def launch(self,jobdir,job_email=None,job_email_options='bae'):
cmds = self.commands(jobdir)
pbsfile = self.pbs_path()
outlog = self.outlog_path()
pbs = PBS(pbsfile,outlog,cmds,self.processor.walltime_str,self.processor.memreq_mb,self.processor.ppn,job_email,job_email_options)
pbs.write()
jobid = pbs.submit()
if jobid == '' or jobid == '0':
# TODO: raise exception
print('ERROR:failed to launch job on cluster')
return False
else:
self.set_status(JOB_RUNNING)
self.set_jobid(jobid)
self.set_jobstartdate_today()
#save record on redcap for the job that has been launch
project=self.assessor_label.split('-x-')[0]
SM_name=self.get_processor_name()
data,record_id=XnatUtils.create_record_redcap(project, SM_name)
run=XnatUtils.save_job_redcap(data,record_id)
if not run:
print(' ->ERROR: did not send the job to redcap for jobID <'+str(jobid)+'>: '+record_id)
return True
def launch(self, jobdir, job_email=None, job_email_options='bae'):
cmds = self.commands(jobdir)
pbsfile = self.pbs_path()
outlog = self.outlog_path()
pbs = PBS(pbsfile, outlog, cmds, self.processor.walltime_str,
self.processor.memreq_mb, self.processor.ppn, job_email,
job_email_options)
pbs.write()
jobid = pbs.submit()
if jobid == '' or jobid == '0':
# TODO: raise exception
print('ERROR:failed to launch job on cluster')
return False
else:
self.set_status(JOB_RUNNING)
self.set_jobid(jobid)
self.set_jobstartdate_today()
#save record on redcap for the job that has been launch
project = self.assessor_label.split('-x-')[0]
SM_name = self.get_processor_name()
data, record_id = XnatUtils.create_record_redcap(project, SM_name)
run = XnatUtils.save_job_redcap(data, record_id)
if not run:
print(' ->ERROR: did not send the job to redcap for jobID <' +
str(jobid) + '>: ' + record_id)
return True
def launch(
self, jobdir, job_email=None, job_email_options=DEFAULT_EMAIL_OPTS, xnat_host=None, writeonly=False, pbsdir=None
):
"""
Method to launch a job on the grid
:param jobdir: absolute path to where the data will be stored on the node
:param job_email: who to email if the job fails
:param job_email_options: grid-specific job email options (e.g.,
fails, starts, exits etc)
:param xnat_host: set the XNAT_HOST in the PBS job
:param writeonly: write the job files without submitting them
:param pbsdir: folder to store the pbs file
:raises: cluster.ClusterLaunchException if the jobid is 0 or empty
as returned by pbs.submit() method
:return: True if the job failed
"""
cmds = self.commands(jobdir)
pbsfile = self.pbs_path(writeonly, pbsdir)
outlog = self.outlog_path()
pbs = PBS(
pbsfile,
outlog,
cmds,
self.processor.walltime_str,
self.processor.memreq_mb,
self.processor.ppn,
job_email,
job_email_options,
xnat_host,
)
pbs.write()
if writeonly:
mes_format = """ filepath: {path}"""
LOGGER.info(mes_format.format(path=pbsfile))
return True
else:
jobid = pbs.submit()
if jobid == "" or jobid == "0":
LOGGER.error("failed to launch job on cluster")
raise cluster.ClusterLaunchException
else:
self.set_launch(jobid)
return True
def build_task(self,
csess,
jobdir,
job_email=None,
job_email_options=DEFAULT_EMAIL_OPTS,
xnat_host=None):
"""
Method to build a job
"""
(old_proc_status,old_qc_status,_) = self.get_statuses()
try:
cmds = self.build_commands(csess, jobdir)
batch_file = self.batch_path()
outlog = self.outlog_path()
batch = PBS(batch_file,
outlog,
cmds,
self.processor.walltime_str,
self.processor.memreq_mb,
self.processor.ppn,
job_email,
job_email_options,
xnat_host)
LOGGER.info('writing:' + batch_file)
batch.write()
new_proc_status = JOB_RUNNING
new_qc_status = JOB_PENDING
except NeedInputsException as e:
new_proc_status = NEED_INPUTS
new_qc_status = e.value
except NoDataException as e:
new_proc_status = NO_DATA
new_qc_status = e.value
if new_proc_status != old_proc_status or new_qc_status != old_qc_status:
self.set_proc_and_qc_status(new_proc_status, new_qc_status)
return (new_proc_status,new_qc_status)
def launch(self, jobdir, job_email=None, job_email_options=DAX_SETTINGS.get_email_opts(), xnat_host=None, writeonly=False, pbsdir=None):
"""
Method to launch a job on the grid
:param jobdir: absolute path to where the data will be stored on the node
:param job_email: who to email if the job fails
:param job_email_options: grid-specific job email options (e.g.,
fails, starts, exits etc)
:param xnat_host: set the XNAT_HOST in the PBS job
:param writeonly: write the job files without submitting them
:param pbsdir: folder to store the pbs file
:raises: cluster.ClusterLaunchException if the jobid is 0 or empty
as returned by pbs.submit() method
:return: True if the job failed
"""
cmds = self.commands(jobdir)
pbsfile = self.pbs_path(writeonly, pbsdir)
outlog = self.outlog_path()
outlog_dir = os.path.dirname(outlog)
mkdirp(outlog_dir)
pbs = PBS(pbsfile, outlog, cmds, self.processor.walltime_str, self.processor.memreq_mb,
self.processor.ppn, job_email, job_email_options, xnat_host)
pbs.write()
if writeonly:
mes_format = """ filepath: {path}"""
LOGGER.info(mes_format.format(path=pbsfile))
return True
else:
jobid = pbs.submit()
if jobid == '' or jobid == '0':
LOGGER.error('failed to launch job on cluster')
raise cluster.ClusterLaunchException
else:
self.set_launch(jobid)
return True