def cancel(self):
super().cancel()
# Recreate the full job id
jobid = str(self._jobid)
if self._pbs_server:
jobid += '.' + self._pbs_server
getlogger().debug('cancelling job (id=%s)' % jobid)
self._run_command('qdel %s' % jobid, settings().job_submit_timeout)
def submit(self):
cmd = 'sbatch %s' % self.script_filename
completed = _run_strict(cmd, timeout=settings().job_submit_timeout)
jobid_match = re.search(r'Submitted batch job (?P<jobid>\d+)',
completed.stdout)
if not jobid_match:
raise JobError(
'could not retrieve the job id of the submitted job')
self._jobid = int(jobid_match.group('jobid'))
def wait(self):
super().wait()
# Quickly return in case we have finished already
if self._state in self._completion_states:
return
intervals = itertools.cycle(settings().job_poll_intervals)
self._update_state()
while self._state not in self._completion_states:
time.sleep(next(intervals))
self._update_state()
def submit(self):
# `-o` and `-e` options are only recognized in command line by the PBS
# Slurm wrappers.
cmd = 'qsub -o %s -e %s %s' % (self.stdout, self.stderr,
self.script_filename)
completed = self._run_command(cmd, settings().job_submit_timeout)
jobid_match = re.search(r'^(?P<jobid>\S+)', completed.stdout)
if not jobid_match:
raise JobError('could not retrieve the job id '
'of the submitted job')
jobid, *info = jobid_match.group('jobid').split('.', maxsplit=2)
self._jobid = int(jobid)
if info:
self._pbs_server = info[0]
def wait(self, job):
# Quickly return in case we have finished already
if slurm_state_completed(job.state):
if self.is_array(job):
self._merge_files(job)
return
intervals = itertools.cycle(settings().job_poll_intervals)
self._update_state(job)
while not slurm_state_completed(job.state):
time.sleep(next(intervals))
self._update_state(job)
if self.is_array(job):
self._merge_files(job)
def wait(self, job):
# Quickly return in case we have finished already
if slurm_state_completed(job.state):
if self.is_array(job):
self._merge_files(job)
return
intervals = itertools.cycle(settings().job_poll_intervals)
self._update_state(job)
while not slurm_state_completed(job.state):
if job.max_pending_time and slurm_state_pending(job.state):
if datetime.now() - self._submit_time >= job.max_pending_time:
self.cancel(job)
raise JobError('maximum pending time exceeded',
jobid=job.jobid)
time.sleep(next(intervals))
self._update_state(job)
if self.is_array(job):
self._merge_files(job)
def cancel(self):
super().cancel()
getlogger().debug('cancelling job (id=%s)' % self._jobid)
_run_strict('scancel %s' % self._jobid,
timeout=settings().job_submit_timeout)
self._is_cancelling = True
def wait(self):
super().wait()
intervals = itertools.cycle(settings().job_poll_intervals)
while not self.finished():
time.sleep(next(intervals))
def wait(self, job):
intervals = itertools.cycle(settings().job_poll_intervals)
while not self.finished(job):
time.sleep(next(intervals))
