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switched to more general and universal subprocess command for launching

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This commit is contained in:
P.M. Sutter 2014-01-03 19:35:51 -06:00
parent d8108d3a8e
commit 079656a8da
1 changed files with 79 additions and 29 deletions
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108
python_tools/void_python_tools/backend/launchers.py
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@ -87,8 +87,12 @@ def launchGenerate(sample, binPath, workDir=None, inputDataDir=None,
if regenerate or not (continueRun and jobSuccessful(logFile, "Done!\n")): if regenerate or not (continueRun and jobSuccessful(logFile, "Done!\n")):
file(parmFile, mode="w").write(conf) file(parmFile, mode="w").write(conf)
cmd = "%s --configFile=%s &> %s" % (binPath,parmFile,logFile) arg1 = "-configFile=%s" % parmFile
os.system(cmd) log = open(logFile, 'w')
subprocess.call([binPath, arg1], stdout=log, stderr=log)
log.close()
#cmd = "%s --configFile=%s >& %s" % (binPath,parmFile,logFile)
#os.system(cmd)
if jobSuccessful(logFile, "Done!\n"): if jobSuccessful(logFile, "Done!\n"):
print "done" print "done"
else: else:
@ -204,10 +208,16 @@ def launchGenerate(sample, binPath, workDir=None, inputDataDir=None,
file(parmFile, mode="w").write(conf) file(parmFile, mode="w").write(conf)
if (prevSubSample == -1): if (prevSubSample == -1):
cmd = "%s --configFile=%s &> %s" % (binPath,parmFile,logFile) #cmd = "%s --configFile=%s &> %s" % (binPath,parmFile,logFile)
log = open(logFile, 'w')
else: else:
cmd = "%s --configFile=%s &>> %s" % (binPath,parmFile,logFile) #cmd = "%s --configFile=%s &>> %s" % (binPath,parmFile,logFile)
os.system(cmd) log = open(logFile, 'a')
arg1 = "--configFile=%s" % parmFile
subprocess.call([binPath, arg1], stdout=log, stderr=log)
#subprocess.call([binPath, arg1], stdout=log, stderr=log)
log.close()
#os.system(cmd)
# remove intermediate files # remove intermediate files
if (prevSubSample != -1): if (prevSubSample != -1):
@ -322,24 +332,49 @@ def launchZobov(sample, binPath, zobovDir=None, logDir=None, continueRun=None,
if os.access(zobovDir+"/voidDesc_"+sampleName+".out", os.F_OK): if os.access(zobovDir+"/voidDesc_"+sampleName+".out", os.F_OK):
os.unlink(zobovDir+"/voidDesc_"+sampleName+".out") os.unlink(zobovDir+"/voidDesc_"+sampleName+".out")
cmd = "%s/vozinit %s 0.1 1.0 %g %s %g %s %s %s &> %s" % \ #cmd = "%s/vozinit %s 0.1 1.0 %g %s %g %s %s %s &> %s" % \
(binPath, datafile, numZobovDivisions, \ # (binPath, datafile, numZobovDivisions, \
"_"+sampleName, numZobovThreads, \ # "_"+sampleName, numZobovThreads, \
binPath, zobovDir, maskIndex, logFile) # binPath, zobovDir, maskIndex, logFile)
os.system(cmd) #os.system(cmd)
cmd = [binPath+"/vozinit", datafile, "0.1", "1.0", str(numZobovDivisions), \
"_"+sampleName, str(numZobovThreads), \
binPath, zobovDir, str(maskIndex)]
log = open(logFile, 'w')
subprocess.call(cmd, stdout=log, stderr=log)
log.close()
#cmd = "./%s >> %s 2>&1" % (vozScript, logFile)
#os.system(cmd)
cmd = ["./%s" % vozScript]
log = open(logFile, 'a')
subprocess.call(cmd, stdout=log, stderr=log)
log.close()
cmd = "./%s >> %s 2>&1" % (vozScript, logFile)
os.system(cmd)
# cmd = "%s/jozov %s %s %s %s %s %g %s >> %s 2>&1" % \ # cmd = "%s/jozov %s %s %s %s %s %g %s >> %s 2>&1" % \
cmd = "%s/../c_tools/zobov2/jozov2/jozov2 %s %s %s %s %s %g %s >> %s 2>&1" % \ #cmd = "%s/../c_tools/zobov2/jozov2/jozov2 %s %s %s %s %s %g %s >> %s 2>&1" % \
(binPath, \ # (binPath, \
# zobovDir+"/adj_"+sampleName+".dat", \
# zobovDir+"/vol_"+sampleName+".dat", \
# zobovDir+"/voidPart_"+sampleName+".dat", \
# zobovDir+"/voidZone_"+sampleName+".dat", \
# zobovDir+"/voidDesc_"+sampleName+".out", \
# maxDen, maskIndex, logFile)
#os.system(cmd)
cmd = [binPath+"../c_tools/zobov2/jozov2/jozov2", \
zobovDir+"/adj_"+sampleName+".dat", \ zobovDir+"/adj_"+sampleName+".dat", \
zobovDir+"/vol_"+sampleName+".dat", \ zobovDir+"/vol_"+sampleName+".dat", \
zobovDir+"/voidPart_"+sampleName+".dat", \ zobovDir+"/voidPart_"+sampleName+".dat", \
zobovDir+"/voidZone_"+sampleName+".dat", \ zobovDir+"/voidZone_"+sampleName+".dat", \
zobovDir+"/voidDesc_"+sampleName+".out", \ zobovDir+"/voidDesc_"+sampleName+".out", \
maxDen, maskIndex, logFile) str(maxDen), str(maskIndex)]
os.system(cmd) log = open(logFile, 'a')
subprocess.call(cmd, stdout=log, stderr=log)
log.close()
# don't need the subbox files
for fileName in glob.glob(zobovDir+"/part._"+sampleName+".*"):
os.unlink(fileName)
if jobSuccessful(logFile, "Done!\n"): if jobSuccessful(logFile, "Done!\n"):
print "done" print "done"
@ -412,11 +447,14 @@ def launchPrune(sample, binPath,
cmd += useComovingFlag cmd += useComovingFlag
cmd += " --outputDir=" + zobovDir cmd += " --outputDir=" + zobovDir
cmd += " --sampleName=" + str(sampleName) cmd += " --sampleName=" + str(sampleName)
cmd += " &> " + logFile #cmd += " &> " + logFile
f=file("run_prune.sh",mode="w") #f=file("run_prune.sh",mode="w")
f.write(cmd) #f.write(cmd)
f.close() #f.close()
os.system(cmd) #os.system(cmd)
log = open(logFile, 'w')
subprocess.call(cmd, stdout=log, stderr=log, shell=True)
log.close()
if jobSuccessful(logFile, "NetCDF: Not a valid ID\n") or \ if jobSuccessful(logFile, "NetCDF: Not a valid ID\n") or \
jobSuccessful(logFile, "Done!\n"): jobSuccessful(logFile, "Done!\n"):
@ -485,9 +523,12 @@ def launchVoidOverlap(sample1, sample2, sample1Dir, sample2Dir,
if matchMethod == "useID": cmd += " --useID" if matchMethod == "useID": cmd += " --useID"
cmd += periodicLine cmd += periodicLine
cmd += " --outfile=" + outputFile cmd += " --outfile=" + outputFile
cmd += " &> " + logFile #cmd += " &> " + logFile
open("temp.par",'w').write(cmd) #open("temp.par",'w').write(cmd)
os.system(cmd) #os.system(cmd)
log = open(logFile, 'w')
subprocess.call(cmd, stdout=log, stderr=log, shell=True)
log.close()
if jobSuccessful(logFile, "Done!\n"): if jobSuccessful(logFile, "Done!\n"):
print "done" print "done"
@ -650,9 +691,14 @@ def launchStack(sample, stack, binPath, thisDataPortion=None, logDir=None,
fp.close() fp.close()
if not (continueRun and jobSuccessful(logFile, "Done!\n")): if not (continueRun and jobSuccessful(logFile, "Done!\n")):
cmd = "%s --configFile=%s &> %s" % \ #cmd = "%s --configFile=%s &> %s" % \
(binPath, parmFile, logFile) # (binPath, parmFile, logFile)
os.system(cmd) #os.system(cmd)
cmd = "%s --configFile=%s" % \
(binPath, parmFile)
log = open(logFile, 'w')
subprocess.call(cmd, stdout=log, stderr=log, shell=True)
log.close()
if jobSuccessful(logFile, "Done!\n"): if jobSuccessful(logFile, "Done!\n"):
print "done" print "done"
@ -1721,8 +1767,12 @@ def launchVelocityStack(sample, stack, binPath,
parameters="--velocityField=%s --voidCenters=%s --Rmax=%e --L0=%e --numBins=%d" % (velField_file, voidCenters, Rmax, Boxsize, numBins) parameters="--velocityField=%s --voidCenters=%s --Rmax=%e --L0=%e --numBins=%d" % (velField_file, voidCenters, Rmax, Boxsize, numBins)
if not (continueRun and jobSuccessful(logFile, "Done!\n")): if not (continueRun and jobSuccessful(logFile, "Done!\n")):
cmd = "%s %s &> %s" % (binPath,parameters,logFile) #cmd = "%s %s &> %s" % (binPath,parameters,logFile)
os.system(cmd) #os.system(cmd)
cmd = "%s %s" % (binPath,parameters)
log = open(logFile, 'w')
subprocess.call(cmd, stdout=log, stderr=log, shell=True)
log.close()
if jobSuccessful(logFile, "Done!\n"): if jobSuccessful(logFile, "Done!\n"):
print "done" print "done"
else: else: