From a4ac6859fc707cbff32475792fc358af0c674ed7 Mon Sep 17 00:00:00 2001
From: Bernie <florbitous@gmail.com>
Date: Fri, 26 Aug 2011 13:32:44 +1000
Subject: [PATCH] Modified to load each module separately, work around bug in
 PBS qsub

---
 cluster_job.py | 21 +++++++++++----------
 1 file changed, 11 insertions(+), 10 deletions(-)

diff --git a/cluster_job.py b/cluster_job.py
index 61814ca..5f19d62 100644
--- a/cluster_job.py
+++ b/cluster_job.py
@@ -21,13 +21,13 @@ def waitForJobCompletion(jobID):
         sleep(10)
 
 def runJobAndWait(script):
-    #print jobScript
+    print(script)
     jobID = script.launch()
     #print jobID
     waitForJobCompletion(jobID)
 
 class PBS_Script(object):
-    def __init__(self, command, walltime=None, name=None, memInGB=None, queue='batch', moduleList=None):
+    def __init__(self, command, walltime=None, name=None, memInGB=None, queue='batch', moduleList=None, logDir=None):
         self.command = command
         if queue in ['batch', 'smp']:
             self.queue = queue
@@ -37,13 +37,17 @@ def __init__(self, command, walltime=None, name=None, memInGB=None, queue='batch
         self.memInGB = memInGB
         self.walltime = walltime
         self.moduleList = moduleList
+        self.logDir = logDir
 
     def __str__(self):
         script = ['#!/bin/bash']
-        # XXX hack
-        script.append('#PBS -o log/%s' % self.name)
-        script.append('#PBS -e log/%s' % self.name)
+        # XXX fixme 
+        # should include job id in the output name.
+        # should use the proper log directory.
         script.append('#PBS -q %s' % self.queue)
+        if self.logDir:
+           script.append('#PBS -o %s' % self.logDir)
+           script.append('#PBS -e %s' % self.logDir)
         if self.name:
             script.append('#PBS -N %s' % self.name)
         if self.memInGB:
@@ -54,7 +58,8 @@ def __str__(self):
         if self.walltime:
             script.append('#PBS -l walltime=%s' % self.walltime)
         if type(self.moduleList) == list and len(self.moduleList) > 0:
-            script.append('module load %s' % ' '.join(self.moduleList))
+            for item in self.moduleList:
+               script.append('module load %s' % item)
         script.append('cd $PBS_O_WORKDIR')
         script.append(self.command)
         return '\n'.join(script) + '\n'
@@ -70,7 +75,3 @@ def launch(self):
             return stdout
         else:
             raise(Exception('qsub command failed with exit status: ' + str(returnCode)))
-
-#waitForJobCompletion(jobID)
-#jobScript = PBS_Script("sleep 50", "00:00:50", "sleepy", "1")
-#runJobAndWait(jobScript)