def __init__(self, account=None, workdir=None, settings=None, wallTime=None, memory=None, cores=None, modules=None): wallTime = wallTime or "48:00:00" memory = memory or 4194304 ClusterConnection.__init__(self, account=account, workdir=workdir, settings=settings, memory=memory, cores=cores, modules=modules, wallTime=wallTime) self.submitCommand = "qsub" self.jobListCommand = "qstat" self.jobTemplate = PBSJobTemplate
def __init__( self, account=None, workdir=None, settings=None, wallTime=None, memory=None, cores=None, modules=None, preamble=None, debug=False, ): if wallTime == None: wallTime = "48:00:00" if memory == None: memory = 4000 # if modules == None: # modules = ["python", "ruby"] ClusterConnection.__init__( self, account=account, workdir=workdir, settings=settings, memory=memory, cores=cores, modules=modules, wallTime=wallTime, preamble=preamble, debug=debug, ) self.submitCommand = "sbatch" self.jobListCommand = "squeue" self.jobTemplate = SLURMJobTemplate
def __init__(self, account=None, workdir=None, settings=None, wallTime=None, memory=None, cores=None, modules=None): if wallTime == None: wallTime = "48:00:00" if memory == None: memory = 4000 #if modules == None: # modules = ["python", "ruby"] ClusterConnection.__init__(self, account=account, workdir=workdir, settings=settings, memory=memory, cores=cores, modules=modules, wallTime=wallTime) self.submitCommand = "sbatch" self.jobListCommand = "squeue" self.jobTemplate = SLURMJobTemplate
def __init__(self, account=None, workDirBase=None, remoteSettingsPath=None): ClusterConnection.__init__(self, account, workDirBase, remoteSettingsPath) self.wallTime = "48:00:00" self.cores = 1 self.memory = 4000 self.modules = ["python"] self.submitCommand = "sbatch"
def __init__(self, account=None, workdir=None, settings=None, wallTime=None, memory=None, cores=None, modules=None): if wallTime == None: wallTime = "48:00" if memory == None: memory = 4194304 #if modules == None: # modules = ["java", "python"] ClusterConnection.__init__(self, account=account, workdir=workdir, settings=settings, memory=memory, cores=cores, modules=modules, wallTime=wallTime) self.submitCommand = "bsub" self.jobListCommand = "bjobs" self.jobTemplate = LSFJobTemplate
def __init__(self, account=None, workDirBase=None, remoteSettingsPath=None, memory=4194304, cores=1): ClusterConnection.__init__(self, account, workDirBase, remoteSettingsPath) self.wallTime = "48:00" self.cores = 1 self.modules = ["java", "python"] self.submitCommand = "bsub"
def submit(self, script=None, jobDir=None, jobName=None, stdout=None, stderr=None): pstdout, pstderr = ClusterConnection.submit(self, script, jobDir, jobName, stdout, stderr) if pstderr != None: print >>sys.stderr, pstderr print >>sys.stderr, pstdout assert pstdout.startswith("Submitted batch job"), pstdout jobId = int(pstdout.split()[-1]) return self._writeJobFile(jobDir, jobName, {"SLURMID": jobId}, append=True)
def __init__(self, account=None, workdir=None, settings=None, wallTime=None, memory=None, cores=None, modules=None): if wallTime == None: wallTime = "48:00:00" if memory == None: memory = 4194304 ClusterConnection.__init__(self, account=account, workdir=workdir, settings=settings, memory=memory, cores=cores, modules=modules, wallTime=wallTime) self.submitCommand = "qsub" self.jobListCommand = "qstat" self.jobTemplate = PBSJobTemplate
def submit(self, script=None, jobDir=None, jobName=None, stdout=None, stderr=None): pstdout, pstderr = ClusterConnection.submit(self, script, jobDir, jobName, stdout, stderr) if pstderr != None: print >> sys.stderr, pstderr print >> sys.stderr, pstdout assert pstdout.startswith("Submitted batch job"), pstdout jobId = int(pstdout.split()[-1]) return self._writeJobFile(jobDir, jobName, {"SLURMID": jobId}, append=True)
def submit(self, script=None, jobDir=None, jobName=None, stdout=None, stderr=None): pstdout, pstderr = ClusterConnection.submit(self, script, jobDir, jobName, stdout, stderr) if pstderr != None: print >> sys.stderr, pstderr print >> sys.stderr, pstdout assert pstdout.startswith("Your job "), pstdout #Use regular expression to find the job id searchObj = re.search( r'[0-9]+ \(', pstdout) print pstdout jobId = '' if searchObj: jobId = searchObj.group()[:-2] else: print >> sys.stderr, 'Error in parsing the SGE job id!' return self._writeJobFile(jobDir, jobName, {"SGEID":jobId}, append=True)