def distributedCommand(stage, comm, options):
time = getStageOptions(options, stage, 'walltime')
mods = getStageOptions(options, stage, 'modules')
queue = getStageOptions(options, stage, 'queue')
mem = getStageOptions(options, stage, 'memInGB')
logDir = options['pipeline']['logDir']
script = PBS_Script(command=comm, walltime=time, name=stage, memInGB=mem, queue=queue, moduleList=mods, logDir=logDir)
runJobAndWait(script)
def distributedCommand(stage, comm, options):
#stageOptions = options['stages'][stage]
#time = stageOptions.get('walltime', defaultWalltime)
#mods = stageOptions.get('modules', defaultModules)
#queue = stageOptions.get('queue', defaultQueue)
#mem = stageOptions.get('memInGB', defaultMemInGB)
time = getStageOptions(options, stage, 'walltime')
mods = getStageOptions(options, stage, 'modules')
queue = getStageOptions(options, stage, 'queue')
mem = getStageOptions(options, stage, 'memInGB')
script = PBS_Script(command=comm, walltime=time, name=stage, memInGB=mem, queue=queue, moduleList=mods)
#print script
runJobAndWait(script)
def distributedCommand(stage, comm, options):
time = getStageOptions(options, stage, 'walltime')
mods = getStageOptions(options, stage, 'modules')
queue = getStageOptions(options, stage, 'queue')
mem = getStageOptions(options, stage, 'memInGB')
logDir = options['pipeline']['logDir']
script = PBS_Script(command=comm,
walltime=time,
name=stage,
memInGB=mem,
queue=queue,
moduleList=mods,
logDir=logDir)
runJobAndWait(script)
def distributedCommand(stage, comm, options):
#stageOptions = options['stages'][stage]
#time = stageOptions.get('walltime', defaultWalltime)
#mods = stageOptions.get('modules', defaultModules)
#queue = stageOptions.get('queue', defaultQueue)
#mem = stageOptions.get('memInGB', defaultMemInGB)
time = getStageOptions(options, stage, 'walltime')
mods = getStageOptions(options, stage, 'modules')
queue = getStageOptions(options, stage, 'queue')
mem = getStageOptions(options, stage, 'memInGB')
script = PBS_Script(command=comm,
walltime=time,
name=stage,
memInGB=mem,
queue=queue,
moduleList=mods)
#print script
runJobAndWait(script)
def distributedCommand(stage, comm, options):
time = getStageOptions(options, stage, "walltime")
mods = getStageOptions(options, stage, "modules")
queue = getStageOptions(options, stage, "queue")
mem = getStageOptions(options, stage, "memInGB")
logDir = options.pipeline["logDir"]
verbosity = options.pipeline["verbose"]
script = PBS_Script(
command=comm, walltime=time, name=stage, memInGB=mem, queue=queue, moduleList=mods, logDir=logDir
)
return runJobAndWait(script, stage, logDir, verbosity)
def distributedCommand(stage, comm, options):
time = getStageOptions(options, stage, 'walltime')
mods = getStageOptions(options, stage, 'modules')
queue = getStageOptions(options, stage, 'queue')
mem = getStageOptions(options, stage, 'memInGB')
logDir = options.pipeline['logDir']
verbosity = options.pipeline['verbose']
manager = options.pipeline['manager']
if manager == 'slurm':
script = SLURM_Script(command=comm, walltime=time, name=stage, memInGB=mem, queue=queue, moduleList=mods, logDir=logDir)
else:
script = PBS_Script(command=comm, walltime=time, name=stage, memInGB=mem, queue=queue, moduleList=mods, logDir=logDir)
manager = 'pbs'
return runJobAndWait(script, stage, logDir, manager=manager, verbose=verbosity)
#!/bin/env python
# simple test for the job submission tools
from cluster_job import (PBS_Script, runJobAndWait)
from utils import mkDir
logDirName='log'
mkDir(logDirName)
script = PBS_Script(command='echo hello world', walltime='0:1:0', name='pipeline_test_job', memInGB=1, logDir=logDirName)
print('before job has run')
runJobAndWait(script, 'test_stage', logDir=logDirName, verbose=1)
print('after job has run')