qtoolkit.io.sge module

class qtoolkit.io.sge.SGEIO(get_job_executable: str = 'qstat')

Bases: PBSIOBase

CANCEL_CMD: str | None = 'qdel'

SUBMIT_CMD: str | None = 'qsub'

default_unit: str = 'M'

extract_job_id(stdout: str) → str | None

Extract the job ID from the submission output.

extract_job_id_from_cancel(stderr: str) → str | None

Extract the job ID from the cancellation output.

header_template: str = '#$ -cwd $${cwd}\n#$ -q $${queue}\n#$ -N $${job_name}\n#$ -P $${device}\n#$ -l $${select}\n#$ -l h_rt=$${walltime}\n#$ -l s_rt=$${soft_walltime}\n#$ -pe $${model}\n#$ -binding $${place}\n#$ -W group_list=$${group_list}\n#$ -M $${mail_user}\n#$ -m $${mail_type}\n#$ -o $${qout_path}\n#$ -e $${qerr_path}\n#$ -p $${priority}\n#$ -r $${rerunnable}\n#$ -t $${array}\n$${qverbatim}\n'

header_template_file: str = 'sge'

job_id_regex: str | None = '^\\d+(\\.[\\w.-]+)?(\\[\\d+(-\\d+)?(,\\d+)*\\])?$'

parse_job_output(exit_code: int, stdout: str | bytes, stderr: str | bytes, job_id: str | None = None) → QJob | None

Parse the output of the qstat command for a single job.

parse_jobs_list_output(exit_code: int, stdout: str | bytes, stderr: str | bytes, job_ids: list[str] | None = None) → list[QJob]

Parse the output of the qstat command for a list of jobs.

power_labels: ClassVar[dict] = {'g': 2, 'k': 0, 'm': 1, 't': 3}

sanitize_options(options: dict) → dict

Sanitize the values in the options used to generate the header.

Parameters:

options – Dictionary of options to sanitize.

Returns:

Sanitized options.

Return type:

dict

system_name: str = 'SGE'

class qtoolkit.io.sge.SGEState(value)

Bases: QSubState

DELETION = 'd'

DELETION_RUNNING = 'dr'

DELETION_RUNNING_RESUBMIT = 'dRr'

DELETION_SUSPENDED_ALARM = 'dT'

DELETION_SUSPENDED_JOB = 'ds'

DELETION_SUSPENDED_QUEUE = 'dS'

DELETION_SUSPENDED_RESUBMIT_ALARM = 'dRT'

DELETION_SUSPENDED_RESUBMIT_JOB = 'dRs'

DELETION_SUSPENDED_RESUBMIT_QUEUE = 'dRS'

DELETION_TRANSFERRING = 'dt'

DELETION_TRANSFERRING_RESUBMIT = 'dRt'

ERROR_PENDING = 'Eqw'

ERROR_PENDING_HOLD = 'Ehqw'

ERROR_PENDING_HOLD_REQUEUE = 'EhRqw'

FINISHED = 'z'

HOLD = 'hqw'

JOB_SUSPENDED = 's'

QUEUED_WAITING = 'qw'

RESTARTED = 'R'

RUNNING = 'r'

TRANSFERRING = 't'

WAITING = 'w'

property qstate: QState