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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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2 changes: 1 addition & 1 deletion nipype/pipeline/plugins/base.py
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Original file line number Diff line number Diff line change
Expand Up @@ -281,7 +281,7 @@ 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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10 changes: 6 additions & 4 deletions nipype/pipeline/plugins/pbs.py
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Expand Up @@ -47,18 +47,20 @@ def __init__(self, **kwargs):
super(PBSPlugin, self).__init__(template, **kwargs)

def _is_pending(self, taskid):
result = CommandLine('qstat {}'.format(taskid),
result = CommandLine('qstat -f {}'.format(taskid),
environ=dict(os.environ),
terminal_output='allatonce',
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@oesteban oesteban Dec 22, 2017 •
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I would suggest changing terminal_output to 'file_split'

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@oesteban why? & where can I read about file_split, it seems to be not documented yet (http://nipype.readthedocs.io/en/latest/interfaces/generated/interfaces.base/core.html#parameters)?

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@achetverikov you can read about terminal outputs here
http://nipype.readthedocs.io/en/latest/devel/interface_specs.html#controlling-outputs-to-terminal

resource_monitor=False,
ignore_exception=True).run()

stdout = result.runtime.stdout
stderr = result.runtime.stderr
errmsg = 'Unknown Job Id' # %s' % taskid
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('qsub', environ=dict(os.environ),
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