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.