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)
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"
