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FIX: PBS plugin fix #2344

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Merged
merged 6 commits into from
Jan 19, 2018
Merged

FIX: PBS plugin fix #2344

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ccf2b41
Fixed PBS plugin to work with the Donders Torque cluster
achetverikov Dec 15, 2017
b10062f
Fixed small bug in plugins/base.py: string inf was supposed to be a n…
achetverikov Dec 15, 2017
1fb84b1
Merge branch 'master' into pbs_plugin_fix
achetverikov Jan 18, 2018
6c9f69f
Added myself to .zenodo.json
achetverikov Jan 18, 2018
5836856
Merged .zenodo.json conflict
achetverikov Jan 18, 2018
eff7b43
Changed PBS plugin output to file_split
achetverikov Jan 18, 2018
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5 changes: 5 additions & 0 deletions .zenodo.json
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Original file line number Diff line number Diff line change
Expand Up @@ -568,6 +568,11 @@
"affiliation": "University College London",
"name": "Mancini, Matteo",
"orcid": "0000-0001-7194-4568"
},
{
"affiliation": "Donders Institute for Brain, Cognition and Behavior, Center for Cognitive Neuroimaging",
"name": "Chetverikov, Andrey",
"orcid": "0000-0003-2767-6310"
}
],
"keywords": [
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2 changes: 1 addition & 1 deletion nipype/pipeline/plugins/base.py
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Expand Up @@ -284,7 +284,7 @@ def _send_procs_to_workers(self, updatehash=False, graph=None):

if len(jobids) > 0:
# send all available jobs
logger.info('Pending[%d] Submitting[%d] jobs Slots[%d]',
logger.info('Pending[%d] Submitting[%d] jobs Slots[%s]',
num_jobs, len(jobids[:slots]), slots or 'inf')

for jobid in jobids[:slots]:
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20 changes: 11 additions & 9 deletions nipype/pipeline/plugins/pbs.py
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Expand Up @@ -49,18 +49,20 @@ def __init__(self, **kwargs):
super(PBSPlugin, self).__init__(template, **kwargs)

def _is_pending(self, taskid):
result = CommandLine(
'qstat {}'.format(taskid),
environ=dict(os.environ),
terminal_output='allatonce',
resource_monitor=False,
ignore_exception=True).run()
errmsg = 'Unknown Job Id' # %s' % taskid
result = CommandLine('qstat -f {}'.format(taskid),
environ=dict(os.environ),
terminal_output='file_split',
resource_monitor=False,
ignore_exception=True).run()

stdout = result.runtime.stdout
stderr = result.runtime.stderr
errmsg = 'Unknown Job Id'
success = 'Job has finished'
if success in e: # Fix for my PBS
if (success in stderr) or ('job_state = C' in stdout):
return False
else:
return errmsg not in e
return errmsg not in stderr

def _submit_batchtask(self, scriptfile, node):
cmd = CommandLine(
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