Esempio n. 1
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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)
Esempio n. 2
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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)
Esempio n. 3
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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)
Esempio n. 4
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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)
Esempio n. 5
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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)
Esempio n. 6
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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)
Esempio n. 7
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#!/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')