pysqa.wrapper.sge.SunGridEngineCommands

class pysqa.wrapper.sge.SunGridEngineCommands

Bases: SchedulerCommands

__init__()

Methods

__init__()
convert_queue_status(queue_status_output)	Convert the queue status output to a pandas DataFrame.
dependencies(dependency_list)	Returns the list of dependencies for a job.
get_job_id_from_output(queue_submit_output)	Extracts the job ID from the output of the job submission command.
render_submission_template(command[, ...])	Generate the job submission template.

Attributes

delete_job_command	Return the command to delete a job.
enable_reservation_command	Return the command to enable job reservation.
get_queue_status_command	Return the command to get the queue status.
submit_job_command	Return the command to submit a job.

static convert_queue_status(queue_status_output: str) → DataFrame

Convert the queue status output to a pandas DataFrame.

Parameters:

queue_status_output – The output of the queue status command.

Returns:

A pandas DataFrame containing the converted queue status.

property delete_job_command: list[str]

Return the command to delete a job.

static dependencies(dependency_list: list[str]) → list

Returns the list of dependencies for a job.

Parameters:

dependency_list (list[str]) – The list of dependencies.

Returns:

The list of dependencies.

Return type:

list

property enable_reservation_command: list[str]

Return the command to enable job reservation.

static get_job_id_from_output(queue_submit_output: str) → int

Extracts the job ID from the output of the job submission command.

property get_queue_status_command: list[str]

Return the command to get the queue status.

static render_submission_template(command: str, submission_template: str | Template = '#!/bin/bash\n#$ -N {{job_name}}\n#$ -wd {{working_directory}}\n{%- if cores %}\n#$ -pe {{partition}} {{cores}}\n{%- endif %}\n{%- if memory_max %}\n#$ -l h_vmem={{memory_max}}\n{%- endif %}\n{%- if run_time_max %}\n#$ -l h_rt={{run_time_max}}\n{%- endif %}\n#$ -o time.out\n#$ -e error.out\n\n{{command}}\n', job_name: str = 'pysqa', working_directory: str = '/home/docs/checkouts/readthedocs.org/user_builds/pysqa/checkouts/latest/docs', cores: int = 1, memory_max: int | str | None = None, run_time_max: int | None = None, dependency_list: list[int] | None = None, **kwargs) → str

Generate the job submission template.

Parameters:

• command (str, optional) – The command to be executed.

• job_name (str, optional) – The job name. Defaults to “pysqa”.

• working_directory (str, optional) – The working directory. Defaults to “.”.

• cores (int, optional) – The number of cores. Defaults to 1.

• memory_max (int, optional) – The maximum memory. Defaults to None.

• run_time_max (int, optional) – The maximum run time. Defaults to None.

• dependency_list (list[int], optional) – The list of dependency job IDs. Defaults to None.

• submission_template (str) – Submission script template pysqa.wrapper.flux.template

Returns:

The rendered job submission template.

Return type:

str

property submit_job_command: list[str]

Return the command to submit a job.