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, re-use 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.