pyiron_base.jobs.job.extension.server.queuestatus module

Set of functions to interact with the queuing system directly from within pyiron - optimized for the Sun grid engine.

pyiron_base.jobs.job.extension.server.queuestatus.queue_check_job_is_waiting_or_running(item)

Check if a job is still listed in the queue system as either waiting or running.

Parameters:

item (int, GenericJob) – Provide either the job_ID or the full hamiltonian

Returns:

[True/False]

Return type:

bool

pyiron_base.jobs.job.extension.server.queuestatus.queue_delete_job(item)

Delete a job from the queuing system

Parameters:

item (int, pyiron_base.jobs.job.generic.GenericJob) – Provide either the job_ID or the full hamiltonian

Returns:

Output from the queuing system as string - optimized for the Sun grid engine

Return type:

str

pyiron_base.jobs.job.extension.server.queuestatus.queue_enable_reservation(item)

Enable a reservation for a particular job within the queuing system

Parameters:

item (int, pyiron_base.jobs.job.generic.GenericJob) – Provide either the job_ID or the full hamiltonian

Returns:

Output from the queuing system as string - optimized for the Sun grid engine

Return type:

str

pyiron_base.jobs.job.extension.server.queuestatus.queue_info_by_job_id(job_id)

Display the queuing system info of job by qstat | grep shell command as dictionary

Parameters:

job_id (int) – query for a specific job_id

Returns:

Dictionary with the output from the queuing system - optimized for the Sun grid engine

Return type:

dict

pyiron_base.jobs.job.extension.server.queuestatus.queue_is_empty()

Check if the queue table is currently empty - no more jobs to wait for.

Returns:

True if the table is empty, else False - optimized for the Sun grid engine

Return type:

bool

pyiron_base.jobs.job.extension.server.queuestatus.queue_table(job_ids=None, working_directory_lst=None, project_only=True, full_table=False)

Display the queuing system table as pandas.Dataframe

Parameters:

  • job_ids (list) – check for a specific list of job IDs - empty list by default

  • working_directory_lst (list) – list of working directories to include - empty list by default

  • project_only (bool) – Query only for jobs within the current project - True by default

  • full_table (bool) – Return all entries from the queuing system without filtering - False by default

Returns:

Output from the queuing system - optimized for the Sun grid engine

Return type:

pandas.DataFrame

pyiron_base.jobs.job.extension.server.queuestatus.retrieve_job(job, try_collecting=False)

Retrieve a job from remote server and check if it has a “finished status”. Optionally try to collect its output.

Parameters:

  • job – pyiron job

  • try_collecting (bool) – whether to run collect if not finished - default=False

Returns:

returns None

pyiron_base.jobs.job.extension.server.queuestatus.update_from_remote(project, recursive=True, ignore_exceptions=False, try_collecting=False)

Update jobs from the remote server

Parameters:

  • project – Project instance the jobs is located in

  • recursive (bool) – search subprojects [True/False] - default=True

  • ignore_exceptions (bool) – ignore eventual exceptions when retrieving jobs - default=False

  • try_collecting (bool) – try to collect jobs that don’t have a status counting as finished - default=False

Returns:

returns None if ignore_exceptions is False or when no error occured. returns a list with job ids when errors occured, but were ignored

pyiron_base.jobs.job.extension.server.queuestatus.validate_que_request(item)

Internal function to convert the job_ID or hamiltonian to the queuing system ID.

Parameters:

item (int, pyiron_base.jobs.job.generic.GenericJob) – Provide either the job_ID or the full hamiltonian

Returns:

queuing system ID

Return type:

int

pyiron_base.jobs.job.extension.server.queuestatus.wait_for_job(job, interval_in_s=5, max_iterations=100)

Sleep until the job is finished but maximum interval_in_s * max_iterations seconds.

Parameters:

  • job (pyiron_base.job.utils.GenericJob) – Job to wait for

  • interval_in_s (int) – interval when the job status is queried from the database - default 5 sec.

  • max_iterations (int) – maximum number of iterations - default 100

Raises:

ValueError – max_iterations reached, job still running

pyiron_base.jobs.job.extension.server.queuestatus.wait_for_jobs(project, interval_in_s=5, max_iterations=100, recursive=True, ignore_exceptions=False, try_collecting=False)

Wait for the calculation in the project to be finished

Parameters:

  • project – Project instance the jobs is located in

  • interval_in_s (int) – interval when the job status is queried from the database - default 5 sec.

  • max_iterations (int) – maximum number of iterations - default 100

  • recursive (bool) – search subprojects [True/False] - default=True

  • ignore_exceptions (bool) – ignore eventual exceptions when retrieving jobs - default=False

  • try_collecting (bool) – try to run collect for fetched jobs that don’t have a status counting as finished - default=False

Raises:

ValueError – max_iterations reached, but jobs still running