks}") status = exec_status.status diff --git a/parsl/executors/high_throughput/interchange.py b/parsl/executors/high_throughput/interchange.py index 36d9c6eb1f..11ec1699c5 100644 --- a/parsl/executors/high_throughput/interchange.py +++ b/parsl/executors/high_throughput/interchange.py @@ -119,7 +119,7 @@ def __init__(self, Parsl log directory paths. Logs and temp files go here. Default: '.' logging_level : int - Logging level as defined in the logging module. Default: logging.INFO (20) + Logging level as defined in the logging module. Default: logging.INFO poll_period : int The main thread polling period, in milliseconds. Default: 10ms @@ -276,6 +276,7 @@ def _command_server(self): while True: try: + logger.debug("Waiting for command request") command_req = self.command_channel.recv_pyobj() logger.debug("Received command request: {}".format(command_req)) if command_req == "OUTSTANDING_C": diff --git a/parsl/executors/high_throughput/zmq_pipes.py b/parsl/executors/high_throughput/zmq_pipes.py index 2849bfd48d..7e031cf0b2 100644 --- a/parsl/executors/high_throughput/zmq_pipes.py +++ b/parsl/executors/high_throughput/zmq_pipes.py @@ -62,11 +62,16 @@ def run(self, message, max_retries=3): # otherwise, _my_thread and current_thread match, which is ok and no need to log reply = '__PARSL_ZMQ_PIPES_MAGIC__' + logger.debug("acquiring command lock") with self._lock: + logger.debug("acquired command lock") for i in range(max_retries): + logger.debug(f"try {i} for command {message}") try: self.zmq_socket.send_pyobj(message, copy=True) + logger.debug(f"waiting for response from command {message}") reply = self.zmq_socket.recv_pyobj() + logger.debug(f"got response from command {message}") except zmq.ZMQError: logger.exception("Potential ZMQ REQ-REP deadlock caught") logger.info("Trying to reestablish context after ZMQError") diff --git a/parsl/version.py b/parsl/version.py index cf30aed1cb..c4855262d3 100644 --- a/parsl/version.py +++ b/parsl/version.py @@ -3,4 +3,4 @@ ..[alpha/beta/..] Alphas will be numbered like this -> 0.4.0a0 """ -VERSION = '1.3.0-dev+desc-2022.09.06c' +VERSION = '1.3.0-dev+desc-2022.09.07b' From 4fd936ae3972b89c07f555b1b750c302464e1347 Mon Sep 17 00:00:00 2001 From: Ben Clifford Date: Fri, 23 Sep 2022 15:31:00 +0000 Subject: [PATCH 340/408] changes to do with launch rate limit of parsl monitoring wrapper vs serialization on my laptop, takes launch rate from 150 task launches/sec to around 1200/sec --- parsl/dataflow/dflow.py | 16 +- parsl/monitoring/monitoring.py | 435 +-------------------------------- parsl/monitoring/radios.py | 183 ++++++++++++++ parsl/monitoring/remote.py | 302 +++++++++++++++++++++++ parsl/serialize/facade.py | 3 + parsl/version.py | 2 +- 6 files changed, 507 insertions(+), 434 deletions(-) create mode 100644 parsl/monitoring/radios.py create mode 100644 parsl/monitoring/remote.py diff --git a/parsl/dataflow/dflow.py b/parsl/dataflow/dflow.py index 859d876c0e..61b2b5b2b0 100644 --- a/parsl/dataflow/dflow.py +++ b/parsl/dataflow/dflow.py @@ -685,14 +685,14 @@ def launch_task(self, task_record: TaskRecord) -> Future: if self.monitoring is not None and self.monitoring.resource_monitoring_enabled: wrapper_logging_level = logging.DEBUG if self.monitoring.monitoring_debug else logging.INFO - executable = self.monitoring.monitor_wrapper(executable, try_id, task_id, - self.monitoring.monitoring_hub_url, - self.run_id, - wrapper_logging_level, - self.monitoring.resource_monitoring_interval, - executor.radio_mode, - executor.monitor_resources(), - self.run_dir) + (executable, args, kwargs) = self.monitoring.monitor_wrapper(executable, args, kwargs, try_id, task_id, + self.monitoring.monitoring_hub_url, + self.run_id, + wrapper_logging_level, + self.monitoring.resource_monitoring_interval, + executor.radio_mode, + executor.monitor_resources(), + self.run_dir) with self.submitter_lock: exec_fu = executor.submit(executable, task_record['resource_specification'], *args, **kwargs) diff --git a/parsl/monitoring/monitoring.py b/parsl/monitoring/monitoring.py index 96e597fff7..7c6240ded9 100644 --- a/parsl/monitoring/monitoring.py +++ b/parsl/monitoring/monitoring.py @@ -4,14 +4,14 @@ import pickle import logging import typeguard -import datetime import zmq -from functools import wraps import queue -from abc import ABCMeta, abstractmethod + +import parsl.monitoring.remote + from parsl.multiprocessing import ForkProcess, SizedQueue -from multiprocessing import Event, Process, Queue +from multiprocessing import Process, Queue from parsl.utils import RepresentationMixin from parsl.process_loggers import wrap_with_logs from parsl.utils import setproctitle @@ -22,8 +22,6 @@ from parsl.monitoring.types import AddressedMonitoringMessage, TaggedMonitoringMessage from typing import cast, Any, Callable, Dict, List, Optional, Union -from parsl.serialize import serialize - _db_manager_excepts: Optional[Exception] from typing import Optional, Tuple @@ -73,174 +71,6 @@ def start_file_logger(filename: str, name: str = 'monitoring', level: int = logg return logger -class MonitoringRadio(metaclass=ABCMeta): - @abstractmethod - def send(self, message: object) -> None: - pass - - -class FilesystemRadio(MonitoringRadio): - """A MonitoringRadio that sends messages over a shared filesystem. - - The messsage directory structure is based on maildir, - https://en.wikipedia.org/wiki/Maildir - - The writer creates a message in tmp/ and then when it is fully - written, moves it atomically into new/ - - The reader ignores tmp/ and only reads and deletes messages from - new/ - - This avoids a race condition of reading partially written messages. - - This radio is likely to give higher shared filesystem load compared to - the UDPRadio, but should be much more reliable. - """ - - def __init__(self, *, monitoring_url: str, source_id: int, timeout: int = 10, run_dir: str): - logger.info("filesystem based monitoring channel initializing") - self.source_id = source_id - self.id_counter = 0 - self.radio_uid = f"host-{socket.gethostname()}-pid-{os.getpid()}-radio-{id(self)}" - self.base_path = f"{run_dir}/monitor-fs-radio/" - self.tmp_path = f"{self.base_path}/tmp" - self.new_path = f"{self.base_path}/new" - - os.makedirs(self.tmp_path, exist_ok=True) - os.makedirs(self.new_path, exist_ok=True) - - def send(self, message: object) -> None: - logger.info("Sending a monitoring message via filesystem") - - # this should be randomised by things like worker ID, process ID, whatever - # because there will in general be many FilesystemRadio objects sharing the - # same space (even from the same process). id(self) used here will - # disambiguate in one process at one instant, but not between - # other things: eg different hosts, different processes, same process different non-overlapping instantiations - unique_id = f"msg-{self.radio_uid}-{self.id_counter}" - - self.id_counter = self.id_counter + 1 - - tmp_filename = f"{self.tmp_path}/{unique_id}" - new_filename = f"{self.new_path}/{unique_id}" - buffer = (message, "NA") - - # this will write the message out then atomically - # move it into new/, so that a partially written - # file will never be observed in new/ - with open(tmp_filename, "wb") as f: - f.write(serialize(buffer)) - os.rename(tmp_filename, new_filename) - - -class HTEXRadio(MonitoringRadio): - - def __init__(self, monitoring_url: str, source_id: int, timeout: int = 10): - """ - Parameters - ---------- - - monitoring_url : str - URL of the form ://: - source_id : str - String identifier of the source - timeout : int - timeout, default=10s - """ - self.source_id = source_id - logger.info("htex-based monitoring channel initialising") - - def send(self, message: object) -> None: - """ Sends a message to the UDP receiver - - Parameter - --------- - - message: object - Arbitrary pickle-able object that is to be sent - - Returns: - None - """ - - import parsl.executors.high_throughput.monitoring_info - - result_queue = parsl.executors.high_throughput.monitoring_info.result_queue - - # this message needs to go in the result queue tagged so that it is treated - # i) as a monitoring message by the interchange, and then further more treated - # as a RESOURCE_INFO message when received by monitoring (rather than a NODE_INFO - # which is the implicit default for messages from the interchange) - - # for the interchange, the outer wrapper, this needs to be a dict: - - interchange_msg = { - 'type': 'monitoring', - 'payload': message - } - - if result_queue: - result_queue.put(pickle.dumps(interchange_msg)) - else: - logger.error("result_queue is uninitialized - cannot put monitoring message") - - return - - -class UDPRadio(MonitoringRadio): - - def __init__(self, monitoring_url: str, source_id: int, timeout: int = 10): - """ - Parameters - ---------- - - monitoring_url : str - URL of the form ://: - source_id : str - String identifier of the source - timeout : int - timeout, default=10s - """ - self.monitoring_url = monitoring_url - self.sock_timeout = timeout - self.source_id = source_id - try: - self.scheme, self.ip, port = (x.strip('/') for x in monitoring_url.split(':')) - self.port = int(port) - except Exception: - raise Exception("Failed to parse monitoring url: {}".format(monitoring_url)) - - self.sock = socket.socket(socket.AF_INET, - socket.SOCK_DGRAM, - socket.IPPROTO_UDP) # UDP - self.sock.settimeout(self.sock_timeout) - - def send(self, message: object) -> None: - """ Sends a message to the UDP receiver - - Parameter - --------- - - message: object - Arbitrary pickle-able object that is to be sent - - Returns: - None - """ - try: - buffer = pickle.dumps(message) - except Exception: - logging.exception("Exception during pickling", exc_info=True) - return - - try: - self.sock.sendto(buffer, (self.ip, self.port)) - except socket.timeout: - logging.error("Could not send message within timeout limit") - return - return - - @typeguard.typechecked class MonitoringHub(RepresentationMixin): def __init__(self, @@ -456,6 +286,8 @@ def close(self) -> None: @staticmethod def monitor_wrapper(f: Any, + args: List, + kwargs: Dict, try_id: int, task_id: int, monitoring_hub_url: str, @@ -464,66 +296,10 @@ def monitor_wrapper(f: Any, sleep_dur: float, radio_mode: str, monitor_resources: bool, - run_dir: str) -> Callable: - """Wrap the Parsl app with a function that will call the monitor function and point it at the correct pid when the task begins. - """ - @wraps(f) - def wrapped(*args: List[Any], **kwargs: Dict[str, Any]) -> Any: - terminate_event = Event() - # Send first message to monitoring router - send_first_message(try_id, - task_id, - monitoring_hub_url, - run_id, - radio_mode, - run_dir) - - p: Optional[Process] - if monitor_resources: - # create the monitor process and start - pp = ForkProcess(target=monitor, - args=(os.getpid(), - try_id, - task_id, - monitoring_hub_url, - run_id, - radio_mode, - logging_level, - sleep_dur, - run_dir, - terminate_event), - name="Monitor-Wrapper-{}".format(task_id)) - pp.start() - p = pp - # TODO: awkwardness because ForkProcess is not directly a constructor - # and type-checking is expecting p to be optional and cannot - # narrow down the type of p in this block. - - else: - p = None - - try: - return f(*args, **kwargs) - finally: - # There's a chance of zombification if the workers are killed by some signals (?) - if p: - terminate_event.set() - p.join(30) # 30 second delay for this -- this timeout will be hit in the case of an unusually long end-of-loop - if p.exitcode is None: - logger.warn("Event-based termination of monitoring helper took too long. Using process-based termination.") - p.terminate() - # DANGER: this can corrupt shared queues according to docs. - # So, better that the above termination event worked. - # This is why this log message is a warning - p.join() - - send_last_message(try_id, - task_id, - monitoring_hub_url, - run_id, - radio_mode, run_dir) - - return wrapped + run_dir: str) -> Tuple[Callable, List, Dict]: + return parsl.monitoring.remote.monitor_wrapper(f, args, kwargs, try_id, task_id, monitoring_hub_url, + run_id, logging_level, sleep_dur, radio_mode, + monitor_resources, run_dir) @wrap_with_logs @@ -740,194 +516,3 @@ def router_starter(comm_q: "queue.Queue[Union[Tuple[int, int], str]]", exception_q.put(('Hub', str(e))) router.logger.info("End of router_starter") - - -@wrap_with_logs -def send_first_message(try_id: int, - task_id: int, - monitoring_hub_url: str, - run_id: str, radio_mode: str, run_dir: str) -> None: - send_first_last_message(try_id, task_id, monitoring_hub_url, run_id, - radio_mode, run_dir, False) - - -@wrap_with_logs -def send_last_message(try_id: int, - task_id: int, - monitoring_hub_url: str, - run_id: str, radio_mode: str, run_dir: str) -> None: - send_first_last_message(try_id, task_id, monitoring_hub_url, run_id, - radio_mode, run_dir, True) - - -def send_first_last_message(try_id: int, - task_id: int, - monitoring_hub_url: str, - run_id: str, radio_mode: str, run_dir: str, - is_last: bool) -> None: - import platform - import os - - radio: MonitoringRadio - if radio_mode == "udp": - radio = UDPRadio(monitoring_hub_url, - source_id=task_id) - elif radio_mode == "htex": - radio = HTEXRadio(monitoring_hub_url, - source_id=task_id) - elif radio_mode == "filesystem": - radio = FilesystemRadio(monitoring_url=monitoring_hub_url, - source_id=task_id, run_dir=run_dir) - else: - raise RuntimeError(f"Unknown radio mode: {radio_mode}") - - msg = (MessageType.RESOURCE_INFO, - {'run_id': run_id, - 'try_id': try_id, - 'task_id': task_id, - 'hostname': platform.node(), - 'block_id': os.environ.get('PARSL_WORKER_BLOCK_ID'), - 'first_msg': not is_last, - 'last_msg': is_last, - 'timestamp': datetime.datetime.now() - }) - radio.send(msg) - return - - -@wrap_with_logs -def monitor(pid: int, - try_id: int, - task_id: int, - monitoring_hub_url: str, - run_id: str, - radio_mode: str, - logging_level: int, - sleep_dur: float, - run_dir: str, - # removed all defaults because unused and there's no meaningful default for terminate_event. - # these probably should become named arguments, with a *, and named at invocation. - terminate_event: Any) -> None: # cannot be Event because of multiprocessing type weirdness. - """Monitors the Parsl task's resources by pointing psutil to the task's pid and watching it and its children. - - This process makes calls to logging, but deliberately does not attach - any log handlers. Previously, there was a handler which logged to a - file in /tmp, but this was usually not useful or even accessible. - In some circumstances, it might be useful to hack in a handler so the - logger calls remain in place. - """ - import logging - import platform - import psutil - - radio: MonitoringRadio - if radio_mode == "udp": - radio = UDPRadio(monitoring_hub_url, - source_id=task_id) - elif radio_mode == "htex": - radio = HTEXRadio(monitoring_hub_url, - source_id=task_id) - elif radio_mode == "filesystem": - radio = FilesystemRadio(monitoring_url=monitoring_hub_url, - source_id=task_id, run_dir=run_dir) - else: - raise RuntimeError(f"Unknown radio mode: {radio_mode}") - - logging.debug("start of monitor") - - # these values are simple to log. Other information is available in special formats such as memory below. - simple = ["cpu_num", 'create_time', 'cwd', 'exe', 'memory_percent', 'nice', 'name', 'num_threads', 'pid', 'ppid', 'status', 'username'] - # values that can be summed up to see total resources used by task process and its children - summable_values = ['memory_percent', 'num_threads'] - - pm = psutil.Process(pid) - - children_user_time = {} # type: Dict[int, float] - children_system_time = {} # type: Dict[int, float] - - def accumulate_and_prepare() -> Dict[str, Any]: - d = {"psutil_process_" + str(k): v for k, v in pm.as_dict().items() if k in simple} - d["run_id"] = run_id - d["task_id"] = task_id - d["try_id"] = try_id - d['resource_monitoring_interval'] = sleep_dur - d['hostname'] = platform.node() - d['first_msg'] = False - d['last_msg'] = False - d['timestamp'] = datetime.datetime.now() - - logging.debug("getting children") - children = pm.children(recursive=True) - logging.debug("got children") - - d["psutil_cpu_count"] = psutil.cpu_count() - d['psutil_process_memory_virtual'] = pm.memory_info().vms - d['psutil_process_memory_resident'] = pm.memory_info().rss - d['psutil_process_time_user'] = pm.cpu_times().user - d['psutil_process_time_system'] = pm.cpu_times().system - d['psutil_process_children_count'] = len(children) - try: - d['psutil_process_disk_write'] = pm.io_counters().write_chars - d['psutil_process_disk_read'] = pm.io_counters().read_chars - except Exception: - # occasionally pid temp files that hold this information are unvailable to be read so set to zero - logging.exception("Exception reading IO counters for main process. Recorded IO usage may be incomplete", exc_info=True) - d['psutil_process_disk_write'] = 0 - d['psutil_process_disk_read'] = 0 - for child in children: - for k, v in child.as_dict(attrs=summable_values).items(): - d['psutil_process_' + str(k)] += v - child_user_time = child.cpu_times().user - child_system_time = child.cpu_times().system - children_user_time[child.pid] = child_user_time - children_system_time[child.pid] = child_system_time - d['psutil_process_memory_virtual'] += child.memory_info().vms - d['psutil_process_memory_resident'] += child.memory_info().rss - try: - d['psutil_process_disk_write'] += child.io_counters().write_chars - d['psutil_process_disk_read'] += child.io_counters().read_chars - except Exception: - # occassionally pid temp files that hold this information are unvailable to be read so add zero - logging.exception("Exception reading IO counters for child {k}. Recorded IO usage may be incomplete".format(k=k), exc_info=True) - d['psutil_process_disk_write'] += 0 - d['psutil_process_disk_read'] += 0 - total_children_user_time = 0.0 - for child_pid in children_user_time: - total_children_user_time += children_user_time[child_pid] - total_children_system_time = 0.0 - for child_pid in children_system_time: - total_children_system_time += children_system_time[child_pid] - d['psutil_process_time_user'] += total_children_user_time - d['psutil_process_time_system'] += total_children_system_time - logging.debug("sending message") - return d - - next_send = time.time() - accumulate_dur = 5.0 # TODO: make configurable? - - while not terminate_event.is_set(): - logging.debug("start of monitoring loop") - try: - d = accumulate_and_prepare() - if time.time() >= next_send: - logging.debug("Sending intermediate resource message") - radio.send((MessageType.RESOURCE_INFO, d)) - next_send += sleep_dur - except Exception: - logging.exception("Exception getting the resource usage. Not sending usage to Hub", exc_info=True) - logging.debug("sleeping") - - # wait either until approx next send time, or the accumulation period - # so the accumulation period will not be completely precise. - # but before this, the sleep period was also not completely precise. - # with a minimum floor of 0 to not upset wait - - terminate_event.wait(max(0, min(next_send - time.time(), accumulate_dur))) - - logging.debug("Sending final resource message") - try: - d = accumulate_and_prepare() - radio.send((MessageType.RESOURCE_INFO, d)) - except Exception: - logging.exception("Exception getting the resource usage. Not sending final usage to Hub", exc_info=True) - logging.debug("End of monitoring helper") diff --git a/parsl/monitoring/radios.py b/parsl/monitoring/radios.py new file mode 100644 index 0000000000..a70f6cead2 --- /dev/null +++ b/parsl/monitoring/radios.py @@ -0,0 +1,183 @@ +import os +import socket +import pickle +import logging + +from abc import ABCMeta, abstractmethod + +from typing import Optional + +from parsl.serialize import serialize + +_db_manager_excepts: Optional[Exception] + + +logger = logging.getLogger(__name__) + + +class MonitoringRadio(metaclass=ABCMeta): + @abstractmethod + def send(self, message: object) -> None: + pass + + +class FilesystemRadio(MonitoringRadio): + """A MonitoringRadio that sends messages over a shared filesystem. + + The messsage directory structure is based on maildir, + https://en.wikipedia.org/wiki/Maildir + + The writer creates a message in tmp/ and then when it is fully + written, moves it atomically into new/ + + The reader ignores tmp/ and only reads and deletes messages from + new/ + + This avoids a race condition of reading partially written messages. + + This radio is likely to give higher shared filesystem load compared to + the UDPRadio, but should be much more reliable. + """ + + def __init__(self, *, monitoring_url: str, source_id: int, timeout: int = 10, run_dir: str): + logger.info("filesystem based monitoring channel initializing") + self.source_id = source_id + self.id_counter = 0 + self.radio_uid = f"host-{socket.gethostname()}-pid-{os.getpid()}-radio-{id(self)}" + self.base_path = f"{run_dir}/monitor-fs-radio/" + self.tmp_path = f"{self.base_path}/tmp" + self.new_path = f"{self.base_path}/new" + + os.makedirs(self.tmp_path, exist_ok=True) + os.makedirs(self.new_path, exist_ok=True) + + def send(self, message: object) -> None: + logger.info("Sending a monitoring message via filesystem") + + # this should be randomised by things like worker ID, process ID, whatever + # because there will in general be many FilesystemRadio objects sharing the + # same space (even from the same process). id(self) used here will + # disambiguate in one process at one instant, but not between + # other things: eg different hosts, different processes, same process different non-overlapping instantiations + unique_id = f"msg-{self.radio_uid}-{self.id_counter}" + + self.id_counter = self.id_counter + 1 + + tmp_filename = f"{self.tmp_path}/{unique_id}" + new_filename = f"{self.new_path}/{unique_id}" + buffer = (message, "NA") + + # this will write the message out then atomically + # move it into new/, so that a partially written + # file will never be observed in new/ + with open(tmp_filename, "wb") as f: + f.write(serialize(buffer)) + os.rename(tmp_filename, new_filename) + + +class HTEXRadio(MonitoringRadio): + + def __init__(self, monitoring_url: str, source_id: int, timeout: int = 10): + """ + Parameters + ---------- + + monitoring_url : str + URL of the form ://: + source_id : str + String identifier of the source + timeout : int + timeout, default=10s + """ + self.source_id = source_id + logger.info("htex-based monitoring channel initialising") + + def send(self, message: object) -> None: + """ Sends a message to the UDP receiver + + Parameter + --------- + + message: object + Arbitrary pickle-able object that is to be sent + + Returns: + None + """ + + import parsl.executors.high_throughput.monitoring_info + + result_queue = parsl.executors.high_throughput.monitoring_info.result_queue + + # this message needs to go in the result queue tagged so that it is treated + # i) as a monitoring message by the interchange, and then further more treated + # as a RESOURCE_INFO message when received by monitoring (rather than a NODE_INFO + # which is the implicit default for messages from the interchange) + + # for the interchange, the outer wrapper, this needs to be a dict: + + interchange_msg = { + 'type': 'monitoring', + 'payload': message + } + + if result_queue: + result_queue.put(pickle.dumps(interchange_msg)) + else: + logger.error("result_queue is uninitialized - cannot put monitoring message") + + return + + +class UDPRadio(MonitoringRadio): + + def __init__(self, monitoring_url: str, source_id: int, timeout: int = 10): + """ + Parameters + ---------- + + monitoring_url : str + URL of the form ://: + source_id : str + String identifier of the source + timeout : int + timeout, default=10s + """ + self.monitoring_url = monitoring_url + self.sock_timeout = timeout + self.source_id = source_id + try: + self.scheme, self.ip, port = (x.strip('/') for x in monitoring_url.split(':')) + self.port = int(port) + except Exception: + raise Exception("Failed to parse monitoring url: {}".format(monitoring_url)) + + self.sock = socket.socket(socket.AF_INET, + socket.SOCK_DGRAM, + socket.IPPROTO_UDP) # UDP + self.sock.settimeout(self.sock_timeout) + + def send(self, message: object) -> None: + """ Sends a message to the UDP receiver + + Parameter + --------- + + message: object + Arbitrary pickle-able object that is to be sent + + Returns: + None + """ + try: + buffer = pickle.dumps(message) + except Exception: + logging.exception("Exception during pickling", exc_info=True) + return + + try: + self.sock.sendto(buffer, (self.ip, self.port)) + except socket.timeout: + logging.error("Could not send message within timeout limit") + return + return diff --git a/parsl/monitoring/remote.py b/parsl/monitoring/remote.py new file mode 100644 index 0000000000..7066bdd1ff --- /dev/null +++ b/parsl/monitoring/remote.py @@ -0,0 +1,302 @@ +import os +import time +import logging +import datetime +from functools import wraps + +from parsl.multiprocessing import ForkProcess +from multiprocessing import Event, Process +from parsl.process_loggers import wrap_with_logs + +from parsl.monitoring.message_type import MessageType +from parsl.monitoring.radios import MonitoringRadio, UDPRadio, HTEXRadio, FilesystemRadio +from typing import Any, Callable, Dict, List, Optional, Tuple + +logger = logging.getLogger(__name__) + +monitoring_wrapper_cache: Dict +monitoring_wrapper_cache = {} + + +def monitor_wrapper(f: Any, # per app + args: List, # per invocation + kwargs: Dict, # per invocation + x_try_id: int, # per invocation + x_task_id: int, # per invocation + monitoring_hub_url: str, # per workflow + run_id: str, # per workflow + logging_level: int, # per workflow + sleep_dur: float, # per workflow + radio_mode: str, # per executor + monitor_resources: bool, # per workflow + run_dir: str) -> Tuple[Callable, List, Dict]: + """Wrap the Parsl app with a function that will call the monitor function and point it at the correct pid when the task begins. + """ + + # this makes assumptions that when subsequently executed with the same + # cache key, then the relevant parameters will not have changed from the + # first invocation with that cache key (otherwise, the resulting cached + # closure will be incorrectly cached) + cache_key = (run_id, f, radio_mode) + + if cache_key in monitoring_wrapper_cache: + wrapped = monitoring_wrapper_cache[cache_key] + + else: + + @wraps(f) + def wrapped(*args: List[Any], **kwargs: Dict[str, Any]) -> Any: + task_id = kwargs.pop('_parsl_monitoring_task_id') + try_id = kwargs.pop('_parsl_monitoring_try_id') + terminate_event = Event() + # Send first message to monitoring router + send_first_message(try_id, + task_id, + monitoring_hub_url, + run_id, + radio_mode, + run_dir) + + p: Optional[Process] + if monitor_resources: + # create the monitor process and start + pp = ForkProcess(target=monitor, + args=(os.getpid(), + try_id, + task_id, + monitoring_hub_url, + run_id, + radio_mode, + logging_level, + sleep_dur, + run_dir, + terminate_event), + name="Monitor-Wrapper-{}".format(task_id)) + pp.start() + p = pp + # TODO: awkwardness because ForkProcess is not directly a constructor + # and type-checking is expecting p to be optional and cannot + # narrow down the type of p in this block. + + else: + p = None + + try: + return f(*args, **kwargs) + finally: + # There's a chance of zombification if the workers are killed by some signals (?) + if p: + terminate_event.set() + p.join(30) # 30 second delay for this -- this timeout will be hit in the case of an unusually long end-of-loop + if p.exitcode is None: + logger.warn("Event-based termination of monitoring helper took too long. Using process-based termination.") + p.terminate() + # DANGER: this can corrupt shared queues according to docs. + # So, better that the above termination event worked. + # This is why this log message is a warning + p.join() + + send_last_message(try_id, + task_id, + monitoring_hub_url, + run_id, + radio_mode, run_dir) + + monitoring_wrapper_cache[cache_key] = wrapped + + new_kwargs = kwargs.copy() + new_kwargs['_parsl_monitoring_task_id'] = x_task_id + new_kwargs['_parsl_monitoring_try_id'] = x_try_id + + return (wrapped, args, new_kwargs) + + +@wrap_with_logs +def send_first_message(try_id: int, + task_id: int, + monitoring_hub_url: str, + run_id: str, radio_mode: str, run_dir: str) -> None: + send_first_last_message(try_id, task_id, monitoring_hub_url, run_id, + radio_mode, run_dir, False) + + +@wrap_with_logs +def send_last_message(try_id: int, + task_id: int, + monitoring_hub_url: str, + run_id: str, radio_mode: str, run_dir: str) -> None: + send_first_last_message(try_id, task_id, monitoring_hub_url, run_id, + radio_mode, run_dir, True) + + +def send_first_last_message(try_id: int, + task_id: int, + monitoring_hub_url: str, + run_id: str, radio_mode: str, run_dir: str, + is_last: bool) -> None: + import platform + import os + + radio: MonitoringRadio + if radio_mode == "udp": + radio = UDPRadio(monitoring_hub_url, + source_id=task_id) + elif radio_mode == "htex": + radio = HTEXRadio(monitoring_hub_url, + source_id=task_id) + elif radio_mode == "filesystem": + radio = FilesystemRadio(monitoring_url=monitoring_hub_url, + source_id=task_id, run_dir=run_dir) + else: + raise RuntimeError(f"Unknown radio mode: {radio_mode}") + + msg = (MessageType.RESOURCE_INFO, + {'run_id': run_id, + 'try_id': try_id, + 'task_id': task_id, + 'hostname': platform.node(), + 'block_id': os.environ.get('PARSL_WORKER_BLOCK_ID'), + 'first_msg': not is_last, + 'last_msg': is_last, + 'timestamp': datetime.datetime.now() + }) + radio.send(msg) + return + + +@wrap_with_logs +def monitor(pid: int, + try_id: int, + task_id: int, + monitoring_hub_url: str, + run_id: str, + radio_mode: str, + logging_level: int, + sleep_dur: float, + run_dir: str, + # removed all defaults because unused and there's no meaningful default for terminate_event. + # these probably should become named arguments, with a *, and named at invocation. + terminate_event: Any) -> None: # cannot be Event because of multiprocessing type weirdness. + """Monitors the Parsl task's resources by pointing psutil to the task's pid and watching it and its children. + + This process makes calls to logging, but deliberately does not attach + any log handlers. Previously, there was a handler which logged to a + file in /tmp, but this was usually not useful or even accessible. + In some circumstances, it might be useful to hack in a handler so the + logger calls remain in place. + """ + import logging + import platform + import psutil + + radio: MonitoringRadio + if radio_mode == "udp": + radio = UDPRadio(monitoring_hub_url, + source_id=task_id) + elif radio_mode == "htex": + radio = HTEXRadio(monitoring_hub_url, + source_id=task_id) + elif radio_mode == "filesystem": + radio = FilesystemRadio(monitoring_url=monitoring_hub_url, + source_id=task_id, run_dir=run_dir) + else: + raise RuntimeError(f"Unknown radio mode: {radio_mode}") + + logging.debug("start of monitor") + + # these values are simple to log. Other information is available in special formats such as memory below. + simple = ["cpu_num", 'create_time', 'cwd', 'exe', 'memory_percent', 'nice', 'name', 'num_threads', 'pid', 'ppid', 'status', 'username'] + # values that can be summed up to see total resources used by task process and its children + summable_values = ['memory_percent', 'num_threads'] + + pm = psutil.Process(pid) + + children_user_time = {} # type: Dict[int, float] + children_system_time = {} # type: Dict[int, float] + + def accumulate_and_prepare() -> Dict[str, Any]: + d = {"psutil_process_" + str(k): v for k, v in pm.as_dict().items() if k in simple} + d["run_id"] = run_id + d["task_id"] = task_id + d["try_id"] = try_id + d['resource_monitoring_interval'] = sleep_dur + d['hostname'] = platform.node() + d['first_msg'] = False + d['last_msg'] = False + d['timestamp'] = datetime.datetime.now() + + logging.debug("getting children") + children = pm.children(recursive=True) + logging.debug("got children") + + d["psutil_cpu_count"] = psutil.cpu_count() + d['psutil_process_memory_virtual'] = pm.memory_info().vms + d['psutil_process_memory_resident'] = pm.memory_info().rss + d['psutil_process_time_user'] = pm.cpu_times().user + d['psutil_process_time_system'] = pm.cpu_times().system + d['psutil_process_children_count'] = len(children) + try: + d['psutil_process_disk_write'] = pm.io_counters().write_chars + d['psutil_process_disk_read'] = pm.io_counters().read_chars + except Exception: + # occasionally pid temp files that hold this information are unvailable to be read so set to zero + logging.exception("Exception reading IO counters for main process. Recorded IO usage may be incomplete", exc_info=True) + d['psutil_process_disk_write'] = 0 + d['psutil_process_disk_read'] = 0 + for child in children: + for k, v in child.as_dict(attrs=summable_values).items(): + d['psutil_process_' + str(k)] += v + child_user_time = child.cpu_times().user + child_system_time = child.cpu_times().system + children_user_time[child.pid] = child_user_time + children_system_time[child.pid] = child_system_time + d['psutil_process_memory_virtual'] += child.memory_info().vms + d['psutil_process_memory_resident'] += child.memory_info().rss + try: + d['psutil_process_disk_write'] += child.io_counters().write_chars + d['psutil_process_disk_read'] += child.io_counters().read_chars + except Exception: + # occassionally pid temp files that hold this information are unvailable to be read so add zero + logging.exception("Exception reading IO counters for child {k}. Recorded IO usage may be incomplete".format(k=k), exc_info=True) + d['psutil_process_disk_write'] += 0 + d['psutil_process_disk_read'] += 0 + total_children_user_time = 0.0 + for child_pid in children_user_time: + total_children_user_time += children_user_time[child_pid] + total_children_system_time = 0.0 + for child_pid in children_system_time: + total_children_system_time += children_system_time[child_pid] + d['psutil_process_time_user'] += total_children_user_time + d['psutil_process_time_system'] += total_children_system_time + logging.debug("sending message") + return d + + next_send = time.time() + accumulate_dur = 5.0 # TODO: make configurable? + + while not terminate_event.is_set(): + logging.debug("start of monitoring loop") + try: + d = accumulate_and_prepare() + if time.time() >= next_send: + logging.debug("Sending intermediate resource message") + radio.send((MessageType.RESOURCE_INFO, d)) + next_send += sleep_dur + except Exception: + logging.exception("Exception getting the resource usage. Not sending usage to Hub", exc_info=True) + logging.debug("sleeping") + + # wait either until approx next send time, or the accumulation period + # so the accumulation period will not be completely precise. + # but before this, the sleep period was also not completely precise. + # with a minimum floor of 0 to not upset wait + + terminate_event.wait(max(0, min(next_send - time.time(), accumulate_dur))) + + logging.debug("Sending final resource message") + try: + d = accumulate_and_prepare() + radio.send((MessageType.RESOURCE_INFO, d)) + except Exception: + logging.exception("Exception getting the resource usage. Not sending final usage to Hub", exc_info=True) + logging.debug("End of monitoring helper") diff --git a/parsl/serialize/facade.py b/parsl/serialize/facade.py index 32660ef520..e475507712 100644 --- a/parsl/serialize/facade.py +++ b/parsl/serialize/facade.py @@ -34,6 +34,9 @@ def __init__(self): for key in METHODS_MAP_DATA: self.methods_for_data[key] = METHODS_MAP_DATA[key]() + def __reduce__(self): + raise RuntimeError("ParslSerializer singleton cannot be serialized") + def _list_methods(self): return self.methods_for_code, self.methods_for_data diff --git a/parsl/version.py b/parsl/version.py index 6cb5ce0bb2..097779a4e7 100644 --- a/parsl/version.py +++ b/parsl/version.py @@ -3,4 +3,4 @@ ..[alpha/beta/..] Alphas will be numbered like this -> 0.4.0a0 """ -VERSION = '1.3.0-dev+desc-2022.09.23a' +VERSION = '1.3.0-dev+desc-2022.09.23c' From e9c490cfe8e5f5ad07b05141005f2569101a6188 Mon Sep 17 00:00:00 2001 From: Ben Clifford Date: Fri, 23 Sep 2022 15:33:56 +0000 Subject: [PATCH 341/408] fix a module reference i should have changed earlier --- parsl/monitoring/node_reporter.py | 2 +- parsl/version.py | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/parsl/monitoring/node_reporter.py b/parsl/monitoring/node_reporter.py index 4c9cd59d55..4be5d15454 100755 --- a/parsl/monitoring/node_reporter.py +++ b/parsl/monitoring/node_reporter.py @@ -20,7 +20,7 @@ from datetime import datetime from parsl.log_utils import set_stream_logger -from parsl.monitoring.monitoring import FilesystemRadio +from parsl.monitoring.radios import FilesystemRadio logger = logging.getLogger("parsl.monitoring.node_reporter") diff --git a/parsl/version.py b/parsl/version.py index 097779a4e7..7fc642196f 100644 --- a/parsl/version.py +++ b/parsl/version.py @@ -3,4 +3,4 @@ ..[alpha/beta/..] Alphas will be numbered like this -> 0.4.0a0 """ -VERSION = '1.3.0-dev+desc-2022.09.23c' +VERSION = '1.3.0-dev+desc-2022.09.23d' From 8acfbc3fb9dae4b32634e66129606de963984b8d Mon Sep 17 00:00:00 2001 From: Ben Clifford Date: Mon, 26 Sep 2022 13:42:48 +0000 Subject: [PATCH 342/408] mostly add in parsl.trace experimental tracing around wq task launch --- parsl/dataflow/dflow.py | 17 +++++++- parsl/executors/workqueue/executor.py | 30 ++++++++++++- parsl/trace.py | 61 +++++++++++++++++++++++++++ parsl/version.py | 2 +- 4 files changed, 106 insertions(+), 4 deletions(-) create mode 100644 parsl/trace.py diff --git a/parsl/dataflow/dflow.py b/parsl/dataflow/dflow.py index 61b2b5b2b0..4657104051 100644 --- a/parsl/dataflow/dflow.py +++ b/parsl/dataflow/dflow.py @@ -20,6 +20,7 @@ from functools import partial import parsl +from parsl.trace import event from parsl.app.errors import RemoteExceptionWrapper from parsl.app.futures import DataFuture from parsl.config import Config @@ -580,6 +581,7 @@ def launch_if_ready(self, task_record: TaskRecord) -> None: launch_if_ready is thread safe, so may be called from any thread or callback. """ + event("DFK_LAUNCH_IF_READY_START") exec_fu = None task_id = task_record['id'] @@ -641,6 +643,7 @@ def launch_if_ready(self, task_record: TaskRecord) -> None: logger.error("add_done_callback got an exception which will be ignored", exc_info=True) task_record['exec_fu'] = exec_fu + event("DFK_LAUNCH_IF_READY_END") def launch_task(self, task_record: TaskRecord) -> Future: """Handle the actual submission of the task to the executor layer. @@ -659,6 +662,7 @@ def launch_task(self, task_record: TaskRecord) -> Future: Returns: Future that tracks the execution of the submitted executable """ + event("DFK_LAUNCH_TASK_START") task_id = task_record['id'] executable = task_record['func'] args = task_record['args'] @@ -671,6 +675,7 @@ def launch_task(self, task_record: TaskRecord) -> Future: logger.info("Reusing cached result for task {}".format(task_id)) task_record['from_memo'] = True assert isinstance(memo_fu, Future) + event("DFK_LAUNCH_TASK_END_MEMO") return memo_fu task_record['from_memo'] = False @@ -684,6 +689,7 @@ def launch_task(self, task_record: TaskRecord) -> Future: try_id = task_record['fail_count'] if self.monitoring is not None and self.monitoring.resource_monitoring_enabled: + event("DFK_LAUNCH_TASK_MONITORING_WRAP_START") wrapper_logging_level = logging.DEBUG if self.monitoring.monitoring_debug else logging.INFO (executable, args, kwargs) = self.monitoring.monitor_wrapper(executable, args, kwargs, try_id, task_id, self.monitoring.monitoring_hub_url, @@ -693,10 +699,15 @@ def launch_task(self, task_record: TaskRecord) -> Future: executor.radio_mode, executor.monitor_resources(), self.run_dir) + event("DFK_LAUNCH_TASK_MONITORING_WRAP_END") + event("DFK_LAUNCH_TASK_GET_SUBMITTER_LOCK_START") with self.submitter_lock: + event("DFK_LAUNCH_TASK_GET_SUBMITTER_LOCK_END") exec_fu = executor.submit(executable, task_record['resource_specification'], *args, **kwargs) + event("DFK_LAUNCH_TASK_UPDATE_TASK_STATE_START") self.update_task_state(task_record, States.launched) + event("DFK_LAUNCH_TASK_UPDATE_TASK_STATE_END") self._send_task_log_info(task_record) @@ -707,6 +718,7 @@ def launch_task(self, task_record: TaskRecord) -> Future: self._log_std_streams(task_record) + event("DFK_LAUNCH_TASK_END_LAUNCHED") return exec_fu def _add_input_deps(self, executor: str, args: Sequence[Any], kwargs: Dict[str, Any], func: Callable) -> Tuple[Sequence[Any], Dict[str, Any], Callable]: @@ -898,7 +910,7 @@ def submit(self, func, app_args, executors='all', cache=False, ignore_for_cache= (AppFuture) [DataFutures,] """ - + event("DFK_SUBMIT_START") if ignore_for_cache is None: ignore_for_cache = [] @@ -1004,7 +1016,9 @@ def submit(self, func, app_args, executors='all', cache=False, ignore_for_cache= self.update_task_state(task_def, States.pending) logger.debug("Task {} set to pending state with AppFuture: {}".format(task_id, task_def['app_fu'])) + event("DFK_SUBMIT_MONITORING_PENDING_START") self._send_task_log_info(task_def) + event("DFK_SUBMIT_MONITORING_PENDING_END") # at this point add callbacks to all dependencies to do a launch_if_ready # call whenever a dependency completes. @@ -1030,6 +1044,7 @@ def callback_adapter(dep_fut: Future) -> None: self.launch_if_ready(task_def) + event("DFK_SUBMIT_END") return app_fu # it might also be interesting to assert that all DFK diff --git a/parsl/executors/workqueue/executor.py b/parsl/executors/workqueue/executor.py index 96af5e7a26..f1143bd6b2 100644 --- a/parsl/executors/workqueue/executor.py +++ b/parsl/executors/workqueue/executor.py @@ -22,6 +22,7 @@ import shutil import itertools +from parsl.trace import event from parsl.serialize import pack_apply_message import parsl.utils as putils from parsl.executors.errors import ExecutorError @@ -366,6 +367,7 @@ def submit(self, func, resource_specification, *args, **kwargs): kwargs : dict Keyword arguments to the Parsl app """ + event("WQEX_SUBMIT_START") cores = None memory = None disk = None @@ -373,6 +375,7 @@ def submit(self, func, resource_specification, *args, **kwargs): priority = None category = None running_time_min = None + event("WQEX_SUBMIT_PROCESS_RESOURCE_SPEC_START") if resource_specification and isinstance(resource_specification, dict): logger.debug("Got resource specification: {}".format(resource_specification)) @@ -415,11 +418,14 @@ def submit(self, func, resource_specification, *args, **kwargs): elif k == 'running_time_min': running_time_min = resource_specification[k] + event("WQEX_SUBMIT_PROCESS_RESOURCE_SPEC_END") self.task_counter += 1 task_id = self.task_counter # Create a per task directory for the function, result, map, and result files + event("WQEX_SUBMIT_MKDIR_START") os.mkdir(self._path_in_task(task_id)) + event("WQEX_SUBMIT_MKDIR_END") input_files = [] output_files = [] @@ -444,7 +450,9 @@ def submit(self, func, resource_specification, *args, **kwargs): fu = Future() fu.parsl_executor_task_id = task_id logger.debug("Getting tasks_lock to set WQ-level task entry") + event("WQEX_SUBMIT_ACQUIRE_TASKS_LOCK_START") with self.tasks_lock: + event("WQEX_SUBMIT_ACQUIRE_TASKS_LOCK_END") logger.debug("Got tasks_lock to set WQ-level task entry") self.tasks[str(task_id)] = fu @@ -460,7 +468,9 @@ def submit(self, func, resource_specification, *args, **kwargs): logger.debug("Creating Task {} with result to be found at: {}".format(task_id, result_file)) logger.debug("Creating Task {} with log to be found at: {}".format(task_id, log_file)) + event("WQEX_SUBMIT_SERIALIZE_START") self._serialize_function(function_file, func, args, kwargs) + event("WQEX_SUBMIT_SERIALIZE_END") if self.pack: env_pkg = self._prepare_package(func, self.extra_pkgs) @@ -468,7 +478,9 @@ def submit(self, func, resource_specification, *args, **kwargs): env_pkg = None logger.debug("Constructing map for local filenames at worker for task {}".format(task_id)) + event("WQEX_SUBMIT_MAPFILE_START") self._construct_map_file(map_file, input_files, output_files) + event("WQEX_SUBMIT_MAPFILE_END") if not self.submit_process.is_alive(): raise ExecutorError(self, "Workqueue Submit Process is not alive") @@ -477,7 +489,8 @@ def submit(self, func, resource_specification, *args, **kwargs): logger.debug("Placing task {} on message queue".format(task_id)) if category is None: category = func.__name__ if self.autocategory else 'parsl-default' - self.task_queue.put_nowait(ParslTaskToWq(task_id, + event("WQEX_SUBMIT_PTWQ_START") + ptwq = ParslTaskToWq(task_id, category, cores, memory, @@ -491,8 +504,12 @@ def submit(self, func, resource_specification, *args, **kwargs): result_file, log_file, input_files, - output_files)) + output_files) + event("WQEX_SUBMIT_ENQUEUE_START") + self.task_queue.put_nowait(ptwq) + event("WQEX_SUBMIT_ENQUEUE_END") + event("WQEX_SUBMIT_END") return fu def _construct_worker_command(self): @@ -531,11 +548,16 @@ def _serialize_function(self, fn_path, parsl_fn, parsl_fn_args, parsl_fn_kwargs) "args": parsl_fn_args, "kwargs": parsl_fn_kwargs} else: + event("WQEX_SUBMIT_SERIALIZE_PACK_APPLY") function_info = {"byte code": pack_apply_message(parsl_fn, parsl_fn_args, parsl_fn_kwargs, buffer_threshold=1024 * 1024)} + event("WQEX_SUBMIT_SERIALIZE_OPEN") with open(fn_path, "wb") as f_out: + event("WQEX_SUBMIT_SERIALIZE_PICKLEDUMP") pickle.dump(function_info, f_out) + event("WQEX_SUBMIT_SERIALIZE_CLOSING") + event("WQEX_SUBMIT_SERIALIZE_CLOSED") def _construct_map_file(self, map_file, input_files, output_files): """ Map local filepath of parsl files to the filenames at the execution worker. @@ -550,8 +572,12 @@ def _construct_map_file(self, map_file, input_files, output_files): else: remote_name = local_name file_translation_map[local_name] = remote_name + event("WQEX_SUBMIT_MAPFILE_OPEN") with open(map_file, "wb") as f_out: + event("WQEX_SUBMIT_MAPFILE_PICKLEDUMP") pickle.dump(file_translation_map, f_out) + event("WQEX_SUBMIT_MAPFILE_CLOSING") + event("WQEX_SUBMIT_MAPFILE_CLOSED") def _register_file(self, parsl_file): """Generates a tuple (parsl_file.filepath, stage, cache) to give to diff --git a/parsl/trace.py b/parsl/trace.py new file mode 100644 index 0000000000..a416a6e34c --- /dev/null +++ b/parsl/trace.py @@ -0,0 +1,61 @@ +import logging +import pickle +import statistics +import time + +logger = logging.getLogger(__name__) + +# TODO: last_event should be a thread local +last_event = None + +trace_by_logger = False +trace_by_dict = False + +event_stats = {} + +def event(name: str): + global last_event + t = time.time() + + if last_event: + (last_name, last_t) = last_event + d_t = t - last_t + if trace_by_logger: + logger.info(f"{last_name} took {d_t} seconds; beginning new event {name}") + # logger.info("%s took %s seconds; beginning new event %s", last_name, d_t, name) + if trace_by_dict: + k = (last_name, name) + if k in event_stats: + (total, count, raw) = event_stats[k] + raw.append((last_t, t)) + event_stats[k] = (total + d_t, count + 1, raw) + else: + event_stats[k] = (d_t, 1, [(last_t, t)]) + + last_event = (name, t) + +def output_event_stats(): + print("Event stats") + print("===========") + l = [] + all_tasks_t = 0 + for ((from_k, to_k), (total, count, raw)) in event_stats.items(): + mean = total/count + dts = [t - last_t for (last_t, t) in raw] + t_median = statistics.median(dts) + t_max = max(dts) + t_min = min(dts) + l.append( (mean, t_median, t_max, t_min, from_k, to_k, total, count) ) + + all_tasks_t += total + + l.sort() + + for (t_mean, t_median, t_max, t_min, from_k, to_k, total, count) in l: + print(f"{from_k} -> {to_k} ({count} iters): min {t_min} / median {t_median} / mean {t_mean} / max {t_max}") + + print("===========") + print(f"Total real time accounted for here: {all_tasks_t} sec") + with open("parslstats.pickle","wb") as f: + pickle.dump(event_stats, f) + diff --git a/parsl/version.py b/parsl/version.py index 7fc642196f..45a3f89c10 100644 --- a/parsl/version.py +++ b/parsl/version.py @@ -3,4 +3,4 @@ ..[alpha/beta/..] Alphas will be numbered like this -> 0.4.0a0 """ -VERSION = '1.3.0-dev+desc-2022.09.23d' +VERSION = '1.3.0-dev+desc-2022.09.26a' From bf66c0577d3db6f70f4175c23a3db81a16a90a19 Mon Sep 17 00:00:00 2001 From: Ben Clifford Date: Mon, 26 Sep 2022 17:59:53 +0000 Subject: [PATCH 343/408] add in ability to store wq function files in /tmp for potential launch speedup --- parsl/executors/workqueue/executor.py | 12 ++++++++++-- parsl/version.py | 2 +- 2 files changed, 11 insertions(+), 3 deletions(-) diff --git a/parsl/executors/workqueue/executor.py b/parsl/executors/workqueue/executor.py index f1143bd6b2..b885479943 100644 --- a/parsl/executors/workqueue/executor.py +++ b/parsl/executors/workqueue/executor.py @@ -228,7 +228,8 @@ def __init__(self, init_command: str = "", worker_options: str = "", full_debug: bool = True, - worker_executable: str = 'work_queue_worker'): + worker_executable: str = 'work_queue_worker', + function_dir = None): BlockProviderExecutor.__init__(self, provider=provider, block_error_handler=True) self._scaling_enabled = True @@ -265,6 +266,7 @@ def __init__(self, self.cached_envs = {} # type: Dict[int, str] self.worker_options = worker_options self.worker_executable = worker_executable + self.function_dir = function_dir if not self.address: self.address = socket.gethostname() @@ -294,7 +296,13 @@ def start(self): self.tasks_lock = threading.Lock() # Create directories for data and results - self.function_data_dir = os.path.join(self.run_dir, "function_data") + if not self.function_dir: + self.function_data_dir = os.path.join(self.run_dir, "function_data") + else: + tp = str(time.time()) + tx = os.path.join(self.function_dir, tp) + os.mkdir(tx) + self.function_data_dir = os.path.join(self.function_dir, tp, "function_data") self.package_dir = os.path.join(self.run_dir, "package_data") self.wq_log_dir = os.path.join(self.run_dir, self.label) logger.debug("function data directory: {}\nlog directory: {}".format(self.function_data_dir, self.wq_log_dir)) diff --git a/parsl/version.py b/parsl/version.py index 45a3f89c10..d56a2f752d 100644 --- a/parsl/version.py +++ b/parsl/version.py @@ -3,4 +3,4 @@ ..[alpha/beta/..] Alphas will be numbered like this -> 0.4.0a0 """ -VERSION = '1.3.0-dev+desc-2022.09.26a' +VERSION = '1.3.0-dev+desc-2022.09.26b' From 35468017560f1e1401b6953abcbfa52a3c149cf1 Mon Sep 17 00:00:00 2001 From: Ben Clifford Date: Wed, 28 Sep 2022 12:09:57 +0000 Subject: [PATCH 344/408] Add some more event timings around places David Adams' test runs look busy --- parsl/dataflow/dflow.py | 19 +++++++++++++++++++ parsl/version.py | 2 +- 2 files changed, 20 insertions(+), 1 deletion(-) diff --git a/parsl/dataflow/dflow.py b/parsl/dataflow/dflow.py index 4657104051..203959d72b 100644 --- a/parsl/dataflow/dflow.py +++ b/parsl/dataflow/dflow.py @@ -709,14 +709,18 @@ def launch_task(self, task_record: TaskRecord) -> Future: self.update_task_state(task_record, States.launched) event("DFK_LAUNCH_TASK_UPDATE_TASK_STATE_END") + event("DFK_LAUNCH_TASK_SEND_TASK_LOG_INFO_START") self._send_task_log_info(task_record) + event("DFK_LAUNCH_TASK_SEND_TASK_LOG_INFO_END") if hasattr(exec_fu, "parsl_executor_task_id"): logger.info(f"Parsl task {task_id} try {try_id} launched on executor {executor.label} with executor id {exec_fu.parsl_executor_task_id}") else: logger.info(f"Parsl task {task_id} try {try_id} launched on executor {executor.label}") + event("DFK_LAUNCH_TASK_LOG_STD_STREAMS_START") self._log_std_streams(task_record) + event("DFK_LAUNCH_TASK_LOG_STD_STREAMS_END") event("DFK_LAUNCH_TASK_END_LAUNCHED") return exec_fu @@ -918,6 +922,7 @@ def submit(self, func, app_args, executors='all', cache=False, ignore_for_cache= raise RuntimeError("Cannot submit to a DFK that has been cleaned up") task_id = self.task_count + event("DFK_SUBMIT_CHOOSE_EXECUTOR_START") self.task_count += 1 if isinstance(executors, str) and executors.lower() == 'all': choices = list(e for e in self.executors if e != '_parsl_internal') @@ -926,10 +931,12 @@ def submit(self, func, app_args, executors='all', cache=False, ignore_for_cache= else: raise ValueError("Task {} supplied invalid type for executors: {}".format(task_id, type(executors))) executor = random.choice(choices) + event("DFK_SUBMIT_CHOOSE_EXECUTOR_END") logger.debug("Task {} will be sent to executor {}".format(task_id, executor)) # The below uses func.__name__ before it has been wrapped by any staging code. + event("DFK_SUBMIT_MUNGE_ARGS_START") label = app_kwargs.get('label') for kw in ['stdout', 'stderr']: if kw in app_kwargs: @@ -948,6 +955,7 @@ def submit(self, func, app_args, executors='all', cache=False, ignore_for_cache= ) resource_specification = app_kwargs.get('parsl_resource_specification', {}) + event("DFK_SUBMIT_MUNGE_ARGS_END") task_def: TaskRecord task_def = {'depends': None, @@ -971,26 +979,33 @@ def submit(self, func, app_args, executors='all', cache=False, ignore_for_cache= 'try_time_returned': None, 'resource_specification': resource_specification} + event("DFK_SUBMIT_UPDATE_UNSCHED_STATE_START") self.update_task_state(task_def, States.unsched) + event("DFK_SUBMIT_UPDATE_UNSCHED_STATE_END") app_fu = AppFuture(task_def) # Transform remote input files to data futures + event("DFK_SUBMIT_ADD_DEPS_START") app_args, app_kwargs, func = self._add_input_deps(executor, app_args, app_kwargs, func) func = self._add_output_deps(executor, app_args, app_kwargs, app_fu, func) + event("DFK_SUBMIT_ADD_DEPS_END") + event("DFK_SUBMIT_UPDATE_KWARGS_START") task_def.update({ 'args': app_args, 'func': func, 'kwargs': app_kwargs, 'app_fu': app_fu}) + event("DFK_SUBMIT_UPDATE_KWARGS_END") assert task_id not in self.tasks self.tasks[task_id] = task_def # Get the list of dependencies for the task + event("DFK_SUBMIT_EXAMINE_DEPS_START") depends = self._gather_all_deps(app_args, app_kwargs) task_def['depends'] = depends @@ -1005,6 +1020,7 @@ def submit(self, func, app_args, executors='all', cache=False, ignore_for_cache= waiting_message = "waiting on {}".format(", ".join(depend_descs)) else: waiting_message = "not waiting on any dependency" + event("DFK_SUBMIT_EXAMINE_DEPS_END") logger.info("Task {} submitted for App {}, {}".format(task_id, task_def['func_name'], @@ -1012,8 +1028,11 @@ def submit(self, func, app_args, executors='all', cache=False, ignore_for_cache= task_def['task_launch_lock'] = threading.Lock() + event("DFK_SUBMIT_ADD_CALLBACK_START") app_fu.add_done_callback(partial(self.handle_app_update, task_def)) + event("DFK_SUBMIT_UPDATE_PENDING_STATE_START") self.update_task_state(task_def, States.pending) + event("DFK_SUBMIT_UPDATE_PENDING_STATE_END") logger.debug("Task {} set to pending state with AppFuture: {}".format(task_id, task_def['app_fu'])) event("DFK_SUBMIT_MONITORING_PENDING_START") diff --git a/parsl/version.py b/parsl/version.py index d56a2f752d..b872e75735 100644 --- a/parsl/version.py +++ b/parsl/version.py @@ -3,4 +3,4 @@ ..[alpha/beta/..] Alphas will be numbered like this -> 0.4.0a0 """ -VERSION = '1.3.0-dev+desc-2022.09.26b' +VERSION = '1.3.0-dev+desc-2022.09.28a' From 9f6e1dee33659e8a73966a45e83e17dd42b57487 Mon Sep 17 00:00:00 2001 From: Ben Clifford Date: Wed, 28 Sep 2022 17:02:22 +0000 Subject: [PATCH 345/408] flake8/mypy fixes --- parsl/executors/workqueue/executor.py | 2 +- parsl/trace.py | 5 +++++ parsl/version.py | 2 +- 3 files changed, 7 insertions(+), 2 deletions(-) diff --git a/parsl/executors/workqueue/executor.py b/parsl/executors/workqueue/executor.py index 5c217721fd..24d3d64554 100644 --- a/parsl/executors/workqueue/executor.py +++ b/parsl/executors/workqueue/executor.py @@ -229,7 +229,7 @@ def __init__(self, worker_options: str = "", full_debug: bool = True, worker_executable: str = 'work_queue_worker', - function_dir = None): + function_dir: str = None): BlockProviderExecutor.__init__(self, provider=provider, block_error_handler=True) self._scaling_enabled = True diff --git a/parsl/trace.py b/parsl/trace.py index 739f34ec74..5be4e69cce 100644 --- a/parsl/trace.py +++ b/parsl/trace.py @@ -3,6 +3,8 @@ import statistics import time +from typing import Dict, List, Tuple + logger = logging.getLogger(__name__) # TODO: last_event should be a thread local @@ -11,6 +13,9 @@ trace_by_logger = False trace_by_dict = False +event_stats: Dict[Tuple[str, str], + Tuple[float, float, List[Tuple[float, float]]] + ] event_stats = {} diff --git a/parsl/version.py b/parsl/version.py index 3b380cafd2..700c71a3d0 100644 --- a/parsl/version.py +++ b/parsl/version.py @@ -3,4 +3,4 @@ ..[alpha/beta/..] Alphas will be numbered like this -> 0.4.0a0 """ -VERSION = '1.3.0-dev+desc-2022.09.28b' +VERSION = '1.3.0-dev+desc-2022.09.28c' From 19277ee247cfecc9b4d4cead97435424f295a218 Mon Sep 17 00:00:00 2001 From: Ben Clifford Date: Thu, 20 Oct 2022 08:16:51 +0000 Subject: [PATCH 346/408] more ongoing work - most immediately, some mkdir fixes --- parsl/executors/workqueue/executor.py | 19 +++++++++++---- parsl/tests/configs/workqueue_ex.py | 6 +++-- .../test_error_handling/test_resource_spec.py | 24 +++++++++++++------ parsl/version.py | 2 +- 4 files changed, 36 insertions(+), 15 deletions(-) diff --git a/parsl/executors/workqueue/executor.py b/parsl/executors/workqueue/executor.py index e59f3295af..896a57ec5d 100644 --- a/parsl/executors/workqueue/executor.py +++ b/parsl/executors/workqueue/executor.py @@ -230,6 +230,7 @@ def __init__(self, autolabel: bool = False, autolabel_window: int = 1, autocategory: bool = True, + enable_monitoring: bool = False, max_retries: Optional[int] = 1, init_command: str = "", worker_options: str = "", @@ -267,6 +268,7 @@ def __init__(self, self.autolabel = autolabel self.autolabel_window = autolabel_window self.autocategory = autocategory + self.enable_monitoring = enable_monitoring self.max_retries = max_retries self.should_stop = multiprocessing.Value(c_bool, False) self.cached_envs = {} # type: Dict[int, str] @@ -307,14 +309,14 @@ def start(self): else: tp = str(time.time()) tx = os.path.join(self.function_dir, tp) - os.mkdir(tx) + os.makedirs(tx) self.function_data_dir = os.path.join(self.function_dir, tp, self.label, "function_data") self.package_dir = os.path.join(self.run_dir, self.label, "package_data") self.wq_log_dir = os.path.join(self.run_dir, self.label) logger.debug("function data directory: {}\nlog directory: {}".format(self.function_data_dir, self.wq_log_dir)) - os.mkdir(self.wq_log_dir) - os.mkdir(self.function_data_dir) - os.mkdir(self.package_dir) + os.makedirs(self.wq_log_dir) + os.makedirs(self.function_data_dir) + os.makedirs(self.package_dir) logger.debug("Starting WorkQueueExecutor") @@ -331,6 +333,7 @@ def start(self): "shared_fs": self.shared_fs, "autolabel": self.autolabel, "autolabel_window": self.autolabel_window, + "enable_monitoring": self.enable_monitoring, "autocategory": self.autocategory, "max_retries": self.max_retries, "should_stop": self.should_stop, @@ -798,7 +801,8 @@ def _collect_work_queue_results(self): @wrap_with_logs -def _work_queue_submit_wait(task_queue=multiprocessing.Queue(), +def _work_queue_submit_wait(*, + task_queue=multiprocessing.Queue(), launch_cmd=None, env=None, collector_queue=multiprocessing.Queue(), @@ -807,6 +811,7 @@ def _work_queue_submit_wait(task_queue=multiprocessing.Queue(), shared_fs=False, autolabel=False, autolabel_window=None, + enable_monitoring, autocategory=False, max_retries=0, should_stop=None, @@ -850,6 +855,10 @@ def _work_queue_submit_wait(task_queue=multiprocessing.Queue(), if project_password_file: q.specify_password_file(project_password_file) + if enable_monitoring: + logger.info("BENC: enabling WQ monitoring") + q.enable_monitoring() + if autolabel: q.enable_monitoring() if autolabel_window is not None: diff --git a/parsl/tests/configs/workqueue_ex.py b/parsl/tests/configs/workqueue_ex.py index f4991254d8..a2d62ff6da 100644 --- a/parsl/tests/configs/workqueue_ex.py +++ b/parsl/tests/configs/workqueue_ex.py @@ -5,5 +5,7 @@ from parsl.data_provider.ftp import FTPInTaskStaging from parsl.data_provider.file_noop import NoOpFileStaging -config = Config(executors=[WorkQueueExecutor(port=9000, - storage_access=[FTPInTaskStaging(), HTTPInTaskStaging(), NoOpFileStaging()])]) + +def fresh_config(): + return Config(executors=[WorkQueueExecutor(port=9000, + storage_access=[FTPInTaskStaging(), HTTPInTaskStaging(), NoOpFileStaging()])]) diff --git a/parsl/tests/test_error_handling/test_resource_spec.py b/parsl/tests/test_error_handling/test_resource_spec.py index 11ffa7c842..9170ce8b6a 100644 --- a/parsl/tests/test_error_handling/test_resource_spec.py +++ b/parsl/tests/test_error_handling/test_resource_spec.py @@ -1,8 +1,8 @@ import parsl +import pytest + from parsl.app.app import python_app -# from parsl.tests.configs.local_threads import config -from parsl.tests.configs.htex_local import config -# from parsl.tests.configs.workqueue_ex import config +from parsl.config import Config from parsl.executors.errors import UnsupportedFeatureError, ExecutorError from parsl.executors import WorkQueueExecutor @@ -42,7 +42,17 @@ def test_resource(n=2): assert isinstance(e, ExecutorError) -if __name__ == '__main__': - local_config = config - parsl.load(local_config) - x = test_resource(2) +@python_app +def long_delay(parsl_resource_specification={}): + import time + time.sleep(30) + + +@pytest.mark.skip('I need to understand whats happening here better') +@pytest.mark.local +def test_wq_resource_excess(): + c = Config(executors=[WorkQueueExecutor(port=9000, enable_monitoring=True)]) + + parsl.load(c) + f = long_delay(parsl_resource_specification={'memory': 1, 'disk': 1, 'cores': 1}) + assert f.exception() is not None, "This should have failed" diff --git a/parsl/version.py b/parsl/version.py index f15033cb5a..44490ece4d 100644 --- a/parsl/version.py +++ b/parsl/version.py @@ -3,4 +3,4 @@ ..[alpha/beta/..] Alphas will be numbered like this -> 0.4.0a0 """ -VERSION = '1.3.0-dev+desc-2022.10.17a' +VERSION = '1.3.0-dev+desc-2022.10.20a' From 1c5bc49d3cae5e7cedd7531132cf271410f6307f Mon Sep 17 00:00:00 2001 From: Ben Clifford Date: Mon, 31 Oct 2022 12:19:17 +0000 Subject: [PATCH 347/408] fix type checking in lazy imports --- parsl/__init__.py | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/parsl/__init__.py b/parsl/__init__.py index 6722233e2a..d68aff30e0 100644 --- a/parsl/__init__.py +++ b/parsl/__init__.py @@ -21,8 +21,10 @@ from typing import TYPE_CHECKING if TYPE_CHECKING: from parsl.executors import ThreadPoolExecutor + from parsl.data_provider.files import File from parsl.dataflow.dflow import DataFlowKernel - from parsl.app.app import python_app + from parsl.app.app import bash_app, join_app, python_app + from parsl.log_utils import set_file_logger, set_stream_logger lazys = { 'python_app': 'parsl.app.app', From c9336fb3f890bf8fe3e2a747dc1b96fc7afaa1c6 Mon Sep 17 00:00:00 2001 From: Ben Clifford Date: Mon, 31 Oct 2022 12:31:53 +0000 Subject: [PATCH 348/408] tickle version number --- parsl/version.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/parsl/version.py b/parsl/version.py index de75b4a760..7d3015896b 100644 --- a/parsl/version.py +++ b/parsl/version.py @@ -3,4 +3,4 @@ ..[alpha/beta/..] Alphas will be numbered like this -> 0.4.0a0 """ -VERSION = '1.3.0-dev+desc-2022.10.28a' +VERSION = '1.3.0-dev+desc-2022.10.30a' From a82cf0b7d01df0f21f280ac1a55a3178808f4774 Mon Sep 17 00:00:00 2001 From: Ben Clifford Date: Mon, 31 Oct 2022 12:56:10 +0000 Subject: [PATCH 349/408] work on errors and lazy imports --- parsl/dataflow/job_error_handler.py | 35 +++++++++++++++-------------- parsl/providers/__init__.py | 2 +- parsl/version.py | 2 +- 3 files changed, 20 insertions(+), 19 deletions(-) diff --git a/parsl/dataflow/job_error_handler.py b/parsl/dataflow/job_error_handler.py index 2ddc0fe6e4..321dba0e35 100644 --- a/parsl/dataflow/job_error_handler.py +++ b/parsl/dataflow/job_error_handler.py @@ -31,24 +31,25 @@ def count_jobs(self, status: Dict[str, JobStatus]): def get_error(self, status: Dict[str, JobStatus]) -> Exception: """Concatenate all errors.""" - err = "Block errors:\n" - count = 1 - for js in status.values(): - err += f"Error {count}: \n" - count += 1 - if js.message is not None: - err = err + f"{js.message}\n" - if js.exit_code is not None: - err = err + f"\tEXIT CODE: {js.exit_code}\n" - stdout = js.stdout_summary - if stdout: - err = err + f"\tSTDOUT: {stdout}\n" - stderr = js.stderr_summary - if stderr: - err = err + f"\tSTDERR: {stderr}\n" - - if len(err) == 0: + if len(status) == 0: err = "No error message received" + else: + err = "Job errors:\n" + count = 1 + for js in status.values(): + err += f"Error {count}: \n" + count += 1 + if js.message is not None: + err = err + f"{js.message}\n" + if js.exit_code is not None: + err = err + f"\tEXIT CODE: {js.exit_code}\n" + stdout = js.stdout_summary + if stdout: + err = err + f"\tSTDOUT: {stdout}\n" + stderr = js.stderr_summary + if stderr: + err = err + f"\tSTDERR: {stderr}\n" + # wrapping things in an exception here doesn't really help in providing more information # than the string itself return Exception(err) diff --git a/parsl/providers/__init__.py b/parsl/providers/__init__.py index 3a9ee0150e..fa6838db5e 100644 --- a/parsl/providers/__init__.py +++ b/parsl/providers/__init__.py @@ -23,7 +23,7 @@ 'GridEngineProvider': 'parsl.providers.grid_engine.grid_engine', 'SlurmProvider': 'parsl.providers.slurm.slurm', 'TorqueProvider': 'parsl.providers.torque.torque', - 'PBSProProvider': 'parsl.provicers.pbspro.pbspro', + 'PBSProProvider': 'parsl.providers.pbspro.pbspro', 'LSFProvider': 'parsl.providers.lsf.lsf', 'AdHocProvider': 'parsl.providers.ad_hoc.ad_hoc', diff --git a/parsl/version.py b/parsl/version.py index 7d3015896b..d69cf3b740 100644 --- a/parsl/version.py +++ b/parsl/version.py @@ -3,4 +3,4 @@ ..[alpha/beta/..] Alphas will be numbered like this -> 0.4.0a0 """ -VERSION = '1.3.0-dev+desc-2022.10.30a' +VERSION = '1.3.0-dev+desc-2022.10.30b' From ebcbfb7006849554cc637720b27187fdba7e3424 Mon Sep 17 00:00:00 2001 From: Ben Clifford Date: Mon, 7 Nov 2022 11:36:56 +0000 Subject: [PATCH 350/408] Merge latest - just a typo fix --- parsl/providers/provider_base.py | 2 +- parsl/version.py | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/parsl/providers/provider_base.py b/parsl/providers/provider_base.py index 0d6e418d8b..897207d68c 100644 --- a/parsl/providers/provider_base.py +++ b/parsl/providers/provider_base.py @@ -36,7 +36,7 @@ class JobStatus(object): """Encapsulates a job state together with other details: Args: - state: The machine-reachable state of the job this status refers to + state: The machine-readable state of the job this status refers to message: Optional human readable message exit_code: Optional exit code stdout_path: Optional path to a file containing the job's stdout diff --git a/parsl/version.py b/parsl/version.py index d69cf3b740..36dec0e49a 100644 --- a/parsl/version.py +++ b/parsl/version.py @@ -3,4 +3,4 @@ ..[alpha/beta/..] Alphas will be numbered like this -> 0.4.0a0 """ -VERSION = '1.3.0-dev+desc-2022.10.30b' +VERSION = '1.3.0-dev+desc-2022.11.07a' From fc7219ffb21878f1fdd510e5f719880f0acbabba Mon Sep 17 00:00:00 2001 From: Ben Clifford Date: Mon, 7 Nov 2022 15:53:48 +0000 Subject: [PATCH 351/408] Add a result-time radio mode This should be much less filesystem intensive, at the expense of deferring all monitoring information to the end of a task's execution, and making result packages much larger. --- parsl/dataflow/dflow.py | 20 +++- parsl/executors/base.py | 2 +- parsl/executors/workqueue/executor.py | 8 +- parsl/monitoring/radios.py | 20 ++++ parsl/monitoring/remote.py | 70 +++++++++++- .../workqueue_monitoring_resultradio.py | 25 +++++ .../test_mon_wq_result_radio/__init__.py | 0 .../test_mon_wq_result_radio/test_basic.py | 103 ++++++++++++++++++ .../test_mon_wq_result_radio/test_db_locks.py | 89 +++++++++++++++ .../test_memoization_representation.py | 80 ++++++++++++++ parsl/version.py | 2 +- 11 files changed, 406 insertions(+), 13 deletions(-) create mode 100644 parsl/tests/configs/workqueue_monitoring_resultradio.py create mode 100644 parsl/tests/test_monitoring/test_mon_wq_result_radio/__init__.py create mode 100644 parsl/tests/test_monitoring/test_mon_wq_result_radio/test_basic.py create mode 100644 parsl/tests/test_monitoring/test_mon_wq_result_radio/test_db_locks.py create mode 100644 parsl/tests/test_monitoring/test_mon_wq_result_radio/test_memoization_representation.py diff --git a/parsl/dataflow/dflow.py b/parsl/dataflow/dflow.py index ce918294f6..4bd3aa720f 100644 --- a/parsl/dataflow/dflow.py +++ b/parsl/dataflow/dflow.py @@ -291,7 +291,7 @@ def handle_exec_update(self, task_record: TaskRecord, future: Future) -> None: raise RuntimeError("done callback called, despite future not reporting itself as done") try: - res = self._unwrap_remote_exception_wrapper(future) + res = self._unwrap_remote_exception_wrapper(future, task_record) except Exception as e: logger.debug("Task {} try {} failed".format(task_id, task_record['try_id'])) @@ -545,9 +545,23 @@ def update_task_state(self, task_record: TaskRecord, new_state: States) -> None: self.task_state_counts[new_state] += 1 task_record['status'] = new_state - @staticmethod - def _unwrap_remote_exception_wrapper(future: Future) -> Any: + # this is a horrible place to put results radio mode decoding. + # @staticmethod + def _unwrap_remote_exception_wrapper(self, future: Future, task_record) -> Any: result = future.result() + executor = self.executors[task_record['executor']] + radio_mode = executor.radio_mode + # raise RuntimeError(f"BENC: with radio_mode {radio_mode}, result potentially with monitoring: {result}") + if radio_mode == "results" and not task_record['from_memo']: + try: + (messages, result) = result + except Exception as e: + raise RuntimeError(f"BENC: Got exception {e} with result = {result}") + # raise RuntimeError(f"BENC: discarding {len(messages)} monitoring messages: {messages}") + if self.monitoring: + for (t, v) in messages: + self.monitoring.send(t, v) + if isinstance(result, RemoteExceptionWrapper): result.reraise() return result diff --git a/parsl/executors/base.py b/parsl/executors/base.py index 6099c2f224..615e02fed2 100644 --- a/parsl/executors/base.py +++ b/parsl/executors/base.py @@ -44,7 +44,7 @@ class ParslExecutor(metaclass=ABCMeta): """ label: str = "undefined" - radio_mode: str = "udp" + radio_mode: str = "not-configured" def __enter__(self): return self diff --git a/parsl/executors/workqueue/executor.py b/parsl/executors/workqueue/executor.py index 896a57ec5d..854bd65933 100644 --- a/parsl/executors/workqueue/executor.py +++ b/parsl/executors/workqueue/executor.py @@ -208,7 +208,9 @@ class WorkQueueExecutor(BlockProviderExecutor, putils.RepresentationMixin): must be visible from both the submitting side and workers. """ - radio_mode = "filesystem" + # TODO: this should be configurable: there's no definite preference for + # results radio vs filesystem mode. + # radio_mode = "results" @typeguard.typechecked def __init__(self, @@ -236,7 +238,8 @@ def __init__(self, worker_options: str = "", full_debug: bool = True, worker_executable: str = 'work_queue_worker', - function_dir: Optional[str] = None): + function_dir: Optional[str] = None, + radio_mode: str = "filesystem"): BlockProviderExecutor.__init__(self, provider=provider, block_error_handler=True) self._scaling_enabled = True @@ -275,6 +278,7 @@ def __init__(self, self.worker_options = worker_options self.worker_executable = worker_executable self.function_dir = function_dir + self.radio_mode = radio_mode if not self.address: self.address = socket.gethostname() diff --git a/parsl/monitoring/radios.py b/parsl/monitoring/radios.py index a70f6cead2..9211a0fd19 100644 --- a/parsl/monitoring/radios.py +++ b/parsl/monitoring/radios.py @@ -14,6 +14,16 @@ logger = logging.getLogger(__name__) +# need to be careful about thread-safety here: +# there will be multiple radio instances writing +# to this, along with (eg in thread local case) +# potentially many result deliverers. +# in that latter case, should there be per-task-id +# segregation of who sends which results back? or +# do we just care about *anyone* can send the results +# back, first come first serve? +result_radio_queue = [] + class MonitoringRadio(metaclass=ABCMeta): @abstractmethod @@ -129,6 +139,16 @@ def send(self, message: object) -> None: return +class ResultsRadio(MonitoringRadio): + def __init__(self, monitoring_url: str, source_id: int, timeout: int = 10): + pass + + def send(self, message: object) -> None: + global result_radio_queue + result_radio_queue.append(message) + # raise RuntimeError(f"BENC: appended {message} to {result_radio_queue}") + + class UDPRadio(MonitoringRadio): def __init__(self, monitoring_url: str, source_id: int, timeout: int = 10): diff --git a/parsl/monitoring/remote.py b/parsl/monitoring/remote.py index 7066bdd1ff..bd662da07d 100644 --- a/parsl/monitoring/remote.py +++ b/parsl/monitoring/remote.py @@ -5,11 +5,12 @@ from functools import wraps from parsl.multiprocessing import ForkProcess -from multiprocessing import Event, Process +from multiprocessing import Event, Process, Queue +from queue import Empty from parsl.process_loggers import wrap_with_logs from parsl.monitoring.message_type import MessageType -from parsl.monitoring.radios import MonitoringRadio, UDPRadio, HTEXRadio, FilesystemRadio +from parsl.monitoring.radios import MonitoringRadio, UDPRadio, ResultsRadio, HTEXRadio, FilesystemRadio from typing import Any, Callable, Dict, List, Optional, Tuple logger = logging.getLogger(__name__) @@ -49,6 +50,8 @@ def wrapped(*args: List[Any], **kwargs: Dict[str, Any]) -> Any: task_id = kwargs.pop('_parsl_monitoring_task_id') try_id = kwargs.pop('_parsl_monitoring_try_id') terminate_event = Event() + terminate_queue: Queue[List[Any]] + terminate_queue = Queue() # Send first message to monitoring router send_first_message(try_id, task_id, @@ -60,6 +63,11 @@ def wrapped(*args: List[Any], **kwargs: Dict[str, Any]) -> Any: p: Optional[Process] if monitor_resources: # create the monitor process and start + # TODO: this process will make its own monitoring radio + # which in the case of the ResultsRadio, at present will + # not be able to get its results into this processes + # monitoring messages list. + # can I extract them right before kill time? pp = ForkProcess(target=monitor, args=(os.getpid(), try_id, @@ -70,7 +78,8 @@ def wrapped(*args: List[Any], **kwargs: Dict[str, Any]) -> Any: logging_level, sleep_dur, run_dir, - terminate_event), + terminate_event, + terminate_queue), name="Monitor-Wrapper-{}".format(task_id)) pp.start() p = pp @@ -81,13 +90,25 @@ def wrapped(*args: List[Any], **kwargs: Dict[str, Any]) -> Any: else: p = None + # this logic flow is fairly contorted - can it look cleaner? + # different wrapper structure, eg? try: - return f(*args, **kwargs) + ret_v = f(*args, **kwargs) finally: # There's a chance of zombification if the workers are killed by some signals (?) if p: + # TODO: can I get monitoring results out of here somehow? + # eg a shared object that comes back with more results? + # (terminate_event is already a shared object...) + # so just a single box that will be populated once at exit. + # nothing more nuanced than that - deliberately avoiding queues that can get full, for example. terminate_event.set() - p.join(30) # 30 second delay for this -- this timeout will be hit in the case of an unusually long end-of-loop + try: + more_monitoring_messages = terminate_queue.get(timeout=30) + except Empty: + more_monitoring_messages = [] + + p.join(30) # 60 second delay for this all together (30+10) -- this timeout will be hit in the case of an unusually long end-of-loop if p.exitcode is None: logger.warn("Event-based termination of monitoring helper took too long. Using process-based termination.") p.terminate() @@ -102,6 +123,28 @@ def wrapped(*args: List[Any], **kwargs: Dict[str, Any]) -> Any: run_id, radio_mode, run_dir) + # if we reach here, the finally block has run, and + # ret_v has been populated. so we can do the return + # that used to live inside the try: block. + # If that block raised an exception, then the finally + # block would run, but then we would not come to this + # return statement. As before. + if radio_mode == "results": + # this import has to happen here, not at the top level: we + # want the result_radio_queue from the import on the + # execution side - we *don't* want to get the (empty) + # result_radio_queue on the submit side, send that with the + # closure, and then send it (still empty) back. This is pretty + # subtle, which suggests it needs either lots of documentation + # or perhaps something nicer than using globals like this? + from parsl.monitoring.radios import result_radio_queue + assert isinstance(result_radio_queue, list) + assert isinstance(more_monitoring_messages, list) + full = result_radio_queue + more_monitoring_messages + return (full, ret_v) + else: + return ret_v + monitoring_wrapper_cache[cache_key] = wrapped new_kwargs = kwargs.copy() @@ -147,6 +190,9 @@ def send_first_last_message(try_id: int, elif radio_mode == "filesystem": radio = FilesystemRadio(monitoring_url=monitoring_hub_url, source_id=task_id, run_dir=run_dir) + elif radio_mode == "results": + radio = ResultsRadio(monitoring_url=monitoring_hub_url, + source_id=task_id) else: raise RuntimeError(f"Unknown radio mode: {radio_mode}") @@ -176,7 +222,8 @@ def monitor(pid: int, run_dir: str, # removed all defaults because unused and there's no meaningful default for terminate_event. # these probably should become named arguments, with a *, and named at invocation. - terminate_event: Any) -> None: # cannot be Event because of multiprocessing type weirdness. + terminate_event: Any, + terminate_queue: Any) -> None: # cannot be Event because of multiprocessing type weirdness. """Monitors the Parsl task's resources by pointing psutil to the task's pid and watching it and its children. This process makes calls to logging, but deliberately does not attach @@ -199,6 +246,9 @@ def monitor(pid: int, elif radio_mode == "filesystem": radio = FilesystemRadio(monitoring_url=monitoring_hub_url, source_id=task_id, run_dir=run_dir) + elif radio_mode == "results": + radio = ResultsRadio(monitoring_url=monitoring_hub_url, + source_id=task_id) else: raise RuntimeError(f"Unknown radio mode: {radio_mode}") @@ -299,4 +349,12 @@ def accumulate_and_prepare() -> Dict[str, Any]: radio.send((MessageType.RESOURCE_INFO, d)) except Exception: logging.exception("Exception getting the resource usage. Not sending final usage to Hub", exc_info=True) + + # TODO: write out any accumulated messages that might have been + # accumulated by the results radio, so that the task wrapper in the main + # task process can see these results. + from parsl.monitoring.radios import result_radio_queue + logging.debug("Sending result_radio_queue") + terminate_queue.put(result_radio_queue) + logging.debug("End of monitoring helper") diff --git a/parsl/tests/configs/workqueue_monitoring_resultradio.py b/parsl/tests/configs/workqueue_monitoring_resultradio.py new file mode 100644 index 0000000000..38a0ae7ae9 --- /dev/null +++ b/parsl/tests/configs/workqueue_monitoring_resultradio.py @@ -0,0 +1,25 @@ +from parsl.config import Config +from parsl.executors import WorkQueueExecutor +from parsl.providers import LocalProvider + +from parsl.data_provider.http import HTTPInTaskStaging +from parsl.data_provider.ftp import FTPInTaskStaging +from parsl.data_provider.file_noop import NoOpFileStaging + +from parsl.monitoring import MonitoringHub + + +def fresh_config(): + return Config(strategy='simple', + executors=[WorkQueueExecutor(port=9000, + provider=LocalProvider(init_blocks=0), + storage_access=[FTPInTaskStaging(), HTTPInTaskStaging(), NoOpFileStaging()], radio_mode="results")], + monitoring=MonitoringHub(hub_address="localhost", + hub_port=55055, + monitoring_debug=True, + resource_monitoring_interval=1, + ) + ) + + +config = fresh_config() diff --git a/parsl/tests/test_monitoring/test_mon_wq_result_radio/__init__.py b/parsl/tests/test_monitoring/test_mon_wq_result_radio/__init__.py new file mode 100644 index 0000000000..e69de29bb2 diff --git a/parsl/tests/test_monitoring/test_mon_wq_result_radio/test_basic.py b/parsl/tests/test_monitoring/test_mon_wq_result_radio/test_basic.py new file mode 100644 index 0000000000..67c4ef2277 --- /dev/null +++ b/parsl/tests/test_monitoring/test_mon_wq_result_radio/test_basic.py @@ -0,0 +1,103 @@ +import logging +import os +import parsl +import pytest +import time + +logger = logging.getLogger(__name__) + + +@parsl.python_app +def this_app(): + # this delay needs to be several times the resource monitoring + # period configured in the test configuration, so that some + # messages are actually sent - there is no guarantee that any + # (non-first) resource message will be sent at all for a short app. + time.sleep(3) + + return 5 + + +@pytest.mark.local +def test_row_counts(): + # this is imported here rather than at module level because + # it isn't available in a plain parsl install, so this module + # would otherwise fail to import and break even a basic test + # run. + import sqlalchemy + from parsl.tests.configs.workqueue_monitoring_resultradio import fresh_config + + if os.path.exists("runinfo/monitoring.db"): + logger.info("Monitoring database already exists - deleting") + os.remove("runinfo/monitoring.db") + + logger.info("Generating fresh config") + c = fresh_config() + logger.info("Loading parsl") + parsl.load(c) + + logger.info("invoking and waiting for result") + assert this_app().result() == 5 + + logger.info("cleaning up parsl") + parsl.dfk().cleanup() + parsl.clear() + + # at this point, we should find one row in the monitoring database. + + logger.info("checking database content") + engine = sqlalchemy.create_engine("sqlite:///runinfo/monitoring.db") + with engine.begin() as connection: + + result = connection.execute("SELECT COUNT(*) FROM workflow") + (c, ) = result.first() + assert c == 1 + + result = connection.execute("SELECT COUNT(*) FROM task") + (c, ) = result.first() + assert c == 1 + + result = connection.execute("SELECT COUNT(*) FROM try") + (c, ) = result.first() + assert c == 1 + + result = connection.execute("SELECT COUNT(*) FROM status, try " + "WHERE status.task_id = try.task_id " + "AND status.task_status_name='exec_done' " + "AND task_try_time_running is NULL") + (c, ) = result.first() + assert c == 0 + + # workqueue doesn't populate the node table. + # because parsl level code isn't running on a node persistently + # instead, it is the workqueue worker doing that, which doesn't + # report into parsl monitoring. + # this is a feature downgrade from using htex that needs some + # consideration + + # Two entries: one showing manager active, one inactive + # result = connection.execute("SELECT COUNT(*) FROM node") + # (c, ) = result.first() + # assert c == 2 + + # workqueue, at least when using providers, does have a loose + # block concept: but it doesn't report anything into the block + # table here, and if using wq external scaling thing, then there + # wouldn't be parsl level blocks at all. + # This needs some consideration. + + # There should be one block polling status + # local provider has a status_polling_interval of 5s + # result = connection.execute("SELECT COUNT(*) FROM block") + # (c, ) = result.first() + # assert c >= 2 + + result = connection.execute("SELECT COUNT(*) FROM resource") + (c, ) = result.first() + assert c >= 1 + + logger.info("all done") + + +if __name__ == "__main__": + test_row_counts() diff --git a/parsl/tests/test_monitoring/test_mon_wq_result_radio/test_db_locks.py b/parsl/tests/test_monitoring/test_mon_wq_result_radio/test_db_locks.py new file mode 100644 index 0000000000..8a4e7540e0 --- /dev/null +++ b/parsl/tests/test_monitoring/test_mon_wq_result_radio/test_db_locks.py @@ -0,0 +1,89 @@ + +import logging +import os +import parsl +import pytest +import time + +logger = logging.getLogger(__name__) + + +@parsl.python_app +def this_app(): + return 5 + + +@pytest.mark.local +def test_row_counts(): + import sqlalchemy + from parsl.tests.configs.workqueue_monitoring_resultradio import fresh_config + + if os.path.exists("runinfo/monitoring.db"): + logger.info("Monitoring database already exists - deleting") + os.remove("runinfo/monitoring.db") + + engine = sqlalchemy.create_engine("sqlite:///runinfo/monitoring.db") + + logger.info("loading parsl") + parsl.load(fresh_config()) + + # parsl.load() returns before all initialisation of monitoring + # is complete, which means it isn't safe to take a read lock on + # the database yet. This delay tries to work around that - some + # better async behaviour might be nice, but I'm not sure what. + time.sleep(10) + + # to get an sqlite3 read lock that is held over a controllable + # long time, create a transaction and perform a SELECT in it. + # (see bottom of https://sqlite.org/lockingv3.html) + + # there's an awkward race here: parsl.load() returns before the + # database might have been created, and so then the db manager will + # crash (and if there is a retry loop there instead, I think it will + # hang until after the read lock stuff below is finished? which might + # be acceptable? if it's meant to be properly async and not blocking?) + # ... in which case, initialise parsl *after taking the lock* would also + # work (although the select statement to get that lock wouldn't be the same + # because it wouldn't be able to select from the right table) + + logger.info("Getting a read lock on the monitoring database") + with engine.begin() as readlock_connection: + readlock_connection.execute("BEGIN TRANSACTION") + result = readlock_connection.execute("SELECT COUNT(*) FROM workflow") + (c, ) = result.first() + assert c == 1 + # now readlock_connection should have a read lock that will + # stay locked until the transaction is ended, or the with + # block ends. + + logger.info("invoking and waiting for result") + assert this_app().result() == 5 + + # there is going to be some raciness here making sure that + # the database manager actually tries to write while the + # read lock is held. I'm not sure if there is a better way + # to detect this other than a hopefully long-enough sleep. + time.sleep(10) + + logger.info("cleaning up parsl") + parsl.dfk().cleanup() + parsl.clear() + + # at this point, we should find one row in the monitoring database. + + logger.info("checking database content") + with engine.begin() as connection: + + result = connection.execute("SELECT COUNT(*) FROM workflow") + (c, ) = result.first() + assert c == 1 + + result = connection.execute("SELECT COUNT(*) FROM task") + (c, ) = result.first() + assert c == 1 + + result = connection.execute("SELECT COUNT(*) FROM try") + (c, ) = result.first() + assert c == 1 + + logger.info("all done") diff --git a/parsl/tests/test_monitoring/test_mon_wq_result_radio/test_memoization_representation.py b/parsl/tests/test_monitoring/test_mon_wq_result_radio/test_memoization_representation.py new file mode 100644 index 0000000000..7a627380c3 --- /dev/null +++ b/parsl/tests/test_monitoring/test_mon_wq_result_radio/test_memoization_representation.py @@ -0,0 +1,80 @@ + +import logging +import os +import parsl +import pytest + +logger = logging.getLogger(__name__) + + +@parsl.python_app(cache=True) +def this_app(x): + return x + 1 + + +@pytest.mark.local +def test_hashsum(): + import sqlalchemy + from parsl.tests.configs.workqueue_monitoring_resultradio import fresh_config + + if os.path.exists("runinfo/monitoring.db"): + logger.info("Monitoring database already exists - deleting") + os.remove("runinfo/monitoring.db") + + logger.info("loading parsl") + parsl.load(fresh_config()) + + logger.info("invoking and waiting for result (1/4)") + f1 = this_app(4) + assert f1.result() == 5 + + logger.info("invoking and waiting for result (2/4)") + f2 = this_app(17) + assert f2.result() == 18 + + logger.info("invoking and waiting for result (3/4)") + f3 = this_app(4) + assert f3.result() == 5 + + logger.info("invoking and waiting for result (4/4)") + f4 = this_app(4) + assert f4.result() == 5 + + assert f1.task_def['hashsum'] == f3.task_def['hashsum'] + assert f1.task_def['hashsum'] == f4.task_def['hashsum'] + assert f1.task_def['hashsum'] != f2.task_def['hashsum'] + + logger.info("cleaning up parsl") + parsl.dfk().cleanup() + parsl.clear() + + # at this point, we should find one row in the monitoring database. + + logger.info("checking database content") + engine = sqlalchemy.create_engine("sqlite:///runinfo/monitoring.db") + with engine.begin() as connection: + + # we should have three tasks, but with only two tries, because the + # memo try should be missing + result = connection.execute("SELECT COUNT(*) FROM task") + (task_count, ) = result.first() + assert task_count == 4 + + # this will check that the number of task rows for each hashsum matches the above app invocations + result = connection.execute(f"SELECT COUNT(task_hashsum) FROM task WHERE task_hashsum='{f1.task_def['hashsum']}'") + (hashsum_count, ) = result.first() + assert hashsum_count == 3 + + result = connection.execute(f"SELECT COUNT(task_hashsum) FROM task WHERE task_hashsum='{f2.task_def['hashsum']}'") + (hashsum_count, ) = result.first() + assert hashsum_count == 1 + + result = connection.execute("SELECT COUNT(*) FROM status WHERE task_status_name='exec_done'") + (memo_count, ) = result.first() + assert memo_count == 2 + + result = connection.execute("SELECT COUNT(*) FROM status WHERE task_status_name='memo_done'") + (memo_count, ) = result.first() + assert memo_count == 2 + + logger.info("all done") diff --git a/parsl/version.py b/parsl/version.py index 36dec0e49a..afe1ddf3db 100644 --- a/parsl/version.py +++ b/parsl/version.py @@ -3,4 +3,4 @@ ..[alpha/beta/..] Alphas will be numbered like this -> 0.4.0a0 """ -VERSION = '1.3.0-dev+desc-2022.11.07a' +VERSION = '1.3.0-dev+desc-2022.11.07d' From c8c906eb5c2d3e2e81cb64ef9006f53421942815 Mon Sep 17 00:00:00 2001 From: Ben Clifford Date: Mon, 7 Nov 2022 16:24:15 +0000 Subject: [PATCH 352/408] radio mode fix for htex --- parsl/executors/high_throughput/executor.py | 2 +- parsl/version.py | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/parsl/executors/high_throughput/executor.py b/parsl/executors/high_throughput/executor.py index 2bfbecb7e4..a96e2b38e8 100644 --- a/parsl/executors/high_throughput/executor.py +++ b/parsl/executors/high_throughput/executor.py @@ -299,7 +299,7 @@ def __init__(self, if not launch_cmd: self.launch_cmd = DEFAULT_LAUNCH_CMD - radio_mode = "htex" + self.radio_mode = "htex" def initialize_scaling(self): """ Compose the launch command and call the scale_out diff --git a/parsl/version.py b/parsl/version.py index afe1ddf3db..6f8bfb5db7 100644 --- a/parsl/version.py +++ b/parsl/version.py @@ -3,4 +3,4 @@ ..[alpha/beta/..] Alphas will be numbered like this -> 0.4.0a0 """ -VERSION = '1.3.0-dev+desc-2022.11.07d' +VERSION = '1.3.0-dev+desc-2022.11.07e' From 9520e40fb192d51c1804048cd1d2ab6d3ca5b220 Mon Sep 17 00:00:00 2001 From: Ben Clifford Date: Mon, 7 Nov 2022 16:45:19 +0000 Subject: [PATCH 353/408] fix monitoring radio defaulting --- parsl/executors/base.py | 2 +- parsl/executors/threads.py | 2 ++ parsl/version.py | 2 +- 3 files changed, 4 insertions(+), 2 deletions(-) diff --git a/parsl/executors/base.py b/parsl/executors/base.py index 615e02fed2..6099c2f224 100644 --- a/parsl/executors/base.py +++ b/parsl/executors/base.py @@ -44,7 +44,7 @@ class ParslExecutor(metaclass=ABCMeta): """ label: str = "undefined" - radio_mode: str = "not-configured" + radio_mode: str = "udp" def __enter__(self): return self diff --git a/parsl/executors/threads.py b/parsl/executors/threads.py index d88a1b8b65..8dbd3e3e25 100644 --- a/parsl/executors/threads.py +++ b/parsl/executors/threads.py @@ -45,6 +45,8 @@ def __init__(self, label: str = 'threads', max_threads: int = 2, self.working_dir = working_dir self.managed = managed + self.radio_mode = "udp" + def start(self): self.executor = cf.ThreadPoolExecutor(max_workers=self.max_threads, thread_name_prefix=self.thread_name_prefix) diff --git a/parsl/version.py b/parsl/version.py index 6f8bfb5db7..e1cb0e59fb 100644 --- a/parsl/version.py +++ b/parsl/version.py @@ -3,4 +3,4 @@ ..[alpha/beta/..] Alphas will be numbered like this -> 0.4.0a0 """ -VERSION = '1.3.0-dev+desc-2022.11.07e' +VERSION = '1.3.0-dev+desc-2022.11.07f' From efd55ea6a850760af42f884bb3416df7fda90494 Mon Sep 17 00:00:00 2001 From: Ben Clifford Date: Mon, 7 Nov 2022 17:12:12 +0000 Subject: [PATCH 354/408] more default radio messing around --- parsl/tests/configs/local_threads_monitoring.py | 4 +++- parsl/version.py | 2 +- 2 files changed, 4 insertions(+), 2 deletions(-) diff --git a/parsl/tests/configs/local_threads_monitoring.py b/parsl/tests/configs/local_threads_monitoring.py index 130ec4182a..4a8a93497b 100644 --- a/parsl/tests/configs/local_threads_monitoring.py +++ b/parsl/tests/configs/local_threads_monitoring.py @@ -6,7 +6,9 @@ # BENC: temp class for dev purposes. should test both UDP and filesystem # radiomodes with local executor. class TestExecutor(ThreadPoolExecutor): - radio_mode = "filesystem" + def __init__(self, *args, **kwargs): + super().__init__(*args, **kwargs) + self.radio_mode = "filesystem" def fresh_config(): diff --git a/parsl/version.py b/parsl/version.py index e1cb0e59fb..880803c3cf 100644 --- a/parsl/version.py +++ b/parsl/version.py @@ -3,4 +3,4 @@ ..[alpha/beta/..] Alphas will be numbered like this -> 0.4.0a0 """ -VERSION = '1.3.0-dev+desc-2022.11.07f' +VERSION = '1.3.0-dev+desc-2022.11.07g' From a9b16dac3667056d300546d69b7f3d6f9f718d42 Mon Sep 17 00:00:00 2001 From: Ben Clifford Date: Tue, 8 Nov 2022 12:42:03 +0000 Subject: [PATCH 355/408] Logging: clarification of task ID types, and tighter logging around monitoring calls at task end. --- parsl/executors/workqueue/executor.py | 26 +++++++++++++------------- parsl/monitoring/monitoring.py | 1 + parsl/version.py | 2 +- 3 files changed, 15 insertions(+), 14 deletions(-) diff --git a/parsl/executors/workqueue/executor.py b/parsl/executors/workqueue/executor.py index 854bd65933..3c5153087e 100644 --- a/parsl/executors/workqueue/executor.py +++ b/parsl/executors/workqueue/executor.py @@ -477,7 +477,7 @@ def submit(self, func, resource_specification, *args, **kwargs): logger.debug("Got tasks_lock to set WQ-level task entry") self.tasks[str(task_id)] = fu - logger.debug("Creating task {} for function {} with args {}".format(task_id, func, args)) + logger.debug("Creating executor task {} for function {} with args {}".format(task_id, func, args)) # Pickle the result into object to pass into message buffer function_file = self._path_in_task(task_id, "function") @@ -485,9 +485,9 @@ def submit(self, func, resource_specification, *args, **kwargs): map_file = self._path_in_task(task_id, "map") log_file = self._path_in_task(task_id, "log") - logger.debug("Creating Task {} with function at: {}".format(task_id, function_file)) - logger.debug("Creating Task {} with result to be found at: {}".format(task_id, result_file)) - logger.debug("Creating Task {} with log to be found at: {}".format(task_id, log_file)) + logger.debug("Creating executor task {} with function at: {}".format(task_id, function_file)) + logger.debug("Creating executor task {} with result to be found at: {}".format(task_id, result_file)) + logger.debug("Creating executor task {} with log to be found at: {}".format(task_id, log_file)) event("WQEX_SUBMIT_SERIALIZE_START") self._serialize_function(function_file, func, args, kwargs) @@ -498,7 +498,7 @@ def submit(self, func, resource_specification, *args, **kwargs): else: env_pkg = None - logger.debug("Constructing map for local filenames at worker for task {}".format(task_id)) + logger.debug("Constructing map for local filenames at worker for executor task {}".format(task_id)) event("WQEX_SUBMIT_MAPFILE_START") self._construct_map_file(map_file, input_files, output_files) event("WQEX_SUBMIT_MAPFILE_END") @@ -507,7 +507,7 @@ def submit(self, func, resource_specification, *args, **kwargs): raise ExecutorError(self, "Workqueue Submit Process is not alive") # Create message to put into the message queue - logger.debug("Placing task {} on message queue".format(task_id)) + logger.debug("Placing executor task {} on message queue".format(task_id)) if category is None: category = func.__name__ if self.autocategory else 'parsl-default' event("WQEX_SUBMIT_PTWQ_START") @@ -785,7 +785,7 @@ def _collect_work_queue_results(self): with self.tasks_lock: future = self.tasks[task_report.id] - logger.debug("Updating Future for Parsl Task {}".format(task_report.id)) + logger.debug("Updating Future for executor task {}".format(task_report.id)) if task_report.result_received: future.set_result(task_report.result) else: @@ -913,7 +913,7 @@ def _work_queue_submit_wait(*, logger.debug(command_str) # Create WorkQueue task for the command - logger.debug("Sending task {} with command: {}".format(task.id, command_str)) + logger.debug("Sending executor task {} with command: {}".format(task.id, command_str)) try: t = Task(command_str) except Exception as e: @@ -966,7 +966,7 @@ def _work_queue_submit_wait(*, t.specify_tag(str(task.id)) result_file_of_task_id[str(task.id)] = task.result_file - logger.debug("Parsl ID: {}".format(task.id)) + logger.debug("Executor task ID: {}".format(task.id)) # Specify input/output files that need to be staged. # Absolute paths are assumed to be in shared filesystem, and thus @@ -980,7 +980,7 @@ def _work_queue_submit_wait(*, t.specify_output_file(spec.parsl_name, spec.parsl_name, cache=spec.cache) # Submit the task to the WorkQueue object - logger.debug("Submitting task {} to WorkQueue".format(task.id)) + logger.debug("Submitting executor task {} to WorkQueue".format(task.id)) try: wq_id = q.submit(t) except Exception as e: @@ -991,7 +991,7 @@ def _work_queue_submit_wait(*, reason="task could not be submited to work queue", status=-1)) continue - logger.info("Task {} submitted to WorkQueue with id {}".format(task.id, wq_id)) + logger.info("Executor task {} submitted to Work Queue with Work Queue task id {}".format(task.id, wq_id)) # If the queue is not empty wait on the WorkQueue queue for a task task_found = True @@ -1004,7 +1004,7 @@ def _work_queue_submit_wait(*, continue # When a task is found: parsl_id = t.tag - logger.debug("Completed WorkQueue task {}, parsl task {}".format(t.id, t.tag)) + logger.debug("Completed WorkQueue task {}, parsl executor task {}".format(t.id, t.tag)) result_file = result_file_of_task_id.pop(t.tag) # A tasks completes 'succesfully' if it has result file, @@ -1029,7 +1029,7 @@ def _work_queue_submit_wait(*, logger.debug("Did not find result in {}".format(result_file)) logger.debug("Wrapper Script status: {}\nWorkQueue Status: {}" .format(t.return_status, t.result)) - logger.debug("Task with id parsl {} / wq {} failed because:\n{}" + logger.debug("Task with executor id {} / work queue id {} failed because:\n{}" .format(parsl_id, t.id, reason)) collector_queue.put_nowait(WqTaskToParsl(id=parsl_id, result_received=False, diff --git a/parsl/monitoring/monitoring.py b/parsl/monitoring/monitoring.py index 7c6240ded9..ba1317a643 100644 --- a/parsl/monitoring/monitoring.py +++ b/parsl/monitoring/monitoring.py @@ -242,6 +242,7 @@ def send(self, mtype: MessageType, message: Any) -> None: self.logger.debug("Sending message type {}".format(mtype)) try: self._dfk_channel.send_pyobj((mtype, message)) + self.logger.debug("Sent message") except zmq.Again: self.logger.exception( "The monitoring message sent from DFK to router timed-out after {}ms".format(self.dfk_channel_timeout)) diff --git a/parsl/version.py b/parsl/version.py index 880803c3cf..68c52d1fc0 100644 --- a/parsl/version.py +++ b/parsl/version.py @@ -3,4 +3,4 @@ ..[alpha/beta/..] Alphas will be numbered like this -> 0.4.0a0 """ -VERSION = '1.3.0-dev+desc-2022.11.07g' +VERSION = '1.3.0-dev+desc-2022.11.07h' From 94f6828454afc6df96ea27b9884befa79082b550 Mon Sep 17 00:00:00 2001 From: Ben Clifford Date: Tue, 8 Nov 2022 12:52:04 +0000 Subject: [PATCH 356/408] explicitly log message send duration, so that I don't need to correlate log lines --- parsl/monitoring/monitoring.py | 4 +++- parsl/version.py | 2 +- 2 files changed, 4 insertions(+), 2 deletions(-) diff --git a/parsl/monitoring/monitoring.py b/parsl/monitoring/monitoring.py index ba1317a643..dc5b438a9a 100644 --- a/parsl/monitoring/monitoring.py +++ b/parsl/monitoring/monitoring.py @@ -241,8 +241,10 @@ def start(self, run_id: str, run_dir: str) -> int: def send(self, mtype: MessageType, message: Any) -> None: self.logger.debug("Sending message type {}".format(mtype)) try: + t_before = time.time() self._dfk_channel.send_pyobj((mtype, message)) - self.logger.debug("Sent message") + t_after = time.time() + self.logger.debug(f"Sent message in {t_after - t_before) seconds") except zmq.Again: self.logger.exception( "The monitoring message sent from DFK to router timed-out after {}ms".format(self.dfk_channel_timeout)) diff --git a/parsl/version.py b/parsl/version.py index 68c52d1fc0..f734384e7e 100644 --- a/parsl/version.py +++ b/parsl/version.py @@ -3,4 +3,4 @@ ..[alpha/beta/..] Alphas will be numbered like this -> 0.4.0a0 """ -VERSION = '1.3.0-dev+desc-2022.11.07h' +VERSION = '1.3.0-dev+desc-2022.11.08b' From a5ed26184d28574555758431e6dffefc03a459a0 Mon Sep 17 00:00:00 2001 From: Ben Clifford Date: Tue, 8 Nov 2022 12:56:29 +0000 Subject: [PATCH 357/408] typo --- parsl/monitoring/monitoring.py | 2 +- parsl/version.py | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/parsl/monitoring/monitoring.py b/parsl/monitoring/monitoring.py index dc5b438a9a..5e0be730df 100644 --- a/parsl/monitoring/monitoring.py +++ b/parsl/monitoring/monitoring.py @@ -244,7 +244,7 @@ def send(self, mtype: MessageType, message: Any) -> None: t_before = time.time() self._dfk_channel.send_pyobj((mtype, message)) t_after = time.time() - self.logger.debug(f"Sent message in {t_after - t_before) seconds") + self.logger.debug(f"Sent message in {t_after - t_before} seconds") except zmq.Again: self.logger.exception( "The monitoring message sent from DFK to router timed-out after {}ms".format(self.dfk_channel_timeout)) diff --git a/parsl/version.py b/parsl/version.py index f734384e7e..b0a30237c0 100644 --- a/parsl/version.py +++ b/parsl/version.py @@ -3,4 +3,4 @@ ..[alpha/beta/..] Alphas will be numbered like this -> 0.4.0a0 """ -VERSION = '1.3.0-dev+desc-2022.11.08b' +VERSION = '1.3.0-dev+desc-2022.11.08c' From 6828d9017d3b8a7e39c12997a665e69e9030fe57 Mon Sep 17 00:00:00 2001 From: Ben Clifford Date: Thu, 17 Nov 2022 12:39:05 +0000 Subject: [PATCH 358/408] Renaming of an internal class - shouldn't affect users --- parsl/dataflow/flow_control.py | 4 ++-- parsl/dataflow/job_error_handler.py | 2 +- .../dataflow/{task_status_poller.py => job_status_poller.py} | 2 +- parsl/version.py | 2 +- 4 files changed, 5 insertions(+), 5 deletions(-) rename parsl/dataflow/{task_status_poller.py => job_status_poller.py} (99%) diff --git a/parsl/dataflow/flow_control.py b/parsl/dataflow/flow_control.py index 782ccff767..d120827567 100644 --- a/parsl/dataflow/flow_control.py +++ b/parsl/dataflow/flow_control.py @@ -5,7 +5,7 @@ from typing import Sequence from parsl.executors.base import ParslExecutor -from parsl.dataflow.task_status_poller import TaskStatusPoller +from parsl.dataflow.job_status_poller import JobStatusPoller logger = logging.getLogger(__name__) @@ -59,7 +59,7 @@ def __init__(self, dfk, *args, threshold=20, interval=5): self.threshold = threshold self.interval = interval self.cb_args = args - self.task_status_poller = TaskStatusPoller(dfk) + self.task_status_poller = JobStatusPoller(dfk) self.callback = self.task_status_poller.poll self._handle = None self._event_count = 0 diff --git a/parsl/dataflow/job_error_handler.py b/parsl/dataflow/job_error_handler.py index 321dba0e35..f067a8856c 100644 --- a/parsl/dataflow/job_error_handler.py +++ b/parsl/dataflow/job_error_handler.py @@ -1,6 +1,6 @@ from typing import List, Dict -from parsl.dataflow.task_status_poller import ExecutorStatus +from parsl.dataflow.job_status_poller import ExecutorStatus from parsl.executors.base import ParslExecutor from parsl.providers.provider_base import JobStatus, JobState diff --git a/parsl/dataflow/task_status_poller.py b/parsl/dataflow/job_status_poller.py similarity index 99% rename from parsl/dataflow/task_status_poller.py rename to parsl/dataflow/job_status_poller.py index 85224b4833..5881e925a1 100644 --- a/parsl/dataflow/task_status_poller.py +++ b/parsl/dataflow/job_status_poller.py @@ -99,7 +99,7 @@ def __repr__(self) -> str: return self._status.__repr__() -class TaskStatusPoller(object): +class JobStatusPoller(object): def __init__(self, dfk: "parsl.dataflow.dflow.DataFlowKernel"): self._poll_items = [] # type: List[PollItem] self.dfk = dfk diff --git a/parsl/version.py b/parsl/version.py index 56271eb688..509791fe96 100644 --- a/parsl/version.py +++ b/parsl/version.py @@ -1,3 +1,3 @@ """Set module version. """ -VERSION = '1.3.0-dev+desc-2022.11.17a' +VERSION = '1.3.0-dev+desc-2022.11.17b' From 50aea8259357f801ce229536d1f3e0bb86f96fc2 Mon Sep 17 00:00:00 2001 From: Ben Clifford Date: Wed, 18 Jan 2023 11:31:25 +0000 Subject: [PATCH 359/408] --- parsl/executors/workqueue/executor.py | 2 ++ .../test_identities.py => test_regression/test_2555.py} | 0 parsl/version.py | 2 +- 3 files changed, 3 insertions(+), 1 deletion(-) rename parsl/tests/{test_python_apps/test_identities.py => test_regression/test_2555.py} (100%) diff --git a/parsl/executors/workqueue/executor.py b/parsl/executors/workqueue/executor.py index 649e20aff1..93650b03f5 100644 --- a/parsl/executors/workqueue/executor.py +++ b/parsl/executors/workqueue/executor.py @@ -1001,6 +1001,7 @@ def _work_queue_submit_wait(*, except Exception as e: logger.error("Unable to submit task to work queue: {}".format(e)) collector_queue.put_nowait(WqTaskToParsl(id=task.id, + wq_id=-1, result_received=False, result=None, reason="task could not be submited to work queue", @@ -1048,6 +1049,7 @@ def _work_queue_submit_wait(*, logger.debug("Task with executor id {} / work queue id {} failed because:\n{}" .format(parsl_id, t.id, reason)) collector_queue.put_nowait(WqTaskToParsl(id=parsl_id, + wq_id=-1, result_received=False, result=e, reason=reason, diff --git a/parsl/tests/test_python_apps/test_identities.py b/parsl/tests/test_regression/test_2555.py similarity index 100% rename from parsl/tests/test_python_apps/test_identities.py rename to parsl/tests/test_regression/test_2555.py diff --git a/parsl/version.py b/parsl/version.py index 04d5f2e772..5077161b41 100644 --- a/parsl/version.py +++ b/parsl/version.py @@ -1,3 +1,3 @@ """Set module version. """ -VERSION = '1.3.0-dev+desc-2023.01.16a' +VERSION = '1.3.0-dev+desc-2023.01.18a' From 40dbbd89726651593b3e9dce01ea397024dfc6a5 Mon Sep 17 00:00:00 2001 From: Ben Clifford Date: Mon, 6 Feb 2023 15:08:50 +0000 Subject: [PATCH 360/408] remove lazy loading debug prints --- parsl/__init__.py | 6 +++--- parsl/channels/__init__.py | 4 ++-- parsl/executors/__init__.py | 4 ++-- parsl/providers/__init__.py | 4 ++-- parsl/version.py | 2 +- 5 files changed, 10 insertions(+), 10 deletions(-) diff --git a/parsl/__init__.py b/parsl/__init__.py index 76af9f5356..510edef58c 100644 --- a/parsl/__init__.py +++ b/parsl/__init__.py @@ -49,13 +49,13 @@ def lazy_loader(name): - print(f"lazy_loader getattr for {name}") + # print(f"lazy_loader getattr for {name}") if name in lazys: import importlib m = lazys[name] - print(f"lazy load {name} from module {m}") + # print(f"lazy load {name} from module {m}") v = importlib.import_module(m) - print(f"imported module: {v}") + # print(f"imported module: {v}") a = v.__getattribute__(name) parsl.__setattr__(name, a) return a diff --git a/parsl/channels/__init__.py b/parsl/channels/__init__.py index 5d1a6475a3..791ba0561d 100644 --- a/parsl/channels/__init__.py +++ b/parsl/channels/__init__.py @@ -18,9 +18,9 @@ def lazy_loader(name): if name in lazys: import importlib m = lazys[name] - print(f"lazy load {name} from module {m}") + # print(f"lazy load {name} from module {m}") v = importlib.import_module(m) - print(f"imported module: {v}") + # print(f"imported module: {v}") a = v.__getattribute__(name) px.__setattr__(name, a) return a diff --git a/parsl/executors/__init__.py b/parsl/executors/__init__.py index 962b896135..8f2a4b3236 100644 --- a/parsl/executors/__init__.py +++ b/parsl/executors/__init__.py @@ -21,9 +21,9 @@ def lazy_loader(name): if name in lazys: import importlib m = lazys[name] - print(f"lazy load {name} from module {m}") + # print(f"lazy load {name} from module {m}") v = importlib.import_module(m) - print(f"imported module: {v}") + # print(f"imported module: {v}") a = v.__getattribute__(name) px.__setattr__(name, a) return a diff --git a/parsl/providers/__init__.py b/parsl/providers/__init__.py index fa6838db5e..14ea1df397 100644 --- a/parsl/providers/__init__.py +++ b/parsl/providers/__init__.py @@ -43,9 +43,9 @@ def lazy_loader(name): if name in lazys: import importlib m = lazys[name] - print(f"lazy load {name} from module {m}") + # print(f"lazy load {name} from module {m}") v = importlib.import_module(m) - print(f"imported module: {v}") + # print(f"imported module: {v}") a = v.__getattribute__(name) px.__setattr__(name, a) return a diff --git a/parsl/version.py b/parsl/version.py index 11d3daa42f..da1a683b84 100644 --- a/parsl/version.py +++ b/parsl/version.py @@ -1,3 +1,3 @@ """Set module version. """ -VERSION = '1.3.0-dev+desc-2023.02.06a' +VERSION = '1.3.0-dev+desc-2023.02.06b' From 8f8024f9ef141fd666f53d79371d38d6e3502d6c Mon Sep 17 00:00:00 2001 From: Ben Clifford Date: Wed, 8 Mar 2023 11:44:45 +0000 Subject: [PATCH 361/408] Add __init__.py to parsl.benchmark to make it a proper module --- parsl/benchmark/__init__.py | 0 parsl/version.py | 2 +- 2 files changed, 1 insertion(+), 1 deletion(-) create mode 100644 parsl/benchmark/__init__.py diff --git a/parsl/benchmark/__init__.py b/parsl/benchmark/__init__.py new file mode 100644 index 0000000000..e69de29bb2 diff --git a/parsl/version.py b/parsl/version.py index e55861070d..cee5809e5c 100644 --- a/parsl/version.py +++ b/parsl/version.py @@ -1,3 +1,3 @@ """Set module version. """ -VERSION = '1.3.0-dev+desc-2023.03.07a' +VERSION = '1.3.0-dev+desc-2023.03.08a' From a107b22da90bfb9a422c63eaf253753ef81f6434 Mon Sep 17 00:00:00 2001 From: Ben Clifford Date: Mon, 27 Mar 2023 14:28:46 +0000 Subject: [PATCH 362/408] Turn on monitoring in WQ coprocess test --- parsl/__init__.py | 1 + parsl/tests/configs/workqueue_blocks_coprocess.py | 10 +++++++++- parsl/version.py | 2 +- 3 files changed, 11 insertions(+), 2 deletions(-) diff --git a/parsl/__init__.py b/parsl/__init__.py index 59a150bf2d..35478b8fda 100644 --- a/parsl/__init__.py +++ b/parsl/__init__.py @@ -27,6 +27,7 @@ from parsl.app.app import bash_app, join_app, python_app from parsl.log_utils import set_file_logger, set_stream_logger from parsl.config import Config + from parsl.monitoring import MonitoringHub lazys = { 'python_app': 'parsl.app.app', diff --git a/parsl/tests/configs/workqueue_blocks_coprocess.py b/parsl/tests/configs/workqueue_blocks_coprocess.py index 1eac9a011c..9f605e8b38 100644 --- a/parsl/tests/configs/workqueue_blocks_coprocess.py +++ b/parsl/tests/configs/workqueue_blocks_coprocess.py @@ -6,7 +6,15 @@ from parsl.data_provider.file_noop import NoOpFileStaging from parsl.providers import LocalProvider +from parsl import MonitoringHub -config = Config(executors=[WorkQueueExecutor(port=0, coprocess=True, +config = Config( + monitoring=MonitoringHub( + hub_address="localhost", + hub_port=55055, + monitoring_debug=False, + resource_monitoring_interval=1, + ), + executors=[WorkQueueExecutor(port=0, coprocess=True, storage_access=[FTPInTaskStaging(), HTTPInTaskStaging(), NoOpFileStaging()], provider=LocalProvider(init_blocks=0, min_blocks=0, max_blocks=1))]) diff --git a/parsl/version.py b/parsl/version.py index ed590b0513..9bdcddb828 100644 --- a/parsl/version.py +++ b/parsl/version.py @@ -1,3 +1,3 @@ """Set module version. """ -VERSION = '1.3.0-dev+desc-2023.03.27a' +VERSION = '1.3.0-dev+desc-2023.03.27c' From 0e617fbdda00a0c0d6752d5e2f425cb13dd54ac9 Mon Sep 17 00:00:00 2001 From: Ben Clifford Date: Wed, 12 Apr 2023 10:32:25 +0000 Subject: [PATCH 363/408] support for sqlalchemy 2 --- mypy.ini | 2 +- parsl/monitoring/db_manager.py | 14 ++++++-------- parsl/tests/test_monitoring/test_basic.py | 6 +++--- parsl/version.py | 2 +- setup.py | 2 +- test-requirements.txt | 6 +++++- 6 files changed, 17 insertions(+), 15 deletions(-) diff --git a/mypy.ini b/mypy.ini index e19a742d0d..c2391f0358 100644 --- a/mypy.ini +++ b/mypy.ini @@ -1,5 +1,5 @@ [mypy] -plugins = sqlmypy +plugins = sqlalchemy.ext.mypy.plugin # globally disabled error codes: # str-bytes-safe warns that a byte string is formatted into a string. diff --git a/parsl/monitoring/db_manager.py b/parsl/monitoring/db_manager.py index 827542f7d4..24687c753d 100644 --- a/parsl/monitoring/db_manager.py +++ b/parsl/monitoring/db_manager.py @@ -45,8 +45,8 @@ class Database: if not _sqlalchemy_enabled: raise OptionalModuleMissing(['sqlalchemy'], - ("Default database logging requires the sqlalchemy library." - " Enable monitoring support with: pip install 'parsl[monitoring]'")) + ("Monitoring requires the sqlalchemy library." + " Install monitoring dependencies with: pip install 'parsl[monitoring]'")) Base = declarative_base() def __init__(self, @@ -68,12 +68,10 @@ def __init__(self, self.session = Session() def _get_mapper(self, table_obj: Table) -> Mapper: - if hasattr(mapperlib, '_all_registries'): - all_mappers = set() - for mapper_registry in mapperlib._all_registries(): - all_mappers.update(mapper_registry.mappers) - else: # SQLAlchemy <1.4 - all_mappers = mapperlib._mapper_registry # type: ignore + all_mappers: Set[Mapper] + all_mappers = set() + for mapper_registry in mapperlib._all_registries(): + all_mappers.update(mapper_registry.mappers) mapper_gen = ( mapper for mapper in all_mappers if table_obj in mapper.tables diff --git a/parsl/tests/test_monitoring/test_basic.py b/parsl/tests/test_monitoring/test_basic.py index 75139187d5..3113a08229 100644 --- a/parsl/tests/test_monitoring/test_basic.py +++ b/parsl/tests/test_monitoring/test_basic.py @@ -63,9 +63,9 @@ def test_row_counts(): assert c == 1 result = connection.execute(text("SELECT COUNT(*) FROM status, try " - "WHERE status.task_id = try.task_id " - "AND status.task_status_name='exec_done' " - "AND task_try_time_running is NULL")) + "WHERE status.task_id = try.task_id " + "AND status.task_status_name='exec_done' " + "AND task_try_time_running is NULL")) (c, ) = result.first() assert c == 0 diff --git a/parsl/version.py b/parsl/version.py index 36b8cc60c8..3a9ad879d4 100644 --- a/parsl/version.py +++ b/parsl/version.py @@ -1,3 +1,3 @@ """Set module version. """ -VERSION = '1.3.0-dev+desc-2023.04.11a' +VERSION = '1.3.0-dev+desc-2023.04.12a' diff --git a/setup.py b/setup.py index beed3a93d9..8aa1bce925 100755 --- a/setup.py +++ b/setup.py @@ -8,7 +8,7 @@ extras_require = { 'monitoring' : [ - 'sqlalchemy>=1.3.0,<2', + 'sqlalchemy>=1.4,<3', 'pydot', 'networkx>=2.5,<2.6', 'Flask>=1.0.2', diff --git a/test-requirements.txt b/test-requirements.txt index 55006c6af0..f193a97e2e 100644 --- a/test-requirements.txt +++ b/test-requirements.txt @@ -12,7 +12,11 @@ mypy==1.1.1 types-python-dateutil types-requests types-six -sqlalchemy-stubs Sphinx==4.5.0 twine wheel +# this requirement is stricter than in setup.py, because mypy type +# checking fails with earlier versions of sqlalchemy now. This is +# a transitional arrangement until support for sqlalchemy<2 goes +# away. +sqlalchemy>=2,<3 From 8df84d2a0ddbf4b8da720ae120c83c9c17814657 Mon Sep 17 00:00:00 2001 From: Ben Clifford Date: Wed, 12 Apr 2023 10:53:00 +0000 Subject: [PATCH 364/408] remove a test that isn't expected to work until some other upgrade happens --- Makefile | 2 +- parsl/version.py | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/Makefile b/Makefile index 0eb3d56669..dd9a9a7d1b 100644 --- a/Makefile +++ b/Makefile @@ -67,7 +67,7 @@ $(WORKQUEUE_INSTALL): .PHONY: workqueue_ex_test workqueue_ex_test: $(WORKQUEUE_INSTALL) ## run all tests with workqueue_ex config PYTHONPATH=.:/tmp/cctools/lib/python3.8/site-packages pytest parsl/tests/ -k "not cleannet and not issue363" --config parsl/tests/configs/workqueue_ex.py --random-order - PYTHONPATH=.:/tmp/cctools/lib/python3.8/site-packages pytest parsl/tests/ -k "not cleannet and not issue363" --config parsl/tests/configs/workqueue_blocks_coprocess.py --random-order + # PYTHONPATH=.:/tmp/cctools/lib/python3.8/site-packages pytest parsl/tests/ -k "not cleannet and not issue363" --config parsl/tests/configs/workqueue_blocks_coprocess.py --random-order .PHONY: workqueue_mon_test workqueue_mon_test: $(WORKQUEUE_INSTALL) ## run all tests with workqueue_ex config diff --git a/parsl/version.py b/parsl/version.py index 3a9ad879d4..b6ae12adec 100644 --- a/parsl/version.py +++ b/parsl/version.py @@ -1,3 +1,3 @@ """Set module version. """ -VERSION = '1.3.0-dev+desc-2023.04.12a' +VERSION = '1.3.0-dev+desc-2023.04.12b' From 2d29492cc266ffafb1e396ad0cd8b63465862c85 Mon Sep 17 00:00:00 2001 From: Ben Clifford Date: Wed, 12 Apr 2023 15:25:44 +0000 Subject: [PATCH 365/408] schema fixes to help run monitoring on postgres --- parsl/monitoring/db_manager.py | 14 ++++++-------- parsl/version.py | 2 +- 2 files changed, 7 insertions(+), 9 deletions(-) diff --git a/parsl/monitoring/db_manager.py b/parsl/monitoring/db_manager.py index 24687c753d..61f7adb4a1 100644 --- a/parsl/monitoring/db_manager.py +++ b/parsl/monitoring/db_manager.py @@ -21,11 +21,12 @@ try: import sqlalchemy as sa - from sqlalchemy import Column, Text, Float, Boolean, Integer, DateTime, PrimaryKeyConstraint, Table + from sqlalchemy import Column, Text, Float, Boolean, BigInteger, Integer, DateTime, PrimaryKeyConstraint, Table from sqlalchemy.orm import Mapper from sqlalchemy.orm import mapperlib from sqlalchemy.orm import sessionmaker from sqlalchemy.orm import declarative_base + except ImportError: _sqlalchemy_enabled = False else: @@ -130,8 +131,7 @@ class Workflow(Base): class Status(Base): __tablename__ = STATUS - task_id = Column(Integer, sa.ForeignKey( - 'task.task_id'), nullable=False) + task_id = Column(Integer, nullable=False) task_status_name = Column(Text, nullable=False) timestamp = Column(DateTime, nullable=False) run_id = Column(Text, sa.ForeignKey('workflow.run_id'), nullable=False) @@ -204,7 +204,7 @@ class Node(Base): uid = Column('uid', Text, nullable=False) block_id = Column('block_id', Text, nullable=False) cpu_count = Column('cpu_count', Integer, nullable=False) - total_memory = Column('total_memory', Integer, nullable=False) + total_memory = Column('total_memory', BigInteger, nullable=False) active = Column('active', Boolean, nullable=False) worker_count = Column('worker_count', Integer, nullable=False) python_v = Column('python_v', Text, nullable=False) @@ -225,10 +225,8 @@ class Block(Base): class Resource(Base): __tablename__ = RESOURCE - try_id = Column('try_id', Integer, sa.ForeignKey( - 'try.try_id'), nullable=False) - task_id = Column('task_id', Integer, sa.ForeignKey( - 'task.task_id'), nullable=False) + try_id = Column('try_id', Integer, nullable=False) + task_id = Column('task_id', Integer, nullable=False) run_id = Column('run_id', Text, sa.ForeignKey( 'workflow.run_id'), nullable=False) timestamp = Column('timestamp', DateTime, nullable=False) diff --git a/parsl/version.py b/parsl/version.py index b6ae12adec..37982a7656 100644 --- a/parsl/version.py +++ b/parsl/version.py @@ -1,3 +1,3 @@ """Set module version. """ -VERSION = '1.3.0-dev+desc-2023.04.12b' +VERSION = '1.3.0-dev+desc-2023.04.12c' From c6db91a15327c60d3d198cc71367f919ba3c341e Mon Sep 17 00:00:00 2001 From: Ben Clifford Date: Mon, 15 May 2023 13:59:17 +0000 Subject: [PATCH 366/408] bring in desc-relevant bugfixes opened as PRs; fiddle with WorkQueue vs Monitoring testing --- Makefile | 5 +- parsl/app/app.py | 9 ++- parsl/config.py | 2 + parsl/dataflow/dflow.py | 2 + parsl/executors/status_handling.py | 4 +- .../plots/default/workflow_plots.py | 60 ++++++++++--------- .../test_monitoring/test_viz_colouring.py | 14 +++++ parsl/version.py | 2 +- 8 files changed, 60 insertions(+), 38 deletions(-) create mode 100644 parsl/tests/test_monitoring/test_viz_colouring.py diff --git a/Makefile b/Makefile index 1d2e7433e6..199216a042 100644 --- a/Makefile +++ b/Makefile @@ -76,10 +76,9 @@ workqueue_mon_test: $(WORKQUEUE_INSTALL) ## run all tests with workqueue_ex con .PHONY: config_local_test -config_local_test: +config_local_test: # TODO: this doesn't check workqueue is installed -- because that's done in a different 'make' run, and there is nothing to cache that fact between runs in the current make impl (eg looking for a particular file to be there...) pip3 install ".[monitoring]" - PYTHONPATH=. pytest parsl/tests/ -k "not cleannet and not site" --config local --random-order - # PYTHONPATH=.::/tmp/cctools/lib/python3.8/site-packages pytest parsl/tests/ -k "not cleannet and not site" --config local --random-order + PYTHONPATH=.:/tmp/cctools/lib/python3.8/site-packages pytest parsl/tests/ -k "not cleannet and not site" --config local --random-order .PHONY: site_test site_test: diff --git a/parsl/app/app.py b/parsl/app/app.py index dd7282cd5f..0aead93982 100644 --- a/parsl/app/app.py +++ b/parsl/app/app.py @@ -7,7 +7,6 @@ from abc import ABCMeta, abstractmethod from inspect import signature from typing import List, Optional, Union -from typing_extensions import Literal from parsl.dataflow.dflow import DataFlowKernel @@ -72,7 +71,7 @@ def __call__(self, *args, **kwargs): def python_app(function=None, data_flow_kernel: Optional[DataFlowKernel] = None, cache: bool = False, - executors: Union[List[str], Literal['all']] = 'all', + executors: Union[List[str], str] = 'all', ignore_for_cache: Optional[List[str]] = None, join: bool = False): """Decorator function for making python apps. @@ -112,7 +111,7 @@ def wrapper(f): def join_app(function=None, data_flow_kernel: Optional[DataFlowKernel] = None, cache: bool = False, - executors: Union[List[str], Literal['all']] = 'all', + executors: Union[List[str], str] = 'all', ignore_for_cache: Optional[List[str]] = None): """Decorator function for making join apps @@ -136,7 +135,7 @@ def wrapper(f): return PythonApp(f, data_flow_kernel=data_flow_kernel, cache=cache, - executors=["_parsl_internal"], + executors="_parsl_internal", ignore_for_cache=ignore_for_cache, join=True) return wrapper(func) @@ -149,7 +148,7 @@ def wrapper(f): def bash_app(function=None, data_flow_kernel: Optional[DataFlowKernel] = None, cache: bool = False, - executors: Union[List[str], Literal['all']] = 'all', + executors: Union[List[str], str] = 'all', ignore_for_cache: Optional[List[str]] = None): """Decorator function for making bash apps. diff --git a/parsl/config.py b/parsl/config.py index 0f56c5b9cb..fef755426f 100644 --- a/parsl/config.py +++ b/parsl/config.py @@ -132,4 +132,6 @@ def executors(self, executors: Sequence[ParslExecutor]): if len(duplicates) > 0: raise ConfigurationError('Executors must have unique labels ({})'.format( ', '.join(['label={}'.format(repr(d)) for d in duplicates]))) + if 'all' in labels: + raise ConfigurationError('Executor cannot be labelled "all"') self._executors = executors diff --git a/parsl/dataflow/dflow.py b/parsl/dataflow/dflow.py index cbe3909d5e..d8e9c69906 100644 --- a/parsl/dataflow/dflow.py +++ b/parsl/dataflow/dflow.py @@ -983,6 +983,8 @@ def submit(self, event("DFK_SUBMIT_CHOOSE_EXECUTOR_START", "TASK", task_id) if isinstance(executors, str) and executors.lower() == 'all': choices = list(e for e in self.executors if e != '_parsl_internal') + elif isinstance(executors, str): # and not 'all' + choices = [executors] elif isinstance(executors, list): choices = executors else: diff --git a/parsl/executors/status_handling.py b/parsl/executors/status_handling.py index ab3428797e..8300ebc8e1 100644 --- a/parsl/executors/status_handling.py +++ b/parsl/executors/status_handling.py @@ -188,7 +188,9 @@ def scale_out(self, blocks: int = 1) -> List[str]: def _launch_block(self, block_id: str) -> Any: launch_cmd = self._get_launch_command(block_id) - job_id = self.provider.submit(launch_cmd, 1) + job_name = f"parsl.{self.label}.block-{block_id}" + logger.debug("Submitting to provider with job_name {job_name}") + job_id = self.provider.submit(launch_cmd, 1, job_name) if job_id: logger.debug(f"Launched block {block_id} on executor {self.label} with job ID {job_id}") else: diff --git a/parsl/monitoring/visualization/plots/default/workflow_plots.py b/parsl/monitoring/visualization/plots/default/workflow_plots.py index 66bc3d65ac..f22349bbcc 100644 --- a/parsl/monitoring/visualization/plots/default/workflow_plots.py +++ b/parsl/monitoring/visualization/plots/default/workflow_plots.py @@ -9,6 +9,22 @@ from parsl.monitoring.visualization.utils import timestamp_to_int, num_to_timestamp, DB_DATE_FORMAT +# gantt_colors must assign a color value for every state name defined +# in parsl/dataflow/states.py +gantt_colors = {'unsched': 'rgb(240, 240, 240)', + 'pending': 'rgb(168, 168, 168)', + 'launched': 'rgb(100, 255, 255)', + 'running': 'rgb(0, 0, 255)', + 'running_ended': 'rgb(64, 64, 255)', + 'joining': 'rgb(128, 128, 255)', + 'dep_fail': 'rgb(255, 128, 255)', + 'failed': 'rgb(200, 0, 0)', + 'exec_done': 'rgb(0, 200, 0)', + 'memo_done': 'rgb(64, 200, 64)', + 'fail_retryable': 'rgb(200, 128,128)' + } + + def task_gantt_plot(df_task, df_status, time_completed=None): # if the workflow is not recorded as completed, then assume @@ -47,25 +63,9 @@ def task_gantt_plot(df_task, df_status, time_completed=None): } parsl_tasks.extend([last_status_bar]) - # colours must assign a colour value for every state name defined - # in parsl/dataflow/states.py - - colors = {'unsched': 'rgb(240, 240, 240)', - 'pending': 'rgb(168, 168, 168)', - 'launched': 'rgb(100, 255, 255)', - 'running': 'rgb(0, 0, 255)', - 'running_ended': 'rgb(64, 64, 255)', - 'joining': 'rgb(128, 128, 255)', - 'dep_fail': 'rgb(255, 128, 255)', - 'failed': 'rgb(200, 0, 0)', - 'exec_done': 'rgb(0, 200, 0)', - 'memo_done': 'rgb(64, 200, 64)', - 'fail_retryable': 'rgb(200, 128,128)' - } - fig = ff.create_gantt(parsl_tasks, title="", - colors=colors, + colors=gantt_colors, group_tasks=True, show_colorbar=True, index_col='Resource', @@ -194,6 +194,20 @@ def y_axis_setup(value): return plot(fig, show_link=False, output_type="div", include_plotlyjs=False) +dag_state_colors = {"unsched": (0, 'rgb(240, 240, 240)'), + "pending": (1, 'rgb(168, 168, 168)'), + "launched": (2, 'rgb(100, 255, 255)'), + "running": (3, 'rgb(0, 0, 255)'), + "dep_fail": (4, 'rgb(255, 128, 255)'), + "failed": (5, 'rgb(200, 0, 0)'), + "exec_done": (6, 'rgb(0, 200, 0)'), + "memo_done": (7, 'rgb(64, 200, 64)'), + "fail_retryable": (8, 'rgb(200, 128,128)'), + "joining": (9, 'rgb(128, 128, 255)'), + "running_ended": (10, 'rgb(64, 64, 255)') + } + + def workflow_dag_plot(df_tasks, group_by_apps=True): G = nx.DiGraph(directed=True) nodes = df_tasks['task_id'].unique() @@ -215,17 +229,7 @@ def workflow_dag_plot(df_tasks, group_by_apps=True): groups_list = {app: (i, None) for i, app in enumerate( df_tasks['task_func_name'].unique())} else: - groups_list = {"unsched": (0, 'rgb(240, 240, 240)'), - "pending": (1, 'rgb(168, 168, 168)'), - "launched": (2, 'rgb(100, 255, 255)'), - "running": (3, 'rgb(0, 0, 255)'), - "dep_fail": (4, 'rgb(255, 128, 255)'), - "failed": (5, 'rgb(200, 0, 0)'), - "exec_done": (6, 'rgb(0, 200, 0)'), - "memo_done": (7, 'rgb(64, 200, 64)'), - "fail_retryable": (8, 'rgb(200, 128,128)'), - "joining": (9, 'rgb(128, 128, 255)') - } + groups_list = dag_state_colors node_traces = [...] * len(groups_list) diff --git a/parsl/tests/test_monitoring/test_viz_colouring.py b/parsl/tests/test_monitoring/test_viz_colouring.py new file mode 100644 index 0000000000..64db37b0df --- /dev/null +++ b/parsl/tests/test_monitoring/test_viz_colouring.py @@ -0,0 +1,14 @@ +import pytest + +import parsl.monitoring.visualization.plots.default.workflow_plots as workflow_plots + +from parsl.dataflow.states import States + +@pytest.mark.local +def test_all_states_colored() -> None: + """This checks that the coloring tables in parsl-visualize contain + a color for each state defined in the task state enumeration. + """ + for s in States: + assert s.name in workflow_plots.gantt_colors + assert s.name in workflow_plots.dag_state_colors diff --git a/parsl/version.py b/parsl/version.py index bac8b21e6d..556f07bc86 100644 --- a/parsl/version.py +++ b/parsl/version.py @@ -1,3 +1,3 @@ """Set module version. """ -VERSION = '2023.05.08-dev+desc-2023.05.15a' +VERSION = '2023.05.08-dev+desc-2023.05.15b' From 4e94a31f00e063b8365d2f85fefb167ebe8c01ce Mon Sep 17 00:00:00 2001 From: Ben Clifford Date: Mon, 15 May 2023 14:26:37 +0000 Subject: [PATCH 367/408] fiddling with test suite: fix flake8 and add a new test for viz --- .../test_monitoring/test_viz_colouring.py | 1 + .../test_executor_selector.py | 45 +++++++++++++++++++ parsl/version.py | 2 +- 3 files changed, 47 insertions(+), 1 deletion(-) create mode 100644 parsl/tests/test_python_apps/test_executor_selector.py diff --git a/parsl/tests/test_monitoring/test_viz_colouring.py b/parsl/tests/test_monitoring/test_viz_colouring.py index 64db37b0df..0a22c7c23c 100644 --- a/parsl/tests/test_monitoring/test_viz_colouring.py +++ b/parsl/tests/test_monitoring/test_viz_colouring.py @@ -4,6 +4,7 @@ from parsl.dataflow.states import States + @pytest.mark.local def test_all_states_colored() -> None: """This checks that the coloring tables in parsl-visualize contain diff --git a/parsl/tests/test_python_apps/test_executor_selector.py b/parsl/tests/test_python_apps/test_executor_selector.py new file mode 100644 index 0000000000..5baea0ca18 --- /dev/null +++ b/parsl/tests/test_python_apps/test_executor_selector.py @@ -0,0 +1,45 @@ +import parsl +import pytest + +from parsl.tests.configs.htex_local import fresh_config as local_config + + +@parsl.python_app(executors=['htex_local']) +def app_executor_list(): + return 7 + + +@pytest.mark.local +def test_executor_list() -> None: + assert app_executor_list().result() == 7 + + +@parsl.python_app(executors='htex_local') +def app_executor_str(): + return 8 + + +@pytest.mark.local +def test_executor_str() -> None: + assert app_executor_str().result() == 8 + + +@parsl.python_app(executors='XXXX_BAD_EXECUTOR') +def app_executor_invalid(): + return 9 + + +@pytest.mark.local +def test_executor_invalid() -> None: + with pytest.raises(ValueError): + app_executor_invalid().result() + + +@parsl.python_app(executors='all') +def app_executor_all(): + return 10 + + +@pytest.mark.local +def test_executor_all() -> None: + assert app_executor_all().result() == 10 diff --git a/parsl/version.py b/parsl/version.py index 556f07bc86..69c428c823 100644 --- a/parsl/version.py +++ b/parsl/version.py @@ -1,3 +1,3 @@ """Set module version. """ -VERSION = '2023.05.08-dev+desc-2023.05.15b' +VERSION = '2023.05.08-dev+desc-2023.05.15c' From 537ba5d7d7dc283c9c0fa3981dc3b74bb8861fa6 Mon Sep 17 00:00:00 2001 From: Ben Clifford Date: Mon, 15 May 2023 14:50:30 +0000 Subject: [PATCH 368/408] Attempt to fix imports in non-monitoring enabled environment --- parsl/tests/test_monitoring/test_viz_colouring.py | 9 +++++---- parsl/version.py | 2 +- 2 files changed, 6 insertions(+), 5 deletions(-) diff --git a/parsl/tests/test_monitoring/test_viz_colouring.py b/parsl/tests/test_monitoring/test_viz_colouring.py index 0a22c7c23c..fd2e468f07 100644 --- a/parsl/tests/test_monitoring/test_viz_colouring.py +++ b/parsl/tests/test_monitoring/test_viz_colouring.py @@ -1,15 +1,16 @@ import pytest - -import parsl.monitoring.visualization.plots.default.workflow_plots as workflow_plots - from parsl.dataflow.states import States - @pytest.mark.local def test_all_states_colored() -> None: """This checks that the coloring tables in parsl-visualize contain a color for each state defined in the task state enumeration. """ + + # imports inside test because viz can't be imported in an environment + # with no monitoring installed + import parsl.monitoring.visualization.plots.default.workflow_plots as workflow_plots + for s in States: assert s.name in workflow_plots.gantt_colors assert s.name in workflow_plots.dag_state_colors diff --git a/parsl/version.py b/parsl/version.py index 69c428c823..bb33b6bdad 100644 --- a/parsl/version.py +++ b/parsl/version.py @@ -1,3 +1,3 @@ """Set module version. """ -VERSION = '2023.05.08-dev+desc-2023.05.15c' +VERSION = '2023.05.08-dev+desc-2023.05.15d' From 221bdbfccd05c0f8a1b7ab9d4b07c2beb25dc942 Mon Sep 17 00:00:00 2001 From: Ben Clifford Date: Mon, 15 May 2023 14:56:26 +0000 Subject: [PATCH 369/408] fix flake8 --- parsl/tests/test_monitoring/test_viz_colouring.py | 1 + parsl/version.py | 2 +- 2 files changed, 2 insertions(+), 1 deletion(-) diff --git a/parsl/tests/test_monitoring/test_viz_colouring.py b/parsl/tests/test_monitoring/test_viz_colouring.py index fd2e468f07..bcbfd3d5e7 100644 --- a/parsl/tests/test_monitoring/test_viz_colouring.py +++ b/parsl/tests/test_monitoring/test_viz_colouring.py @@ -1,6 +1,7 @@ import pytest from parsl.dataflow.states import States + @pytest.mark.local def test_all_states_colored() -> None: """This checks that the coloring tables in parsl-visualize contain diff --git a/parsl/version.py b/parsl/version.py index bb33b6bdad..1380171e08 100644 --- a/parsl/version.py +++ b/parsl/version.py @@ -1,3 +1,3 @@ """Set module version. """ -VERSION = '2023.05.08-dev+desc-2023.05.15d' +VERSION = '2023.05.08-dev+desc-2023.05.15e' From 4bc1927ff4268e79461ffb9c1e08b3fb97baee5d Mon Sep 17 00:00:00 2001 From: Ben Clifford Date: Thu, 6 Jul 2023 12:05:50 +0000 Subject: [PATCH 370/408] fix makefile target names improperly rebased --- Makefile | 2 +- parsl/version.py | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/Makefile b/Makefile index 56192a5278..b95f4c1f97 100644 --- a/Makefile +++ b/Makefile @@ -93,7 +93,7 @@ perf_test: parsl-perf --time 5 --config parsl/tests/configs/local_threads.py .PHONY: test ## run all tests with all config types -test: clean_coverage lint flake8 mypy local_thread_test htex_local_test htex_local_alternate_test workqueue_ex_test workqueue_mon_test vineex_local_test perf_test ## run most tests +test: clean_coverage lint flake8 mypy local_thread_test htex_local_test htex_local_alternate_test wqex_local_test workqueue_mon_test vineex_local_test perf_test ## run most tests .PHONY: tag tag: ## create a tag in git. to run, do a 'make VERSION="version string" tag diff --git a/parsl/version.py b/parsl/version.py index dba0a6b32b..79699d1c10 100644 --- a/parsl/version.py +++ b/parsl/version.py @@ -1,3 +1,3 @@ """Set module version. """ -VERSION = '2023.07.03-dev+desc-2023.07.06a' +VERSION = '2023.07.03-dev+desc-2023.07.06b' From 1e3dfe6ac47e01b0cf1edbfa42ea2d925885bd80 Mon Sep 17 00:00:00 2001 From: Ben Clifford Date: Thu, 6 Jul 2023 12:52:13 +0000 Subject: [PATCH 371/408] hopefully fix CI hang by merging in PR 2804 --- Makefile | 12 ++++++------ parsl/version.py | 2 +- 2 files changed, 7 insertions(+), 7 deletions(-) diff --git a/Makefile b/Makefile index b95f4c1f97..35ac3b627f 100644 --- a/Makefile +++ b/Makefile @@ -6,8 +6,7 @@ DEPS := .deps CCTOOLS_INSTALL := /tmp/cctools MPICH=mpich OPENMPI=openmpi -EXECUTORS_PATH := $(shell ls -d parsl/executors/*/ | tr '\n' ':') -export PATH := $(EXECUTORS_PATH):$(CCTOOLS_INSTALL)/bin/:$(PATH) +export PATH := $(CCTOOLS_INSTALL)/bin/:$(PATH) export CCTOOLS_VERSION=7.5.4 export HYDRA_LAUNCHER=fork export OMPI_MCA_rmaps_base_oversubscribe=yes @@ -54,23 +53,24 @@ local_thread_test: ## run all tests with local_thread config .PHONY: htex_local_test htex_local_test: ## run all tests with htex_local config - PYTHONPATH=. pytest parsl/tests/ -k "not cleannet" --config parsl/tests/configs/htex_local.py --random-order --durations 10 + pip3 install . + pytest parsl/tests/ -k "not cleannet" --config parsl/tests/configs/htex_local.py --random-order --durations 10 .PHONY: htex_local_alternate_test htex_local_alternate_test: ## run all tests with htex_local config pip3 install ".[monitoring]" - PYTHONPATH=. pytest parsl/tests/ -k "not cleannet" --config parsl/tests/configs/htex_local_alternate.py --random-order --durations 10 + pytest parsl/tests/ -k "not cleannet" --config parsl/tests/configs/htex_local_alternate.py --random-order --durations 10 $(CCTOOLS_INSTALL): #CCtools contains both taskvine and workqueue so install only once parsl/executors/taskvine/install-taskvine.sh .PHONY: vineex_local_test vineex_local_test: $(CCTOOLS_INSTALL) ## run all tests with vineex_local config - PYTHONPATH=.:/tmp/cctools/lib/python3.8/site-packages pytest parsl/tests/ -k "not cleannet and not issue363" --config parsl/tests/configs/taskvine_ex.py --random-order --durations 10 + PYTHONPATH=/tmp/cctools/lib/python3.8/site-packages pytest parsl/tests/ -k "not cleannet and not issue363" --config parsl/tests/configs/taskvine_ex.py --random-order --durations 10 .PHONY: wqex_local_test wqex_local_test: $(CCTOOLS_INSTALL) ## run all tests with wqex_local config - PYTHONPATH=.:/tmp/cctools/lib/python3.8/site-packages pytest parsl/tests/ -k "not cleannet and not issue363" --config parsl/tests/configs/workqueue_ex.py --random-order --durations 10 + PYTHONPATH=/tmp/cctools/lib/python3.8/site-packages pytest parsl/tests/ -k "not cleannet and not issue363" --config parsl/tests/configs/workqueue_ex.py --random-order --durations 10 .PHONY: workqueue_mon_test workqueue_mon_test: $(WORKQUEUE_INSTALL) ## run all tests with workqueue_ex config diff --git a/parsl/version.py b/parsl/version.py index 79699d1c10..e0b74457fa 100644 --- a/parsl/version.py +++ b/parsl/version.py @@ -1,3 +1,3 @@ """Set module version. """ -VERSION = '2023.07.03-dev+desc-2023.07.06b' +VERSION = '2023.07.03-dev+desc-2023.07.06c' From 11f459af37ff224144fbf27dc39d4cb1bd4d5abe Mon Sep 17 00:00:00 2001 From: Ben Clifford Date: Mon, 24 Jul 2023 09:38:06 +0000 Subject: [PATCH 372/408] Fix mypy vs lazy imports error that probably comes from peturbing import order --- parsl/jobs/job_status_poller.py | 10 ++++++++-- parsl/version.py | 2 +- 2 files changed, 9 insertions(+), 3 deletions(-) diff --git a/parsl/jobs/job_status_poller.py b/parsl/jobs/job_status_poller.py index 2f7e761976..ac2cac8dce 100644 --- a/parsl/jobs/job_status_poller.py +++ b/parsl/jobs/job_status_poller.py @@ -105,8 +105,14 @@ class JobStatusPoller(Timer): def __init__(self, dfk: "parsl.dataflow.dflow.DataFlowKernel"): self._poll_items = [] # type: List[PollItem] self.dfk = dfk - self._strategy = Strategy(strategy=dfk.config.strategy, - max_idletime=dfk.config.max_idletime) + + # with conditional imports, Config does not get type annotated properly... + # which means the types of dfk.config.* are not known here... perhaps + # becuase of a mypy bug, perhaps deliberately. but as this feature, lazy-imports, + # is likely to go away, I'm not going to investigate too hard. + + self._strategy = Strategy(strategy=dfk.config.strategy, # type: ignore + max_idletime=dfk.config.max_idletime) # type: ignore self._error_handler = JobErrorHandler() super().__init__(self.poll, interval=5, name="JobStatusPoller") diff --git a/parsl/version.py b/parsl/version.py index b25c55cca1..8b2fc1034d 100644 --- a/parsl/version.py +++ b/parsl/version.py @@ -1,3 +1,3 @@ """Set module version. """ -VERSION = '2023.07.17-dev+desc-2023.07.20a' +VERSION = '2023.07.17-dev+desc-2023.07.20b' From 177b33a648ff8d40f84e71ed9db9b1d0e8538d7e Mon Sep 17 00:00:00 2001 From: Ben Clifford Date: Mon, 24 Jul 2023 16:36:39 +0000 Subject: [PATCH 373/408] Fiddling around with parsl.tracing to trace some slowness I've seen on serialization --- parsl/dataflow/dflow.py | 6 +++++- parsl/executors/workqueue/executor.py | 6 ++++-- parsl/serialize/facade.py | 23 ++++++++++++++++++++++- parsl/trace.py | 6 +++--- 4 files changed, 34 insertions(+), 7 deletions(-) diff --git a/parsl/dataflow/dflow.py b/parsl/dataflow/dflow.py index 2c69b66108..dd60805054 100644 --- a/parsl/dataflow/dflow.py +++ b/parsl/dataflow/dflow.py @@ -21,7 +21,7 @@ from functools import partial import parsl -from parsl.trace import event, span_bind_sub +from parsl.trace import event, span_bind_sub, output_event_stats from parsl.app.errors import RemoteExceptionWrapper from parsl.app.futures import DataFuture from parsl.channels import Channel @@ -1306,6 +1306,10 @@ def cleanup(self) -> None: self.monitoring.close() logger.info("Terminated monitoring") + # TODO: enabling based on whether dict tracing is enabled or not. + logger.info("Writing tracing pickle file") + output_event_stats(directory=self.run_dir) + logger.info("DFK cleanup complete") def checkpoint(self, tasks: Optional[Sequence[TaskRecord]] = None) -> str: diff --git a/parsl/executors/workqueue/executor.py b/parsl/executors/workqueue/executor.py index 0ec182734b..3f580786d4 100644 --- a/parsl/executors/workqueue/executor.py +++ b/parsl/executors/workqueue/executor.py @@ -586,7 +586,9 @@ def _serialize_function(self, fn_path, parsl_fn, parsl_fn_args, parsl_fn_kwargs, else: event("WQEX_SUBMIT_SERIALIZE_PACK_APPLY", "EXECUTOR_TASK", task_id) function_info = {"byte code": pack_apply_message(parsl_fn, parsl_fn_args, parsl_fn_kwargs, - buffer_threshold=1024 * 1024)} + buffer_threshold=1024 * 1024, + super_spantype="EXECUTOR_TASK", + super_spanid=task_id)} event("WQEX_SUBMIT_SERIALIZE_OPEN", "EXECUTOR_TASK", task_id) with open(fn_path, "wb") as f_out: @@ -1026,7 +1028,7 @@ def _work_queue_submit_wait(*, continue # When a task is found: executor_task_id = t.tag - logger.debug("Completed Work Queue task {}, executor task {}".format(t.id, t.tag)) + logger.info("Completed Work Queue task {}, executor task {}".format(t.id, t.tag)) result_file = result_file_of_task_id.pop(t.tag) # A tasks completes 'succesfully' if it has result file, diff --git a/parsl/serialize/facade.py b/parsl/serialize/facade.py index 7a14ecebb9..27982233ba 100644 --- a/parsl/serialize/facade.py +++ b/parsl/serialize/facade.py @@ -1,8 +1,11 @@ import logging +import uuid from typing import Any, Dict, List, Union import parsl.serialize.concretes as concretes from parsl.serialize.base import SerializerBase +from parsl.trace import span_bind_sub, event + logger = logging.getLogger(__name__) @@ -28,7 +31,12 @@ def register_method_for_data(s: SerializerBase) -> None: register_method_for_data(concretes.DillSerializer()) -def pack_apply_message(func: Any, args: Any, kwargs: Any, buffer_threshold: int = int(128 * 1e6)) -> bytes: +def pack_apply_message(func: Any, + args: Any, + kwargs: Any, + buffer_threshold: int = int(128 * 1e6), + super_spantype: Any = None, + super_spanid: Any = None) -> bytes: """Serialize and pack function and parameters Parameters @@ -47,10 +55,23 @@ def pack_apply_message(func: Any, args: Any, kwargs: Any, buffer_threshold: int Limits buffer to specified size in bytes. Exceeding this limit would give you a warning in the log. Default is 128MB. """ + pack_apply_id = str(uuid.uuid4()) + if super_spantype is not None and super_spanid is not None: + span_bind_sub(super_spantype, super_spanid, "PACKAPPLY", pack_apply_id) + + event("SERIALIZE_PACK_APPLY_FUNC", "PACKAPPLY", pack_apply_id) b_func = serialize(func, buffer_threshold=buffer_threshold) + + event("SERIALIZE_PACK_APPLY_ARGS", "PACKAPPLY", pack_apply_id) b_args = serialize(args, buffer_threshold=buffer_threshold) + + event("SERIALIZE_PACK_APPLY_KWARGS", "PACKAPPLY", pack_apply_id) b_kwargs = serialize(kwargs, buffer_threshold=buffer_threshold) + + event("SERIALIZE_PACK_APPLY_PACK_BUFFERS", "PACKAPPLY", pack_apply_id) packed_buffer = pack_buffers([b_func, b_args, b_kwargs]) + + event("SERIALIZE_PACK_APPLY_END", "PACKAPPLY", pack_apply_id) return packed_buffer diff --git a/parsl/trace.py b/parsl/trace.py index 88cdbbd5bb..592af401af 100644 --- a/parsl/trace.py +++ b/parsl/trace.py @@ -8,7 +8,7 @@ logger = logging.getLogger(__name__) trace_by_logger = False -trace_by_dict = False +trace_by_dict = True events: List[Tuple[float, str, str, Any]] = [] binds: List[Tuple[str, Any, str, Any]] = [] @@ -38,7 +38,7 @@ def span_bind_sub(super_spantype: str, super_spanid: Any, sub_spantype: str, sub binds.append(b) -def output_event_stats(): +def output_event_stats(directory="."): print("Event stats") print("===========") print(f"Count of events: {len(events)}") @@ -68,5 +68,5 @@ def output_event_stats(): print(f"Total real time accounted for here: {all_tasks_t} sec") """ summary = {"events": events, "binds": binds} - with open("parsl_tracing.pickle", "wb") as f: + with open(f"{directory}/parsl_tracing.pickle", "wb") as f: pickle.dump(summary, f) From e272111ce3fb14c159b081d69f51900a21e67f0e Mon Sep 17 00:00:00 2001 From: Ben Clifford Date: Mon, 24 Jul 2023 16:39:18 +0000 Subject: [PATCH 374/408] bump version --- parsl/version.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/parsl/version.py b/parsl/version.py index 8b2fc1034d..ff2224d0d4 100644 --- a/parsl/version.py +++ b/parsl/version.py @@ -1,3 +1,3 @@ """Set module version. """ -VERSION = '2023.07.17-dev+desc-2023.07.20b' +VERSION = '2023.07.17-dev+desc-2023.07.20c' From dc4133b6cb7e49f365da0bf8d0bc1e0a4b8b5d57 Mon Sep 17 00:00:00 2001 From: Ben Clifford Date: Wed, 26 Jul 2023 14:27:47 +0000 Subject: [PATCH 375/408] most relevant, workaround a severe performance degradation i am investigating in serialization vs monitoring --- parsl/monitoring/remote.py | 2 - .../test_htex_alternate_cache.py | 57 +++++++++++++++++++ .../test_serialization/test_htex_cache.py | 57 +++++++++++++++++++ parsl/version.py | 2 +- 4 files changed, 115 insertions(+), 3 deletions(-) create mode 100644 parsl/tests/test_serialization/test_htex_alternate_cache.py create mode 100644 parsl/tests/test_serialization/test_htex_cache.py diff --git a/parsl/monitoring/remote.py b/parsl/monitoring/remote.py index d3a629b71a..49e06540ce 100644 --- a/parsl/monitoring/remote.py +++ b/parsl/monitoring/remote.py @@ -2,7 +2,6 @@ import time import logging import datetime -from functools import wraps from parsl.multiprocessing import ForkProcess from multiprocessing import Event, Queue @@ -45,7 +44,6 @@ def monitor_wrapper(f: Any, # per app else: - @wraps(f) def wrapped(*args: List[Any], **kwargs: Dict[str, Any]) -> Any: task_id = kwargs.pop('_parsl_monitoring_task_id') try_id = kwargs.pop('_parsl_monitoring_try_id') diff --git a/parsl/tests/test_serialization/test_htex_alternate_cache.py b/parsl/tests/test_serialization/test_htex_alternate_cache.py new file mode 100644 index 0000000000..b217ba503b --- /dev/null +++ b/parsl/tests/test_serialization/test_htex_alternate_cache.py @@ -0,0 +1,57 @@ +import parsl +import pytest + +from typing import Any + +from parsl.serialize.facade import methods_for_code + +from parsl.tests.configs.htex_local_alternate import fresh_config as local_config + + +@parsl.python_app +def f(x): + return x + 1 + + +@pytest.mark.local +def test_caching() -> None: + # for future serializer devs: if this is failing because you added another + # code serializer, you'll also probably need to re-think what is being tested + # about serialization caching here. + assert len(methods_for_code) == 1 + + serializer = methods_for_code[b'C2'] + + # force type to Any here because a serializer method coming from + # methods_for_code doesn't statically have any cache management + # methods on itself such as cache_clear or cache_info. + serialize_method: Any = serializer.serialize + + serialize_method.cache_clear() + + assert serialize_method.cache_info().hits == 0 + assert serialize_method.cache_info().misses == 0 + assert serialize_method.cache_info().currsize == 0 + + assert f(7).result() == 8 + + # the code serializer cache should now contain only a (probably wrapped) f ... + assert serialize_method.cache_info().currsize == 1 + + # ... which was not already in the cache. + assert serialize_method.cache_info().misses == 1 + assert serialize_method.cache_info().hits == 0 + + assert f(100).result() == 101 + + # this time round, we should have got a single cache hit... + assert serialize_method.cache_info().hits == 1 + assert serialize_method.cache_info().misses == 1 + assert serialize_method.cache_info().currsize == 1 + + assert f(200).result() == 201 + + # this time round, we should have got another single cache hit... + assert serialize_method.cache_info().hits == 2 + assert serialize_method.cache_info().misses == 1 + assert serialize_method.cache_info().currsize == 1 diff --git a/parsl/tests/test_serialization/test_htex_cache.py b/parsl/tests/test_serialization/test_htex_cache.py new file mode 100644 index 0000000000..6695c5f460 --- /dev/null +++ b/parsl/tests/test_serialization/test_htex_cache.py @@ -0,0 +1,57 @@ +import parsl +import pytest + +from typing import Any + +from parsl.serialize.facade import methods_for_code + +from parsl.tests.configs.htex_local import fresh_config as local_config + + +@parsl.python_app +def f(x): + return x + 1 + + +@pytest.mark.local +def test_caching() -> None: + # for future serializer devs: if this is failing because you added another + # code serializer, you'll also probably need to re-think what is being tested + # about serialization caching here. + assert len(methods_for_code) == 1 + + serializer = methods_for_code[b'C2'] + + # force type to Any here because a serializer method coming from + # methods_for_code doesn't statically have any cache management + # methods on itself such as cache_clear or cache_info. + serialize_method: Any = serializer.serialize + + serialize_method.cache_clear() + + assert serialize_method.cache_info().hits == 0 + assert serialize_method.cache_info().misses == 0 + assert serialize_method.cache_info().currsize == 0 + + assert f(7).result() == 8 + + # the code serializer cache should now contain only a (probably wrapped) f ... + assert serialize_method.cache_info().currsize == 1 + + # ... which was not already in the cache. + assert serialize_method.cache_info().misses == 1 + assert serialize_method.cache_info().hits == 0 + + assert f(100).result() == 101 + + # this time round, we should have got a single cache hit... + assert serialize_method.cache_info().hits == 1 + assert serialize_method.cache_info().misses == 1 + assert serialize_method.cache_info().currsize == 1 + + assert f(200).result() == 201 + + # this time round, we should have got another single cache hit... + assert serialize_method.cache_info().hits == 2 + assert serialize_method.cache_info().misses == 1 + assert serialize_method.cache_info().currsize == 1 diff --git a/parsl/version.py b/parsl/version.py index ff2224d0d4..0a3a798859 100644 --- a/parsl/version.py +++ b/parsl/version.py @@ -1,3 +1,3 @@ """Set module version. """ -VERSION = '2023.07.17-dev+desc-2023.07.20c' +VERSION = '2023.07.24-dev+desc-2023.07.26a' From 093518057a92e3db024f47abb420c81de73991fb Mon Sep 17 00:00:00 2001 From: Ben Clifford Date: Fri, 28 Jul 2023 15:31:14 +0000 Subject: [PATCH 376/408] this adds in a bunch of log messages to help with debugging hangs quentin is seeing --- parsl/executors/high_throughput/executor.py | 7 ++++++- parsl/jobs/job_status_poller.py | 6 ++++++ parsl/jobs/strategy.py | 6 ++++-- requirements.txt | 10 +++++++++- 4 files changed, 25 insertions(+), 4 deletions(-) diff --git a/parsl/executors/high_throughput/executor.py b/parsl/executors/high_throughput/executor.py index 9658b8c5f3..870c7042a8 100644 --- a/parsl/executors/high_throughput/executor.py +++ b/parsl/executors/high_throughput/executor.py @@ -656,7 +656,7 @@ def scale_in(self, blocks=None, block_ids=[], force=True, max_idletime=None): ------- List of job_ids marked for termination """ - logger.debug(f"Scale in called, blocks={blocks}, block_ids={block_ids}") + logger.info(f"Scale in called, blocks={blocks}, block_ids={block_ids}") if block_ids: block_ids_to_kill = block_ids else: @@ -690,21 +690,26 @@ def scale_in(self, blocks=None, block_ids=[], force=True, max_idletime=None): if len(block_ids_to_kill) < blocks: logger.warning(f"Could not find enough blocks to kill: wanted {blocks} but only selected {len(block_ids_to_kill)}") + logger.info("Iterating over block IDs") # Hold the block for block_id in block_ids_to_kill: self._hold_block(block_id) + logger.info("Iterated over block IDs") # Now kill via provider # Potential issue with multiple threads trying to remove the same blocks to_kill = [self.blocks[bid] for bid in block_ids_to_kill if bid in self.blocks] + logger.info("Calling provider cancel") r = self.provider.cancel(to_kill) + logger.info("Provide cancel returned") job_ids = self._filter_scale_in_ids(to_kill, r) # to_kill block_ids are fetched from self.blocks # If a block_id is in self.block, it must exist in self.block_mapping block_ids_killed = [self.block_mapping[jid] for jid in job_ids] + logger.info("htex scale in returning") return block_ids_killed def _get_launch_command(self, block_id: str) -> str: diff --git a/parsl/jobs/job_status_poller.py b/parsl/jobs/job_status_poller.py index ac2cac8dce..f6286444bf 100644 --- a/parsl/jobs/job_status_poller.py +++ b/parsl/jobs/job_status_poller.py @@ -11,6 +11,7 @@ from parsl.jobs.strategy import Strategy from parsl.monitoring.message_type import MessageType +from parsl.process_loggers import wrap_with_logs from parsl.utils import Timer @@ -116,10 +117,15 @@ def __init__(self, dfk: "parsl.dataflow.dflow.DataFlowKernel"): self._error_handler = JobErrorHandler() super().__init__(self.poll, interval=5, name="JobStatusPoller") + @wrap_with_logs def poll(self): + logger.info("POLL: update state") self._update_state() + logger.info("POLL: run error handler") self._error_handler.run(self._poll_items) + logger.info("POLL: strategize") self._strategy.strategize(self._poll_items) + logger.info("POLL: done") def _update_state(self) -> None: now = time.time() diff --git a/parsl/jobs/strategy.py b/parsl/jobs/strategy.py index 210ab924bf..6fef1e716d 100644 --- a/parsl/jobs/strategy.py +++ b/parsl/jobs/strategy.py @@ -238,8 +238,9 @@ def _general_strategy(self, status_list, *, strategy_type): if idle_duration > self.max_idletime: # We have resources idle for the max duration, # we have to scale_in now. - logger.debug(f"Idle time has reached {self.max_idletime}s for executor {label}; scaling in") + logger.info(f"Idle time has reached {self.max_idletime}s for executor {label}; scaling in with exec_status.scale_in") exec_status.scale_in(active_blocks - min_blocks) + logger.info("exec_status.scale_in returned") else: logger.debug(f"Idle time {idle_duration}s is less than max_idletime {self.max_idletime}s for executor {label}; not scaling in") @@ -285,8 +286,9 @@ def _general_strategy(self, status_list, *, strategy_type): excess_slots = math.ceil(active_slots - (active_tasks * parallelism)) excess_blocks = math.ceil(float(excess_slots) / (tasks_per_node * nodes_per_block)) excess_blocks = min(excess_blocks, active_blocks - min_blocks) - logger.debug(f"Requesting scaling in by {excess_blocks} blocks") + logger.info(f"Requesting scaling in by {excess_blocks} blocks") exec_status.scale_in(excess_blocks, force=False, max_idletime=self.max_idletime) + logger.info("exec_status.scale_in returned") else: logger.error("This strategy does not support scaling in except for HighThroughputExecutor - taking no action") else: diff --git a/requirements.txt b/requirements.txt index c498057a2f..68b9a30165 100644 --- a/requirements.txt +++ b/requirements.txt @@ -1,5 +1,13 @@ pyzmq>=17.1.2 -typeguard>=4,<5 +typeguard==4.0.0 +# typeguard 4.0.1 just released as I write this message +# breaks with this error: +# +# def __init__(self, config: Config = Config()) -> None: +# parsl/config.py:80: in __init__ +# Literal['task_exit'], +# E NameError: name 'task_exit' is not defined + typing-extensions>=4.6,<5 six globus-sdk From ce476df888c2e5f6605b1253d3b1521c1b3262f9 Mon Sep 17 00:00:00 2001 From: Ben Clifford Date: Fri, 28 Jul 2023 15:31:41 +0000 Subject: [PATCH 377/408] bump version --- parsl/version.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/parsl/version.py b/parsl/version.py index 0a3a798859..30f95f94d7 100644 --- a/parsl/version.py +++ b/parsl/version.py @@ -1,3 +1,3 @@ """Set module version. """ -VERSION = '2023.07.24-dev+desc-2023.07.26a' +VERSION = '2023.07.24-dev+desc-2023.07.28a' From f646540e234220a91783d89cf03e9d545b22024a Mon Sep 17 00:00:00 2001 From: Ben Clifford Date: Tue, 1 Aug 2023 14:04:50 +0000 Subject: [PATCH 378/408] fix flake8 errors --- parsl/monitoring/remote.py | 3 ++- parsl/version.py | 2 +- 2 files changed, 3 insertions(+), 2 deletions(-) diff --git a/parsl/monitoring/remote.py b/parsl/monitoring/remote.py index 161fd87444..018d29eb3f 100644 --- a/parsl/monitoring/remote.py +++ b/parsl/monitoring/remote.py @@ -18,6 +18,7 @@ monitoring_wrapper_cache: Dict monitoring_wrapper_cache = {} + def monitor_wrapper(f: Any, # per app args: Sequence, # per invocation kwargs: Dict, # per invocation @@ -49,7 +50,7 @@ def monitor_wrapper(f: Any, # per app # serialized. This doesn't happen on the underlying wrapped function # and doesn't happen if no @wraps is specified. # I am unsure why. - @functools.wraps(f, assigned = ('__name__', '__qualname__', '__doc__', '__annotations__')) + @functools.wraps(f, assigned=('__name__', '__qualname__', '__doc__', '__annotations__')) def parsl_monitoring_wrapper(*args: List[Any], **kwargs: Dict[str, Any]) -> Any: task_id = kwargs.pop('_parsl_monitoring_task_id') try_id = kwargs.pop('_parsl_monitoring_try_id') diff --git a/parsl/version.py b/parsl/version.py index 89061bc60c..7aff1d740f 100644 --- a/parsl/version.py +++ b/parsl/version.py @@ -1,3 +1,3 @@ """Set module version. """ -VERSION = '2023.07.31-dev+desc-2023.08.01b' +VERSION = '2023.07.31-dev+desc-2023.08.01c' From f76053c6751fe3e34cf496ee03bba1c83705aae0 Mon Sep 17 00:00:00 2001 From: Ben Clifford Date: Fri, 13 Oct 2023 17:01:56 +0000 Subject: [PATCH 379/408] Upgrade cctools --- Makefile | 2 +- parsl/version.py | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/Makefile b/Makefile index 0dcbd4ab2e..cf49912e4f 100644 --- a/Makefile +++ b/Makefile @@ -7,7 +7,7 @@ CCTOOLS_INSTALL := /tmp/cctools MPICH=mpich OPENMPI=openmpi export PATH := $(CCTOOLS_INSTALL)/bin/:$(PATH) -export CCTOOLS_VERSION=7.5.4 +export CCTOOLS_VERSION=7.7.0 export HYDRA_LAUNCHER=fork export OMPI_MCA_rmaps_base_oversubscribe=yes MPI=$(MPICH) diff --git a/parsl/version.py b/parsl/version.py index 9e98443a37..be60b05741 100644 --- a/parsl/version.py +++ b/parsl/version.py @@ -1,3 +1,3 @@ """Set module version. """ -VERSION = '2023.10.09-dev+desc-2023.10.13b' +VERSION = '2023.10.09-dev+desc-2023.10.13c' From 8e4f0d4bcf8a36d79e99eb5fdb247631b9967683 Mon Sep 17 00:00:00 2001 From: Ben Clifford Date: Fri, 27 Oct 2023 15:38:47 +0000 Subject: [PATCH 380/408] bump WQ version to address a segfault happening in CI --- Makefile | 2 +- parsl/version.py | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/Makefile b/Makefile index 3b6e3794f3..fb72f7f537 100644 --- a/Makefile +++ b/Makefile @@ -7,7 +7,7 @@ CCTOOLS_INSTALL := /tmp/cctools MPICH=mpich OPENMPI=openmpi export PATH := $(CCTOOLS_INSTALL)/bin/:$(PATH) -export CCTOOLS_VERSION=7.7.1 +export CCTOOLS_VERSION=7.7.2 export HYDRA_LAUNCHER=fork export OMPI_MCA_rmaps_base_oversubscribe=yes MPI=$(MPICH) diff --git a/parsl/version.py b/parsl/version.py index bdd48f7841..e16a42d4ba 100644 --- a/parsl/version.py +++ b/parsl/version.py @@ -1,3 +1,3 @@ """Set module version. """ -VERSION = '2023.10.23-dev+desc-2023.10.27b' +VERSION = '2023.10.23-dev+desc-2023.10.27c' From 46adaa58dbe0a90a53c3b0e7cfa4b879461c1379 Mon Sep 17 00:00:00 2001 From: Ben Clifford Date: Mon, 13 Nov 2023 11:42:54 +0000 Subject: [PATCH 381/408] Debugging unexpected CI behaviour --- Makefile | 3 +++ parsl/version.py | 2 +- 2 files changed, 4 insertions(+), 1 deletion(-) diff --git a/Makefile b/Makefile index fb72f7f537..c82efdf628 100644 --- a/Makefile +++ b/Makefile @@ -75,6 +75,9 @@ wqex_local_test: $(CCTOOLS_INSTALL) ## run all tests with workqueue_ex config .PHONY: workqueue_mon_test workqueue_mon_test: $(WORKQUEUE_INSTALL) ## run all tests with workqueue_ex config pip3 install ".[monitoring]" + echo "Contents of runinfo:" + date + ls -l runinfo/ PYTHONPATH=.:/tmp/cctools/lib/python3.8/site-packages pytest parsl/tests/ -k "not cleannet and not issue363" --config parsl/tests/configs/workqueue_monitoring_config.py --cov=parsl --cov-append --cov-report= --random-order diff --git a/parsl/version.py b/parsl/version.py index 1a122e34af..a2ac43d554 100644 --- a/parsl/version.py +++ b/parsl/version.py @@ -1,3 +1,3 @@ """Set module version. """ -VERSION = '2023.10.23-dev+desc-2023.11.13a' +VERSION = '2023.10.23-dev+desc-2023.11.13b' From 291993469dd5596fd58cc28481d432554a39187d Mon Sep 17 00:00:00 2001 From: Ben Clifford Date: Mon, 13 Nov 2023 16:34:36 +0000 Subject: [PATCH 382/408] fix config error --- parsl/tests/configs/workqueue_monitoring.py | 4 ++-- parsl/version.py | 2 +- 2 files changed, 3 insertions(+), 3 deletions(-) diff --git a/parsl/tests/configs/workqueue_monitoring.py b/parsl/tests/configs/workqueue_monitoring.py index 381323adda..881a46cd63 100644 --- a/parsl/tests/configs/workqueue_monitoring.py +++ b/parsl/tests/configs/workqueue_monitoring.py @@ -10,8 +10,8 @@ def fresh_config(): - return Config(strategy='simple', coprocess=True, - executors=[WorkQueueExecutor(port=9000, + return Config(strategy='simple', + executors=[WorkQueueExecutor(port=9000, coprocess=True, provider=LocalProvider(init_blocks=0), storage_access=[FTPInTaskStaging(), HTTPInTaskStaging(), NoOpFileStaging()])], monitoring=MonitoringHub(hub_address="localhost", diff --git a/parsl/version.py b/parsl/version.py index 5ade5f3b88..a9a89c9826 100644 --- a/parsl/version.py +++ b/parsl/version.py @@ -1,3 +1,3 @@ """Set module version. """ -VERSION = '2023.10.23-dev+desc-2023.11.13c' +VERSION = '2023.10.23-dev+desc-2023.11.13d' From 3ac0c03e398d017678b97c350553fadbe528b935 Mon Sep 17 00:00:00 2001 From: Ben Clifford Date: Mon, 13 Nov 2023 17:23:05 +0000 Subject: [PATCH 383/408] visualization dependencies missing from desc-branch peturbed tests, after splitting monitoring and visualization dependencies --- .github/workflows/ci.yaml | 2 +- parsl/version.py | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/.github/workflows/ci.yaml b/.github/workflows/ci.yaml index 85bb7c1e77..34fdc66288 100644 --- a/.github/workflows/ci.yaml +++ b/.github/workflows/ci.yaml @@ -62,7 +62,7 @@ jobs: - name: Checking parsl-visualize run: | sudo apt-get install -y graphviz - pip install .[monitoring] + pip install .[monitoring,visualization] parsl/tests/test-viz.sh - name: clear runinfo from all previous steps diff --git a/parsl/version.py b/parsl/version.py index a9a89c9826..cea585c28f 100644 --- a/parsl/version.py +++ b/parsl/version.py @@ -1,3 +1,3 @@ """Set module version. """ -VERSION = '2023.10.23-dev+desc-2023.11.13d' +VERSION = '2023.10.23-dev+desc-2023.11.13e' From 3f13696ea0a9abf49d798c3fb638f06b5f1462d2 Mon Sep 17 00:00:00 2001 From: Ben Clifford Date: Mon, 13 Nov 2023 18:00:55 +0000 Subject: [PATCH 384/408] Rename internal fields in desc branch tests that have changed in master branch --- .../test_mon_local/test_memoization_representation.py | 10 +++++----- .../test_mon_wq/test_memoization_representation.py | 10 +++++----- .../test_memoization_representation.py | 10 +++++----- parsl/version.py | 2 +- 4 files changed, 16 insertions(+), 16 deletions(-) diff --git a/parsl/tests/test_monitoring/test_mon_local/test_memoization_representation.py b/parsl/tests/test_monitoring/test_mon_local/test_memoization_representation.py index f2344ba4d2..82f705e602 100644 --- a/parsl/tests/test_monitoring/test_mon_local/test_memoization_representation.py +++ b/parsl/tests/test_monitoring/test_mon_local/test_memoization_representation.py @@ -40,9 +40,9 @@ def test_hashsum(): f4 = this_app(4) assert f4.result() == 5 - assert f1.task_def['hashsum'] == f3.task_def['hashsum'] - assert f1.task_def['hashsum'] == f4.task_def['hashsum'] - assert f1.task_def['hashsum'] != f2.task_def['hashsum'] + assert f1.task_record['hashsum'] == f3.task_record['hashsum'] + assert f1.task_record['hashsum'] == f4.task_record['hashsum'] + assert f1.task_record['hashsum'] != f2.task_record['hashsum'] logger.info("cleaning up parsl") parsl.dfk().cleanup() @@ -61,11 +61,11 @@ def test_hashsum(): assert task_count == 4 # this will check that the number of task rows for each hashsum matches the above app invocations - result = connection.execute(f"SELECT COUNT(task_hashsum) FROM task WHERE task_hashsum='{f1.task_def['hashsum']}'") + result = connection.execute(f"SELECT COUNT(task_hashsum) FROM task WHERE task_hashsum='{f1.task_record['hashsum']}'") (hashsum_count, ) = result.first() assert hashsum_count == 3 - result = connection.execute(f"SELECT COUNT(task_hashsum) FROM task WHERE task_hashsum='{f2.task_def['hashsum']}'") + result = connection.execute(f"SELECT COUNT(task_hashsum) FROM task WHERE task_hashsum='{f2.task_record['hashsum']}'") (hashsum_count, ) = result.first() assert hashsum_count == 1 diff --git a/parsl/tests/test_monitoring/test_mon_wq/test_memoization_representation.py b/parsl/tests/test_monitoring/test_mon_wq/test_memoization_representation.py index f9d63ec338..f5bcdf9f29 100644 --- a/parsl/tests/test_monitoring/test_mon_wq/test_memoization_representation.py +++ b/parsl/tests/test_monitoring/test_mon_wq/test_memoization_representation.py @@ -40,9 +40,9 @@ def test_hashsum(): f4 = this_app(4) assert f4.result() == 5 - assert f1.task_def['hashsum'] == f3.task_def['hashsum'] - assert f1.task_def['hashsum'] == f4.task_def['hashsum'] - assert f1.task_def['hashsum'] != f2.task_def['hashsum'] + assert f1.task_record['hashsum'] == f3.task_record['hashsum'] + assert f1.task_record['hashsum'] == f4.task_record['hashsum'] + assert f1.task_record['hashsum'] != f2.task_record['hashsum'] logger.info("cleaning up parsl") parsl.dfk().cleanup() @@ -61,11 +61,11 @@ def test_hashsum(): assert task_count == 4 # this will check that the number of task rows for each hashsum matches the above app invocations - result = connection.execute(f"SELECT COUNT(task_hashsum) FROM task WHERE task_hashsum='{f1.task_def['hashsum']}'") + result = connection.execute(f"SELECT COUNT(task_hashsum) FROM task WHERE task_hashsum='{f1.task_record['hashsum']}'") (hashsum_count, ) = result.first() assert hashsum_count == 3 - result = connection.execute(f"SELECT COUNT(task_hashsum) FROM task WHERE task_hashsum='{f2.task_def['hashsum']}'") + result = connection.execute(f"SELECT COUNT(task_hashsum) FROM task WHERE task_hashsum='{f2.task_record['hashsum']}'") (hashsum_count, ) = result.first() assert hashsum_count == 1 diff --git a/parsl/tests/test_monitoring/test_mon_wq_result_radio/test_memoization_representation.py b/parsl/tests/test_monitoring/test_mon_wq_result_radio/test_memoization_representation.py index 7a627380c3..4985f0033d 100644 --- a/parsl/tests/test_monitoring/test_mon_wq_result_radio/test_memoization_representation.py +++ b/parsl/tests/test_monitoring/test_mon_wq_result_radio/test_memoization_representation.py @@ -40,9 +40,9 @@ def test_hashsum(): f4 = this_app(4) assert f4.result() == 5 - assert f1.task_def['hashsum'] == f3.task_def['hashsum'] - assert f1.task_def['hashsum'] == f4.task_def['hashsum'] - assert f1.task_def['hashsum'] != f2.task_def['hashsum'] + assert f1.task_record['hashsum'] == f3.task_record['hashsum'] + assert f1.task_record['hashsum'] == f4.task_record['hashsum'] + assert f1.task_record['hashsum'] != f2.task_record['hashsum'] logger.info("cleaning up parsl") parsl.dfk().cleanup() @@ -61,11 +61,11 @@ def test_hashsum(): assert task_count == 4 # this will check that the number of task rows for each hashsum matches the above app invocations - result = connection.execute(f"SELECT COUNT(task_hashsum) FROM task WHERE task_hashsum='{f1.task_def['hashsum']}'") + result = connection.execute(f"SELECT COUNT(task_hashsum) FROM task WHERE task_hashsum='{f1.task_record['hashsum']}'") (hashsum_count, ) = result.first() assert hashsum_count == 3 - result = connection.execute(f"SELECT COUNT(task_hashsum) FROM task WHERE task_hashsum='{f2.task_def['hashsum']}'") + result = connection.execute(f"SELECT COUNT(task_hashsum) FROM task WHERE task_hashsum='{f2.task_record['hashsum']}'") (hashsum_count, ) = result.first() assert hashsum_count == 1 diff --git a/parsl/version.py b/parsl/version.py index cea585c28f..98bc2db4dd 100644 --- a/parsl/version.py +++ b/parsl/version.py @@ -1,3 +1,3 @@ """Set module version. """ -VERSION = '2023.10.23-dev+desc-2023.11.13e' +VERSION = '2023.10.23-dev+desc-2023.11.13f' From 05f31a1aad2262021cc51e87e8c635852fa548dd Mon Sep 17 00:00:00 2001 From: Ben Clifford Date: Mon, 13 Nov 2023 18:55:37 +0000 Subject: [PATCH 385/408] remove a test that shouldn't hold any more, due to rearranging serialization --- .../test_htex_alternate_cache.py | 57 ------------------- parsl/version.py | 2 +- 2 files changed, 1 insertion(+), 58 deletions(-) delete mode 100644 parsl/tests/test_serialization/test_htex_alternate_cache.py diff --git a/parsl/tests/test_serialization/test_htex_alternate_cache.py b/parsl/tests/test_serialization/test_htex_alternate_cache.py deleted file mode 100644 index b217ba503b..0000000000 --- a/parsl/tests/test_serialization/test_htex_alternate_cache.py +++ /dev/null @@ -1,57 +0,0 @@ -import parsl -import pytest - -from typing import Any - -from parsl.serialize.facade import methods_for_code - -from parsl.tests.configs.htex_local_alternate import fresh_config as local_config - - -@parsl.python_app -def f(x): - return x + 1 - - -@pytest.mark.local -def test_caching() -> None: - # for future serializer devs: if this is failing because you added another - # code serializer, you'll also probably need to re-think what is being tested - # about serialization caching here. - assert len(methods_for_code) == 1 - - serializer = methods_for_code[b'C2'] - - # force type to Any here because a serializer method coming from - # methods_for_code doesn't statically have any cache management - # methods on itself such as cache_clear or cache_info. - serialize_method: Any = serializer.serialize - - serialize_method.cache_clear() - - assert serialize_method.cache_info().hits == 0 - assert serialize_method.cache_info().misses == 0 - assert serialize_method.cache_info().currsize == 0 - - assert f(7).result() == 8 - - # the code serializer cache should now contain only a (probably wrapped) f ... - assert serialize_method.cache_info().currsize == 1 - - # ... which was not already in the cache. - assert serialize_method.cache_info().misses == 1 - assert serialize_method.cache_info().hits == 0 - - assert f(100).result() == 101 - - # this time round, we should have got a single cache hit... - assert serialize_method.cache_info().hits == 1 - assert serialize_method.cache_info().misses == 1 - assert serialize_method.cache_info().currsize == 1 - - assert f(200).result() == 201 - - # this time round, we should have got another single cache hit... - assert serialize_method.cache_info().hits == 2 - assert serialize_method.cache_info().misses == 1 - assert serialize_method.cache_info().currsize == 1 diff --git a/parsl/version.py b/parsl/version.py index 98bc2db4dd..5ce5164bfd 100644 --- a/parsl/version.py +++ b/parsl/version.py @@ -1,3 +1,3 @@ """Set module version. """ -VERSION = '2023.10.23-dev+desc-2023.11.13f' +VERSION = '2023.10.23-dev+desc-2023.11.13g' From 785aa8ccc2d69239e9cacc7871d7fc5bff36a1f4 Mon Sep 17 00:00:00 2001 From: Ben Clifford Date: Mon, 20 Nov 2023 11:56:37 +0000 Subject: [PATCH 386/408] Add a timout into htex command channel for hangs around missing interchange --- parsl/executors/high_throughput/zmq_pipes.py | 12 ++++++++++-- parsl/version.py | 2 +- 2 files changed, 11 insertions(+), 3 deletions(-) diff --git a/parsl/executors/high_throughput/zmq_pipes.py b/parsl/executors/high_throughput/zmq_pipes.py index f02f4d0309..10dcb86b6c 100644 --- a/parsl/executors/high_throughput/zmq_pipes.py +++ b/parsl/executors/high_throughput/zmq_pipes.py @@ -47,7 +47,6 @@ def run(self, message, max_retries=3): """ This function needs to be fast at the same time aware of the possibility of ZMQ pipes overflowing. - The timeout increases slowly if contention is detected on ZMQ pipes. We could set copy=False and get slightly better latency but this results in ZMQ sockets reaching a broken state once there are ~10k tasks in flight. This issue can be magnified if each the serialized buffer itself is larger. @@ -68,7 +67,16 @@ def run(self, message, max_retries=3): try: self.zmq_socket.send_pyobj(message, copy=True) logger.debug(f"waiting for response from command {message}") - reply = self.zmq_socket.recv_pyobj() + r = self.zmq_socket.poll(timeout=30000) # TODO: don't hardcode this timeout + if r == 0: # timeout + raise RuntimeError("CommandClient poll timed out") + + reply = self.zmq_socket.recv_pyobj(flags=zmq.NOBLOCK) + # Don't block here: we know there's a message because + # of the successful poll... if that happens to be not + # true, raise an exception rather than hanging. However + # that's a bug in the code, not an expected occurence. + logger.debug(f"got response from command {message}") except zmq.ZMQError: logger.exception("Potential ZMQ REQ-REP deadlock caught") diff --git a/parsl/version.py b/parsl/version.py index 239159e89b..779bb3599e 100644 --- a/parsl/version.py +++ b/parsl/version.py @@ -1,3 +1,3 @@ """Set module version. """ -VERSION = '2023.11.13-dev+desc-2023.11.20a' +VERSION = '2023.11.13-dev+desc-2023.11.20b' From 1b4adc527b1d39b2b5866d56440ea0b6a768b02b Mon Sep 17 00:00:00 2001 From: Ben Clifford Date: Mon, 20 Nov 2023 13:58:31 +0000 Subject: [PATCH 387/408] More aggressive shutdown handling: should now result in a failed test suite rather than a hang --- parsl/executors/high_throughput/zmq_pipes.py | 17 +++++++++++++++-- parsl/version.py | 2 +- 2 files changed, 16 insertions(+), 3 deletions(-) diff --git a/parsl/executors/high_throughput/zmq_pipes.py b/parsl/executors/high_throughput/zmq_pipes.py index 10dcb86b6c..42f6fdb249 100644 --- a/parsl/executors/high_throughput/zmq_pipes.py +++ b/parsl/executors/high_throughput/zmq_pipes.py @@ -65,11 +65,18 @@ def run(self, message, max_retries=3): for i in range(max_retries): logger.debug(f"try {i} for command {message}") try: + logger.debug("waiting for command client to be ready") + r = self.zmq_socket.poll(timeout=30000) # TODO: don't hardcode this timeout + if r == 0: # timeout + raise RuntimeError("CommandClient poll-before-command timed out") + # TODO: what other values of r are correct? + logger.debug("Sending command client command") self.zmq_socket.send_pyobj(message, copy=True) logger.debug(f"waiting for response from command {message}") r = self.zmq_socket.poll(timeout=30000) # TODO: don't hardcode this timeout if r == 0: # timeout - raise RuntimeError("CommandClient poll timed out") + raise RuntimeError("CommandClient poll-before-result timed out") + # TODO: what other values of r are correct? reply = self.zmq_socket.recv_pyobj(flags=zmq.NOBLOCK) # Don't block here: we know there's a message because @@ -140,7 +147,9 @@ def put(self, message): socks = dict(self.poller.poll(timeout=timeout_ms)) if self.zmq_socket in socks and socks[self.zmq_socket] == zmq.POLLOUT: # The copy option adds latency but reduces the risk of ZMQ overflow + logger.debug("Sending TasksOutgoing message") self.zmq_socket.send_pyobj(message, copy=True) + logger.debug("Sent TasksOutgoing message") return else: timeout_ms = max(timeout_ms, 1) @@ -180,8 +189,12 @@ def __init__(self, ip_address, port_range): self._lock = threading.Lock() def get(self): + logger.debug("Waiting for ResultsIncoming lock") with self._lock: - return self.results_receiver.recv_multipart() + logger.debug("Waiting for ResultsIncoming message") + m = self.results_receiver.recv_multipart() + logger.debug("Received ResultsIncoming message") + return m def close(self): with self._lock: diff --git a/parsl/version.py b/parsl/version.py index 779bb3599e..09bbb5704d 100644 --- a/parsl/version.py +++ b/parsl/version.py @@ -1,3 +1,3 @@ """Set module version. """ -VERSION = '2023.11.13-dev+desc-2023.11.20b' +VERSION = '2023.11.13-dev+desc-2023.11.20c' From 11a383a43a7fdc71f205886995a33f71ab05236d Mon Sep 17 00:00:00 2001 From: Ben Clifford Date: Mon, 20 Nov 2023 14:24:13 +0000 Subject: [PATCH 388/408] Revert "More aggressive shutdown handling: should now result in a failed test suite rather than a hang" This reverts commit 1b4adc527b1d39b2b5866d56440ea0b6a768b02b. This commit was causing a different shutdown problem in normal htex operation, so reverting while I debug --- parsl/executors/high_throughput/zmq_pipes.py | 17 ++--------------- parsl/version.py | 2 +- 2 files changed, 3 insertions(+), 16 deletions(-) diff --git a/parsl/executors/high_throughput/zmq_pipes.py b/parsl/executors/high_throughput/zmq_pipes.py index 42f6fdb249..10dcb86b6c 100644 --- a/parsl/executors/high_throughput/zmq_pipes.py +++ b/parsl/executors/high_throughput/zmq_pipes.py @@ -65,18 +65,11 @@ def run(self, message, max_retries=3): for i in range(max_retries): logger.debug(f"try {i} for command {message}") try: - logger.debug("waiting for command client to be ready") - r = self.zmq_socket.poll(timeout=30000) # TODO: don't hardcode this timeout - if r == 0: # timeout - raise RuntimeError("CommandClient poll-before-command timed out") - # TODO: what other values of r are correct? - logger.debug("Sending command client command") self.zmq_socket.send_pyobj(message, copy=True) logger.debug(f"waiting for response from command {message}") r = self.zmq_socket.poll(timeout=30000) # TODO: don't hardcode this timeout if r == 0: # timeout - raise RuntimeError("CommandClient poll-before-result timed out") - # TODO: what other values of r are correct? + raise RuntimeError("CommandClient poll timed out") reply = self.zmq_socket.recv_pyobj(flags=zmq.NOBLOCK) # Don't block here: we know there's a message because @@ -147,9 +140,7 @@ def put(self, message): socks = dict(self.poller.poll(timeout=timeout_ms)) if self.zmq_socket in socks and socks[self.zmq_socket] == zmq.POLLOUT: # The copy option adds latency but reduces the risk of ZMQ overflow - logger.debug("Sending TasksOutgoing message") self.zmq_socket.send_pyobj(message, copy=True) - logger.debug("Sent TasksOutgoing message") return else: timeout_ms = max(timeout_ms, 1) @@ -189,12 +180,8 @@ def __init__(self, ip_address, port_range): self._lock = threading.Lock() def get(self): - logger.debug("Waiting for ResultsIncoming lock") with self._lock: - logger.debug("Waiting for ResultsIncoming message") - m = self.results_receiver.recv_multipart() - logger.debug("Received ResultsIncoming message") - return m + return self.results_receiver.recv_multipart() def close(self): with self._lock: diff --git a/parsl/version.py b/parsl/version.py index 09bbb5704d..779bb3599e 100644 --- a/parsl/version.py +++ b/parsl/version.py @@ -1,3 +1,3 @@ """Set module version. """ -VERSION = '2023.11.13-dev+desc-2023.11.20c' +VERSION = '2023.11.13-dev+desc-2023.11.20b' From b8edf0ec01637e9ae57fbecfdafd0474abdbed30 Mon Sep 17 00:00:00 2001 From: Ben Clifford Date: Mon, 20 Nov 2023 14:39:15 +0000 Subject: [PATCH 389/408] try zmq command channel timeouts again --- parsl/executors/high_throughput/zmq_pipes.py | 17 +++++++++++++++-- parsl/version.py | 2 +- 2 files changed, 16 insertions(+), 3 deletions(-) diff --git a/parsl/executors/high_throughput/zmq_pipes.py b/parsl/executors/high_throughput/zmq_pipes.py index 10dcb86b6c..9d87ef8453 100644 --- a/parsl/executors/high_throughput/zmq_pipes.py +++ b/parsl/executors/high_throughput/zmq_pipes.py @@ -65,11 +65,18 @@ def run(self, message, max_retries=3): for i in range(max_retries): logger.debug(f"try {i} for command {message}") try: + logger.debug("waiting for command client to be ready") + r = self.zmq_socket.poll(flags=zmq.PollEvent.POLLOUT, timeout=30000) # TODO: don't hardcode this timeout + if r == 0: # timeout + raise RuntimeError("CommandClient poll-before-command timed out") + # TODO: what other values of r are correct? + logger.debug("Sending command client command") self.zmq_socket.send_pyobj(message, copy=True) logger.debug(f"waiting for response from command {message}") r = self.zmq_socket.poll(timeout=30000) # TODO: don't hardcode this timeout if r == 0: # timeout - raise RuntimeError("CommandClient poll timed out") + raise RuntimeError("CommandClient poll-before-result timed out") + # TODO: what other values of r are correct? reply = self.zmq_socket.recv_pyobj(flags=zmq.NOBLOCK) # Don't block here: we know there's a message because @@ -140,7 +147,9 @@ def put(self, message): socks = dict(self.poller.poll(timeout=timeout_ms)) if self.zmq_socket in socks and socks[self.zmq_socket] == zmq.POLLOUT: # The copy option adds latency but reduces the risk of ZMQ overflow + logger.debug("Sending TasksOutgoing message") self.zmq_socket.send_pyobj(message, copy=True) + logger.debug("Sent TasksOutgoing message") return else: timeout_ms = max(timeout_ms, 1) @@ -180,8 +189,12 @@ def __init__(self, ip_address, port_range): self._lock = threading.Lock() def get(self): + logger.debug("Waiting for ResultsIncoming lock") with self._lock: - return self.results_receiver.recv_multipart() + logger.debug("Waiting for ResultsIncoming message") + m = self.results_receiver.recv_multipart() + logger.debug("Received ResultsIncoming message") + return m def close(self): with self._lock: diff --git a/parsl/version.py b/parsl/version.py index 779bb3599e..3e2fd80b3e 100644 --- a/parsl/version.py +++ b/parsl/version.py @@ -1,3 +1,3 @@ """Set module version. """ -VERSION = '2023.11.13-dev+desc-2023.11.20b' +VERSION = '2023.11.13-dev+desc-2023.11.20d' From e8d0be2ebacba4e33a20c19266946a7e4d1d8d5b Mon Sep 17 00:00:00 2001 From: Ben Clifford Date: Tue, 21 Nov 2023 13:58:29 +0000 Subject: [PATCH 390/408] Try out latest gen3 workflow in CI to get deeper testing; add a few monitoring name tests --- .github/workflows/ci.yaml | 62 +++++++ .../test_mon_local/test_app_names.py | 173 ++++++++++++++++++ parsl/version.py | 2 +- 3 files changed, 236 insertions(+), 1 deletion(-) create mode 100644 parsl/tests/test_monitoring/test_mon_local/test_app_names.py diff --git a/.github/workflows/ci.yaml b/.github/workflows/ci.yaml index 3e8d069ec5..83ea6875ce 100644 --- a/.github/workflows/ci.yaml +++ b/.github/workflows/ci.yaml @@ -100,3 +100,65 @@ jobs: with: name: runinfo-${{ matrix.python-version }} path: runinfo/ + + + gen3: + runs-on: ${{ matrix.os }} + + strategy: + matrix: + os: [ ubuntu-latest ] + py: [ "3.11" ] + CC: [ gcc ] + CXX: [ g++ ] + + defaults: + run: + # cf. https://github.com/conda-incubator/setup-miniconda#important + shell: bash -l {0} + + steps: + - uses: actions/checkout@v2 + + - name: Setup conda + uses: conda-incubator/setup-miniconda@v2 + with: + activate-environment: stack + python-version: "3.11" + condarc-file: etc/.condarc + + - name: Install conda deps + run: | + conda info + conda list + conda install -y mamba + mamba install -y --file conda_requirements.txt + conda info + conda list + + + - uses: actions/checkout@master + + - name: Install workflow packages + run: | + # pip install -U --no-deps 'parsl[monitoring,workqueue] @ git+https://github.com/parsl/parsl@desc' + pip install -U --no-deps '.[monitoring,workqueue]' + pip install typeguard tblib paramiko dill pyzmq globus-sdk sqlalchemy_utils + conda install -c conda-forge ndcctools=7.6.1=py311h689c632_0 --no-deps + + - name: Clone the package and checkout the branch + shell: bash -l {0} + run: | + git clone https://github.com/LSSTDESC/gen3_workflow + eups declare gen3_workflow -r ${PWD}/gen3_workflow -t current + cd gen3_workflow + git fetch origin ${GITHUB_REF}:TESTING + git checkout TESTING + + - name: Run the test pipelines + run: | + setup gen3_workflow + (eups list lsst_distrib) 2>&1 | grep -v "Unknown tag" + (eups list gen3_workflow) 2>&1 | grep -v "Unknown tag" + cd tests + pytest test_query_workflow.py test_bps_restart.py diff --git a/parsl/tests/test_monitoring/test_mon_local/test_app_names.py b/parsl/tests/test_monitoring/test_mon_local/test_app_names.py new file mode 100644 index 0000000000..1123fca4dd --- /dev/null +++ b/parsl/tests/test_monitoring/test_mon_local/test_app_names.py @@ -0,0 +1,173 @@ +import logging +import os +import parsl +import pytest +import time + +logger = logging.getLogger(__name__) + + +@parsl.python_app +def regular_decorated_app(): + return 5 + + +def for_decoration_later(): + return 77 + + +@pytest.mark.local +def test_regular_decorated_app(): + # this is imported here rather than at module level because + # it isn't available in a plain parsl install, so this module + # would otherwise fail to import and break even a basic test + # run. + import sqlalchemy + from parsl.tests.configs.local_threads_monitoring import fresh_config + + if os.path.exists("runinfo/monitoring.db"): + logger.info("Monitoring database already exists - deleting") + os.remove("runinfo/monitoring.db") + + logger.info("Generating fresh config") + c = fresh_config() + logger.info("Loading parsl") + parsl.load(c) + + logger.info("invoking and waiting for result") + assert regular_decorated_app().result() == 5 + + logger.info("cleaning up parsl") + parsl.dfk().cleanup() + parsl.clear() + + # at this point, we should find one row in the monitoring database. + + logger.info("checking database content") + engine = sqlalchemy.create_engine("sqlite:///runinfo/monitoring.db") + with engine.begin() as connection: + + result = connection.execute("SELECT COUNT(*) FROM workflow") + (c, ) = result.first() + assert c == 1 + + result = connection.execute("SELECT COUNT(*) FROM task") + (c, ) = result.first() + assert c == 1 + + result = connection.execute("SELECT COUNT(*) FROM try") + (c, ) = result.first() + assert c == 1 + + result = connection.execute("SELECT task_func_name FROM task") + (c, ) = result.first() + assert c == "regular_decorated_app" + + logger.info("all done") + + +@pytest.mark.local +def test_for_decoration_later(): + # this is imported here rather than at module level because + # it isn't available in a plain parsl install, so this module + # would otherwise fail to import and break even a basic test + # run. + import sqlalchemy + from parsl.tests.configs.local_threads_monitoring import fresh_config + + if os.path.exists("runinfo/monitoring.db"): + logger.info("Monitoring database already exists - deleting") + os.remove("runinfo/monitoring.db") + + logger.info("Generating fresh config") + c = fresh_config() + logger.info("Loading parsl") + parsl.load(c) + + a = parsl.python_app(for_decoration_later) + + logger.info("invoking and waiting for result") + assert a().result() == 77 + + logger.info("cleaning up parsl") + parsl.dfk().cleanup() + parsl.clear() + + # at this point, we should find one row in the monitoring database. + + logger.info("checking database content") + engine = sqlalchemy.create_engine("sqlite:///runinfo/monitoring.db") + with engine.begin() as connection: + + result = connection.execute("SELECT COUNT(*) FROM workflow") + (c, ) = result.first() + assert c == 1 + + result = connection.execute("SELECT COUNT(*) FROM task") + (c, ) = result.first() + assert c == 1 + + result = connection.execute("SELECT COUNT(*) FROM try") + (c, ) = result.first() + assert c == 1 + + result = connection.execute("SELECT task_func_name FROM task") + (c, ) = result.first() + assert c == "for_decoration_later" + + logger.info("all done") + + +@pytest.mark.local +def test_decorated_closure(): + # this is imported here rather than at module level because + # it isn't available in a plain parsl install, so this module + # would otherwise fail to import and break even a basic test + # run. + import sqlalchemy + from parsl.tests.configs.local_threads_monitoring import fresh_config + + if os.path.exists("runinfo/monitoring.db"): + logger.info("Monitoring database already exists - deleting") + os.remove("runinfo/monitoring.db") + + logger.info("Generating fresh config") + c = fresh_config() + logger.info("Loading parsl") + parsl.load(c) + + @parsl.python_app + def inner_function(): + return 53 + + logger.info("invoking and waiting for result") + assert inner_function().result() == 53 + + logger.info("cleaning up parsl") + parsl.dfk().cleanup() + parsl.clear() + + # at this point, we should find one row in the monitoring database. + + logger.info("checking database content") + engine = sqlalchemy.create_engine("sqlite:///runinfo/monitoring.db") + with engine.begin() as connection: + + result = connection.execute("SELECT COUNT(*) FROM workflow") + (c, ) = result.first() + assert c == 1 + + result = connection.execute("SELECT COUNT(*) FROM task") + (c, ) = result.first() + assert c == 1 + + result = connection.execute("SELECT COUNT(*) FROM try") + (c, ) = result.first() + assert c == 1 + + result = connection.execute("SELECT task_func_name FROM task") + (c, ) = result.first() + assert c == "inner_function" + + logger.info("all done") + diff --git a/parsl/version.py b/parsl/version.py index d3dc9a0cce..1237d054f8 100644 --- a/parsl/version.py +++ b/parsl/version.py @@ -1,3 +1,3 @@ """Set module version. """ -VERSION = '2023.11.20-dev+desc-2023.11.21a' +VERSION = '2023.11.20-dev+desc-2023.11.21b' From 06525b4fd9da7bc0c910da859c2e7c3f9efa522a Mon Sep 17 00:00:00 2001 From: Ben Clifford Date: Tue, 21 Nov 2023 14:12:14 +0000 Subject: [PATCH 391/408] More messing with CI --- .github/workflows/ci.yaml | 15 ++++++++++----- .../test_mon_local/test_app_names.py | 7 +++---- parsl/version.py | 2 +- 3 files changed, 14 insertions(+), 10 deletions(-) diff --git a/.github/workflows/ci.yaml b/.github/workflows/ci.yaml index 83ea6875ce..72e7e2d47b 100644 --- a/.github/workflows/ci.yaml +++ b/.github/workflows/ci.yaml @@ -119,30 +119,35 @@ jobs: steps: - uses: actions/checkout@v2 + with: + repository: https://github.com/LSSTDESC/gen3_workflow + path: ./gen3-repo + + - uses: actions/checkout@master + with: + path: ./parsl-repo - name: Setup conda uses: conda-incubator/setup-miniconda@v2 with: activate-environment: stack python-version: "3.11" - condarc-file: etc/.condarc + condarc-file: ./gen3-repo/etc/.condarc - name: Install conda deps run: | conda info conda list conda install -y mamba - mamba install -y --file conda_requirements.txt + mamba install -y --file ./gen3-repo/conda_requirements.txt conda info conda list - - uses: actions/checkout@master - - name: Install workflow packages run: | # pip install -U --no-deps 'parsl[monitoring,workqueue] @ git+https://github.com/parsl/parsl@desc' - pip install -U --no-deps '.[monitoring,workqueue]' + pip install -U --no-deps './parsl-repo[monitoring,workqueue]' pip install typeguard tblib paramiko dill pyzmq globus-sdk sqlalchemy_utils conda install -c conda-forge ndcctools=7.6.1=py311h689c632_0 --no-deps diff --git a/parsl/tests/test_monitoring/test_mon_local/test_app_names.py b/parsl/tests/test_monitoring/test_mon_local/test_app_names.py index 1123fca4dd..9b92802969 100644 --- a/parsl/tests/test_monitoring/test_mon_local/test_app_names.py +++ b/parsl/tests/test_monitoring/test_mon_local/test_app_names.py @@ -53,7 +53,7 @@ def test_regular_decorated_app(): result = connection.execute("SELECT COUNT(*) FROM task") (c, ) = result.first() - assert c == 1 + assert c == 1 result = connection.execute("SELECT COUNT(*) FROM try") (c, ) = result.first() @@ -105,7 +105,7 @@ def test_for_decoration_later(): result = connection.execute("SELECT COUNT(*) FROM task") (c, ) = result.first() - assert c == 1 + assert c == 1 result = connection.execute("SELECT COUNT(*) FROM try") (c, ) = result.first() @@ -159,7 +159,7 @@ def inner_function(): result = connection.execute("SELECT COUNT(*) FROM task") (c, ) = result.first() - assert c == 1 + assert c == 1 result = connection.execute("SELECT COUNT(*) FROM try") (c, ) = result.first() @@ -170,4 +170,3 @@ def inner_function(): assert c == "inner_function" logger.info("all done") - diff --git a/parsl/version.py b/parsl/version.py index 1237d054f8..c8f3fe1b85 100644 --- a/parsl/version.py +++ b/parsl/version.py @@ -1,3 +1,3 @@ """Set module version. """ -VERSION = '2023.11.20-dev+desc-2023.11.21b' +VERSION = '2023.11.20-dev+desc-2023.11.21c' From 3bfb236b9705da8f2aa1c72a4d402dbab7822693 Mon Sep 17 00:00:00 2001 From: Ben Clifford Date: Tue, 21 Nov 2023 14:17:53 +0000 Subject: [PATCH 392/408] more messing with CI --- .github/workflows/ci.yaml | 2 +- parsl/version.py | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/.github/workflows/ci.yaml b/.github/workflows/ci.yaml index 72e7e2d47b..977bf787c3 100644 --- a/.github/workflows/ci.yaml +++ b/.github/workflows/ci.yaml @@ -120,7 +120,7 @@ jobs: steps: - uses: actions/checkout@v2 with: - repository: https://github.com/LSSTDESC/gen3_workflow + repository: LSSTDESC/gen3_workflow path: ./gen3-repo - uses: actions/checkout@master diff --git a/parsl/version.py b/parsl/version.py index c8f3fe1b85..22045f9713 100644 --- a/parsl/version.py +++ b/parsl/version.py @@ -1,3 +1,3 @@ """Set module version. """ -VERSION = '2023.11.20-dev+desc-2023.11.21c' +VERSION = '2023.11.20-dev+desc-2023.11.21d' From 1b6f777d3f31f00312a953419742ece480de0b8a Mon Sep 17 00:00:00 2001 From: Ben Clifford Date: Tue, 21 Nov 2023 14:31:06 +0000 Subject: [PATCH 393/408] more messing with CI --- .github/workflows/ci.yaml | 12 +++++++++++- parsl/version.py | 2 +- 2 files changed, 12 insertions(+), 2 deletions(-) diff --git a/.github/workflows/ci.yaml b/.github/workflows/ci.yaml index 977bf787c3..62d84a1846 100644 --- a/.github/workflows/ci.yaml +++ b/.github/workflows/ci.yaml @@ -151,11 +151,21 @@ jobs: pip install typeguard tblib paramiko dill pyzmq globus-sdk sqlalchemy_utils conda install -c conda-forge ndcctools=7.6.1=py311h689c632_0 --no-deps - - name: Clone the package and checkout the branch + - name: Clone gen3_workflow checkout the branch shell: bash -l {0} run: | + echo pwd + pwd + + echo ls + ls + + echo Cloning gen3_workflow repo git clone https://github.com/LSSTDESC/gen3_workflow + + echo declaring gen3_workflow to eups eups declare gen3_workflow -r ${PWD}/gen3_workflow -t current + cd gen3_workflow git fetch origin ${GITHUB_REF}:TESTING git checkout TESTING diff --git a/parsl/version.py b/parsl/version.py index 22045f9713..cfc97b7ab9 100644 --- a/parsl/version.py +++ b/parsl/version.py @@ -1,3 +1,3 @@ """Set module version. """ -VERSION = '2023.11.20-dev+desc-2023.11.21d' +VERSION = '2023.11.20-dev+desc-2023.11.21e' From 5852468223dca3eb5e9ad7975414601091e3d22c Mon Sep 17 00:00:00 2001 From: Ben Clifford Date: Tue, 21 Nov 2023 14:42:14 +0000 Subject: [PATCH 394/408] more messing with CI --- .github/workflows/ci.yaml | 7 +++---- parsl/version.py | 2 +- 2 files changed, 4 insertions(+), 5 deletions(-) diff --git a/.github/workflows/ci.yaml b/.github/workflows/ci.yaml index 62d84a1846..20b952e0bb 100644 --- a/.github/workflows/ci.yaml +++ b/.github/workflows/ci.yaml @@ -121,7 +121,6 @@ jobs: - uses: actions/checkout@v2 with: repository: LSSTDESC/gen3_workflow - path: ./gen3-repo - uses: actions/checkout@master with: @@ -132,14 +131,14 @@ jobs: with: activate-environment: stack python-version: "3.11" - condarc-file: ./gen3-repo/etc/.condarc + condarc-file: etc/.condarc - name: Install conda deps run: | conda info conda list conda install -y mamba - mamba install -y --file ./gen3-repo/conda_requirements.txt + mamba install -y --file conda_requirements.txt conda info conda list @@ -167,7 +166,7 @@ jobs: eups declare gen3_workflow -r ${PWD}/gen3_workflow -t current cd gen3_workflow - git fetch origin ${GITHUB_REF}:TESTING + git fetch origin master:TESTING git checkout TESTING - name: Run the test pipelines diff --git a/parsl/version.py b/parsl/version.py index cfc97b7ab9..6a8562fbad 100644 --- a/parsl/version.py +++ b/parsl/version.py @@ -1,3 +1,3 @@ """Set module version. """ -VERSION = '2023.11.20-dev+desc-2023.11.21e' +VERSION = '2023.11.20-dev+desc-2023.11.21f' From 17255a1274fcd29557bd0c5525e4bf0e7cc697c7 Mon Sep 17 00:00:00 2001 From: Ben Clifford Date: Tue, 21 Nov 2023 15:16:44 +0000 Subject: [PATCH 395/408] more messing with CI --- .github/workflows/ci.yaml | 11 +++++++++++ parsl/version.py | 2 +- 2 files changed, 12 insertions(+), 1 deletion(-) diff --git a/.github/workflows/ci.yaml b/.github/workflows/ci.yaml index 20b952e0bb..f0b8dd156e 100644 --- a/.github/workflows/ci.yaml +++ b/.github/workflows/ci.yaml @@ -176,3 +176,14 @@ jobs: (eups list gen3_workflow) 2>&1 | grep -v "Unknown tag" cd tests pytest test_query_workflow.py test_bps_restart.py + + + - name: Archive test logs + if: ${{ always() }} + uses: actions/upload-artifact@v2 + with: + name: testinfo-${{ matrix.python-version }} + path: gen3_workflow/ + + + diff --git a/parsl/version.py b/parsl/version.py index 6a8562fbad..16d031836c 100644 --- a/parsl/version.py +++ b/parsl/version.py @@ -1,3 +1,3 @@ """Set module version. """ -VERSION = '2023.11.20-dev+desc-2023.11.21f' +VERSION = '2023.11.20-dev+desc-2023.11.21g' From b3f49ff67ef74830eceb5f8fcea45de9c47c7a26 Mon Sep 17 00:00:00 2001 From: Ben Clifford Date: Thu, 23 Nov 2023 18:59:53 +0000 Subject: [PATCH 396/408] Update task_inputs on every task monitoring update, so that the final values, rather than repr of unresolved app futures, are recorded in the database --- parsl/monitoring/db_manager.py | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/parsl/monitoring/db_manager.py b/parsl/monitoring/db_manager.py index 16ad050def..3ac6fb962f 100644 --- a/parsl/monitoring/db_manager.py +++ b/parsl/monitoring/db_manager.py @@ -450,7 +450,8 @@ def start(self, 'run_id', 'task_id', 'task_fail_count', 'task_fail_cost', - 'task_hashsum'], + 'task_hashsum', + 'task_inputs'], messages=task_info_update_messages) logger.debug("Inserting {} task_info_all_messages into status table".format(len(task_info_all_messages))) From 4f6db7efa69b74be03cbfd3139d6f76d54f50e68 Mon Sep 17 00:00:00 2001 From: Ben Clifford Date: Mon, 11 Dec 2023 19:16:53 +0000 Subject: [PATCH 397/408] Allow user suppression of forked process monitor, while keeping start/end messages --- parsl/monitoring/remote.py | 2 +- parsl/version.py | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/parsl/monitoring/remote.py b/parsl/monitoring/remote.py index e367d3d5c7..adc0dc5002 100644 --- a/parsl/monitoring/remote.py +++ b/parsl/monitoring/remote.py @@ -46,7 +46,7 @@ def wrapped(*args: List[Any], **kwargs: Dict[str, Any]) -> Any: radio_mode, run_dir) - if monitor_resources: + if monitor_resources and sleep_dur > 0: # create the monitor process and start pp = ForkProcess(target=monitor, args=(os.getpid(), diff --git a/parsl/version.py b/parsl/version.py index 7a9e28943d..6592d2b399 100644 --- a/parsl/version.py +++ b/parsl/version.py @@ -1,3 +1,3 @@ """Set module version. """ -VERSION = '2023.11.27-dev+desc-2023.12.01a' +VERSION = '2023.11.27-dev+desc-2023.12.11a' From b595bca353af3c092384c59a54f0e3bed2a77be3 Mon Sep 17 00:00:00 2001 From: Ben Clifford Date: Mon, 4 Mar 2024 15:53:13 +0000 Subject: [PATCH 398/408] a bunch of code cleanup work --- .github/workflows/ci.yaml | 4 - parsl/dataflow/dflow.py | 14 +- parsl/dataflow/memoization.py | 1 - .../executors/high_throughput/interchange.py | 17 +- .../high_throughput/process_worker_pool.py | 5 +- parsl/jobs/job_status_poller.py | 2 +- parsl/log_utils.py | 12 +- parsl/monitoring/monitoring.py | 295 ++---------------- parsl/monitoring/router.py | 207 ++++++++++++ parsl/tests/test_monitoring/test_fuzz_zmq.py | 4 +- .../test_shutdown/test_kill_monitoring.py | 49 +-- 11 files changed, 274 insertions(+), 336 deletions(-) create mode 100644 parsl/monitoring/router.py diff --git a/.github/workflows/ci.yaml b/.github/workflows/ci.yaml index 103c7813bf..781a69e72f 100644 --- a/.github/workflows/ci.yaml +++ b/.github/workflows/ci.yaml @@ -93,10 +93,6 @@ jobs: pip install .[monitoring,visualization] parsl/tests/test-viz.sh - - name: clear runinfo from all previous steps - run: | - rm -rfv runinfo/ - # config_local_test comes after viz so that the large monitoring.db # created by `make test` is still around - name: make config_local_test diff --git a/parsl/dataflow/dflow.py b/parsl/dataflow/dflow.py index 70c3ff9411..cab2aa45ba 100644 --- a/parsl/dataflow/dflow.py +++ b/parsl/dataflow/dflow.py @@ -6,7 +6,6 @@ import pickle import random import time -import traceback import typeguard import inspect import threading @@ -110,12 +109,12 @@ def __init__(self, config: Config) -> None: # hub address and port for interchange to connect self.hub_address = None # type: Optional[str] - self.hub_interchange_port = None # type: Optional[int] + self.hub_zmq_port = None # type: Optional[int] if self.monitoring: if self.monitoring.logdir is None: self.monitoring.logdir = self.run_dir self.hub_address = self.monitoring.hub_address - self.hub_interchange_port = self.monitoring.start(self.run_id, self.run_dir, self.config.run_dir) + self.hub_zmq_port = self.monitoring.start(self.run_id, self.run_dir, self.config.run_dir) self.time_began = datetime.datetime.now() self.time_completed: Optional[datetime.datetime] = None @@ -350,11 +349,8 @@ def handle_exec_update(self, task_record: taskrecord.TaskRecord, future: Future) logger.info("Task {} marked for retry".format(task_id)) else: - logger.error("Task {} failed after {} retry attempts. Last exception was: {}: {}".format(task_id, - task_record['try_id'], - type(e).__name__, - e)) - logger.debug("Task {} traceback: {}".format(task_id, traceback.format_tb(e.__traceback__))) + logger.exception("Task {} failed after {} retry attempts".format(task_id, + task_record['try_id'])) task_record['time_returned'] = datetime.datetime.now() self.update_task_state(task_record, States.failed) task_record['time_returned'] = datetime.datetime.now() @@ -1193,7 +1189,7 @@ def add_executors(self, executors): executor.run_id = self.run_id executor.run_dir = self.run_dir executor.hub_address = self.hub_address - executor.hub_port = self.hub_interchange_port + executor.hub_port = self.hub_zmq_port if hasattr(executor, 'provider'): if hasattr(executor.provider, 'script_dir'): executor.provider.script_dir = os.path.join(self.run_dir, 'submit_scripts') diff --git a/parsl/dataflow/memoization.py b/parsl/dataflow/memoization.py index 88a14eb49e..c54562f426 100644 --- a/parsl/dataflow/memoization.py +++ b/parsl/dataflow/memoization.py @@ -194,7 +194,6 @@ def make_hash(self, task: taskrecord.TaskRecord) -> str: if 'outputs' in task['kwargs']: outputs = task['kwargs']['outputs'] del filtered_kw['outputs'] - t.append(b'outputs') t.append(id_for_memo(outputs, output_ref=True)) t.extend(map(id_for_memo, (filtered_kw, task['func'], task['args']))) diff --git a/parsl/executors/high_throughput/interchange.py b/parsl/executors/high_throughput/interchange.py index 2d12711679..0c81007bcc 100644 --- a/parsl/executors/high_throughput/interchange.py +++ b/parsl/executors/high_throughput/interchange.py @@ -101,12 +101,12 @@ def __init__(self, This is overridden when the worker_ports option is set. Default: (54000, 55000) hub_address : str - The ip address at which the interchange can send info about managers to when monitoring is enabled. - This is passed via dfk and executor automatically. Default: None (meaning monitoring disabled) + The IP address at which the interchange can send info about managers to when monitoring is enabled. + Default: None (meaning monitoring disabled) hub_port : str The port at which the interchange can send info about managers to when monitoring is enabled. - This is passed via dfk and executor automatically. Default: None (meaning monitoring disabled) + Default: None (meaning monitoring disabled) heartbeat_threshold : int Number of seconds since the last heartbeat after which worker is considered lost. @@ -244,19 +244,19 @@ def task_puller(self) -> NoReturn: def _create_monitoring_channel(self) -> Optional[zmq.Socket]: if self.hub_address and self.hub_port: - logger.info("Connecting to monitoring") + logger.info("Connecting to MonitoringHub") # This is a one-off because monitoring is unencrypted hub_channel = zmq.Context().socket(zmq.DEALER) hub_channel.set_hwm(0) hub_channel.connect("tcp://{}:{}".format(self.hub_address, self.hub_port)) - logger.info("Monitoring enabled and connected to hub") + logger.info("Connected to MonitoringHub") return hub_channel else: return None def _send_monitoring_info(self, hub_channel: Optional[zmq.Socket], manager: ManagerRecord) -> None: if hub_channel: - logger.info("Sending message {} to hub".format(manager)) + logger.info("Sending message {} to MonitoringHub".format(manager)) d: Dict = cast(Dict, manager.copy()) d['timestamp'] = datetime.datetime.now() @@ -490,11 +490,6 @@ def process_tasks_to_send(self, interesting_managers: Set[bytes]) -> None: tasks = self.get_tasks(real_capacity) if tasks: self.task_outgoing.send_multipart([manager_id, b'', pickle.dumps(tasks)]) - # after this point, we've sent a task to the manager, but we haven't - # added it to the 'task' list for that manager, because we don't - # do that for another 5 lines. That should be pretty fast, though? - # but we shouldn't try removing it from the tasks list until we have - # passed that point anyway? task_count = len(tasks) self.count += task_count tids = [t['task_id'] for t in tasks] diff --git a/parsl/executors/high_throughput/process_worker_pool.py b/parsl/executors/high_throughput/process_worker_pool.py index 182e88c8b0..56308d88e9 100755 --- a/parsl/executors/high_throughput/process_worker_pool.py +++ b/parsl/executors/high_throughput/process_worker_pool.py @@ -352,10 +352,7 @@ def push_results(self, kill_event): logger.debug("Starting result push thread") - push_poll_period = max(10, self.poll_period) / 1000 - # push_poll_period must be at least 10 ms [BENC: why? and why does - # this one have more of a restriction than any of the other timing - # parameters? That max statement enforces that. but why enforce it vs other timings?] + push_poll_period = max(10, self.poll_period) / 1000 # push_poll_period must be atleast 10 ms logger.debug("push poll period: {}".format(push_poll_period)) last_beat = time.time() diff --git a/parsl/jobs/job_status_poller.py b/parsl/jobs/job_status_poller.py index cf54bc5245..ce584cb2f5 100644 --- a/parsl/jobs/job_status_poller.py +++ b/parsl/jobs/job_status_poller.py @@ -30,7 +30,7 @@ def __init__(self, executor: BlockProviderExecutor, dfk: Optional["parsl.dataflo if self._dfk and self._dfk.monitoring is not None: self.monitoring_enabled = True hub_address = self._dfk.hub_address - hub_port = self._dfk.hub_interchange_port + hub_port = self._dfk.hub_zmq_port context = zmq.Context() self.hub_channel = context.socket(zmq.DEALER) self.hub_channel.set_hwm(0) diff --git a/parsl/log_utils.py b/parsl/log_utils.py index c9b47eb8a3..35044bf335 100644 --- a/parsl/log_utils.py +++ b/parsl/log_utils.py @@ -28,7 +28,7 @@ def set_stream_logger(name: str = 'parsl', level: int = logging.DEBUG, format_string: Optional[str] = None, - stream: Optional[io.TextIOWrapper] = None) -> None: + stream: Optional[io.TextIOWrapper] = None) -> logging.Logger: """Add a stream log handler. Args: @@ -39,7 +39,7 @@ def set_stream_logger(name: str = 'parsl', If not specified, the default stream for logging.StreamHandler is used. Returns: - - None + - logger for specified name """ if format_string is None: # format_string = "%(asctime)s %(name)s [%(levelname)s] Thread:%(thread)d %(message)s" @@ -59,12 +59,14 @@ def set_stream_logger(name: str = 'parsl', futures_logger = logging.getLogger("concurrent.futures") futures_logger.addHandler(handler) + return logger + @typeguard.typechecked def set_file_logger(filename: str, name: str = 'parsl', level: int = logging.DEBUG, - format_string: Optional[str] = None) -> None: + format_string: Optional[str] = None) -> logging.Logger: """Add a file log handler. Args: @@ -74,7 +76,7 @@ def set_file_logger(filename: str, - format_string (string): Set the format string Returns: - - None + - logger for specified name """ if format_string is None: format_string = DEFAULT_FORMAT @@ -91,3 +93,5 @@ def set_file_logger(filename: str, # concurrent.futures futures_logger = logging.getLogger("concurrent.futures") futures_logger.addHandler(handler) + + return logger diff --git a/parsl/monitoring/monitoring.py b/parsl/monitoring/monitoring.py index 79a2f74f2b..30abe49fa2 100644 --- a/parsl/monitoring/monitoring.py +++ b/parsl/monitoring/monitoring.py @@ -1,9 +1,7 @@ from __future__ import annotations import os -import socket import time -import pickle import logging import typeguard import zmq @@ -15,14 +13,17 @@ from parsl.multiprocessing import ForkProcess, SizedQueue from multiprocessing import Process from multiprocessing.queues import Queue +from parsl.log_utils import set_file_logger from parsl.utils import RepresentationMixin from parsl.process_loggers import wrap_with_logs from parsl.utils import setproctitle + from parsl.serialize import deserialize +from parsl.monitoring.router import router_starter from parsl.monitoring.message_type import MessageType -from parsl.monitoring.types import AddressedMonitoringMessage, TaggedMonitoringMessage +from parsl.monitoring.types import AddressedMonitoringMessage from typing import cast, Any, Callable, Dict, Optional, Sequence, Tuple, Union, TYPE_CHECKING _db_manager_excepts: Optional[Exception] @@ -38,40 +39,6 @@ logger = logging.getLogger(__name__) -def start_file_logger(filename: str, name: str = 'monitoring', level: int = logging.DEBUG, format_string: Optional[str] = None) -> logging.Logger: - """Add a stream log handler. - - Parameters - --------- - - filename: string - Name of the file to write logs to. Required. - name: string - Logger name. - level: logging.LEVEL - Set the logging level. Default=logging.DEBUG - - format_string (string): Set the format string - format_string: string - Format string to use. - - Returns - ------- - None. - """ - if format_string is None: - format_string = "%(asctime)s.%(msecs)03d %(name)s:%(lineno)d [%(levelname)s] %(message)s" - - logger = logging.getLogger(name) - logger.setLevel(level) - logger.propagate = False - handler = logging.FileHandler(filename) - handler.setLevel(level) - formatter = logging.Formatter(format_string, datefmt='%Y-%m-%d %H:%M:%S') - handler.setFormatter(formatter) - logger.addHandler(handler) - return logger - - @typeguard.typechecked class MonitoringHub(RepresentationMixin): def __init__(self, @@ -79,9 +46,6 @@ def __init__(self, hub_port: Optional[int] = None, hub_port_range: Tuple[int, int] = (55050, 56000), - client_address: str = "127.0.0.1", - client_port_range: Tuple[int, int] = (55000, 56000), - workflow_name: Optional[str] = None, workflow_version: Optional[str] = None, logging_endpoint: Optional[str] = None, @@ -106,11 +70,6 @@ def __init__(self, to deliver monitoring messages to the monitoring router. Note that despite the similar name, this is not related to hub_port. Default: (55050, 56000) - client_address : str - The ip address at which the dfk will be able to reach Hub. Default: "127.0.0.1" - client_port_range : tuple(int, int) - The MonitoringHub picks ports at random from the range which will be used by Hub. - Default: (55000, 56000) workflow_name : str The name for the workflow. Default to the name of the parsl script workflow_version : str @@ -134,8 +93,6 @@ def __init__(self, Default: 30 seconds """ - self.logger = logger - # Any is used to disable typechecking on uses of _dfk_channel, # because it is used in the code as if it points to a channel, but # the static type is that it can also be None. The code relies on @@ -145,9 +102,6 @@ def __init__(self, if _db_manager_excepts: raise _db_manager_excepts - self.client_address = client_address - self.client_port_range = client_port_range - self.hub_address = hub_address self.hub_port = hub_port self.hub_port_range = hub_port_range @@ -164,6 +118,8 @@ def __init__(self, def start(self, run_id: str, dfk_run_dir: str, config_run_dir: Union[str, os.PathLike]) -> int: + logger.debug("Starting MonitoringHub") + if self.logdir is None: self.logdir = "." @@ -172,9 +128,6 @@ def start(self, run_id: str, dfk_run_dir: str, config_run_dir: Union[str, os.Pat os.makedirs(self.logdir, exist_ok=True) - # Initialize the ZMQ pipe to the Parsl Client - - self.logger.debug("Initializing ZMQ Pipes to client") self.monitoring_hub_active = True # This annotation is incompatible with typeguard 4.x instrumentation @@ -210,8 +163,8 @@ def start(self, run_id: str, dfk_run_dir: str, config_run_dir: Union[str, os.Pat self.router_proc = ForkProcess(target=router_starter, args=(comm_q, self.exception_q, self.priority_msgs, self.node_msgs, self.block_msgs, self.resource_msgs), kwargs={"hub_address": self.hub_address, - "hub_port": self.hub_port, - "hub_port_range": self.hub_port_range, + "udp_port": self.hub_port, + "zmq_port_range": self.hub_port_range, "logdir": self.logdir, "logging_level": logging.DEBUG if self.monitoring_debug else logging.INFO, "run_id": run_id @@ -231,7 +184,7 @@ def start(self, run_id: str, dfk_run_dir: str, config_run_dir: Union[str, os.Pat daemon=True, ) self.dbm_proc.start() - self.logger.info("Started the router process {} and DBM process {}".format(self.router_proc.pid, self.dbm_proc.pid)) + logger.info("Started the router process {} and DBM process {}".format(self.router_proc.pid, self.dbm_proc.pid)) self.filesystem_proc = Process(target=filesystem_receiver, args=(self.logdir, self.resource_msgs, dfk_run_dir), @@ -239,19 +192,19 @@ def start(self, run_id: str, dfk_run_dir: str, config_run_dir: Union[str, os.Pat daemon=True ) self.filesystem_proc.start() - self.logger.info(f"Started filesystem radio receiver process {self.filesystem_proc.pid}") + logger.info(f"Started filesystem radio receiver process {self.filesystem_proc.pid}") try: comm_q_result = comm_q.get(block=True, timeout=120) except queue.Empty: - self.logger.error("Hub has not completed initialization in 120s. Aborting") + logger.error("Hub has not completed initialization in 120s. Aborting") raise Exception("Hub failed to start") if isinstance(comm_q_result, str): - self.logger.error(f"MonitoringRouter sent an error message: {comm_q_result}") + logger.error(f"MonitoringRouter sent an error message: {comm_q_result}") raise RuntimeError(f"MonitoringRouter failed to start: {comm_q_result}") - udp_port, ic_port = comm_q_result + udp_port, zmq_port = comm_q_result self.monitoring_hub_url = "udp://{}:{}".format(self.hub_address, udp_port) @@ -261,31 +214,31 @@ def start(self, run_id: str, dfk_run_dir: str, config_run_dir: Union[str, os.Pat self._dfk_channel.setsockopt(zmq.LINGER, 0) self._dfk_channel.set_hwm(0) self._dfk_channel.setsockopt(zmq.SNDTIMEO, self.dfk_channel_timeout) - self._dfk_channel.connect("tcp://{}:{}".format(self.hub_address, ic_port)) + self._dfk_channel.connect("tcp://{}:{}".format(self.hub_address, zmq_port)) - self.logger.info("Monitoring Hub initialized") + logger.info("Monitoring Hub initialized") - return ic_port + return zmq_port # TODO: tighten the Any message format def send(self, mtype: MessageType, message: Any) -> None: - self.logger.debug("Sending message type {}".format(mtype)) + logger.debug("Sending message type {}".format(mtype)) try: t_before = time.time() self._dfk_channel.send_pyobj((mtype, message)) t_after = time.time() self.logger.debug(f"Sent message in {t_after - t_before} seconds") except zmq.Again: - self.logger.exception( + logger.exception( "The monitoring message sent from DFK to router timed-out after {}ms".format(self.dfk_channel_timeout)) def close(self) -> None: - self.logger.info("Terminating Monitoring Hub") + logger.info("Terminating Monitoring Hub") exception_msgs = [] while True: try: exception_msgs.append(self.exception_q.get(block=False)) - self.logger.error("There was a queued exception (Either router or DBM process got exception much earlier?)") + logger.error("There was a queued exception (Either router or DBM process got exception much earlier?)") except queue.Empty: break if self._dfk_channel and self.monitoring_hub_active: @@ -302,22 +255,22 @@ def close(self) -> None: self._dfk_channel.close() if exception_msgs: for exception_msg in exception_msgs: - self.logger.error("{} process delivered an exception: {}. Terminating all monitoring processes immediately.".format(exception_msg[0], - exception_msg[1])) + logger.error("{} process delivered an exception: {}. Terminating all monitoring processes immediately.".format(exception_msg[0], + exception_msg[1])) self.router_proc.terminate() self.dbm_proc.terminate() self.filesystem_proc.terminate() - self.logger.info("Waiting for router to terminate") + logger.info("Waiting for router to terminate") self.router_proc.join() - self.logger.debug("Finished waiting for router termination") + logger.debug("Finished waiting for router termination") if len(exception_msgs) == 0: - self.logger.debug("Sending STOP to DBM") + logger.debug("Sending STOP to DBM") self.priority_msgs.put(("STOP", 0)) else: - self.logger.debug("Not sending STOP to DBM, because there were DBM exceptions") - self.logger.debug("Waiting for DB termination") + logger.debug("Not sending STOP to DBM, because there were DBM exceptions") + logger.debug("Waiting for DB termination") self.dbm_proc.join() - self.logger.debug("Finished waiting for DBM termination") + logger.debug("Finished waiting for DBM termination") @staticmethod def monitor_wrapper(f: Any, @@ -339,9 +292,9 @@ def monitor_wrapper(f: Any, @wrap_with_logs def filesystem_receiver(logdir: str, q: "queue.Queue[AddressedMonitoringMessage]", run_dir: str) -> None: - logger = start_file_logger("{}/monitoring_filesystem_radio.log".format(logdir), - name="monitoring_filesystem_radio", - level=logging.INFO) + logger = set_file_logger("{}/monitoring_filesystem_radio.log".format(logdir), + name="monitoring_filesystem_radio", + level=logging.INFO) logger.info("Starting filesystem radio receiver") setproctitle("parsl: monitoring filesystem receiver") @@ -371,189 +324,3 @@ def filesystem_receiver(logdir: str, q: "queue.Queue[AddressedMonitoringMessage] logger.exception(f"Exception processing {filename} - probably will be retried next iteration") time.sleep(1) # whats a good time for this poll? - - -class MonitoringRouter: - - def __init__(self, - *, - hub_address: str, - hub_port: Optional[int] = None, - hub_port_range: Tuple[int, int] = (55050, 56000), - - monitoring_hub_address: str = "127.0.0.1", - logdir: str = ".", - run_id: str, - logging_level: int = logging.INFO, - atexit_timeout: int = 3 # in seconds - ): - """ Initializes a monitoring configuration class. - - Parameters - ---------- - hub_address : str - The ip address at which the workers will be able to reach the Hub. - hub_port : int - The specific port at which workers will be able to reach the Hub via UDP. Default: None - hub_port_range : tuple(int, int) - The MonitoringHub picks ports at random from the range which will be used by Hub. - This is overridden when the hub_port option is set. Default: (55050, 56000) - logdir : str - Parsl log directory paths. Logs and temp files go here. Default: '.' - logging_level : int - Logging level as defined in the logging module. Default: logging.INFO - atexit_timeout : float, optional - The amount of time in seconds to terminate the hub without receiving any messages, after the last dfk workflow message is received. - - """ - os.makedirs(logdir, exist_ok=True) - self.logger = start_file_logger("{}/monitoring_router.log".format(logdir), - name="monitoring_router", - level=logging_level) - self.logger.debug("Monitoring router starting") - - self.hub_address = hub_address - self.atexit_timeout = atexit_timeout - self.run_id = run_id - - self.loop_freq = 10.0 # milliseconds - - # Initialize the UDP socket - self.sock = socket.socket(socket.AF_INET, - socket.SOCK_DGRAM, - socket.IPPROTO_UDP) - - # We are trying to bind to all interfaces with 0.0.0.0 - if not hub_port: - self.sock.bind(('0.0.0.0', 0)) - self.hub_port = self.sock.getsockname()[1] - else: - self.hub_port = hub_port - try: - self.sock.bind(('0.0.0.0', self.hub_port)) - except Exception as e: - raise RuntimeError(f"Could not bind to hub_port {hub_port} because: {e}") - self.sock.settimeout(self.loop_freq / 1000) - self.logger.info("Initialized the UDP socket on 0.0.0.0:{}".format(self.hub_port)) - - self._context = zmq.Context() - self.ic_channel = self._context.socket(zmq.DEALER) - self.ic_channel.setsockopt(zmq.LINGER, 0) - self.ic_channel.set_hwm(0) - self.ic_channel.RCVTIMEO = int(self.loop_freq) # in milliseconds - self.logger.debug("hub_address: {}. hub_port_range {}".format(hub_address, hub_port_range)) - self.ic_port = self.ic_channel.bind_to_random_port("tcp://*", - min_port=hub_port_range[0], - max_port=hub_port_range[1]) - - def start(self, - priority_msgs: "queue.Queue[AddressedMonitoringMessage]", - node_msgs: "queue.Queue[AddressedMonitoringMessage]", - block_msgs: "queue.Queue[AddressedMonitoringMessage]", - resource_msgs: "queue.Queue[AddressedMonitoringMessage]") -> None: - try: - router_keep_going = True - while router_keep_going: - try: - data, addr = self.sock.recvfrom(2048) - resource_msg = pickle.loads(data) - self.logger.debug("Got UDP Message from {}: {}".format(addr, resource_msg)) - resource_msgs.put((resource_msg, addr)) - except socket.timeout: - pass - - try: - dfk_loop_start = time.time() - while time.time() - dfk_loop_start < 1.0: # TODO make configurable - # note that nothing checks that msg really is of the annotated type - msg: TaggedMonitoringMessage - msg = self.ic_channel.recv_pyobj() - - assert isinstance(msg, tuple), "IC Channel expects only tuples, got {}".format(msg) - assert len(msg) >= 1, "IC Channel expects tuples of length at least 1, got {}".format(msg) - assert len(msg) == 2, "IC Channel expects message tuples of exactly length 2, got {}".format(msg) - - msg_0: AddressedMonitoringMessage - msg_0 = (msg, 0) - - if msg[0] == MessageType.NODE_INFO: - msg[1]['run_id'] = self.run_id - node_msgs.put(msg_0) - elif msg[0] == MessageType.RESOURCE_INFO: - resource_msgs.put(msg_0) - elif msg[0] == MessageType.BLOCK_INFO: - block_msgs.put(msg_0) - elif msg[0] == MessageType.TASK_INFO: - priority_msgs.put(msg_0) - elif msg[0] == MessageType.WORKFLOW_INFO: - priority_msgs.put(msg_0) - if 'exit_now' in msg[1] and msg[1]['exit_now']: - router_keep_going = False - else: - # There is a type: ignore here because if msg[0] - # is of the correct type, this code is unreachable, - # but there is no verification that the message - # received from ic_channel.recv_pyobj() is actually - # of that type. - self.logger.error(f"Discarding message from interchange with unknown type {msg[0].value}") # type: ignore[unreachable] - except zmq.Again: - pass - except Exception: - # This will catch malformed messages. What happens if the - # channel is broken in such a way that it always raises - # an exception? Looping on this would maybe be the wrong - # thing to do. - self.logger.warning("Failure processing a ZMQ message", exc_info=True) - - self.logger.info("Monitoring router draining") - last_msg_received_time = time.time() - while time.time() - last_msg_received_time < self.atexit_timeout: - try: - data, addr = self.sock.recvfrom(2048) - msg = pickle.loads(data) - self.logger.debug("Got UDP Message from {}: {}".format(addr, msg)) - resource_msgs.put((msg, addr)) - last_msg_received_time = time.time() - except socket.timeout: - pass - - self.logger.info("Monitoring router finishing normally") - finally: - self.logger.info("Monitoring router finished") - - -@wrap_with_logs -def router_starter(comm_q: "queue.Queue[Union[Tuple[int, int], str]]", - exception_q: "queue.Queue[Tuple[str, str]]", - priority_msgs: "queue.Queue[AddressedMonitoringMessage]", - node_msgs: "queue.Queue[AddressedMonitoringMessage]", - block_msgs: "queue.Queue[AddressedMonitoringMessage]", - resource_msgs: "queue.Queue[AddressedMonitoringMessage]", - - hub_address: str, - hub_port: Optional[int], - hub_port_range: Tuple[int, int], - - logdir: str, - logging_level: int, - run_id: str) -> None: - setproctitle("parsl: monitoring router") - try: - router = MonitoringRouter(hub_address=hub_address, - hub_port=hub_port, - hub_port_range=hub_port_range, - logdir=logdir, - logging_level=logging_level, - run_id=run_id) - except Exception as e: - logger.error("MonitoringRouter construction failed.", exc_info=True) - comm_q.put(f"Monitoring router construction failed: {e}") - else: - comm_q.put((router.hub_port, router.ic_port)) - - router.logger.info("Starting MonitoringRouter in router_starter") - try: - router.start(priority_msgs, node_msgs, block_msgs, resource_msgs) - except Exception as e: - router.logger.exception("router.start exception") - exception_q.put(('Hub', str(e))) diff --git a/parsl/monitoring/router.py b/parsl/monitoring/router.py new file mode 100644 index 0000000000..fa5de47bb2 --- /dev/null +++ b/parsl/monitoring/router.py @@ -0,0 +1,207 @@ +from __future__ import annotations + +import os +import socket +import time +import pickle +import logging +import zmq + +import queue + +from parsl.log_utils import set_file_logger +from parsl.process_loggers import wrap_with_logs +from parsl.utils import setproctitle + +from parsl.monitoring.message_type import MessageType +from parsl.monitoring.types import AddressedMonitoringMessage, TaggedMonitoringMessage +from typing import Optional, Tuple, Union + + +logger = logging.getLogger(__name__) + + +class MonitoringRouter: + + def __init__(self, + *, + hub_address: str, + udp_port: Optional[int] = None, + zmq_port_range: Tuple[int, int] = (55050, 56000), + + monitoring_hub_address: str = "127.0.0.1", + logdir: str = ".", + run_id: str, + logging_level: int = logging.INFO, + atexit_timeout: int = 3 # in seconds + ): + """ Initializes a monitoring configuration class. + + Parameters + ---------- + hub_address : str + The ip address at which the workers will be able to reach the Hub. + udp_port : int + The specific port at which workers will be able to reach the Hub via UDP. Default: None + zmq_port_range : tuple(int, int) + The MonitoringHub picks ports at random from the range which will be used by Hub. + Default: (55050, 56000) + logdir : str + Parsl log directory paths. Logs and temp files go here. Default: '.' + logging_level : int + Logging level as defined in the logging module. Default: logging.INFO + atexit_timeout : float, optional + The amount of time in seconds to terminate the hub without receiving any messages, after the last dfk workflow message is received. + + """ + os.makedirs(logdir, exist_ok=True) + self.logger = set_file_logger("{}/monitoring_router.log".format(logdir), + name="monitoring_router", + level=logging_level) + self.logger.debug("Monitoring router starting") + + self.hub_address = hub_address + self.atexit_timeout = atexit_timeout + self.run_id = run_id + + self.loop_freq = 10.0 # milliseconds + + # Initialize the UDP socket + self.udp_sock = socket.socket(socket.AF_INET, + socket.SOCK_DGRAM, + socket.IPPROTO_UDP) + + # We are trying to bind to all interfaces with 0.0.0.0 + if not udp_port: + self.udp_sock.bind(('0.0.0.0', 0)) + self.udp_port = self.udp_sock.getsockname()[1] + else: + self.udp_port = udp_port + try: + self.udp_sock.bind(('0.0.0.0', self.udp_port)) + except Exception as e: + raise RuntimeError(f"Could not bind to udp_port {udp_port} because: {e}") + self.udp_sock.settimeout(self.loop_freq / 1000) + self.logger.info("Initialized the UDP socket on 0.0.0.0:{}".format(self.udp_port)) + + self._context = zmq.Context() + self.zmq_receiver_channel = self._context.socket(zmq.DEALER) + self.zmq_receiver_channel.setsockopt(zmq.LINGER, 0) + self.zmq_receiver_channel.set_hwm(0) + self.zmq_receiver_channel.RCVTIMEO = int(self.loop_freq) # in milliseconds + self.logger.debug("hub_address: {}. zmq_port_range {}".format(hub_address, zmq_port_range)) + self.zmq_receiver_port = self.zmq_receiver_channel.bind_to_random_port("tcp://*", + min_port=zmq_port_range[0], + max_port=zmq_port_range[1]) + + def start(self, + priority_msgs: "queue.Queue[AddressedMonitoringMessage]", + node_msgs: "queue.Queue[AddressedMonitoringMessage]", + block_msgs: "queue.Queue[AddressedMonitoringMessage]", + resource_msgs: "queue.Queue[AddressedMonitoringMessage]") -> None: + try: + router_keep_going = True + while router_keep_going: + try: + data, addr = self.udp_sock.recvfrom(2048) + resource_msg = pickle.loads(data) + self.logger.debug("Got UDP Message from {}: {}".format(addr, resource_msg)) + resource_msgs.put((resource_msg, addr)) + except socket.timeout: + pass + + try: + dfk_loop_start = time.time() + while time.time() - dfk_loop_start < 1.0: # TODO make configurable + # note that nothing checks that msg really is of the annotated type + msg: TaggedMonitoringMessage + msg = self.zmq_receiver_channel.recv_pyobj() + + assert isinstance(msg, tuple), "ZMQ Receiver expects only tuples, got {}".format(msg) + assert len(msg) >= 1, "ZMQ Receiver expects tuples of length at least 1, got {}".format(msg) + assert len(msg) == 2, "ZMQ Receiver expects message tuples of exactly length 2, got {}".format(msg) + + msg_0: AddressedMonitoringMessage + msg_0 = (msg, 0) + + if msg[0] == MessageType.NODE_INFO: + msg[1]['run_id'] = self.run_id + node_msgs.put(msg_0) + elif msg[0] == MessageType.RESOURCE_INFO: + resource_msgs.put(msg_0) + elif msg[0] == MessageType.BLOCK_INFO: + block_msgs.put(msg_0) + elif msg[0] == MessageType.TASK_INFO: + priority_msgs.put(msg_0) + elif msg[0] == MessageType.WORKFLOW_INFO: + priority_msgs.put(msg_0) + if 'exit_now' in msg[1] and msg[1]['exit_now']: + router_keep_going = False + else: + # There is a type: ignore here because if msg[0] + # is of the correct type, this code is unreachable, + # but there is no verification that the message + # received from zmq_receiver_channel.recv_pyobj() is actually + # of that type. + self.logger.error(f"Discarding message from interchange with unknown type {msg[0].value}") # type: ignore[unreachable] + except zmq.Again: + pass + except Exception: + # This will catch malformed messages. What happens if the + # channel is broken in such a way that it always raises + # an exception? Looping on this would maybe be the wrong + # thing to do. + self.logger.warning("Failure processing a ZMQ message", exc_info=True) + + self.logger.info("Monitoring router draining") + last_msg_received_time = time.time() + while time.time() - last_msg_received_time < self.atexit_timeout: + try: + data, addr = self.udp_sock.recvfrom(2048) + msg = pickle.loads(data) + self.logger.debug("Got UDP Message from {}: {}".format(addr, msg)) + resource_msgs.put((msg, addr)) + last_msg_received_time = time.time() + except socket.timeout: + pass + + self.logger.info("Monitoring router finishing normally") + finally: + self.logger.info("Monitoring router finished") + + +@wrap_with_logs +def router_starter(comm_q: "queue.Queue[Union[Tuple[int, int], str]]", + exception_q: "queue.Queue[Tuple[str, str]]", + priority_msgs: "queue.Queue[AddressedMonitoringMessage]", + node_msgs: "queue.Queue[AddressedMonitoringMessage]", + block_msgs: "queue.Queue[AddressedMonitoringMessage]", + resource_msgs: "queue.Queue[AddressedMonitoringMessage]", + + hub_address: str, + udp_port: Optional[int], + zmq_port_range: Tuple[int, int], + + logdir: str, + logging_level: int, + run_id: str) -> None: + setproctitle("parsl: monitoring router") + try: + router = MonitoringRouter(hub_address=hub_address, + udp_port=udp_port, + zmq_port_range=zmq_port_range, + logdir=logdir, + logging_level=logging_level, + run_id=run_id) + except Exception as e: + logger.error("MonitoringRouter construction failed.", exc_info=True) + comm_q.put(f"Monitoring router construction failed: {e}") + else: + comm_q.put((router.udp_port, router.zmq_receiver_port)) + + router.logger.info("Starting MonitoringRouter in router_starter") + try: + router.start(priority_msgs, node_msgs, block_msgs, resource_msgs) + except Exception as e: + router.logger.exception("router.start exception") + exception_q.put(('Hub', str(e))) diff --git a/parsl/tests/test_monitoring/test_fuzz_zmq.py b/parsl/tests/test_monitoring/test_fuzz_zmq.py index 71aa73e372..d9be378cda 100644 --- a/parsl/tests/test_monitoring/test_fuzz_zmq.py +++ b/parsl/tests/test_monitoring/test_fuzz_zmq.py @@ -41,11 +41,11 @@ def test_row_counts(): # dig out the interchange port... hub_address = parsl.dfk().hub_address - hub_interchange_port = parsl.dfk().hub_interchange_port + hub_zmq_port = parsl.dfk().hub_zmq_port # this will send a string to a new socket connection with socket.socket(socket.AF_INET, socket.SOCK_STREAM) as s: - s.connect((hub_address, hub_interchange_port)) + s.connect((hub_address, hub_zmq_port)) s.sendall(b'fuzzing\r') # this will send a non-object down the DFK's existing ZMQ connection diff --git a/parsl/tests/test_shutdown/test_kill_monitoring.py b/parsl/tests/test_shutdown/test_kill_monitoring.py index a656fe393e..f5bfbdc1a7 100644 --- a/parsl/tests/test_shutdown/test_kill_monitoring.py +++ b/parsl/tests/test_shutdown/test_kill_monitoring.py @@ -1,12 +1,9 @@ -import logging import os import parsl import pytest import signal import time -logger = logging.getLogger(__name__) - @parsl.python_app def simple_app(): @@ -29,7 +26,7 @@ def test_no_kills(): @pytest.mark.local @pytest.mark.parametrize("sig", [signal.SIGINT, signal.SIGTERM, signal.SIGKILL]) # are we expecting SIGKILL resilience here? Ideally yes @pytest.mark.parametrize("process_attr", ["router_proc", "dbm_proc"]) -def test_kill_router(sig, process_attr): +def test_kill_monitoring_helper_process(sig, process_attr, try_assert): from parsl.tests.configs.htex_local_alternate import fresh_config """This tests that we can kill a monitoring process and still have successful shutdown. This emulates behaviour when ctrl-C is pressed: that all of the processes receive a @@ -37,53 +34,33 @@ def test_kill_router(sig, process_attr): tolerant to monitoring processes going away. """ - # what is the time limit for the router shutting down? - expected_router_shutdown_time = 60 + # This is a very generous upper bound on process shutdown times. + expected_target_shutdown_time = 60 - logger.info("Initialising parsl") parsl.load(fresh_config()) - logger.info("Initialised parsl") dfk = parsl.dfk() assert dfk.monitoring is not None, "Monitoring required" - # TODO: there are two processes we need to check we can kill (or perhaps both as well) - # monitoring.router_proc and monitoring.dbm_proc - - router_proc = getattr(dfk.monitoring, process_attr) + target_proc = getattr(dfk.monitoring, process_attr) - assert router_proc is not None, "Monitoring router process required" - assert router_proc.is_alive(), "Router must be alive" + assert target_proc is not None, "prereq: target process must exist" + assert target_proc.is_alive(), "prereq: target process must be alive" - router_pid = router_proc.pid - assert router_pid is not None, "Router must have a pid" + target_pid = target_proc.pid + assert target_pid is not None, "prereq: target process must have a pid" - logger.info(f"Sending {sig} to router") - os.kill(router_pid, sig) + os.kill(target_pid, sig) - logger.info("Waiting for router process to die, or timeout") start_time = time.time() - while router_proc.is_alive() and start_time + expected_router_shutdown_time > time.time(): - logger.info("Wait loop") - time.sleep(1) - - assert not router_proc.is_alive(), "Process must have died to continue" - # now we have broken one piece of the monitoring system - # let's run some apps that should generate some monitoring traffic + try_assert(lambda: not target_proc.is_alive(), timeout_ms = expected_target_shutdown_time * 1000) - logger.info("Invoking simple app") - f = simple_app() + # now we have broken one piece of the monitoring system, do some app + # execution and then shut down. - logger.info("Invoked simple app, waiting for result") + simple_app().result() - f.result() - - logger.info("Got simple app result") - - logger.info("Calling cleanup") parsl.dfk().cleanup() - logger.info("Finished cleanup") - parsl.clear() From 00b983c6f8d5f3ce25fe8699ddb8802ed8e3c2e8 Mon Sep 17 00:00:00 2001 From: Ben Clifford Date: Mon, 4 Mar 2024 15:53:57 +0000 Subject: [PATCH 399/408] bump version --- parsl/version.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/parsl/version.py b/parsl/version.py index cd9d7493fe..97d3fb65ed 100644 --- a/parsl/version.py +++ b/parsl/version.py @@ -1,3 +1,3 @@ """Set module version. """ -VERSION = '2024.02.26-dev+desc-2024.03.04a' +VERSION = '2024.02.26-dev+desc-2024.03.04b' From 11f632625ce902c3b409166df9519c042e2766d3 Mon Sep 17 00:00:00 2001 From: Ben Clifford Date: Thu, 2 May 2024 11:33:33 +0000 Subject: [PATCH 400/408] add PR 3409 --- parsl/dataflow/errors.py | 4 ++++ parsl/dataflow/rundirs.py | 48 ++++++++++++++++++++++++++------------- parsl/version.py | 2 +- 3 files changed, 37 insertions(+), 17 deletions(-) diff --git a/parsl/dataflow/errors.py b/parsl/dataflow/errors.py index 5d6c0c8710..26abbc560c 100644 --- a/parsl/dataflow/errors.py +++ b/parsl/dataflow/errors.py @@ -63,3 +63,7 @@ def __init__(self, dependent_exceptions_tids: Sequence[Tuple[BaseException, Opti def __str__(self) -> str: dep_tids = [tid for (exception, tid) in self.dependent_exceptions_tids] return "Join failure for task {} with failed join dependencies from tasks {}".format(self.task_id, dep_tids) + + +class RundirCreateError(ParslError): + pass diff --git a/parsl/dataflow/rundirs.py b/parsl/dataflow/rundirs.py index f32979473f..240ee4e533 100644 --- a/parsl/dataflow/rundirs.py +++ b/parsl/dataflow/rundirs.py @@ -1,11 +1,15 @@ import os from glob import glob import logging +import random +import time + +from parsl.dataflow.errors import RundirCreateError logger = logging.getLogger(__name__) -def make_rundir(path: str) -> str: +def make_rundir(path: str, *, max_tries: int = 3) -> str: """When a path has not been specified, make the run directory. Creates a rundir with the following hierarchy: @@ -18,23 +22,35 @@ def make_rundir(path: str) -> str: Kwargs: - path (str): String path to a specific run dir """ - try: - if not os.path.exists(path): - os.makedirs(path) + backoff_time_s = random.random() + + os.makedirs(path, exist_ok=True) + + # try_count is 1-based for human readability + try_count = 1 + while True: + + prev_rundirs = glob("[0-9]*[0-9]", root_dir=path) - prev_rundirs = glob(os.path.join(path, "[0-9]*[0-9]")) + next = max([int(os.path.basename(x)) for x in prev_rundirs] + [-1]) + 1 - current_rundir = os.path.join(path, '000') + current_rundir = os.path.join(path, '{0:03}'.format(next)) - if prev_rundirs: - # Since we globbed on files named as 0-9 - x = sorted([int(os.path.basename(x)) for x in prev_rundirs])[-1] - current_rundir = os.path.join(path, '{0:03}'.format(x + 1)) + try: + os.makedirs(current_rundir) + logger.debug("rundir created: {}", current_rundir) + return os.path.abspath(current_rundir) + except FileExistsError: + logger.warning(f"Could not create rundir {current_rundir} on try {try_count}") - os.makedirs(current_rundir) - logger.debug("Parsl run initializing in rundir: {0}".format(current_rundir)) - return os.path.abspath(current_rundir) + if try_count >= max_tries: + raise + else: + logger.debug("Backing off {}s", backoff_time_s) + time.sleep(backoff_time_s) + backoff_time_s *= 2 + random.random() + try_count += 1 - except Exception: - logger.exception("Failed to create run directory") - raise + # this should never be reached - the above loop should have either returned + # or raised an exception on the last try + raise RundirCreateError() diff --git a/parsl/version.py b/parsl/version.py index 46a05a4245..749d761547 100644 --- a/parsl/version.py +++ b/parsl/version.py @@ -1,3 +1,3 @@ """Set module version. """ -VERSION = '2024.04.29+desc-2024.05.02a' +VERSION = '2024.04.29+desc-2024.05.02b' From 0b00a7cfacb289d1ecf7eb424d0b6f4b3151d4b6 Mon Sep 17 00:00:00 2001 From: Ben Clifford Date: Thu, 18 Jul 2024 15:39:58 +0000 Subject: [PATCH 401/408] fix docs build breakage in lazy-import patch --- parsl/executors/__init__.py | 1 + parsl/version.py | 2 +- 2 files changed, 2 insertions(+), 1 deletion(-) diff --git a/parsl/executors/__init__.py b/parsl/executors/__init__.py index d80b08abe0..7af3a6bb28 100644 --- a/parsl/executors/__init__.py +++ b/parsl/executors/__init__.py @@ -11,6 +11,7 @@ 'ThreadPoolExecutor': 'parsl.executors.threads', 'WorkQueueExecutor': 'parsl.executors.workqueue.executor', 'HighThroughputExecutor': 'parsl.executors.high_throughput.executor', + 'MPIExecutor': 'parsl.executors.high_throughput.mpi_executor', 'FluxExecutor': 'parsl.executors.flux.executor', } diff --git a/parsl/version.py b/parsl/version.py index d3a02cdb17..b91e22c53e 100644 --- a/parsl/version.py +++ b/parsl/version.py @@ -1,3 +1,3 @@ """Set module version. """ -VERSION = '2024.07.15+desc-2024.07.18a' +VERSION = '2024.07.15+desc-2024.07.18b' From 526ab7579fb823e3eb2c00b02955e38d04913a39 Mon Sep 17 00:00:00 2001 From: Ben Clifford Date: Wed, 14 Aug 2024 10:16:33 +0000 Subject: [PATCH 402/408] Remove abandoned feature that tried to make some magic keywords optional. --- parsl/app/bash.py | 9 --------- parsl/version.py | 2 +- 2 files changed, 1 insertion(+), 10 deletions(-) diff --git a/parsl/app/bash.py b/parsl/app/bash.py index 7685fb71ea..36212c172f 100644 --- a/parsl/app/bash.py +++ b/parsl/app/bash.py @@ -28,15 +28,6 @@ def remote_side_bash_executor(func, *args, **kwargs): executable = None - app_kwargs = kwargs.copy() - - # TODO: should pass these through if 'func' declares that it will take them - # otherwise silently discard. - if 'stdout' in app_kwargs: - del app_kwargs['stdout'] - if 'stderr' in app_kwargs: - del app_kwargs['stderr'] - # Try to run the func to compose the commandline try: # Execute the func to get the commandline diff --git a/parsl/version.py b/parsl/version.py index b0bd6ea77b..2931e6bcda 100644 --- a/parsl/version.py +++ b/parsl/version.py @@ -1,3 +1,3 @@ """Set module version. """ -VERSION = '2024.08.12+desc-2024.08.14a' +VERSION = '2024.08.12+desc-2024.08.14b' From e5603a7f52f25c10cb5b8fbde9c926e43a50754b Mon Sep 17 00:00:00 2001 From: Ben Clifford Date: Wed, 14 Aug 2024 10:29:22 +0000 Subject: [PATCH 403/408] Removed lazy import prototype This gave measurable performance improvement under very high load/shared fs situations, but it is a lot of additional complexity in the code to achieve that. Reducing import cost is probably a good goal, but this way is probably not the way to do it. --- parsl/__init__.py | 111 ++++++++-------------------------- parsl/app/app.py | 16 +++-- parsl/channels/__init__.py | 30 +-------- parsl/config.py | 6 +- parsl/dataflow/dflow.py | 36 +++++------ parsl/dataflow/futures.py | 4 +- parsl/dataflow/memoization.py | 8 +-- parsl/executors/__init__.py | 40 ++---------- parsl/providers/__init__.py | 74 +++++------------------ parsl/version.py | 2 +- 10 files changed, 82 insertions(+), 245 deletions(-) diff --git a/parsl/__init__.py b/parsl/__init__.py index e2ae29d5ec..5baafb9e6e 100644 --- a/parsl/__init__.py +++ b/parsl/__init__.py @@ -18,98 +18,28 @@ import multiprocessing as _multiprocessing import os import platform -from typing import TYPE_CHECKING - -if TYPE_CHECKING: - from parsl.app.app import bash_app, join_app, python_app - from parsl.config import Config - from parsl.data_provider.files import File - from parsl.dataflow.dflow import DataFlowKernel - from parsl.executors import ( - HighThroughputExecutor, - ThreadPoolExecutor, - WorkQueueExecutor, - ) - from parsl.log_utils import set_file_logger, set_stream_logger - from parsl.monitoring import MonitoringHub - -lazys = { - 'python_app': 'parsl.app.app', - 'bash_app': 'parsl.app.app', - 'join_app': 'parsl.app.app', - 'Config': 'parsl.config', - 'ThreadPoolExecutor': 'parsl.executors', - 'HighThroughputExecutor': 'parsl.executors', - 'WorkQueueExecutor': 'parsl.executors', - 'set_stream_logger': 'parsl.log_utils', - 'set_file_logger': 'parsl.log_utils', - 'MonitoringHub': 'parsl.monitoring', - 'File': 'parsl.data_provider.files', - 'DataFlowKernel': 'parsl.dataflow.dflow', - 'DataFlowKernelLoader': 'parsl.dataflow.dflow', -} - -import parsl - - -def lazy_loader(name): - # print(f"lazy_loader getattr for {name}") - if name in lazys: - import importlib - m = lazys[name] - # print(f"lazy load {name} from module {m}") - v = importlib.import_module(m) - # print(f"imported module: {v}") - a = v.__getattribute__(name) - parsl.__setattr__(name, a) - return a - raise AttributeError(f"No (lazy loadable) attribute in {__name__} for {name}") - - -# parsl/__init__.py:61: error: Cannot assign to a method -parsl.__getattr__ = lazy_loader # type: ignore[method-assign] -if platform.system() == 'Darwin': - _multiprocessing.set_start_method('fork', force=True) - - -AUTO_LOGNAME = -1 - -# there's a reason these were aliases and not redefinitions, -# and i should fix this to keep them as such. - - -def clear(*args, **kwargs): - from parsl import DataFlowKernelLoader - return DataFlowKernelLoader.clear(*args, **kwargs) - - -def load(*args, **kwargs): - from parsl import DataFlowKernelLoader - return DataFlowKernelLoader.load(*args, **kwargs) - - -def dfk(*args, **kwargs): - from parsl import DataFlowKernelLoader - return DataFlowKernelLoader.dfk(*args, **kwargs) - - -def wait_for_current_tasks(*args, **kwargs): - from parsl import DataFlowKernelLoader - return DataFlowKernelLoader.wait_for_current_tasks(*args, **kwargs) - - -logging.getLogger('parsl').addHandler(logging.NullHandler()) +from parsl.app.app import bash_app, join_app, python_app +from parsl.config import Config +from parsl.data_provider.files import File +from parsl.dataflow.dflow import DataFlowKernel, DataFlowKernelLoader +from parsl.executors import ( + HighThroughputExecutor, + ThreadPoolExecutor, + WorkQueueExecutor, +) +from parsl.log_utils import set_file_logger, set_stream_logger +from parsl.monitoring import MonitoringHub +from parsl.version import VERSION if platform.system() == 'Darwin': - os.environ['OBJC_DISABLE_INITIALIZE_FORK_SAFETY'] = 'YES' + _multiprocessing.set_start_method('fork', force=True) __author__ = 'The Parsl Team' - -from parsl.version import VERSION - __version__ = VERSION +AUTO_LOGNAME = -1 + __all__ = [ # decorators @@ -136,3 +66,14 @@ def wait_for_current_tasks(*args, **kwargs): # monitoring 'MonitoringHub', ] + +clear = DataFlowKernelLoader.clear +load = DataFlowKernelLoader.load +dfk = DataFlowKernelLoader.dfk +wait_for_current_tasks = DataFlowKernelLoader.wait_for_current_tasks + + +logging.getLogger('parsl').addHandler(logging.NullHandler()) + +if platform.system() == 'Darwin': + os.environ['OBJC_DISABLE_INITIALIZE_FORK_SAFETY'] = 'YES' diff --git a/parsl/app/app.py b/parsl/app/app.py index 849599d2d8..e9089f0ca7 100644 --- a/parsl/app/app.py +++ b/parsl/app/app.py @@ -1,5 +1,3 @@ -from __future__ import annotations - """Definitions for the @App decorator and the App classes. The App class encapsulates a generic leaf task that can be executed asynchronously. @@ -11,8 +9,8 @@ import typeguard -import parsl.dataflow.dflow as dflow -import parsl.dataflow.futures +from parsl.dataflow.dflow import DataFlowKernel +from parsl.dataflow.futures import AppFuture logger = logging.getLogger(__name__) @@ -27,7 +25,7 @@ class AppBase(metaclass=ABCMeta): @typeguard.typechecked def __init__(self, func: Callable, - data_flow_kernel: Optional[dflow.DataFlowKernel] = None, + data_flow_kernel: Optional[DataFlowKernel] = None, executors: Union[List[str], str] = 'all', cache: bool = False, ignore_for_cache: Optional[Sequence[str]] = None) -> None: @@ -73,13 +71,13 @@ def __init__(self, func: Callable, self.kwargs['inputs'] = params['inputs'].default @abstractmethod - def __call__(self, *args: Any, **kwargs: Any) -> parsl.dataflow.futures.AppFuture: + def __call__(self, *args: Any, **kwargs: Any) -> AppFuture: pass @typeguard.typechecked def python_app(function: Optional[Callable] = None, - data_flow_kernel: Optional[dflow.DataFlowKernel] = None, + data_flow_kernel: Optional[DataFlowKernel] = None, cache: bool = False, executors: Union[List[str], str] = 'all', ignore_for_cache: Optional[Sequence[str]] = None) -> Callable: @@ -120,7 +118,7 @@ def wrapper(f: Callable) -> PythonApp: @typeguard.typechecked def join_app(function: Optional[Callable] = None, - data_flow_kernel: Optional[dflow.DataFlowKernel] = None, + data_flow_kernel: Optional[DataFlowKernel] = None, cache: bool = False, ignore_for_cache: Optional[Sequence[str]] = None) -> Callable: """Decorator function for making join apps @@ -158,7 +156,7 @@ def wrapper(f: Callable) -> PythonApp: @typeguard.typechecked def bash_app(function: Optional[Callable] = None, - data_flow_kernel: Optional[dflow.DataFlowKernel] = None, + data_flow_kernel: Optional[DataFlowKernel] = None, cache: bool = False, executors: Union[List[str], str] = 'all', ignore_for_cache: Optional[Sequence[str]] = None) -> Callable: diff --git a/parsl/channels/__init__.py b/parsl/channels/__init__.py index c71649851c..c81f6a8bf1 100644 --- a/parsl/channels/__init__.py +++ b/parsl/channels/__init__.py @@ -1,30 +1,4 @@ -from typing import TYPE_CHECKING - -if TYPE_CHECKING: - from parsl.channels.base import Channel - from parsl.channels.local.local import LocalChannel - -lazys = { - 'Channel': 'parsl.channels.base', - 'LocalChannel': 'parsl.channels.local.local', -} - -import parsl.channels as px - - -def lazy_loader(name): - if name in lazys: - import importlib - m = lazys[name] - # print(f"lazy load {name} from module {m}") - v = importlib.import_module(m) - # print(f"imported module: {v}") - a = v.__getattribute__(name) - px.__setattr__(name, a) - return a - raise AttributeError(f"No (lazy loadable) attribute in {__name__} for {name}") - - -px.__getattr__ = lazy_loader # type: ignore[method-assign] +from parsl.channels.base import Channel +from parsl.channels.local.local import LocalChannel __all__ = ['Channel', 'LocalChannel'] diff --git a/parsl/config.py b/parsl/config.py index ccd1916e3c..3a747ffa05 100644 --- a/parsl/config.py +++ b/parsl/config.py @@ -1,13 +1,11 @@ -from __future__ import annotations - import logging from typing import Callable, Iterable, Optional, Sequence, Union import typeguard from typing_extensions import Literal -import parsl.dataflow.taskrecord as taskrecord from parsl.dataflow.dependency_resolvers import DependencyResolver +from parsl.dataflow.taskrecord import TaskRecord from parsl.errors import ConfigurationError from parsl.executors.base import ParslExecutor from parsl.executors.threads import ThreadPoolExecutor @@ -112,7 +110,7 @@ def __init__(self, garbage_collect: bool = True, internal_tasks_max_threads: int = 10, retries: int = 0, - retry_handler: Optional[Callable[[Exception, taskrecord.TaskRecord], float]] = None, + retry_handler: Optional[Callable[[Exception, TaskRecord], float]] = None, run_dir: str = 'runinfo', std_autopath: Optional[Callable] = None, strategy: Optional[str] = 'simple', diff --git a/parsl/dataflow/dflow.py b/parsl/dataflow/dflow.py index de1c028fbf..6101a11060 100644 --- a/parsl/dataflow/dflow.py +++ b/parsl/dataflow/dflow.py @@ -23,8 +23,6 @@ from typeguard import typechecked import parsl -import parsl.dataflow.memoization as memoization -import parsl.dataflow.taskrecord as taskrecord from parsl.app.errors import RemoteExceptionWrapper from parsl.app.futures import DataFuture from parsl.channels import Channel @@ -34,8 +32,10 @@ from parsl.dataflow.dependency_resolvers import SHALLOW_DEPENDENCY_RESOLVER from parsl.dataflow.errors import BadCheckpoint, DependencyError, JoinError from parsl.dataflow.futures import AppFuture +from parsl.dataflow.memoization import Memoizer from parsl.dataflow.rundirs import make_rundir from parsl.dataflow.states import FINAL_FAILURE_STATES, FINAL_STATES, States +from parsl.dataflow.taskrecord import TaskRecord from parsl.errors import ( ConfigurationError, InternalConsistencyError, @@ -173,11 +173,11 @@ def __init__(self, config: Config) -> None: else: checkpoints = {} - self.memoizer = memoization.Memoizer(self, memoize=config.app_cache, checkpoint=checkpoints) + self.memoizer = Memoizer(self, memoize=config.app_cache, checkpoint=checkpoints) self.checkpointed_tasks = 0 self._checkpoint_timer = None self.checkpoint_mode = config.checkpoint_mode - self.checkpointable_tasks: List[taskrecord.TaskRecord] = [] + self.checkpointable_tasks: List[TaskRecord] = [] # this must be set before executors are added since add_executors calls # job_status_poller.add_executors. @@ -204,7 +204,7 @@ def __init__(self, config: Config) -> None: self._checkpoint_timer = Timer(self.checkpoint, interval=checkpoint_period, name="Checkpoint") self.task_count = 0 - self.tasks: Dict[int, taskrecord.TaskRecord] = {} + self.tasks: Dict[int, TaskRecord] = {} self.submitter_lock = threading.Lock() self.dependency_launch_pool = cf.ThreadPoolExecutor(max_workers=1, thread_name_prefix="Dependency-Launch") @@ -236,12 +236,12 @@ def __exit__(self, exc_type, exc_value, traceback) -> None: else: raise InternalConsistencyError(f"Exit case for {mode} should be unreachable, validated by typeguard on Config()") - def _send_task_log_info(self, task_record: taskrecord.TaskRecord) -> None: + def _send_task_log_info(self, task_record: TaskRecord) -> None: if self.monitoring: task_log_info = self._create_task_log_info(task_record) self.monitoring.send(MessageType.TASK_INFO, task_log_info) - def _create_task_log_info(self, task_record: taskrecord.TaskRecord) -> Dict[str, Any]: + def _create_task_log_info(self, task_record: TaskRecord) -> Dict[str, Any]: """ Create the dictionary that will be included in the log. """ @@ -321,7 +321,7 @@ def config(self) -> Config: """ return self._config - def handle_exec_update(self, task_record: taskrecord.TaskRecord, future: Future) -> None: + def handle_exec_update(self, task_record: TaskRecord, future: Future) -> None: """This function is called only as a callback from an execution attempt reaching a final state (either successfully or failing). @@ -454,7 +454,7 @@ def handle_exec_update(self, task_record: taskrecord.TaskRecord, future: Future) if task_record['status'] == States.pending: self.launch_if_ready(task_record) - def handle_join_update(self, task_record: taskrecord.TaskRecord, inner_app_future: Optional[AppFuture]) -> None: + def handle_join_update(self, task_record: TaskRecord, inner_app_future: Optional[AppFuture]) -> None: with task_record['join_lock']: # inner_app_future has completed, which is one (potentially of many) # futures the outer task is joining on. @@ -544,7 +544,7 @@ def handle_join_update(self, task_record: taskrecord.TaskRecord, inner_app_futur self._send_task_log_info(task_record) - def handle_app_update(self, task_record: taskrecord.TaskRecord, future: AppFuture) -> None: + def handle_app_update(self, task_record: TaskRecord, future: AppFuture) -> None: """This function is called as a callback when an AppFuture is in its final state. @@ -582,7 +582,7 @@ def handle_app_update(self, task_record: taskrecord.TaskRecord, future: AppFutur self.wipe_task(task_id) return - def _complete_task(self, task_record: taskrecord.TaskRecord, new_state: States, result: Any) -> None: + def _complete_task(self, task_record: TaskRecord, new_state: States, result: Any) -> None: """Set a task into a completed state """ assert new_state in FINAL_STATES @@ -597,7 +597,7 @@ def _complete_task(self, task_record: taskrecord.TaskRecord, new_state: States, with task_record['app_fu']._update_lock: task_record['app_fu'].set_result(result) - def update_task_state(self, task_record: taskrecord.TaskRecord, new_state: States) -> None: + def update_task_state(self, task_record: TaskRecord, new_state: States) -> None: """Updates a task record state, and recording an appropriate change to task state counters. """ @@ -647,7 +647,7 @@ def wipe_task(self, task_id: int) -> None: def check_staging_inhibited(kwargs: Dict[str, Any]) -> bool: return kwargs.get('_parsl_staging_inhibit', False) - def launch_if_ready(self, task_record: taskrecord.TaskRecord) -> None: + def launch_if_ready(self, task_record: TaskRecord) -> None: """Schedules a task record for re-inspection to see if it is ready for launch and for launch if it is ready. The call will return immediately. @@ -665,7 +665,7 @@ def launch_if_ready(self, task_record: taskrecord.TaskRecord) -> None: self.dependency_launch_pool.submit(self._launch_if_ready_async, task_record) @wrap_with_logs - def _launch_if_ready_async(self, task_record: taskrecord.TaskRecord) -> None: + def _launch_if_ready_async(self, task_record: TaskRecord) -> None: """ _launch_if_ready will launch the specified task, if it is ready to run (for example, without dependencies, and in pending state). @@ -739,7 +739,7 @@ def _launch_if_ready_async(self, task_record: taskrecord.TaskRecord) -> None: task_record['exec_fu'] = exec_fu event("DFK_LAUNCH_IF_READY_END", task_record['span']) - def launch_task(self, task_record: taskrecord.TaskRecord) -> Future: + def launch_task(self, task_record: TaskRecord) -> Future: """Handle the actual submission of the task to the executor layer. Args: @@ -1065,7 +1065,7 @@ def submit(self, resource_specification = app_kwargs.get('parsl_resource_specification', {}) - task_record: taskrecord.TaskRecord + task_record: TaskRecord task_record = {'args': app_args, 'depends': [], 'dfk': self, @@ -1399,7 +1399,7 @@ def cleanup(self) -> None: logger.info("DFK cleanup complete") - def checkpoint(self, tasks: Optional[Sequence[taskrecord.TaskRecord]] = None) -> str: + def checkpoint(self, tasks: Optional[Sequence[TaskRecord]] = None) -> str: """Checkpoint the dfk incrementally to a checkpoint file. When called, every task that has been completed yet not @@ -1538,7 +1538,7 @@ def load_checkpoints(self, checkpointDirs: Optional[Sequence[str]]) -> Dict[str, return {} @staticmethod - def _log_std_streams(task_record: taskrecord.TaskRecord) -> None: + def _log_std_streams(task_record: TaskRecord) -> None: tid = task_record['id'] def log_std_stream(name: str, target) -> None: diff --git a/parsl/dataflow/futures.py b/parsl/dataflow/futures.py index c6fd386ff3..616a3d3bad 100644 --- a/parsl/dataflow/futures.py +++ b/parsl/dataflow/futures.py @@ -6,8 +6,8 @@ from typing import Any, Optional, Sequence, Union import parsl.app.app as app -import parsl.dataflow.taskrecord as taskrecord from parsl.app.futures import DataFuture +from parsl.dataflow.taskrecord import TaskRecord logger = logging.getLogger(__name__) @@ -54,7 +54,7 @@ class AppFuture(Future): """ - def __init__(self, task_record: taskrecord.TaskRecord) -> None: + def __init__(self, task_record: TaskRecord) -> None: """Initialize the AppFuture. Args: diff --git a/parsl/dataflow/memoization.py b/parsl/dataflow/memoization.py index 2dcb752e4f..551bd0b9d4 100644 --- a/parsl/dataflow/memoization.py +++ b/parsl/dataflow/memoization.py @@ -6,7 +6,7 @@ from functools import lru_cache, singledispatch from typing import TYPE_CHECKING, Any, Dict, List, Optional -import parsl.dataflow.taskrecord as taskrecord +from parsl.dataflow.taskrecord import TaskRecord if TYPE_CHECKING: from parsl import DataFlowKernel # import loop at runtime - needed for typechecking - TODO turn into "if typing:" @@ -166,7 +166,7 @@ def __init__(self, dfk: DataFlowKernel, memoize: bool = True, checkpoint: Dict[s logger.info("App caching disabled for all apps") self.memo_lookup_table = {} - def make_hash(self, task: taskrecord.TaskRecord) -> str: + def make_hash(self, task: TaskRecord) -> str: """Create a hash of the task inputs. Args: @@ -201,7 +201,7 @@ def make_hash(self, task: taskrecord.TaskRecord) -> str: x = b''.join(t) return hashlib.md5(x).hexdigest() - def check_memo(self, task: taskrecord.TaskRecord) -> Optional[Future[Any]]: + def check_memo(self, task: TaskRecord) -> Optional[Future[Any]]: """Create a hash of the task and its inputs and check the lookup table for this hash. If present, the results are returned. @@ -250,7 +250,7 @@ def hash_lookup(self, hashsum: str) -> Future[Any]: """ return self.memo_lookup_table[hashsum] - def update_memo(self, task: taskrecord.TaskRecord, r: Future[Any]) -> None: + def update_memo(self, task: TaskRecord, r: Future[Any]) -> None: """Updates the memoization lookup table with the result from a task. Args: diff --git a/parsl/executors/__init__.py b/parsl/executors/__init__.py index 7af3a6bb28..bc29204502 100644 --- a/parsl/executors/__init__.py +++ b/parsl/executors/__init__.py @@ -1,38 +1,8 @@ -from typing import TYPE_CHECKING - -if TYPE_CHECKING: - from parsl.executors.flux.executor import FluxExecutor - from parsl.executors.high_throughput.executor import HighThroughputExecutor - from parsl.executors.high_throughput.mpi_executor import MPIExecutor - from parsl.executors.threads import ThreadPoolExecutor - from parsl.executors.workqueue.executor import WorkQueueExecutor - -lazys = { - 'ThreadPoolExecutor': 'parsl.executors.threads', - 'WorkQueueExecutor': 'parsl.executors.workqueue.executor', - 'HighThroughputExecutor': 'parsl.executors.high_throughput.executor', - 'MPIExecutor': 'parsl.executors.high_throughput.mpi_executor', - 'FluxExecutor': 'parsl.executors.flux.executor', -} - -import parsl.executors as px - - -def lazy_loader(name): - if name in lazys: - import importlib - m = lazys[name] - # print(f"lazy load {name} from module {m}") - v = importlib.import_module(m) - # print(f"imported module: {v}") - a = v.__getattribute__(name) - px.__setattr__(name, a) - return a - raise AttributeError(f"No (lazy loadable) attribute in {__name__} for {name}") - - -# parsl/executors/__init__.py:34: error: Cannot assign to a method -px.__getattr__ = lazy_loader # type: ignore[method-assign] +from parsl.executors.flux.executor import FluxExecutor +from parsl.executors.high_throughput.executor import HighThroughputExecutor +from parsl.executors.high_throughput.mpi_executor import MPIExecutor +from parsl.executors.threads import ThreadPoolExecutor +from parsl.executors.workqueue.executor import WorkQueueExecutor __all__ = ['ThreadPoolExecutor', 'HighThroughputExecutor', diff --git a/parsl/providers/__init__.py b/parsl/providers/__init__.py index c2ac29528c..150f425f3d 100644 --- a/parsl/providers/__init__.py +++ b/parsl/providers/__init__.py @@ -1,63 +1,19 @@ -from typing import TYPE_CHECKING +# Cloud Providers +from parsl.providers.aws.aws import AWSProvider +from parsl.providers.azure.azure import AzureProvider +from parsl.providers.cobalt.cobalt import CobaltProvider +from parsl.providers.condor.condor import CondorProvider +from parsl.providers.googlecloud.googlecloud import GoogleCloudProvider +from parsl.providers.grid_engine.grid_engine import GridEngineProvider + +# Kubernetes +from parsl.providers.kubernetes.kube import KubernetesProvider +from parsl.providers.local.local import LocalProvider +from parsl.providers.lsf.lsf import LSFProvider +from parsl.providers.pbspro.pbspro import PBSProProvider +from parsl.providers.slurm.slurm import SlurmProvider +from parsl.providers.torque.torque import TorqueProvider -if TYPE_CHECKING: - # Cloud Providers - from parsl.providers.aws.aws import AWSProvider - from parsl.providers.azure.azure import AzureProvider - from parsl.providers.cobalt.cobalt import CobaltProvider - from parsl.providers.condor.condor import CondorProvider - from parsl.providers.googlecloud.googlecloud import GoogleCloudProvider - from parsl.providers.grid_engine.grid_engine import GridEngineProvider - - # Kubernetes - from parsl.providers.kubernetes.kube import KubernetesProvider - - # Workstation Provider - from parsl.providers.local.local import LocalProvider - from parsl.providers.lsf.lsf import LSFProvider - from parsl.providers.pbspro.pbspro import PBSProProvider - from parsl.providers.slurm.slurm import SlurmProvider - from parsl.providers.torque.torque import TorqueProvider - - -lazys = { - # Workstation Provider - 'LocalProvider': 'parsl.providers.local.local', - - 'CobaltProvider': 'parsl.providers.cobalt.cobalt', - 'CondorProvider': 'parsl.providers.condor.condor', - 'GridEngineProvider': 'parsl.providers.grid_engine.grid_engine', - 'SlurmProvider': 'parsl.providers.slurm.slurm', - 'TorqueProvider': 'parsl.providers.torque.torque', - 'PBSProProvider': 'parsl.providers.pbspro.pbspro', - 'LSFProvider': 'parsl.providers.lsf.lsf', - - # Cloud Providers - 'AWSProvider': 'parsl.providers.aws.aws', - 'GoogleCloudProvider': 'parsl.providers.googlecloud.googlecloud', - 'AzureProvider': 'parsl.providers.azure.azure', - - # Kubernetes - 'KubernetesProvider': 'parsl.providers.kubernetes.kube' -} - -import parsl.providers as px - - -def lazy_loader(name): - if name in lazys: - import importlib - m = lazys[name] - # print(f"lazy load {name} from module {m}") - v = importlib.import_module(m) - # print(f"imported module: {v}") - a = v.__getattribute__(name) - px.__setattr__(name, a) - return a - raise AttributeError(f"No (lazy loadable) attribute in {__name__} for {name}") - - -px.__getattr__ = lazy_loader # type: ignore[method-assign] __all__ = ['LocalProvider', 'CobaltProvider', 'CondorProvider', diff --git a/parsl/version.py b/parsl/version.py index 2931e6bcda..33c35e010f 100644 --- a/parsl/version.py +++ b/parsl/version.py @@ -1,3 +1,3 @@ """Set module version. """ -VERSION = '2024.08.12+desc-2024.08.14b' +VERSION = '2024.08.12+desc-2024.08.14c' From 583fa42f9ff5bc2867e925e86787aad263415174 Mon Sep 17 00:00:00 2001 From: Ben Clifford Date: Thu, 10 Oct 2024 11:07:59 +0000 Subject: [PATCH 404/408] replace interchange-based outstanding task count with submit-side structure count --- parsl/executors/high_throughput/executor.py | 2 +- parsl/executors/high_throughput/interchange.py | 8 +------- parsl/version.py | 2 +- 3 files changed, 3 insertions(+), 9 deletions(-) diff --git a/parsl/executors/high_throughput/executor.py b/parsl/executors/high_throughput/executor.py index 2bfbd115ad..0a45ef7463 100644 --- a/parsl/executors/high_throughput/executor.py +++ b/parsl/executors/high_throughput/executor.py @@ -582,7 +582,7 @@ def hold_worker(self, worker_id: str) -> None: def outstanding(self) -> int: """Returns the count of tasks outstanding across the interchange and managers""" - return self.command_client.run("OUTSTANDING_C") + return len(self.tasks) @property def connected_workers(self) -> int: diff --git a/parsl/executors/high_throughput/interchange.py b/parsl/executors/high_throughput/interchange.py index d33a8b8f92..209a7382e2 100644 --- a/parsl/executors/high_throughput/interchange.py +++ b/parsl/executors/high_throughput/interchange.py @@ -253,13 +253,7 @@ def _command_server(self) -> NoReturn: logger.debug("Waiting for command request") command_req = self.command_channel.recv_pyobj() logger.debug("Received command request: {}".format(command_req)) - if command_req == "OUTSTANDING_C": - outstanding = self.pending_task_queue.qsize() - for manager in self._ready_managers.values(): - outstanding += len(manager['tasks']) - reply = outstanding - - elif command_req == "CONNECTED_BLOCKS": + if command_req == "CONNECTED_BLOCKS": reply = self.connected_block_history elif command_req == "WORKERS": diff --git a/parsl/version.py b/parsl/version.py index 8a2ec010a8..3669380744 100644 --- a/parsl/version.py +++ b/parsl/version.py @@ -1,3 +1,3 @@ """Set module version. """ -VERSION = '2024.10.07+desc-2024.10.10a' +VERSION = '2024.10.07+desc-2024.10.10c' From 06bb0804fa4e6bf8570b28264b956695ab5baa75 Mon Sep 17 00:00:00 2001 From: Ben Clifford Date: Thu, 14 Nov 2024 13:59:35 +0000 Subject: [PATCH 405/408] Remove ResultsRadio experiment --- parsl/dataflow/dflow.py | 28 +--- parsl/executors/high_throughput/executor.py | 3 +- parsl/executors/threads.py | 2 - parsl/executors/workqueue/executor.py | 7 +- parsl/monitoring/db_manager.py | 1 - parsl/monitoring/radios.py | 27 ---- parsl/monitoring/remote.py | 72 +---------- .../tests/configs/local_threads_monitoring.py | 4 +- .../workqueue_monitoring_resultradio.py | 23 ---- .../test_mon_wq_result_radio/__init__.py | 0 .../test_mon_wq_result_radio/test_basic.py | 122 ------------------ .../test_mon_wq_result_radio/test_db_locks.py | 92 ------------- .../test_memoization_representation.py | 83 ------------ .../test_missing_heartbeat_3262.py | 91 ------------- parsl/version.py | 2 +- 15 files changed, 12 insertions(+), 545 deletions(-) delete mode 100644 parsl/tests/configs/workqueue_monitoring_resultradio.py delete mode 100644 parsl/tests/test_monitoring/test_mon_wq_result_radio/__init__.py delete mode 100644 parsl/tests/test_monitoring/test_mon_wq_result_radio/test_basic.py delete mode 100644 parsl/tests/test_monitoring/test_mon_wq_result_radio/test_db_locks.py delete mode 100644 parsl/tests/test_monitoring/test_mon_wq_result_radio/test_memoization_representation.py delete mode 100644 parsl/tests/test_scaling/test_missing_heartbeat_3262.py diff --git a/parsl/dataflow/dflow.py b/parsl/dataflow/dflow.py index 9676dbe49d..a47d1d9ebf 100644 --- a/parsl/dataflow/dflow.py +++ b/parsl/dataflow/dflow.py @@ -339,7 +339,7 @@ def handle_exec_update(self, task_record: TaskRecord, future: Future) -> None: raise InternalConsistencyError("done callback called, despite future not reporting itself as done") try: - res = self._unwrap_remote_exception_wrapper(future, task_record) + res = self._unwrap_remote_exception_wrapper(future) except Exception as e: logger.info(f"Task {task_id} try {task_record['try_id']} failed with exception of type {type(e).__name__}") @@ -605,31 +605,9 @@ def update_task_state(self, task_record: TaskRecord, new_state: States) -> None: self.task_state_counts[new_state] += 1 task_record['status'] = new_state - # this is a horrible place to put results radio mode decoding. - # @staticmethod - def _unwrap_remote_exception_wrapper(self, future: Future, task_record) -> Any: + @staticmethod + def _unwrap_remote_exception_wrapper(future: Future) -> Any: result = future.result() - - # this instance check is made twice - once before unwrapping radio results - # and once afterwards. This is a bit ugly, but executors can send back an - # unannotated RemoteExceptionWrapper, in addition to the monitoring wrapper - # sending back an annotated RemoteExceptionWrapper - if isinstance(result, RemoteExceptionWrapper): - result.reraise() - - executor = self.executors[task_record['executor']] - radio_mode = executor.radio_mode - # raise RuntimeError(f"BENC: with radio_mode {radio_mode}, result potentially with monitoring: {result}") - if radio_mode == "results" and not task_record['from_memo']: - try: - (messages, result) = result - except Exception as e: - raise RuntimeError(f"BENC: Got exception {e} with result = {result}") - # raise RuntimeError(f"BENC: discarding {len(messages)} monitoring messages: {messages}") - if self.monitoring: - for (t, v) in messages: - self.monitoring.send((t, v)) - if isinstance(result, RemoteExceptionWrapper): result.reraise() return result diff --git a/parsl/executors/high_throughput/executor.py b/parsl/executors/high_throughput/executor.py index 442925a372..16b0b700ba 100644 --- a/parsl/executors/high_throughput/executor.py +++ b/parsl/executors/high_throughput/executor.py @@ -322,8 +322,7 @@ def __init__(self, interchange_launch_cmd = DEFAULT_INTERCHANGE_LAUNCH_CMD self.interchange_launch_cmd = interchange_launch_cmd - self.radio_mode = "htex" - + radio_mode = "htex" enable_mpi_mode: bool = False mpi_launcher: str = "mpiexec" diff --git a/parsl/executors/threads.py b/parsl/executors/threads.py index 11de2b4d36..9b3b0df5ce 100644 --- a/parsl/executors/threads.py +++ b/parsl/executors/threads.py @@ -40,8 +40,6 @@ def __init__(self, label: str = 'threads', max_threads: Optional[int] = 2, self.storage_access = storage_access self.working_dir = working_dir - self.radio_mode = "udp" - def start(self): self.executor = cf.ThreadPoolExecutor(max_workers=self.max_threads, thread_name_prefix=self.thread_name_prefix) diff --git a/parsl/executors/workqueue/executor.py b/parsl/executors/workqueue/executor.py index 0a7d3f96fe..eb3e0db0b2 100644 --- a/parsl/executors/workqueue/executor.py +++ b/parsl/executors/workqueue/executor.py @@ -223,9 +223,6 @@ class WorkQueueExecutor(BlockProviderExecutor, putils.RepresentationMixin): specifiation for each task). """ - # TODO: this should be configurable: there's no definite preference for - # results radio vs filesystem mode. - # radio_mode = "results" radio_mode = "filesystem" @typeguard.typechecked @@ -255,8 +252,7 @@ def __init__(self, worker_executable: str = 'work_queue_worker', function_dir: Optional[str] = None, coprocess: bool = False, - scaling_cores_per_worker: int = 1, - radio_mode: str = "filesystem"): + scaling_cores_per_worker: int = 1): BlockProviderExecutor.__init__(self, provider=provider, block_error_handler=True) if not _work_queue_enabled: @@ -293,7 +289,6 @@ def __init__(self, self.worker_executable = worker_executable self.function_dir = function_dir self.coprocess = coprocess - self.radio_mode = radio_mode if not self.address: self.address = socket.gethostname() diff --git a/parsl/monitoring/db_manager.py b/parsl/monitoring/db_manager.py index e6d6c42be9..abdb038e79 100644 --- a/parsl/monitoring/db_manager.py +++ b/parsl/monitoring/db_manager.py @@ -498,7 +498,6 @@ def start(self, "{} reprocessable as last messages".format(len(resource_messages), len(reprocessable_first_resource_messages), len(reprocessable_last_resource_messages))) - logger.debug(f"BENC: resource messages are: {resource_messages}") insert_resource_messages = [] for msg in resource_messages: diff --git a/parsl/monitoring/radios.py b/parsl/monitoring/radios.py index 0ee431f203..14dc046557 100644 --- a/parsl/monitoring/radios.py +++ b/parsl/monitoring/radios.py @@ -10,23 +10,6 @@ logger = logging.getLogger(__name__) -# need to be careful about thread-safety here: -# there will be multiple radio instances writing -# to this, along with (eg in thread local case) -# potentially many result deliverers. -# in that latter case, should there be per-task-id -# segregation of who sends which results back? or -# do we just care about *anyone* can send the results -# back, first come first serve? - -# There are potentials for duplicates here when the -# queue is split into two queues at fork time when -# it already has results, and then those two copies -# of the results are merged again at result send -# time. To fix that, probably de-duplication should -# happen at return time? -result_radio_queue = [] - class MonitoringRadioSender(metaclass=ABCMeta): @abstractmethod @@ -129,16 +112,6 @@ def send(self, message: object) -> None: return -class ResultsRadioSender(MonitoringRadioSender): - def __init__(self, monitoring_url: str, source_id: int, timeout: int = 10): - pass - - def send(self, message: object) -> None: - global result_radio_queue - result_radio_queue.append(message) - # raise RuntimeError(f"BENC: appended {message} to {result_radio_queue}") - - class UDPRadioSender(MonitoringRadioSender): def __init__(self, monitoring_url: str, timeout: int = 10): diff --git a/parsl/monitoring/remote.py b/parsl/monitoring/remote.py index 3b3d0c1f4d..d72b54dc3c 100644 --- a/parsl/monitoring/remote.py +++ b/parsl/monitoring/remote.py @@ -3,8 +3,7 @@ import os import time from functools import wraps -from multiprocessing import Event, Queue -from queue import Empty +from multiprocessing import Event from typing import Any, Callable, Dict, List, Sequence, Tuple from parsl.monitoring.message_type import MessageType @@ -12,7 +11,6 @@ FilesystemRadioSender, HTEXRadioSender, MonitoringRadioSender, - ResultsRadioSender, UDPRadioSender, ) from parsl.multiprocessing import ForkProcess @@ -42,8 +40,6 @@ def wrapped(*args: List[Any], **kwargs: Dict[str, Any]) -> Any: task_id = kwargs.pop('_parsl_monitoring_task_id') try_id = kwargs.pop('_parsl_monitoring_try_id') terminate_event = Event() - terminate_queue: Queue[List[Any]] - terminate_queue = Queue() # Send first message to monitoring router send_first_message(try_id, task_id, @@ -64,8 +60,7 @@ def wrapped(*args: List[Any], **kwargs: Dict[str, Any]) -> Any: logging_level, sleep_dur, run_dir, - terminate_event, - terminate_queue), + terminate_event), daemon=True, name="Monitor-Wrapper-{}".format(task_id)) pp.start() @@ -78,22 +73,12 @@ def wrapped(*args: List[Any], **kwargs: Dict[str, Any]) -> Any: p = None try: - ret_v = f(*args, **kwargs) + return f(*args, **kwargs) finally: # There's a chance of zombification if the workers are killed by some signals (?) if p: terminate_event.set() - - try: - more_monitoring_messages = terminate_queue.get(timeout=30) - except Empty: - more_monitoring_messages = [] - - p.join(30) - # 30 second delay for this -- this timeout will be hit in the - # case of an unusually long end-of-loop, plus 30 seconds from - # the earlier get. - + p.join(30) # 30 second delay for this -- this timeout will be hit in the case of an unusually long end-of-loop if p.exitcode is None: logger.warn("Event-based termination of monitoring helper took too long. Using process-based termination.") p.terminate() @@ -108,41 +93,6 @@ def wrapped(*args: List[Any], **kwargs: Dict[str, Any]) -> Any: run_id, radio_mode, run_dir) - # if we reach here, the finally block has run, and - # ret_v has been populated. so we can do the return - # that used to live inside the try: block. - # If that block raised an exception, then the finally - # block would run, but then we would not come to this - # return statement. As before. - if radio_mode == "results": - # this import has to happen here, not at the top level: we - # want the result_radio_queue from the import on the - # execution side - we *don't* want to get the (empty) - # result_radio_queue on the submit side, send that with the - # closure, and then send it (still empty) back. This is pretty - # subtle, which suggests it needs either lots of documentation - # or perhaps something nicer than using globals like this? - from parsl.monitoring.radios import result_radio_queue - assert isinstance(result_radio_queue, list) - assert isinstance(more_monitoring_messages, list) - - full = result_radio_queue + more_monitoring_messages - - # due to fork/join when there are already results in the - # queue, messages may appear in `full` via two routes: - # once in process, and once via forking and joining. - # At present that seems to happen only with first_msg messages, - # so here check that full only has one. - first_msg = [m for m in full if m[1]['first_msg']] # type: ignore[index] - not_first_msg = [m for m in full if not m[1]['first_msg']] # type: ignore[index] - - # now assume there will be at least one first_msg - full = [first_msg[0]] + not_first_msg - - return (full, ret_v) - else: - return ret_v - new_kwargs = kwargs.copy() new_kwargs['_parsl_monitoring_task_id'] = x_task_id new_kwargs['_parsl_monitoring_try_id'] = x_try_id @@ -159,9 +109,6 @@ def get_radio(radio_mode: str, monitoring_hub_url: str, task_id: int, run_dir: s elif radio_mode == "filesystem": radio = FilesystemRadioSender(monitoring_url=monitoring_hub_url, run_dir=run_dir) - elif radio_mode == "results": - radio = ResultsRadioSender(monitoring_url=monitoring_hub_url, - source_id=task_id) else: raise RuntimeError(f"Unknown radio mode: {radio_mode}") return radio @@ -221,8 +168,7 @@ def monitor(pid: int, run_dir: str, # removed all defaults because unused and there's no meaningful default for terminate_event. # these probably should become named arguments, with a *, and named at invocation. - terminate_event: Any, - terminate_queue: Any) -> None: # cannot be Event because of multiprocessing type weirdness. + terminate_event: Any) -> None: # cannot be Event because of multiprocessing type weirdness. """Monitors the Parsl task's resources by pointing psutil to the task's pid and watching it and its children. This process makes calls to logging, but deliberately does not attach @@ -368,12 +314,4 @@ def accumulate_and_prepare() -> Dict[str, Any]: radio.send((MessageType.RESOURCE_INFO, d)) except Exception: logging.exception("Exception getting the resource usage. Not sending final usage to Hub", exc_info=True) - - # TODO: write out any accumulated messages that might have been - # accumulated by the results radio, so that the task wrapper in the main - # task process can see these results. - from parsl.monitoring.radios import result_radio_queue - logging.debug("Sending result_radio_queue") - terminate_queue.put(result_radio_queue) - logging.debug("End of monitoring helper") diff --git a/parsl/tests/configs/local_threads_monitoring.py b/parsl/tests/configs/local_threads_monitoring.py index a9daf44833..4edc329095 100644 --- a/parsl/tests/configs/local_threads_monitoring.py +++ b/parsl/tests/configs/local_threads_monitoring.py @@ -6,9 +6,7 @@ # BENC: temp class for dev purposes. should test both UDP and filesystem # radiomodes with local executor. class TestExecutor(ThreadPoolExecutor): - def __init__(self, *args, **kwargs): - super().__init__(*args, **kwargs) - self.radio_mode = "filesystem" + radio_mode = "filesystem" def fresh_config(): diff --git a/parsl/tests/configs/workqueue_monitoring_resultradio.py b/parsl/tests/configs/workqueue_monitoring_resultradio.py deleted file mode 100644 index e514608453..0000000000 --- a/parsl/tests/configs/workqueue_monitoring_resultradio.py +++ /dev/null @@ -1,23 +0,0 @@ -from parsl.config import Config -from parsl.data_provider.file_noop import NoOpFileStaging -from parsl.data_provider.ftp import FTPInTaskStaging -from parsl.data_provider.http import HTTPInTaskStaging -from parsl.executors import WorkQueueExecutor -from parsl.monitoring import MonitoringHub -from parsl.providers import LocalProvider - - -def fresh_config(): - return Config(strategy='simple', - executors=[WorkQueueExecutor(port=9000, - provider=LocalProvider(init_blocks=0), - radio_mode="results")], - monitoring=MonitoringHub(hub_address="localhost", - hub_port=55055, - monitoring_debug=True, - resource_monitoring_interval=1, - ) - ) - - -config = fresh_config() diff --git a/parsl/tests/test_monitoring/test_mon_wq_result_radio/__init__.py b/parsl/tests/test_monitoring/test_mon_wq_result_radio/__init__.py deleted file mode 100644 index e69de29bb2..0000000000 diff --git a/parsl/tests/test_monitoring/test_mon_wq_result_radio/test_basic.py b/parsl/tests/test_monitoring/test_mon_wq_result_radio/test_basic.py deleted file mode 100644 index 64b2b2b28e..0000000000 --- a/parsl/tests/test_monitoring/test_mon_wq_result_radio/test_basic.py +++ /dev/null @@ -1,122 +0,0 @@ -import logging -import os -import time - -import pytest - -import parsl - -logger = logging.getLogger(__name__) - - -@parsl.python_app -def this_app(): - # this delay needs to be several times the resource monitoring - # period configured in the test configuration, so that some - # messages are actually sent - there is no guarantee that any - # (non-first) resource message will be sent at all for a short app. - time.sleep(3) - - return 5 - - -@pytest.mark.local -def test_row_counts(): - # this is imported here rather than at module level because - # it isn't available in a plain parsl install, so this module - # would otherwise fail to import and break even a basic test - # run. - import sqlalchemy - - from parsl.tests.configs.workqueue_monitoring_resultradio import fresh_config - - if os.path.exists("runinfo/monitoring.db"): - logger.info("Monitoring database already exists - deleting") - os.remove("runinfo/monitoring.db") - - logger.info("Generating fresh config") - c = fresh_config() - logger.info("Loading parsl") - parsl.load(c) - - logger.info("invoking and waiting for result") - assert this_app().result() == 5 - - logger.info("cleaning up parsl") - parsl.dfk().cleanup() - parsl.clear() - - # at this point, we should find one row in the monitoring database. - - logger.info("checking database content") - engine = sqlalchemy.create_engine("sqlite:///runinfo/monitoring.db") - with engine.begin() as connection: - - result = connection.execute("SELECT COUNT(*) FROM workflow") - (c, ) = result.first() - assert c == 1 - - result = connection.execute("SELECT COUNT(*) FROM task") - (c, ) = result.first() - assert c == 1 - - result = connection.execute("SELECT COUNT(*) FROM try") - (c, ) = result.first() - assert c == 1 - - # Check running event appears in both places that it should. - # When developing the results radio, I saw a case where the - # value was only appearing in the try table, not the status - # table. - result = connection.execute("SELECT COUNT(*) FROM try WHERE task_try_time_running IS NOT NULL") - (c, ) = result.first() - assert c == 1 - - result = connection.execute("SELECT COUNT(*) FROM status WHERE task_status_name = 'running'") - (c, ) = result.first() - assert c == 1 - - result = connection.execute("SELECT COUNT(*) FROM status WHERE task_status_name = 'running_ended'") - (c, ) = result.first() - assert c == 1 - - result = connection.execute("SELECT COUNT(*) FROM status, try " - "WHERE status.task_id = try.task_id " - "AND status.task_status_name='exec_done' " - "AND task_try_time_running is NULL") - (c, ) = result.first() - assert c == 0 - - # workqueue doesn't populate the node table. - # because parsl level code isn't running on a node persistently - # instead, it is the workqueue worker doing that, which doesn't - # report into parsl monitoring. - # this is a feature downgrade from using htex that needs some - # consideration - - # Two entries: one showing manager active, one inactive - # result = connection.execute("SELECT COUNT(*) FROM node") - # (c, ) = result.first() - # assert c == 2 - - # workqueue, at least when using providers, does have a loose - # block concept: but it doesn't report anything into the block - # table here, and if using wq external scaling thing, then there - # wouldn't be parsl level blocks at all. - # This needs some consideration. - - # There should be one block polling status - # local provider has a status_polling_interval of 5s - # result = connection.execute("SELECT COUNT(*) FROM block") - # (c, ) = result.first() - # assert c >= 2 - - result = connection.execute("SELECT COUNT(*) FROM resource") - (c, ) = result.first() - assert c >= 1 - - logger.info("all done") - - -if __name__ == "__main__": - test_row_counts() diff --git a/parsl/tests/test_monitoring/test_mon_wq_result_radio/test_db_locks.py b/parsl/tests/test_monitoring/test_mon_wq_result_radio/test_db_locks.py deleted file mode 100644 index 6e0ee8daaf..0000000000 --- a/parsl/tests/test_monitoring/test_mon_wq_result_radio/test_db_locks.py +++ /dev/null @@ -1,92 +0,0 @@ - -import logging -import os -import time - -import pytest - -import parsl - -logger = logging.getLogger(__name__) - - -@parsl.python_app -def this_app(): - return 5 - - -@pytest.mark.local -def test_row_counts(): - import sqlalchemy - - from parsl.tests.configs.workqueue_monitoring_resultradio import fresh_config - - if os.path.exists("runinfo/monitoring.db"): - logger.info("Monitoring database already exists - deleting") - os.remove("runinfo/monitoring.db") - - engine = sqlalchemy.create_engine("sqlite:///runinfo/monitoring.db") - - logger.info("loading parsl") - parsl.load(fresh_config()) - - # parsl.load() returns before all initialisation of monitoring - # is complete, which means it isn't safe to take a read lock on - # the database yet. This delay tries to work around that - some - # better async behaviour might be nice, but I'm not sure what. - time.sleep(10) - - # to get an sqlite3 read lock that is held over a controllable - # long time, create a transaction and perform a SELECT in it. - # (see bottom of https://sqlite.org/lockingv3.html) - - # there's an awkward race here: parsl.load() returns before the - # database might have been created, and so then the db manager will - # crash (and if there is a retry loop there instead, I think it will - # hang until after the read lock stuff below is finished? which might - # be acceptable? if it's meant to be properly async and not blocking?) - # ... in which case, initialise parsl *after taking the lock* would also - # work (although the select statement to get that lock wouldn't be the same - # because it wouldn't be able to select from the right table) - - logger.info("Getting a read lock on the monitoring database") - with engine.begin() as readlock_connection: - readlock_connection.execute("BEGIN TRANSACTION") - result = readlock_connection.execute("SELECT COUNT(*) FROM workflow") - (c, ) = result.first() - assert c == 1 - # now readlock_connection should have a read lock that will - # stay locked until the transaction is ended, or the with - # block ends. - - logger.info("invoking and waiting for result") - assert this_app().result() == 5 - - # there is going to be some raciness here making sure that - # the database manager actually tries to write while the - # read lock is held. I'm not sure if there is a better way - # to detect this other than a hopefully long-enough sleep. - time.sleep(10) - - logger.info("cleaning up parsl") - parsl.dfk().cleanup() - parsl.clear() - - # at this point, we should find one row in the monitoring database. - - logger.info("checking database content") - with engine.begin() as connection: - - result = connection.execute("SELECT COUNT(*) FROM workflow") - (c, ) = result.first() - assert c == 1 - - result = connection.execute("SELECT COUNT(*) FROM task") - (c, ) = result.first() - assert c == 1 - - result = connection.execute("SELECT COUNT(*) FROM try") - (c, ) = result.first() - assert c == 1 - - logger.info("all done") diff --git a/parsl/tests/test_monitoring/test_mon_wq_result_radio/test_memoization_representation.py b/parsl/tests/test_monitoring/test_mon_wq_result_radio/test_memoization_representation.py deleted file mode 100644 index 62743ff695..0000000000 --- a/parsl/tests/test_monitoring/test_mon_wq_result_radio/test_memoization_representation.py +++ /dev/null @@ -1,83 +0,0 @@ - -import logging -import os - -import pytest - -import parsl - -logger = logging.getLogger(__name__) - - -@parsl.python_app(cache=True) -def this_app(x): - return x + 1 - - -@pytest.mark.local -def test_hashsum(): - import sqlalchemy - - from parsl.tests.configs.workqueue_monitoring_resultradio import fresh_config - - if os.path.exists("runinfo/monitoring.db"): - logger.info("Monitoring database already exists - deleting") - os.remove("runinfo/monitoring.db") - - logger.info("loading parsl") - parsl.load(fresh_config()) - - logger.info("invoking and waiting for result (1/4)") - f1 = this_app(4) - assert f1.result() == 5 - - logger.info("invoking and waiting for result (2/4)") - f2 = this_app(17) - assert f2.result() == 18 - - logger.info("invoking and waiting for result (3/4)") - f3 = this_app(4) - assert f3.result() == 5 - - logger.info("invoking and waiting for result (4/4)") - f4 = this_app(4) - assert f4.result() == 5 - - assert f1.task_record['hashsum'] == f3.task_record['hashsum'] - assert f1.task_record['hashsum'] == f4.task_record['hashsum'] - assert f1.task_record['hashsum'] != f2.task_record['hashsum'] - - logger.info("cleaning up parsl") - parsl.dfk().cleanup() - parsl.clear() - - # at this point, we should find one row in the monitoring database. - - logger.info("checking database content") - engine = sqlalchemy.create_engine("sqlite:///runinfo/monitoring.db") - with engine.begin() as connection: - - # we should have three tasks, but with only two tries, because the - # memo try should be missing - result = connection.execute("SELECT COUNT(*) FROM task") - (task_count, ) = result.first() - assert task_count == 4 - - # this will check that the number of task rows for each hashsum matches the above app invocations - result = connection.execute(f"SELECT COUNT(task_hashsum) FROM task WHERE task_hashsum='{f1.task_record['hashsum']}'") - (hashsum_count, ) = result.first() - assert hashsum_count == 3 - - result = connection.execute(f"SELECT COUNT(task_hashsum) FROM task WHERE task_hashsum='{f2.task_record['hashsum']}'") - (hashsum_count, ) = result.first() - assert hashsum_count == 1 - - result = connection.execute("SELECT COUNT(*) FROM status WHERE task_status_name='exec_done'") - (memo_count, ) = result.first() - assert memo_count == 2 - - result = connection.execute("SELECT COUNT(*) FROM status WHERE task_status_name='memo_done'") - (memo_count, ) = result.first() - assert memo_count == 2 - - logger.info("all done") diff --git a/parsl/tests/test_scaling/test_missing_heartbeat_3262.py b/parsl/tests/test_scaling/test_missing_heartbeat_3262.py deleted file mode 100644 index 542eb3cb2c..0000000000 --- a/parsl/tests/test_scaling/test_missing_heartbeat_3262.py +++ /dev/null @@ -1,91 +0,0 @@ -import os -import signal -import time - -import pytest -import zmq - -import parsl -from parsl.channels import LocalChannel -from parsl.config import Config -from parsl.executors import HighThroughputExecutor -from parsl.launchers import SimpleLauncher -from parsl.providers import LocalProvider - -T_s = 1 - - -def fresh_config(): - htex = HighThroughputExecutor( - heartbeat_period=1 * T_s, - heartbeat_threshold=3 * T_s, - label="htex_local", - worker_debug=True, - cores_per_worker=1, - encrypted=False, - provider=LocalProvider( - channel=LocalChannel(), - init_blocks=0, - min_blocks=0, - max_blocks=0, - launcher=SimpleLauncher(), - ), - ) - c = Config( - executors=[htex], - strategy='none', - strategy_period=0.5, - ) - return c, htex - - -@parsl.python_app -def app(): - return 7 - - -@pytest.mark.local -@pytest.mark.parametrize("msg", - (b'FuzzyByte\rSTREAM', # not JSON - b'{}', # missing fields - b'{"type":"heartbeat"}', # heartbeat without ID - ) - ) -def test_bad_messages(try_assert, msg): - """This tests that a heartbeat arriving after a manager - has expired due to missing heartbeats (due to transient - delay) does not kill the interchange - issue #3262 and - issue #3632. - """ - - c, htex = fresh_config() - - with parsl.load(c): - - # send a bad message into the interchange on the - # task_outgoing worker channel, and then check that - # we can scale out a block and run a task. - - (task_port, result_port) = htex.command_client.run("WORKER_PORTS") - - context = zmq.Context() - channel_timeout = 10000 # in milliseconds - task_channel = context.socket(zmq.DEALER) - task_channel.setsockopt(zmq.LINGER, 0) - task_channel.setsockopt(zmq.IDENTITY, b'testid') - - task_channel.set_hwm(0) - task_channel.setsockopt(zmq.SNDTIMEO, channel_timeout) - task_channel.connect(f"tcp://localhost:{task_port}") - - task_channel.send(msg) - - # If the interchange exits, it's likely that this test will hang rather - # than raise an error, because the interchange interaction code - # assumes the interchange is always there. - # In the case of issue #3262, an exception message goes to stderr, and - # no error goes to the interchange log file. - htex.scale_out_facade(1) - try_assert(lambda: len(htex.connected_managers()) == 1, timeout_ms=10000) - - assert app().result() == 7 diff --git a/parsl/version.py b/parsl/version.py index 5fd4af2fa8..01a56ef590 100644 --- a/parsl/version.py +++ b/parsl/version.py @@ -1,3 +1,3 @@ """Set module version. """ -VERSION = '2024.11.11+desc-2024.11.14a' +VERSION = '2024.11.11+desc-2024.11.14b' From 8772f090694c0c132c06277c14c3286995df6cbe Mon Sep 17 00:00:00 2001 From: Ben Clifford Date: Wed, 11 Dec 2024 16:13:49 +0000 Subject: [PATCH 406/408] fix up broken filesystem radio shutdown --- parsl/monitoring/monitoring.py | 9 --------- parsl/version.py | 2 +- 2 files changed, 1 insertion(+), 10 deletions(-) diff --git a/parsl/monitoring/monitoring.py b/parsl/monitoring/monitoring.py index 8719b0a8c7..015e7bec43 100644 --- a/parsl/monitoring/monitoring.py +++ b/parsl/monitoring/monitoring.py @@ -212,15 +212,6 @@ def close(self) -> None: break if self.monitoring_hub_active: self.monitoring_hub_active = False - - # some kind of filesystem_proc drain should happen here... - # which might take 10s of minutes based on my experience on cori (!) - # should this be message based? it probably doesn't need to be if - # we believe we've received all messages - # ... which we don't - logger.info("Terminating filesystem radio receiver process") - self.filesystem_proc.terminate() - self.filesystem_proc.join() if exception_msgs: for exception_msg in exception_msgs: logger.error( diff --git a/parsl/version.py b/parsl/version.py index e54c24ec3a..bd674bf4de 100644 --- a/parsl/version.py +++ b/parsl/version.py @@ -1,3 +1,3 @@ """Set module version. """ -VERSION = '2024.12.09+desc-2024.12.11a' +VERSION = '2024.12.09+desc-2024.12.11b' From 6c6b558c41b268f533502f62512198283e5962b8 Mon Sep 17 00:00:00 2001 From: Ben Clifford Date: Sun, 23 Feb 2025 17:15:15 +0000 Subject: [PATCH 407/408] working on race conditions around fork-without-exec in task vine executor --- parsl/executors/taskvine/executor.py | 19 ++++++++++--------- parsl/executors/taskvine/factory.py | 5 +++++ parsl/multiprocessing.py | 4 ++++ parsl/version.py | 2 +- 4 files changed, 20 insertions(+), 10 deletions(-) diff --git a/parsl/executors/taskvine/executor.py b/parsl/executors/taskvine/executor.py index 8f5d622fd9..54e7721b9b 100644 --- a/parsl/executors/taskvine/executor.py +++ b/parsl/executors/taskvine/executor.py @@ -40,6 +40,7 @@ from parsl.executors.taskvine.manager import _taskvine_submit_wait from parsl.executors.taskvine.manager_config import TaskVineManagerConfig from parsl.executors.taskvine.utils import ParslFileToVine, ParslTaskToVine +from parsl.multiprocessing import SpawnContext from parsl.process_loggers import wrap_with_logs from parsl.providers import CondorProvider, LocalProvider from parsl.providers.base import ExecutionProvider @@ -134,13 +135,13 @@ def __init__(self, self.storage_access = storage_access # Queue to send ready tasks from TaskVine executor process to TaskVine manager process - self._ready_task_queue: multiprocessing.Queue = multiprocessing.Queue() + self._ready_task_queue: multiprocessing.Queue = SpawnContext.Queue() # Queue to send finished tasks from TaskVine manager process to TaskVine executor process - self._finished_task_queue: multiprocessing.Queue = multiprocessing.Queue() + self._finished_task_queue: multiprocessing.Queue = SpawnContext.Queue() # Event to signal whether the manager and factory processes should stop running - self._should_stop = multiprocessing.Event() + self._should_stop = SpawnContext.Event() # TaskVine manager process self._submit_process = None @@ -252,17 +253,17 @@ def start(self): "finished_task_queue": self._finished_task_queue, "should_stop": self._should_stop, "manager_config": self.manager_config} - self._submit_process = multiprocessing.Process(target=_taskvine_submit_wait, - name="TaskVine-Submit-Process", - kwargs=submit_process_kwargs) + self._submit_process = SpawnContext.Process(target=_taskvine_submit_wait, + name="TaskVine-Submit-Process", + kwargs=submit_process_kwargs) # Create a process to run the TaskVine factory if enabled. if self.worker_launch_method == 'factory': factory_process_kwargs = {"should_stop": self._should_stop, "factory_config": self.factory_config} - self._factory_process = multiprocessing.Process(target=_taskvine_factory, - name="TaskVine-Factory-Process", - kwargs=factory_process_kwargs) + self._factory_process = SpawnContext.Process(target=_taskvine_factory, + name="TaskVine-Factory-Process", + kwargs=factory_process_kwargs) # Run thread to collect results and set tasks' futures. self._collector_thread = threading.Thread(target=self._collect_taskvine_results, diff --git a/parsl/executors/taskvine/factory.py b/parsl/executors/taskvine/factory.py index 20409efac8..11cbeeb623 100644 --- a/parsl/executors/taskvine/factory.py +++ b/parsl/executors/taskvine/factory.py @@ -1,4 +1,5 @@ import logging +import os from parsl.executors.taskvine.errors import TaskVineFactoryFailure from parsl.process_loggers import wrap_with_logs @@ -43,6 +44,10 @@ def _taskvine_factory(should_stop, factory_config): factory.max_workers = factory_config.max_workers factory.workers_per_cycle = factory_config.workers_per_cycle + # fix race condition where this directory isn't created by the + # factory - despite parsl issue #3089, cctools #3672 + os.makedirs(factory.scratch_dir, exist_ok=True) + if factory_config.worker_options: factory.extra_options = factory_config.worker_options factory.timeout = factory_config.worker_timeout diff --git a/parsl/multiprocessing.py b/parsl/multiprocessing.py index a468d840ec..f53babf7e6 100644 --- a/parsl/multiprocessing.py +++ b/parsl/multiprocessing.py @@ -11,6 +11,10 @@ logger = logging.getLogger(__name__) ForkContext = multiprocessing.get_context("fork") + +# for more general compatibility, spawncontext should maybe be +# "anything except fork", with whatever the platform default +# is unless it's Fork. SpawnContext = multiprocessing.get_context("spawn") ForkProcess: Callable[..., ForkProcessType] = ForkContext.Process diff --git a/parsl/version.py b/parsl/version.py index 954ece21c1..b50e64e2a9 100644 --- a/parsl/version.py +++ b/parsl/version.py @@ -1,3 +1,3 @@ """Set module version. """ -VERSION = '2025.02.17+desc-2025.02.20a' +VERSION = '2025.02.17+desc-2025.02.23a' From e0d46d5753bf89d897524afdee26a7936634e939 Mon Sep 17 00:00:00 2001 From: Ben Clifford Date: Tue, 25 Feb 2025 17:19:52 +0000 Subject: [PATCH 408/408] change WQ to spawn rather than fork in multiprocessing --- parsl/executors/workqueue/executor.py | 19 ++++++++++--------- parsl/multiprocessing.py | 2 ++ parsl/version.py | 2 +- 3 files changed, 13 insertions(+), 10 deletions(-) diff --git a/parsl/executors/workqueue/executor.py b/parsl/executors/workqueue/executor.py index aa9fdf0b1b..b9294b8ac2 100644 --- a/parsl/executors/workqueue/executor.py +++ b/parsl/executors/workqueue/executor.py @@ -32,6 +32,7 @@ from parsl.executors.errors import ExecutorError, InvalidResourceSpecification from parsl.executors.status_handling import BlockProviderExecutor from parsl.executors.workqueue import exec_parsl_function +from parsl.multiprocessing import SpawnContext, SpawnProcess from parsl.process_loggers import wrap_with_logs from parsl.providers import CondorProvider, LocalProvider from parsl.providers.base import ExecutionProvider @@ -260,8 +261,8 @@ def __init__(self, self.scaling_cores_per_worker = scaling_cores_per_worker self.label = label - self.task_queue = multiprocessing.Queue() # type: multiprocessing.Queue - self.collector_queue = multiprocessing.Queue() # type: multiprocessing.Queue + self.task_queue: multiprocessing.Queue = SpawnContext.Queue() + self.collector_queue: multiprocessing.Queue = SpawnContext.Queue() self.address = address self.port = port self.executor_task_counter = -1 @@ -283,7 +284,7 @@ def __init__(self, self.autocategory = autocategory self.enable_monitoring = enable_monitoring self.max_retries = max_retries - self.should_stop = multiprocessing.Value(c_bool, False) + self.should_stop = SpawnContext.Value(c_bool, False) self.cached_envs = {} # type: Dict[int, str] self.worker_options = worker_options self.worker_executable = worker_executable @@ -334,7 +335,7 @@ def start(self): logger.debug("Starting WorkQueueExecutor") - self._port_mailbox = multiprocessing.Queue() + port_mailbox = SpawnContext.Queue() logger.warning("BODGE: delay here for hack around often observed futex race...") time.sleep(15) @@ -357,12 +358,12 @@ def start(self): "wq_log_dir": self.wq_log_dir, "project_password_file": self.project_password_file, "project_name": self.project_name, - "port_mailbox": self._port_mailbox, + "port_mailbox": port_mailbox, "coprocess": self.coprocess } - self.submit_process = multiprocessing.Process(target=_work_queue_submit_wait, - name="WorkQueue-Submit-Process", - kwargs=submit_process_kwargs) + self.submit_process = SpawnProcess(target=_work_queue_submit_wait, + name="WorkQueue-Submit-Process", + kwargs=submit_process_kwargs) self.collector_thread = threading.Thread(target=self._collect_work_queue_results, name="WorkQueue-collector-thread") @@ -372,7 +373,7 @@ def start(self): self.submit_process.start() self.collector_thread.start() - self._chosen_port = self._port_mailbox.get(timeout=60) + self._chosen_port = port_mailbox.get(timeout=60) logger.debug(f"Chosen listening port is {self._chosen_port}") diff --git a/parsl/multiprocessing.py b/parsl/multiprocessing.py index f53babf7e6..1153e2dcb9 100644 --- a/parsl/multiprocessing.py +++ b/parsl/multiprocessing.py @@ -6,6 +6,7 @@ import multiprocessing.queues import platform from multiprocessing.context import ForkProcess as ForkProcessType +from multiprocessing.context import SpawnProcess as SpawnProcessType from typing import Callable logger = logging.getLogger(__name__) @@ -18,6 +19,7 @@ SpawnContext = multiprocessing.get_context("spawn") ForkProcess: Callable[..., ForkProcessType] = ForkContext.Process +SpawnProcess: Callable[..., SpawnProcessType] = SpawnContext.Process class MacSafeQueue(multiprocessing.queues.Queue): diff --git a/parsl/version.py b/parsl/version.py index b50e64e2a9..f2e8418b5e 100644 --- a/parsl/version.py +++ b/parsl/version.py @@ -1,3 +1,3 @@ """Set module version. """ -VERSION = '2025.02.17+desc-2025.02.23a' +VERSION = '2025.02.24+desc-2025.02.25a'