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MRG: fix _is_pending checks #429

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Merged
merged 3 commits into from
Jul 31, 2012
Merged

MRG: fix _is_pending checks #429

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fb236fb
fix: refined pbs to directly use subprocess instead of CommandLine
satra Jul 16, 2012
d5620ff
fix: check for pbs
satra Jul 19, 2012
b1774f9
fix: changed sge to use subprocess directly
satra Jul 19, 2012
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17 changes: 7 additions & 10 deletions nipype/pipeline/plugins/pbs.py
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Original file line number Diff line number Diff line change
Expand Up @@ -3,6 +3,7 @@

import os
from time import sleep
import subprocess

from .base import (SGELikeBatchManagerBase, logger, iflogger, logging)

Expand Down Expand Up @@ -35,16 +36,12 @@ def __init__(self, **kwargs):
super(PBSPlugin, self).__init__(template, **kwargs)

def _is_pending(self, taskid):
cmd = CommandLine('qstat')
cmd.inputs.args = '%s' % taskid
# check pbs task
oldlevel = iflogger.level
iflogger.setLevel(logging.getLevelName('CRITICAL'))
result = cmd.run(ignore_exception=True)
iflogger.setLevel(oldlevel)
if 'Unknown Job Id' in result.runtime.stderr:
return False
return True
proc = subprocess.Popen(["qstat", taskid],
stdout=subprocess.PIPE,
stderr=subprocess.PIPE)
_, e = proc.communicate()
errmsg = 'Unknown Job Id' # %s' % taskid
return errmsg not in e

def _submit_batchtask(self, scriptfile, node):
cmd = CommandLine('qsub', environ=os.environ.data)
Expand Down
18 changes: 7 additions & 11 deletions nipype/pipeline/plugins/sge.py
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Original file line number Diff line number Diff line change
Expand Up @@ -2,12 +2,13 @@
"""

import os
import subprocess
from time import sleep

from .base import (SGELikeBatchManagerBase, logger, iflogger, logging)

from nipype.interfaces.base import CommandLine

from time import sleep

class SGEPlugin(SGELikeBatchManagerBase):
"""Execute using SGE (OGE not tested)
Expand Down Expand Up @@ -36,16 +37,11 @@ def __init__(self, **kwargs):
super(SGEPlugin, self).__init__(template, **kwargs)

def _is_pending(self, taskid):
cmd = CommandLine('qstat')
cmd.inputs.args = '-j %d' % taskid
# check sge task
oldlevel = iflogger.level
iflogger.setLevel(logging.getLevelName('CRITICAL'))
result = cmd.run(ignore_exception=True)
iflogger.setLevel(oldlevel)
if result.runtime.stdout.startswith('='):
return True
return False
proc = subprocess.Popen(["qstat", '-j', taskid],
stdout=subprocess.PIPE,
stderr=subprocess.PIPE)
o, _ = proc.communicate()
return o.startswith('=')

def _submit_batchtask(self, scriptfile, node):
cmd = CommandLine('qsub', environ=os.environ.data)
Expand Down