def run(batchids):
"""
Run the QSTAT command to get the status of given batchids.
Sample output of command:
$ bjobs
JOBID USER STAT QUEUE FROM_HOST EXEC_HOST JOB_NAME SUBMIT_TIME
1722 mashkev RUN normal pdx-lsf-lv0 pdx-lsf-lv0 job300-m Sep 13 17:43
"""
keywords = queueinit.readConfig(queue_dir=queue_dir)
cmd = form_command(keywords)
logger.debug("Executing cmd: %s" % cmd)
qstat = sp.Popen(cmd, shell=True, stdout=sp.PIPE)
lsf_status = process_output(qstat.stdout)
exit_code = qstat.wait()
if not batchids:
batchids = sorted(lsf_status.keys())
for batchid in batchids:
status = lsf_status.get(batchid, "unknown")
print batchid, status
return exit_code
def run(batchids):
"""
Run the QSTAT command to get the status of given batchids.
Sample output of command (note the batch id can be truncated):
$ qstat
Job id Name User Time Use S Queue
---------------- ---------------- ---------------- -------- - -----
97.pdx-pbspro-lv0 job300-muriel-4 mashkevi 00:00:00 R workq
"""
keywords = queueinit.readConfig(queue_dir=queue_dir)
cmd = form_command(keywords)
logger.debug("Executing cmd: %s" % cmd)
qstat = sp.Popen(cmd, shell=True, stdout=sp.PIPE)
pbs_status = process_output(qstat.stdout)
exit_code = qstat.wait()
if not batchids:
batchids = sorted(pbs_status.keys())
for batchid in batchids:
numid = re.sub(r'\D.+', "", batchid)
status = pbs_status.get(numid, "unknown")
print batchid, status
return exit_code
def run(batchids):
"""
Run the QSTAT command to get the status of given batchids.
Sample output of command:
$ condor_q
-- Submitter: Q1@ip-10-159-23-56 : <10.159.23.56:39213> : ip-10-159-23-56.ec2.internal
ID OWNER SUBMITTED RUN_TIME ST PRI SIZE CMD
2.0 smashkevich 12/5 15:40 0+00:00:52 C 0 122.1 inscript_26041.sh
3.0 smashkevich 12/5 16:39 0+00:00:00 I 0 0.0 inscript_5445.sh
"""
keywords = queueinit.readConfig(queue_dir=queue_dir)
cmd = form_command(keywords)
logger.debug("Executing cmd: %s"% cmd)
qstat = sp.Popen(cmd, shell=True, stdout=sp.PIPE)
batch_status = process_output(qstat.stdout)
exit_code = qstat.wait()
if not batchids:
batchids = sorted(batch_status.keys())
for batchid in batchids:
status = batch_status.get(batchid, "unknown")
print batchid, status
return exit_code
def run(batchids):
"""
Run the QSTAT command to get the status of given batchids.
Sample output of command (note the batch id can be truncated):
$ qstat
Job id Name User Time Use S Queue
---------------- ---------------- ---------------- -------- - -----
97.pdx-pbspro-lv0 job300-muriel-4 mashkevi 00:00:00 R workq
"""
keywords = queueinit.readConfig(queue_dir=queue_dir)
for batchid in batchids:
cmd = form_command(keywords, batchid)
logger.debug("Executing cmd: %s"% cmd)
qstat = sp.Popen(cmd, shell=True, stdout = sp.PIPE)
outp = qstat.stdout.read()
pbs_status = process_output(outp)
exit_code = qstat.wait()
print batchid, pbs_status
return exit_code
def cancelJobs(batchids):
"""
Run the QDEL command to cancel given batchids.
Sample output of command:
$ scancel -v 244
scancel: Terminating job 244
"""
keywords = queueinit.readConfig(queue_dir=queue_dir)
cmd = form_command(keywords, batchids)
logger.debug("Executing cmd: %s" % cmd)
qdel = sp.Popen(cmd, shell=True, stdout=sp.PIPE, stderr=sp.STDOUT)
message = process_output(qdel.stdout)
print message
exit_code = qdel.wait()
logger.debug("Exit code from command: %d" % exit_code)
return exit_code
def run(batchids):
"""
Run the QSTAT command to get the status of given batchids.
Sample output of command:
$ squeue
JOBID PARTITION NAME USER ST TIME NODES NODELIST(REASON)
244 batch job100-m mashkevi R 12:36 1 pdx-slurm1-lv01
"""
keywords = queueinit.readConfig(queue_dir=queue_dir)
cmd = form_command(keywords)
logger.debug("Executing cmd: %s" % cmd)
qstat = sp.Popen(cmd, shell=True, stdout=sp.PIPE)
message = process_output(qstat.stdout, batchids)
print message
exit_code = qstat.wait()
return exit_code
def cancelJobs(batchids):
"""
Run the QDEL command to cancel given batchids.
Sample output of command:
$ condor_rm 5
Cluster 5 has been marked for removal.
$ condor_rm 5
Couldn't find/remove all jobs in cluster 5.
"""
keywords = queueinit.readConfig(queue_dir=queue_dir)
cmd = form_command(keywords, batchids)
logger.debug("Executing cmd: %s" % cmd)
qdel = sp.Popen(cmd, shell=True, stdout = sp.PIPE, stderr = sp.STDOUT)
message = process_output(qdel.stdout)
print message
exit_code = qdel.wait()
return exit_code
def cancelJobs(batchids):
"""
Run the QDEL command to cancel given batchids.
Sample output of command:
$ qdel 7938861
mashkevi has registered the job 7938861 for deletion
$ qdel 7938861
job 7938861 is already in deletion
"""
keywords = queueinit.readConfig(queue_dir=queue_dir)
cmd = form_command(keywords, batchids)
logger.debug("Executing cmd: %s" % cmd)
qdel = sp.Popen(cmd, shell=True, stdout=sp.PIPE, stderr=sp.STDOUT)
message = process_output(qdel.stdout)
print message
exit_code = qdel.wait()
return exit_code
def cancelJobs(batchids):
"""
Run the QDEL command to cancel given batchids.
Sample output of command:
$ qdel 7938861
<no output -- exit code is 0 on success, nonzero on failure>
"""
keywords = queueinit.readConfig(queue_dir=queue_dir)
cmd = form_command(keywords, batchids)
logger.debug("Executing cmd: %s" % cmd)
process = sp.Popen(cmd, shell=True, stdout=sp.PIPE, stderr=sp.STDOUT)
exit_code = process.wait()
if exit_code:
result = "ERROR"
else:
result = "cancelled"
for batchid in batchids:
print "%s %s" % (batchid, result)
return exit_code
def cancelJobs(batchids):
"""
Run the QDEL command to cancel given batchids.
Sample output of command:
$ qdel 7938861
<no output -- exit code is 0 on success, nonzero on failure>
"""
keywords = queueinit.readConfig(queue_dir=queue_dir)
cmd = form_command(keywords, batchids)
logger.debug("Executing cmd: %s"% cmd)
process = sp.Popen(cmd, shell=True, stdout = sp.PIPE, stderr = sp.STDOUT)
exit_code = process.wait()
if exit_code:
result = "ERROR"
else:
result = "cancelled"
for batchid in batchids:
print "%s %s" % (batchid, result)
return exit_code
