arc.job.local

A module for running jobs on the local machine. When transitioning to Python 3, use subprocess.run()

arc.job.local.check_job_status(job_id)

Possible statuses: before_submission, running, errored on node xx, done Status line formats:

OGE:

540420 0.45326 xq1340b    user_name       r     10/26/2018 11:08:30 long1@node18.cluster

Slurm:

14428     debug xq1371m2   user_name  R 50-04:04:46      1 node06

PBS (taken from zeldo.dow.com):

                                                                                  Req'd       Req'd       Elap
Job ID                  Username    Queue    Jobname          SessID  NDS   TSK   Memory      Time    S   Time
----------------------- ----------- -------- ---------------- ------ ----- ------ --------- --------- - ---------
2016614.zeldo.local     u780444     workq    scan.pbs          75380     1     10       --  730:00:00 R  00:00:20
2016616.zeldo.local     u780444     workq    scan.pbs          75380     1     10       --  730:00:00 R  00:00:20

arc.job.local.check_running_jobs_ids()

Return a list of int representing job IDs of all jobs submitted by the user on a server

arc.job.local.delete_all_local_arc_jobs(jobs: Optional[List[Union[str, int]]] = None)

Delete all ARC-spawned jobs (with job name starting with a and a digit) from the local server. Make sure you know what you’re doing, so unrelated jobs won’t be deleted… Useful when terminating ARC while some (ghost) jobs are still running.

Parameters

jobs (List[Union[str, int]], optional) – Specific ARC job IDs to delete.

arc.job.local.delete_job(job_id)

Deletes a running job

arc.job.local.execute_command(command, shell=True, no_fail=False)

Execute a command.

Notes

If no_fail == True, then a warning is logged and False is returned so that the calling function can debug the situation.

Parameters

• command – An array of string commands to send.

• shell (bool) – Specifies whether the command should be executed using bash instead of Python

• no_fail (bool) – If True then ARC will not crash if an error is encountered.

Returns: list

lists of stdin, stdout, stderr corresponding to the commands sent

arc.job.local.get_last_modified_time(file_path_1: str, file_path_2: Optional[str] = None) → Optional[datetime.datetime]

Returns the last modified time of file_path_1 if the file exists, else returns the last modified time of file_path_2 if the file exists.

Parameters

• file_path_1 (str) – The path to file 1.

• file_path_2 (str, optional) – The path to file 2.

arc.job.local.rename_output(local_file_path, software)

Rename the output file to “output.out” for consistency between software local_file_path is the full path to the output.out file, software is the software used for the job by which the original output file name is determined

arc.job.local.submit_job(path)

Submit a job path is the job’s folder path, where the submit script is located (without the submit script file name)

arc.job.local.write_file(file_path, file_string)

Write file_string as the file’s content in file_path