def submit_jobs(self,
link,
job_dict=None,
job_archive=None,
stream=sys.stdout):
"""Submit all the jobs in job_dict """
if link is None:
return JobStatus.no_job
if job_dict is None:
job_keys = link.jobs.keys()
else:
job_keys = sorted(job_dict.keys())
# copy & reverse the keys b/c we will be popping item off the back of
# the list
unsubmitted_jobs = job_keys
unsubmitted_jobs.reverse()
failed = False
while unsubmitted_jobs:
njob_to_submit = min(self._jobs_per_cycle, len(unsubmitted_jobs))
if self._dry_run:
njob_to_submit = len(unsubmitted_jobs)
for i in range(njob_to_submit):
job_key = unsubmitted_jobs.pop()
# job_details = job_dict[job_key]
job_details = link.jobs[job_key]
job_config = job_details.job_config
if job_details.status == JobStatus.failed:
clean_job(job_details.logfile, {}, self._dry_run)
# clean_job(job_details.logfile,
# job_details.outfiles, self.args['dry_run'])
job_config['logfile'] = job_details.logfile
new_job_details = self.dispatch_job(link, job_key, job_archive)
if new_job_details.status == JobStatus.failed:
failed = True
clean_job(new_job_details.logfile,
new_job_details.outfiles, self._dry_run)
link.jobs[job_key] = new_job_details
if unsubmitted_jobs:
print('Sleeping %.0f seconds between submission cycles' %
self._time_per_cycle)
time.sleep(self._time_per_cycle)
return failed
def submit_jobs(self, link, job_dict=None, job_archive=None, stream=sys.stdout):
"""Submit all the jobs in job_dict """
if link is None:
return JobStatus.no_job
if job_dict is None:
job_keys = link.jobs.keys()
else:
job_keys = sorted(job_dict.keys())
# copy & reverse the keys b/c we will be popping item off the back of
# the list
unsubmitted_jobs = job_keys
unsubmitted_jobs.reverse()
failed = False
while unsubmitted_jobs:
njob_to_submit = min(self._jobs_per_cycle,
len(unsubmitted_jobs))
if self._dry_run:
njob_to_submit = len(unsubmitted_jobs)
for i in range(njob_to_submit):
job_key = unsubmitted_jobs.pop()
# job_details = job_dict[job_key]
job_details = link.jobs[job_key]
job_config = job_details.job_config
if job_details.status == JobStatus.failed:
clean_job(job_details.logfile, {}, self._dry_run)
# clean_job(job_details.logfile,
# job_details.outfiles, self.args['dry_run'])
job_config['logfile'] = job_details.logfile
new_job_details = self.dispatch_job(link, job_key, job_archive)
if new_job_details.status == JobStatus.failed:
failed = True
clean_job(new_job_details.logfile,
new_job_details.outfiles, self._dry_run)
link.jobs[job_key] = new_job_details
if unsubmitted_jobs:
print('Sleeping %.0f seconds between submission cycles' %
self._time_per_cycle)
time.sleep(self._time_per_cycle)
return failed
def submit_jobs(self,
link,
job_dict=None,
job_archive=None,
stream=sys.stdout):
"""Submit all the jobs in job_dict """
if link is None:
return JobStatus.no_job
if job_dict is None:
job_keys = link.jobs.keys()
else:
job_keys = sorted(job_dict.keys())
# copy & reverse the keys b/c we will be popping item off the back of
# the list
unsubmitted_jobs = list(job_keys)[::-1]
failed = False
if unsubmitted_jobs:
if stream != sys.stdout:
sys.stdout.write('Submitting jobs (%i): ' %
len(unsubmitted_jobs))
sys.stdout.flush()
while unsubmitted_jobs:
status = get_lsf_status()
njob_to_submit = min(self._max_jobs - status['NJOB'],
self._jobs_per_cycle, len(unsubmitted_jobs))
if self._dry_run:
njob_to_submit = len(unsubmitted_jobs)
for i in range(njob_to_submit):
job_key = unsubmitted_jobs.pop()
# job_details = job_dict[job_key]
job_details = link.jobs[job_key]
job_config = job_details.job_config
if job_details.status == JobStatus.failed:
clean_job(job_details.logfile, {}, self._dry_run)
# clean_job(job_details.logfile,
# job_details.outfiles, self.args['dry_run'])
job_config['logfile'] = job_details.logfile
new_job_details = self.dispatch_job(link, job_key, job_archive,
stream)
if new_job_details.status == JobStatus.failed:
failed = True
clean_job(new_job_details.logfile,
new_job_details.outfiles, self._dry_run)
link.jobs[job_key] = new_job_details
if unsubmitted_jobs:
if stream != sys.stdout:
sys.stdout.write('.')
sys.stdout.flush()
stream.write(
'Sleeping %.0f seconds between submission cycles\n' %
self._time_per_cycle)
time.sleep(self._time_per_cycle)
if failed:
return JobStatus.failed
if stream != sys.stdout:
sys.stdout.write('!\n')
return JobStatus.done