def main(pickleConfigFile, primaryConfigSection, workflowClassName):
from configureUtil import getConfigWithPrimaryOptions
runOptions = get_run_options(workflowClassName)
flowOptions, configSections = getConfigWithPrimaryOptions(
pickleConfigFile, primaryConfigSection)
# new logs and marker files to assist automated workflow monitoring:
warningpath = os.path.join(flowOptions.runDir, "workflow.warning.log.txt")
errorpath = os.path.join(flowOptions.runDir, "workflow.error.log.txt")
exitpath = os.path.join(flowOptions.runDir, "workflow.exitcode.txt")
# the exit path should only exist once the workflow completes:
if os.path.exists(exitpath):
if not os.path.isfile(exitpath):
raise Exception("Unexpected filesystem item: '%s'" % (exitpath))
os.unlink(exitpath)
wflow = workflowClassName(flowOptions)
retval = 1
try:
retval = wflow.run(mode=runOptions.mode,
nCores=runOptions.jobs,
memMb=runOptions.memMb,
dataDirRoot=flowOptions.workDir,
mailTo=runOptions.mailTo,
isContinue="Auto",
isForceContinue=True,
isDryRun=runOptions.isDryRun,
isQuiet=runOptions.isQuiet,
schedulerArgList=runOptions.schedulerArgList,
resetTasks=runOptions.resetTasks,
successMsg=wflow.getSuccessMessage(),
retryWindow=0,
retryMode='all',
warningLogFile=warningpath,
errorLogFile=errorpath)
finally:
exitfp = open(exitpath, "w")
exitfp.write("%i\n" % (retval))
exitfp.close()
sys.exit(retval)
def main(pickleConfigFile, primaryConfigSection, workflowClassName) :
from configureUtil import getConfigWithPrimaryOptions
runOptions=get_run_options(workflowClassName)
flowOptions,configSections=getConfigWithPrimaryOptions(pickleConfigFile,primaryConfigSection)
# new logs and marker files to assist automated workflow monitoring:
warningpath=os.path.join(flowOptions.runDir,"manta.warning.log.txt")
errorpath=os.path.join(flowOptions.runDir,"manta.error.log.txt")
exitpath=os.path.join(flowOptions.runDir,"manta.workflow.exitcode.txt")
# the exit path should only exist once the workflow completes:
if os.path.exists(exitpath) :
if not os.path.isfile(exitpath) :
raise Exception("Unexpected filesystem item: '%s'" % (exitpath))
os.unlink(exitpath)
wflow = workflowClassName(flowOptions,configSections)
retval=1
try:
retval=wflow.run(mode=runOptions.mode,
nCores=runOptions.jobs,
memMb=runOptions.memMb,
dataDirRoot=flowOptions.workDir,
mailTo=runOptions.mailTo,
isContinue="Auto",
isForceContinue=True,
isDryRun=runOptions.isDryRun,
isQuiet=runOptions.isQuiet,
schedulerArgList=runOptions.schedulerArgList,
resetTasks=runOptions.resetTasks,
successMsg=wflow.getSuccessMessage(),
warningLogFile=warningpath,
errorLogFile=errorpath)
finally:
exitfp=open(exitpath,"w")
exitfp.write("%i\n" % (retval))
exitfp.close()
sys.exit(retval)