nipype.pipeline.plugins.sge module

Parallel workflow execution via SGE

class nipype.pipeline.plugins.sge.QJobInfo(job_num, job_queue_state, job_time, job_queue_name, job_slots, qsub_command_line)

Bases: object

Information about a single job created by OGE/SGE or similar Each job is responsible for knowing it’s own refresh state :author Hans J. Johnson

is_initializing()

is_job_state_pending()

Return True, unless job is in the “zombie” status

is_pending()

is_running()

is_zombie()

set_state(new_state)

update_info(job_queue_state, job_time, job_queue_name, job_slots)

class nipype.pipeline.plugins.sge.QstatSubstitute(qstat_instant_executable='qstat', qstat_cached_executable='qstat')

Bases: object

A wrapper for Qstat to avoid overloading the SGE/OGS server with rapid continuous qstat requests

add_startup_job(taskid, qsub_command_line)

Parameters:

• taskid – The job id

• qsub_command_line – When initializing, reuse the job_queue_name

Returns:

NONE

is_job_pending(task_id)

print_dictionary()

For debugging

class nipype.pipeline.plugins.sge.SGEPlugin(**kwargs)

Bases: nipype.pipeline.plugins.base.SGELikeBatchManagerBase

Execute using SGE (OGE not tested)

The plugin_args input to run can be used to control the SGE execution. Currently supported options are:

• template : template to use for batch job submission

• qsub_argsarguments to be prepended to the job execution script in the

  qsub call

nipype.pipeline.plugins.sge.qsub_sanitize_job_name(testjobname)

Ensure that qsub job names must begin with a letter.

Numbers and punctuation are not allowed.

>>> qsub_sanitize_job_name('01')
'J01'
>>> qsub_sanitize_job_name('a01')
'a01'

nipype.pipeline.plugins.sge.sge_debug_print(message)

Needed for debugging on big jobs. Once this is fully vetted, it can be removed.