prisms_jobs.interface.torque

Misc functions for interfacing between torque and the prisms_jobs module

Functions

alter(jobid, arg)	qalter a job.
delete(jobid)	qdel a PBS job.
hold(jobid)	qhold a job.
job_id([all, name])	Get job IDs
job_rundir(jobid)	Return the directory job was run in using qstat.
job_status([jobid])	Return job status using qstat
read(job, qsubstr)	Set Job object from string representing a PBS submit script.
release(jobid)	qrls a job.
sub_string(job)	Write Job as a string suitable for torque
submit(substr[, write_submit_script])	Submit a job using qsub.

prisms_jobs.interface.torque._getversion()

Returns the torque version as string or None if no qstat

prisms_jobs.interface.torque._qstat(jobid=None, username='bpuchala', full=False)

Return the stdout of qstat minus the header lines.

By default, ‘username’ is set to the current user. ‘full’ is the ‘-f’ option ‘jobid’ is a string or list of strings of job ids

Returns:str – the text of qstat, minus the header lines

prisms_jobs.interface.torque.alter(jobid, arg)

qalter a job.

Parameters:

• jobid (str) – ID of job to alter
• arg (str) – ‘arg’ is a scontrol command option string. For instance, “-a 201403152300.19”

Returns:

int – qalter returncode

prisms_jobs.interface.torque.delete(jobid)

qdel a PBS job.

Parameters:jobid (str) – ID of job to delete Returns:int – qdel returncode

prisms_jobs.interface.torque.hold(jobid)

qhold a job.

Parameters:jobid (str) – ID of job to hold Returns:int – qhold returncode

prisms_jobs.interface.torque.job_id(all=False, name=None)

Get job IDs

Parameters:

• all (bool) – If True, use qstat to query all user jobs. Else, check
• environment variable for ID of current job. (PBS_JOBID) –
• name (str) – If all==True, use name to filter results.

Returns:

One of str, List(str), or None – Returns a str if all==False and PBS_JOBID exists, a List(str) if all==True, else None.

prisms_jobs.interface.torque.job_rundir(jobid)

Return the directory job was run in using qstat.

Parameters:jobid (str or List(str)) – IDs of jobs to get the run directory Returns:dict – A dict, with id:rundir pairs.

prisms_jobs.interface.torque.job_status(jobid=None)

Return job status using qstat

Parameters:jobid (None, str, or List(str)) – IDs of jobs to query for status. None for all user jobs. Returns:dict of dict – The outer dict uses jobid as key; the inner dict contains:

”name”	Job name
”nodes”	Number of nodes
”procs”	Number of processors
”walltime”	Walltime
”jobstatus”	status (“Q”,”C”,”R”, etc.)
”qstatstr”	result of squeue -f jobid, None if not found
”elapsedtime”	None if not started, else seconds as int
”starttime”	None if not started, else seconds since epoch as int
”completiontime”	None if not completed, else seconds since epoch as int

prisms_jobs.interface.torque.read(job, qsubstr)

Set Job object from string representing a PBS submit script.

• Will read many but not all valid PBS scripts.
• Will ignore any arguments not included in prisms_jobs.Job()’s attributes.
• Will add default optional arguments (i.e. -A, -a, -l pmem=(.*), -l qos=(.*), -M, -m, -p, "Auto:") if not found.
• Will exit() if required arguments (-N, -l walltime=(.*), -l nodes=(.*):ppn=(.*), -q, cd $PBS_O_WORKDIR) not found.
• Will always include -V

Parameters:qsubstr (str) – A submit script as a string

prisms_jobs.interface.torque.release(jobid)

qrls a job.

Parameters:jobid (str) – ID of job to release Returns:int – qrls returncode

prisms_jobs.interface.torque.sub_string(job)

Write Job as a string suitable for torque

Parameters:job (prisms_jobs.Job instance) – Job to be submitted

prisms_jobs.interface.torque.submit(substr, write_submit_script=None)

Submit a job using qsub.

Parameters:

• substr (str) – The submit script string
• write_submit_script (bool, optional) – If true, submit via file skipping lines containing ‘#PBS -N’; otherwise, submit via commandline. If not specified, uses prisms_jobs.config['write_submit_script'].

Returns:

str – ID of submitted job

Raises:

JobsError – If a submission error occurs