Merge branch 'amusecode:main' into main

.github/workflows/inplace.yml → .github/workflows/ci.yml

@@ -1,64 +1,104 @@
 # This workflow will install Python dependencies, run tests and lint with a single version of Python
 # For more information see: https://help.github.com/actions/language-and-framework-guides/using-python-with-github-actions
 
-name: inplace
+name: ci
 
 on:
   push:
-    branches: [ main ]
+    branches:
+     - main
   pull_request:
-    branches: [ main ]
+    branches:
+     - main
+  workflow_dispatch:
 
 jobs:
-  build:
-
-    runs-on: ubuntu-latest
+  test:
+    runs-on: ${{ matrix.os }}
     strategy:
+      fail-fast: false
       matrix:
-        mpi: [ 'mpich', 'openmpi']
-    name: Test AMUSE with ${{ matrix.mpi }}
+        mpi:
+          - mpich
+          - openmpi
+        os:
+          - ubuntu-22.04
+          - ubuntu-20.04
+          # macOS is not ready yet - needs other setup of prerequisites
+          # - macos-12
+          # - macos-11
+        python:
+          - 3.7
+
     steps:
-    - uses: actions/checkout@v3
+
+    - name: Checkout
+      uses: actions/checkout@v3
+
     - name: Setup MPI
+      id:   setup-mpi
       uses: mpi4py/setup-mpi@v1
       with:
         mpi: ${{ matrix.mpi }}
+
+    - name: Show MPI name
+      run:  echo "${{ steps.setup-mpi.outputs.mpi }}"
+
+    - name: Show MPI info
+      run:  mpichversion
+      if:   ${{ matrix.mpi == 'mpich' }}
+
+    - name: Show MPI info
+      run:  ompi_info
+      if:   ${{ matrix.mpi == 'openmpi' }}
+
     - name: Set up JDK 1.8
       uses: actions/setup-java@v3.9.0
       with:
         distribution: 'zulu' # See 'Supported distributions' for available options
         java-version: '17'
-    - name: Set up Python 3.8
+
+    - name: Set up Python
       uses: actions/setup-python@v4
       with:
-        python-version: 3.8
+        python-version: ${{ matrix.python }}
+        cache: 'pip'
+
     - name: Install dependencies
       run: |
         python -m pip install --upgrade pip
         sudo apt-get install gfortran libopenblas-dev libhdf5-openmpi-dev libgsl0-dev cmake libfftw3-3 libfftw3-dev libmpfr6 libmpfr-dev
         pip install numpy scipy matplotlib docutils mpi4py pytest pytest-timeout
         if [ -f requirements.txt ]; then pip install -r requirements.txt; fi
+
     - name: Install amuse
       run: |
         pip install -e .
+        ./configure
+
     - name: build AMUSE framework
       run: |
         make framework
+
     - name: build SSE and BHTree
       run: |
         make sse.code bhtree.code
+
     - name: check installation
       run: |
         amusifier --get-amuse-configmk
         pip list
+
     - name: archive build log
       uses: actions/upload-artifact@v3.1.1
       with:
           name: buildlog
           path: build.log
+
     - name: test core_tests
       run: |
         pytest --pyargs amuse.test.suite.core_tests -s
+
     - name: test compile_tests
       run: |
         ip link show
@@ -67,10 +107,11 @@ jobs:
       env:
         OMPI_MCA_rmaps_base_oversubscribe: 1
         OMPI_MCA_btl_tcp_if_include: lo
+
     - name: test code_tests
       run: |
-        pytest  --pyargs amuse.test.suite.codes_tests.test_bhtree -sv
-        pytest  --pyargs amuse.test.suite.codes_tests.test_sse -sv
+        mpiexec -n 1 pytest --pyargs amuse.test.suite.codes_tests.test_bhtree -sv
+        mpiexec -n 1 pytest --pyargs amuse.test.suite.codes_tests.test_sse -sv
       env:
         OMPI_MCA_rmaps_base_oversubscribe: 1
         OMPI_MCA_btl_tcp_if_include: lo

.github/workflows/python-package.yml

@@ -8,16 +8,13 @@ on:
     branches: [ "main" ]
   pull_request:
     branches: [ "main" ]
-
 jobs:
   build:
-
     runs-on: ubuntu-latest
     strategy:
       fail-fast: false
       matrix:
         python-version: ["3.7", "3.10"]
-
     steps:
     - uses: actions/checkout@v3
     - name: Set up Python ${{ matrix.python-version }}
@@ -30,7 +27,7 @@ jobs:
         python -m pip install flake8 pytest
         # don't install requirements.txt as mpi4py will fail...
         # if [ -f requirements.txt ]; then pip install -r requirements.txt; fi
-        python -m pip install setuptools setuptools_scm wheel docutils numpy h5py
+        python -m pip install --upgrade setuptools setuptools_scm wheel docutils numpy h5py
     - name: Lint with flake8
       run: |
         # stop the build if there are Python syntax errors or undefined names
@@ -43,6 +40,6 @@ jobs:
     - name: Test with pytest (only core tests)
       run: |
         pytest src/amuse/test/suite/core_tests
-    - name: Create packages
-      run: |
-        cd packages && sh generate_packages.sh
+#    - name: Create packages
+#      run: |
+#        cd packages && sh generate_packages.sh

.gitignore

@@ -483,14 +483,16 @@ test_python_sockets_implementation
 
 .idea
 
-src/amuse/community/petar/src
 src/amuse/community/bonsai2/src
-src/amuse/community/*/version.py
-src/amuse/version.py
+doc/interactive_tutorial/_version.py
+src/amuse/test/suite/_version.py
+src/amuse/community/*/_version.py
+src/amuse/_version.py
 src/amuse/community/petar/src
-src/amuse/community/petar/interface.cc
-src/amuse/community/petar/interface.h
 src/amuse/community/seba/src
 packages/amuse*/dist
 packages/dist
 src/amuse/community/phantom/src
+
+# standard directory for a virtualenv
+env/

configure

@@ -1,6 +1,6 @@
 #! /bin/sh
 # Guess values for system-dependent variables and create Makefiles.
-# Generated by GNU Autoconf 2.71 for amuse 2023.3.1.dev41+gaa14f8bf8.d20230322.
+# Generated by GNU Autoconf 2.71 for amuse 2023.7.0.
 #
 #
 # Copyright (C) 1992-1996, 1998-2017, 2020-2021 Free Software Foundation,
@@ -668,8 +668,8 @@ MAKEFLAGS=
 # Identity of this package.
 PACKAGE_NAME='amuse'
 PACKAGE_TARNAME='amuse'
-PACKAGE_VERSION='2023.3.1.dev41+gaa14f8bf8.d20230322'
-PACKAGE_STRING='amuse 2023.3.1.dev41+gaa14f8bf8.d20230322'
+PACKAGE_VERSION='2023.7.0'
+PACKAGE_STRING='amuse 2023.7.0'
 PACKAGE_BUGREPORT=''
 PACKAGE_URL=''
 
@@ -1505,7 +1505,7 @@ if test "$ac_init_help" = "long"; then
   # Omit some internal or obsolete options to make the list less imposing.
   # This message is too long to be a string in the A/UX 3.1 sh.
   cat <<_ACEOF
-\`configure' configures amuse 2023.3.1.dev41+gaa14f8bf8.d20230322 to adapt to many kinds of systems.
+\`configure' configures amuse 2023.7.0 to adapt to many kinds of systems.
 
 Usage: $0 [OPTION]... [VAR=VALUE]...
 
@@ -1571,7 +1571,7 @@ fi
 
 if test -n "$ac_init_help"; then
   case $ac_init_help in
-     short | recursive ) echo "Configuration of amuse 2023.3.1.dev41+gaa14f8bf8.d20230322:";;
+     short | recursive ) echo "Configuration of amuse 2023.7.0:";;
    esac
   cat <<\_ACEOF
 
@@ -1725,7 +1725,7 @@ fi
 test -n "$ac_init_help" && exit $ac_status
 if $ac_init_version; then
   cat <<\_ACEOF
-amuse configure 2023.3.1.dev41+gaa14f8bf8.d20230322
+amuse configure 2023.7.0
 generated by GNU Autoconf 2.71
 
 Copyright (C) 2021 Free Software Foundation, Inc.
@@ -2259,7 +2259,7 @@ cat >config.log <<_ACEOF
 This file contains any messages produced by compilers while
 running configure, to aid debugging if configure makes a mistake.
 
-It was created by amuse $as_me 2023.3.1.dev41+gaa14f8bf8.d20230322, which was
+It was created by amuse $as_me 2023.7.0, which was
 generated by GNU Autoconf 2.71.  Invocation command line was
 
   $ $0$ac_configure_args_raw
@@ -4942,13 +4942,13 @@ ac_compiler_gnu=$ac_cv_c_compiler_gnu
 
         if test -n "$PYTHON"; then
       # If the user set $PYTHON, use it and don't search something else.
-      { printf "%s\n" "$as_me:${as_lineno-$LINENO}: checking whether $PYTHON version is >= 3.5" >&5
-printf %s "checking whether $PYTHON version is >= 3.5... " >&6; }
+      { printf "%s\n" "$as_me:${as_lineno-$LINENO}: checking whether $PYTHON version is >= 3.7" >&5
+printf %s "checking whether $PYTHON version is >= 3.7... " >&6; }
       prog="import sys
 # split strings by '.' and convert to numeric.  Append some zeros
 # because we need at least 4 digits for the hex conversion.
 # map returns an iterator in Python 3.0 and a list in 2.x
-minver = list(map(int, '3.5'.split('.'))) + [0, 0, 0]
+minver = list(map(int, '3.7'.split('.'))) + [0, 0, 0]
 minverhex = 0
 # xrange is not present in Python 3.0 and range returns an iterator
 for i in list(range(0, 4)): minverhex = (minverhex << 8) + minver[i]
@@ -4970,8 +4970,8 @@ fi
     else
       # Otherwise, try each interpreter until we find one that satisfies
       # VERSION.
-      { printf "%s\n" "$as_me:${as_lineno-$LINENO}: checking for a Python interpreter with version >= 3.5" >&5
-printf %s "checking for a Python interpreter with version >= 3.5... " >&6; }
+      { printf "%s\n" "$as_me:${as_lineno-$LINENO}: checking for a Python interpreter with version >= 3.7" >&5
+printf %s "checking for a Python interpreter with version >= 3.7... " >&6; }
 if test ${am_cv_pathless_PYTHON+y}
 then :
   printf %s "(cached) " >&6
@@ -4983,7 +4983,7 @@ else $as_nop
 # split strings by '.' and convert to numeric.  Append some zeros
 # because we need at least 4 digits for the hex conversion.
 # map returns an iterator in Python 3.0 and a list in 2.x
-minver = list(map(int, '3.5'.split('.'))) + [0, 0, 0]
+minver = list(map(int, '3.7'.split('.'))) + [0, 0, 0]
 minverhex = 0
 # xrange is not present in Python 3.0 and range returns an iterator
 for i in list(range(0, 4)): minverhex = (minverhex << 8) + minver[i]
@@ -7776,7 +7776,13 @@ else $as_nop
         fi
         cat confdefs.h - <<_ACEOF >conftest.$ac_ext
 /* end confdefs.h.  */
+ifelse(main, main, , # Avoid conflicting decl of main.
+    /* Override any gcc2 internal prototype to avoid an error.  */
 
+    /* We use char because int might match the return type of a gcc2
+        builtin and then its argument prototype would still apply.  */
+    char main();
+    )
 int
 main (void)
 {
@@ -7860,7 +7866,13 @@ else $as_nop
         fi
         cat confdefs.h - <<_ACEOF >conftest.$ac_ext
 /* end confdefs.h.  */
+ifelse(main, main, , # Avoid conflicting decl of main.
+    /* Override any gcc2 internal prototype to avoid an error.  */
 
+    /* We use char because int might match the return type of a gcc2
+        builtin and then its argument prototype would still apply.  */
+    char main();
+    )
 int
 main (void)
 {
@@ -14322,7 +14334,7 @@ cat >>$CONFIG_STATUS <<\_ACEOF || ac_write_fail=1
 # report actual input values of CONFIG_FILES etc. instead of their
 # values after options handling.
 ac_log="
-This file was extended by amuse $as_me 2023.3.1.dev41+gaa14f8bf8.d20230322, which was
+This file was extended by amuse $as_me 2023.7.0, which was
 generated by GNU Autoconf 2.71.  Invocation command line was
 
   CONFIG_FILES    = $CONFIG_FILES
@@ -14377,7 +14389,7 @@ ac_cs_config_escaped=`printf "%s\n" "$ac_cs_config" | sed "s/^ //; s/'/'\\\\\\\\
 cat >>$CONFIG_STATUS <<_ACEOF || ac_write_fail=1
 ac_cs_config='$ac_cs_config_escaped'
 ac_cs_version="\\
-amuse config.status 2023.3.1.dev41+gaa14f8bf8.d20230322
+amuse config.status 2023.7.0
 configured by $0, generated by GNU Autoconf 2.71,
   with options \\"\$ac_cs_config\\"
 

configure.ac

@@ -21,7 +21,7 @@ AC_ARG_VAR([PYTHON], [Python interpreter])
 
 AC_SUBST(FC_ISO_C_BINDINGS)
 
-AM_PATH_PYTHON([3.5])
+AM_PATH_PYTHON([3.7])
 
 AC_PATH_PROG([PYTHON], [$PYTHON], [])
 AC_ARG_VAR([NVCC], [CUDA compiler command])

doc/install/howto-install-AMUSE.rst

@@ -170,3 +170,56 @@ individual codes can be build with:
     make {code}.code
 
 with {code} the name of the code in lower case. 
+
+Installation on HPC systems using modules (tested for Snellius)
+***************************************************************
+
+Note that the modules on your local HPC system may be differently named.
+
+.. code-block:: sh
+
+    module load 2022
+    module load foss/2022a
+
+Load python.
+
+.. code-block:: sh
+
+    module load Python/3.10.4-GCCcore-11.3.0 # or another version of python, 3.7 or higher
+
+
+Following AMUSE documentation (see above), download/upgrade the python package: (--user is required by Snellius)
+
+.. code-block:: sh
+
+    mkdir MY_PROJECT_DIR
+    cd MY_PROJECT_DIR
+    python3 -m venv env  # initialise a Python virtual environment, which will contain all the packages we install
+    source env/bin/activate  # activate the virtual environment - this must be repeated every time you log in
+    pip install --upgrade pip
+    cd AMUSE_DIR  # change to where you downloaded AMUSE
+    pip install -r requirements.txt --upgrade  # install/upgrade all required packages
+    pip install matplotlib  # not required but highly recommended
+    pip install -e .
+
+Now you can build the AMUSE framework with 
+
+.. code-block:: sh
+
+    make framework
+
+Finally, build AMUSE individual codes by running from the AMUSE directory:
+
+.. code-block:: sh
+
+    make {code}.code
+
+When you log in again (and in your SLURM scripts), you will need to load the same modules and activate the same environment:
+
+.. code-block:: sh
+
+    module load 2022
+    module load foss/2022a
+    module load Python/3.10.4-GCCcore-11.3.0 # or another version of python, 3.7 or higher
+    cd MY_PROJECT_DIR
+    source env/bin/activate