def get_njobs_in_queue(self, username=None):
"""
returns the number of jobs currently in the queu efor the user
:param username: (str) the username of the jobs to count (default is to autodetect)
:return: (int) number of jobs in the queue
"""
queue_logger = self.get_qlogger('qadapter.{}'.format(self.q_name))
# initialize username
if username is None:
username = getpass.getuser()
# run qstat
qstat = Command(self._get_status_cmd(username))
p = qstat.run(timeout=5)
# parse the result
if p[0] == 0:
njobs = self._parse_njobs(p[1], username)
queue_logger.info(
'The number of jobs currently in the queue is: {}'.format(
njobs))
return njobs
# there's a problem talking to qstat server?
msgs = [
'Error trying to get the number of jobs in the queue',
'The error response reads: {}'.format(p[2])
]
log_fancy(queue_logger, msgs, 'error')
return None
def get_njobs_in_queue(self, username=None):
"""
returns the number of jobs currently in the queu efor the user
:param username: (str) the username of the jobs to count (default is to autodetect)
:return: (int) number of jobs in the queue
"""
queue_logger = self.get_qlogger('qadapter.{}'.format(self.q_name))
# initialize username
if username is None:
username = getpass.getuser()
# run qstat
qstat = Command(self._get_status_cmd(username))
p = qstat.run(timeout=5)
# parse the result
if p[0] == 0:
njobs = self._parse_njobs(p[1], username)
queue_logger.info(
'The number of jobs currently in the queue is: {}'.format(
njobs))
return njobs
# there's a problem talking to qstat server?
msgs = ['Error trying to get the number of jobs in the queue',
'The error response reads: {}'.format(p[2])]
log_fancy(queue_logger, msgs, 'error')
return None
def submit_to_queue(self, script_file):
"""
submits the job to the queue and returns the job id
:param script_file: (str) name of the script file to use (String)
:return: (int) job_id
"""
if not os.path.exists(script_file):
raise ValueError(
'Cannot find script file located at: {}'.format(
script_file))
queue_logger = self.get_qlogger('qadapter.{}'.format(self.q_name))
submit_cmd = self.q_commands[self.q_type]["submit_cmd"]
# submit the job
try:
if self.q_type == "Cobalt":
# Cobalt requires scripts to be executable
os.chmod(script_file,stat.S_IRWXU|stat.S_IRGRP|stat.S_IXGRP)
cmd = [submit_cmd, script_file]
#For most of the queues handled by common_adapter, it's best to simply submit the file name
#as an argument. LoadSharingFacility doesn't handle the header section (queue name, nodes, etc)
#when taking file arguments, so the file needs to be passed as stdin to make it work correctly.
if self.q_type == 'LoadSharingFacility':
with open(script_file, 'r') as inputFile:
p = subprocess.Popen([submit_cmd],stdin=inputFile,stdout=subprocess.PIPE,stderr=subprocess.PIPE)
else:
p = subprocess.Popen(cmd, stdout=subprocess.PIPE, stderr=subprocess.PIPE)
p.wait()
# retrieve the returncode. PBS returns 0 if the job was successful
if p.returncode == 0:
try:
job_id = self._parse_jobid(p.stdout.read().decode())
queue_logger.info(
'Job submission was successful and job_id is {}'.format(
job_id))
return job_id
except Exception as ex:
# probably error parsing job code
log_exception(queue_logger,
'Could not parse job id following {} due to error {}...'
.format(submit_cmd, str(ex)))
else:
# some qsub error, e.g. maybe wrong queue specified, don't have permission to submit, etc...
msgs = [
'Error in job submission with {n} file {f} and cmd {c}'.format(
n=self.q_name, f=script_file, c=cmd),
'The error response reads: {}'.format(p.stderr.read())]
log_fancy(queue_logger, msgs, 'error')
except Exception as ex:
# random error, e.g. no qsub on machine!
log_exception(queue_logger,
'Running the command: {} caused an error...'
.format(submit_cmd))
def submit_to_queue(self, script_file):
"""
submits the job to the queue and returns the job id
:param script_file: (str) name of the script file to use (String)
:return: (int) job_id
"""
if not os.path.exists(script_file):
raise ValueError(
'Cannot find script file located at: {}'.format(
script_file))
queue_logger = self.get_qlogger('qadapter.{}'.format(self.q_name))
submit_cmd = self.q_commands[self.q_type]["submit_cmd"]
# submit the job
try:
if self.q_type == "Cobalt":
# Cobalt requires scripts to be executable
os.chmod(script_file, stat.S_IRWXU | stat.S_IRGRP | stat.S_IXGRP)
cmd = [submit_cmd, script_file]
# For most of the queues handled by common_adapter, it's best to simply submit the file name
# as an argument. LoadSharingFacility doesn't handle the header section (queue name, nodes, etc)
# when taking file arguments, so the file needs to be passed as stdin to make it work correctly.
if self.q_type == 'LoadSharingFacility':
with open(script_file, 'r') as inputFile:
p = subprocess.Popen([submit_cmd], stdin=inputFile, stdout=subprocess.PIPE, stderr=subprocess.PIPE)
else:
p = subprocess.Popen(cmd, stdout=subprocess.PIPE, stderr=subprocess.PIPE)
p.wait()
# retrieve the returncode. PBS returns 0 if the job was successful
if p.returncode == 0:
try:
job_id = self._parse_jobid(p.stdout.read().decode())
queue_logger.info(
'Job submission was successful and job_id is {}'.format(
job_id))
return job_id
except Exception as ex:
# probably error parsing job code
log_exception(queue_logger,
'Could not parse job id following {} due to error {}...'
.format(submit_cmd, str(ex)))
else:
# some qsub error, e.g. maybe wrong queue specified, don't have permission to submit, etc...
msgs = [
'Error in job submission with {n} file {f} and cmd {c}'.format(
n=self.q_name, f=script_file, c=cmd),
'The error response reads: {}'.format(p.stderr.read())]
log_fancy(queue_logger, msgs, 'error')
except Exception as ex:
# random error, e.g. no qsub on machine!
log_exception(queue_logger,
'Running the command: {} caused an error...'
.format(submit_cmd))
def submit_to_queue(self, script_file):
"""
submits the job to the queue and returns the job id
:param script_file: (str) name of the script file to use (String)
:return: (int) job_id
"""
if not os.path.exists(script_file):
raise ValueError(
'Cannot find script file located at: {}'.format(script_file))
queue_logger = self.get_qlogger('qadapter.{}'.format(self.q_name))
# submit the job
try:
cmd = [self.submit_cmd, script_file]
p = subprocess.Popen(cmd,
stdout=subprocess.PIPE,
stderr=subprocess.PIPE)
p.wait()
# grab the returncode. PBS returns 0 if the job was successful
if p.returncode == 0:
try:
job_id = self._parse_jobid(p.stdout.read())
queue_logger.info(
'Job submission was successful and job_id is {}'.
format(job_id))
return job_id
except:
# probably error parsing job code
log_exception(
queue_logger,
'Could not parse job id following {}...'.format(
self.submit_cmd))
else:
# some qsub error, e.g. maybe wrong queue specified, don't have permission to submit, etc...
msgs = [
'Error in job submission with {n} file {f} and cmd {c}'.
format(n=self.q_name, f=script_file, c=cmd),
'The error response reads: {}'.format(p.stderr.read())
]
log_fancy(queue_logger, msgs, 'error')
except:
# random error, e.g. no qsub on machine!
log_exception(
queue_logger,
'Running the command: {} caused an error...'.format(
self.submit_cmd))
def submit_to_queue(self, script_file):
"""
submits the job to the queue and returns the job id
:param script_file: (str) name of the script file to use (String)
:return: (int) job_id
"""
if not os.path.exists(script_file):
raise ValueError(
'Cannot find script file located at: {}'.format(
script_file))
queue_logger = self.get_qlogger('qadapter.{}'.format(self.q_name))
# submit the job
try:
cmd = [self.submit_cmd, script_file]
p = subprocess.Popen(cmd, stdout=subprocess.PIPE,
stderr=subprocess.PIPE)
p.wait()
# grab the returncode. PBS returns 0 if the job was successful
if p.returncode == 0:
try:
job_id = self._parse_jobid(p.stdout.read())
queue_logger.info(
'Job submission was successful and job_id is {}'.format(
job_id))
return job_id
except:
# probably error parsing job code
log_exception(queue_logger,
'Could not parse job id following {}...'.format(
self.submit_cmd))
else:
# some qsub error, e.g. maybe wrong queue specified, don't have permission to submit, etc...
msgs = [
'Error in job submission with {n} file {f} and cmd {c}'.format(
n=self.q_name, f=script_file, c=cmd),
'The error response reads: {}'.format(p.stderr.read())]
log_fancy(queue_logger, msgs, 'error')
except:
# random error, e.g. no qsub on machine!
log_exception(queue_logger,
'Running the command: {} caused an error...'.format(
self.submit_cmd))
def submit_to_queue(self, queue_params, script_file):
"""
for documentation, see parent object
"""
if not os.path.exists(script_file):
raise ValueError(
'Cannot find script file located at: {}'.format(script_file))
# initialize logger
slurm_logger = get_fw_logger('rocket.slurm', queue_params.logging_dir)
# submit the job
try:
cmd = ['sbatch', script_file]
p = subprocess.Popen(cmd,
stdout=subprocess.PIPE,
stderr=subprocess.PIPE)
p.wait()
# grab the returncode. SLURM returns 0 if the job was successful
if p.returncode == 0:
try:
# output should of the form '2561553.sdb' or '352353.jessup' - just grab the first part for job id
job_id = int(p.stdout.read().split()[3])
slurm_logger.info(
'Job submission was successful and job_id is {}'.
format(job_id))
return job_id
except:
# probably error parsing job code
log_exception(slurm_logger,
'Could not parse job id following slurm...')
else:
# some qsub error, e.g. maybe wrong queue specified, don't have permission to submit, etc...
msgs = [
'Error in job submission with SLURM file {f} and cmd {c}'.
format(f=script_file, c=cmd)
]
msgs.append('The error response reads: {}'.format(
p.stderr.read()))
log_fancy(slurm_logger, 'error', msgs)
except:
# random error, e.g. no qsub on machine!
log_exception(slurm_logger, 'Running slurm caused an error...')
def get_njobs_in_queue(self, rocket_params, username=None):
"""
for documentation, see parent object
"""
# TODO: (low-priority) parse the qstat -x output as an alternate way to get this working
# tmp_file_name = 'tmp_qstat.xml'
# cmd = ['qstat', '-x']\n
# initialize logger
pbs_logger = get_fw_logger('rocket.pbs', rocket_params.logging_dir)
# initialize username
if username is None:
username = getpass.getuser()
# run qstat
cmd = ['qstat', '-a', '-u', username]
p = subprocess.Popen(cmd, shell=False, stdout=subprocess.PIPE)
p.wait()
# parse the result
if p.returncode == 0:
# lines should have this form
# '1339044.sdb username queuename 2012-02-29-16-43 20460 -- -- -- 00:20 C 00:09'
# count lines that include the username in it
# TODO: only count running or queued jobs. or rather, *don't* count jobs that are 'C'.
outs = p.stdout.readlines()
rx = re.compile(username)
njobs = len(
[line.split() for line in outs if rx.search(line) is not None])
pbs_logger.info(
'The number of jobs currently in the queue is: {}'.format(
njobs))
return njobs
# there's a problem talking to qstat server?
msgs = [
'Error trying to get the number of jobs in the queue using qstat service'
]
msgs.append('The error response reads: {}'.format(p.stderr.read()))
log_fancy(pbs_logger, 'error', msgs)
return None
def get_njobs_in_queue(self, queue_params, username=None):
"""
for documentation, see parent object
"""
# TODO: (low-priority) parse the qstat -x output as an alternate way to get this working
# tmp_file_name = 'tmp_qstat.xml'
# cmd = ['qstat', '-x']\n
# initialize logger
slurm_logger = get_fw_logger('rocket.slurm', queue_params.logging_dir)
# initialize username
if username is None:
username = getpass.getuser()
# run qstat
cmd = ['squeue', '-o "%u"', '-u', username]
p = subprocess.Popen(cmd, shell=False, stdout=subprocess.PIPE)
p.wait()
# parse the result
if p.returncode == 0:
# lines should have this form
# username
# count lines that include the username in it
outs = p.stdout.readlines()
rx = re.compile(username)
njobs = len(
[line.split() for line in outs if rx.search(line) is not None])
slurm_logger.info(
'The number of jobs currently in the queue is: {}'.format(
njobs))
return njobs
# there's a problem talking to qstat server?
msgs = [
'Error trying to get the number of jobs in the queue using squeue service'
]
msgs.append('The error response reads: {}'.format(p.stderr.read()))
log_fancy(slurm_logger, 'error', msgs)
return None
def get_njobs_in_queue(self, rocket_params, username=None):
"""
for documentation, see parent object
"""
# TODO: (low-priority) parse the qstat -x output as an alternate way to get this working
# tmp_file_name = 'tmp_qstat.xml'
# cmd = ['qstat', '-x']\n
# initialize logger
pbs_logger = get_fw_logger('rocket.pbs', rocket_params.logging_dir)
# initialize username
if username is None:
username = getpass.getuser()
# run qstat
cmd = ['qstat', '-a', '-u', username]
p = subprocess.Popen(cmd, shell=False, stdout=subprocess.PIPE)
p.wait()
# parse the result
if p.returncode == 0:
# lines should have this form
# '1339044.sdb username queuename 2012-02-29-16-43 20460 -- -- -- 00:20 C 00:09'
# count lines that include the username in it
# TODO: only count running or queued jobs. or rather, *don't* count jobs that are 'C'.
outs = p.stdout.readlines()
rx = re.compile(username)
njobs = len([line.split() for line in outs if rx.search(line) is not None])
pbs_logger.info('The number of jobs currently in the queue is: {}'.format(njobs))
return njobs
# there's a problem talking to qstat server?
msgs = ['Error trying to get the number of jobs in the queue using qstat service']
msgs.append('The error response reads: {}'.format(p.stderr.read()))
log_fancy(pbs_logger, 'error', msgs)
return None
def get_njobs_in_queue(self, queue_params, username=None):
"""
for documentation, see parent object
"""
# TODO: (low-priority) parse the qstat -x output as an alternate way to get this working
# tmp_file_name = 'tmp_qstat.xml'
# cmd = ['qstat', '-x']\n
# initialize logger
slurm_logger = get_fw_logger('rocket.slurm', queue_params.logging_dir)
# initialize username
if username is None:
username = getpass.getuser()
# run qstat
cmd = ['squeue', '-o "%u"', '-u', username]
p = subprocess.Popen(cmd, shell=False, stdout=subprocess.PIPE)
p.wait()
# parse the result
if p.returncode == 0:
# lines should have this form
# username
# count lines that include the username in it
outs = p.stdout.readlines()
rx = re.compile(username)
njobs = len([line.split() for line in outs if rx.search(line) is not None])
slurm_logger.info('The number of jobs currently in the queue is: {}'.format(njobs))
return njobs
# there's a problem talking to qstat server?
msgs = ['Error trying to get the number of jobs in the queue using squeue service']
msgs.append('The error response reads: {}'.format(p.stderr.read()))
log_fancy(slurm_logger, 'error', msgs)
return None
def submit_to_queue(self, queue_params, script_file):
"""
for documentation, see parent object
"""
if not os.path.exists(script_file):
raise ValueError('Cannot find script file located at: {}'.format(script_file))
# initialize logger
slurm_logger = get_fw_logger('rocket.slurm', queue_params.logging_dir)
# submit the job
try:
cmd = ['sbatch', script_file]
p = subprocess.Popen(cmd, stdout=subprocess.PIPE, stderr=subprocess.PIPE)
p.wait()
# grab the returncode. SLURM returns 0 if the job was successful
if p.returncode == 0:
try:
# output should of the form '2561553.sdb' or '352353.jessup' - just grab the first part for job id
job_id = int(p.stdout.read().split()[3])
slurm_logger.info('Job submission was successful and job_id is {}'.format(job_id))
return job_id
except:
# probably error parsing job code
log_exception(slurm_logger, 'Could not parse job id following slurm...')
else:
# some qsub error, e.g. maybe wrong queue specified, don't have permission to submit, etc...
msgs = ['Error in job submission with SLURM file {f} and cmd {c}'.format(f=script_file, c=cmd)]
msgs.append('The error response reads: {}'.format(p.stderr.read()))
log_fancy(slurm_logger, 'error', msgs)
except:
# random error, e.g. no qsub on machine!
log_exception(slurm_logger, 'Running slurm caused an error...')