def wait_on_job(self, job_id):
if self.cluster_type == "bsub":
print "Waiting on %s.. (started wait @ %s)" \
%(job_id,
time.strftime("%x, %X"))
Mybsub.waitUntilDone(job_id)
print " - Completed at %s" %(time.strftime("%x, %X"))
return True
elif self.cluster_type == "qsub":
print "Waiting on %s.. (started wait @ %s)" \
%(job_id,
time.strftime("%x, %X"))
Mypbm.waitUntilDone(job_id)
print " - Completed at %s" %(time.strftime("%x, %X"))
return True
elif self.cluster_type == "none":
self.jobs[job_id].wait()
else:
raise Exception, "Not implemented yet."
def launch_job(self, cmd, job_name,
ppn=1,
unless_exists=None,
bsub_queue_type="normal"):
"""
Launch job on cluster and return a job id.
if unless_exists flag is given, do not execute command
if the given filename path exists.
Wrapper to Mysge/Mypbm/Mybsub.
"""
job_id = None
script_options = {}
if (unless_exists is not None) and \
os.path.isfile(unless_exists):
print "launch_job: SKIPPING %s since %s exists." \
%(cmd, unless_exists)
return job_id
if self.cluster_type == "bsub":
# Use bsub for submission
job_id = Mybsub.launchJob(cmd, job_name,
script_options,
self.output_dir,
queue_type=bsub_queue_type,
ppn=ppn)
elif self.cluster_type == "qsub":
# Use qsub for submission
job_id = Mypbm.launchJob(cmd, job_name,
script_options,
self.output_dir,
queue_type="long",
ppn=ppn)
elif self.cluster_type == "none":
# Use local machine (multi-cores)
p = subprocess.Popen(cmd, shell=True)
self.jobs[self._curjobid] = p
job_id = self._curjobid
self._curjobid += 1
if job_id is None:
print "WARNING: Job %s not submitted." %(job_name)
return job_id
