From 43e5ed0bb945b7b4b05c9ea1853fc8c3c6de700d Mon Sep 17 00:00:00 2001
From: Luc Papeleux <L.Papeleux@ULiege.be>
Date: Wed, 13 Jul 2022 16:43:06 +0200
Subject: [PATCH] fix launchGuy for non interactive use (at, batch, slurm,...)
by replacing '*Guy.pyw' by '*.py' in runBatch, runSge, runSlurm,... I also
add a test to not close the gui when launching a nonInteractive job
---
cfg/blueberry/launch.cfg | 2 +-
parametricJob.py | 31 +++++++++++++++++++++++--------
postProLoop.py | 8 ++++----
3 files changed, 28 insertions(+), 13 deletions(-)
diff --git a/cfg/blueberry/launch.cfg b/cfg/blueberry/launch.cfg
index 12256a8..d66afc5 100644
--- a/cfg/blueberry/launch.cfg
+++ b/cfg/blueberry/launch.cfg
@@ -1,4 +1,4 @@
-self.pars['NB_THREADS'].val='6'
+self.pars['NB_THREADS'].val='4'
self.pars['NB_TASKS'].val='1'
self.pars['RUNMETHOD'].vals=['interactive','at','batch']
self.pars['RUNMETHOD'].val='batch'
diff --git a/parametricJob.py b/parametricJob.py
index ce51a0f..95d7d01 100644
--- a/parametricJob.py
+++ b/parametricJob.py
@@ -296,7 +296,8 @@ class ParametricJob(PRMSet):
#file.write("jobId=`atq | awk '{if ($1>jobId)jobId=$1} END {print jobId}'`\n")
#file.write("echo \"at JobId = $jobId\"\n")
#file.write('%s -x -i $jobId -d "%s"\n' % (sys.argv[0], os.getcwd()) )
- file.write('%s -x -i %d -d "%s"\n' % (sys.argv[0], launchId, os.getcwd()) )
+ script = re.sub(r'(.+)Gui.pyw',r'\1.py', sys.argv[0]) #if launched through a Gui => use the basic script instead in batch
+ file.write('%s -x -i %d -d "%s"\n' % (script, launchId, os.getcwd()) )
file.close()
os.chmod(scriptname,0o700)
@@ -331,7 +332,9 @@ class ParametricJob(PRMSet):
print("\t\t - '=' means running")
print("\tuse 'atrm %s to kill the job" % batchId)
print("\t\t or 'atrm%s.py' to kill the job" % batchId)
- sys.exit()
+ # to avoid closing the gui
+ if not (re.match(r'(.+)Gui.pyw', sys.argv[0])):
+ sys.exit()
def atrmScript(self, pid):
filename = "atrm%s.py"%pid
@@ -391,7 +394,10 @@ class ParametricJob(PRMSet):
file.write("#$ %s\n" % self.pars['SGEARGS'].val)
import socket
file.write(". %s %s\n" % (cfgfile,socket.gethostname()))
- file.write("%s -x -i $JOB_ID\n" % (sys.argv[0]))
+ #file.write('%s -x -i $jobId -d "%s"\n' % (sys.argv[0], os.getcwd()) )
+ script = re.sub(r'(.+)Gui.pyw',r'\1.py', sys.argv[0])
+ file.write("%s -x -i $JOB_ID\n" % (script))
+ #file.write("%s -x -i $JOB_ID\n" % (sys.argv[0]))
file.close()
# send to sge
print("sending job '%s' to SGE" % jobname)
@@ -415,7 +421,9 @@ class ParametricJob(PRMSet):
print("\tuse './%s' to get results from node disk" % self.cpNodeResultsScriptName(sgeId))
print("\tuse './%s' to clean results from node disk" % self.rmNodeResultsScriptName(sgeId))
print("\tuse './qDel%s.py' to kill your job, get results and clean node disk" % sgeId)
- sys.exit()
+ # to avoid closing the gui
+ if not (re.match(r'(.+)Gui.pyw', sys.argv[0])):
+ sys.exit()
def qDelScriptName(self, jobId):
filename = "qDel%s.py"%jobId
@@ -483,7 +491,8 @@ class ParametricJob(PRMSet):
#file.write("echo 'squeue'\n")
import socket
file.write(". %s %s\n" % (cfgfile, socket.gethostname()))
- file.write("srun %s -x -i $SLURM_JOB_ID \n" % (sys.argv[0]))
+ script = re.sub(r'(.+)Gui.pyw',r'\1.py', sys.argv[0])
+ file.write("srun %s -x -i $SLURM_JOB_ID \n" % (script))
file.close()
os.chmod(scriptname,0o700)
# send to slurm
@@ -508,7 +517,10 @@ class ParametricJob(PRMSet):
print("\tuse ' sstat -a --format=JobID,NTasks,MaxRSS,MaxVMSize -j %s ' to get information about your running job (adapt format to your needs)" % slurmId)
print("\tuse ' scancel %s ' to kill your job" % slurmId)
print("\tuse ' sacct --format=JobID,NTasks,NCPUS,CPUTime,Elapsed,MaxRSS,MaxVMSize -j %s ' to get information about your finished job (adapt format to your needs)" % slurmId)
- sys.exit()
+
+ # to avoid closing the gui
+ if not (re.match(r'(.+)Gui.pyw', sys.argv[0])):
+ sys.exit()
def sCancelScriptName(self, jobId):
filename = "sCancel%s.py"%jobId
@@ -608,7 +620,8 @@ class ParametricJob(PRMSet):
# Lanch the job
import socket
file.write('. %s %s\n' % (cfgfile, socket.gethostname()))
- file.write('%s -x -i $PBS_JOBID\n' % (sys.argv[0]))
+ script = re.sub(r'(.+)Gui.pyw',r'\1.py', sys.argv[0])
+ file.write('%s -x -i $PBS_JOBID\n' % (script))
file.write('qstat -f $PBS_JOBID\n')
file.close()
os.chmod(scriptname,0o700)
@@ -648,7 +661,9 @@ class ParametricJob(PRMSet):
print "\tuse ' qdel %s ' to kill your job" % PbsId
#print "\tuse ' sacct --format=JobID,NTasks,NCPUS,CPUTime,Elapsed,MaxRSS,MaxVMSize -j %s ' to get information about your finished job (adapt format to your needs)" % PbsId
'''
- sys.exit()
+ # to avoid closing the gui
+ if not (re.match(r'(.+)Gui.pyw', sys.argv[0])):
+ sys.exit()
def PBSCancelScriptName(self, jobId):
filename = "qdel%s.py"%jobId
diff --git a/postProLoop.py b/postProLoop.py
index d66fdfe..d09e9e2 100755
--- a/postProLoop.py
+++ b/postProLoop.py
@@ -148,10 +148,10 @@ class PostProLoop(PRMSet):
if shutil.which(self.pars[key].val):
return True
else:
- print "%s is not found (%s)...."%self.pars[key].val
- print "\t Check installation and accessibility..."
- print "\t Use 'externalProgramPathGui' to define the full program path (recommanded)"
- print "\t or add %s in your user path (not recommanded)"%key
+ print ("%s is not found (%s)...."%self.pars[key].val)
+ print ("\t Check installation and accessibility...")
+ print ("\t Use 'externalProgramPathGui' to define the full program path (recommanded)")
+ print ("\t or add %s in your user path (not recommanded)"%key)
return False
'''
if distutils.spawn.find_executable(os.path.splitext(self.pars[key].val)[0]):
--
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