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FIX: TypeError bug for PBS process communication in python3 #1987

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May 3, 2017
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FIX: TypeError bug for PBS process communication in python3 #1987

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12 changes: 5 additions & 7 deletions nipype/pipeline/plugins/pbs.py
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Original file line number Diff line number Diff line change
Expand Up @@ -6,7 +6,6 @@

import os
from time import sleep
import subprocess

from ...interfaces.base import CommandLine
from .base import (SGELikeBatchManagerBase, logger, iflogger, logging)
Expand Down Expand Up @@ -46,13 +45,12 @@ def __init__(self, **kwargs):
super(PBSPlugin, self).__init__(template, **kwargs)

def _is_pending(self, taskid):
# subprocess.Popen requires taskid to be a string
proc = subprocess.Popen(["qstat", str(taskid)],
stdout=subprocess.PIPE,
stderr=subprocess.PIPE)
_, e = proc.communicate()
result = CommandLine('qstat {}'.format(taskid),
environ=dict(os.environ),
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I think you can remove this line if you want to use the default environment

terminal_output='allatonce',
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I'm not sure 'allatonce' generates both stdout and stderr in the runtime object. Have you checked?

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allatonce doesn't stream but still separates stdout and stderr

ignore_exception=True).run()
errmsg = 'Unknown Job Id' # %s' % taskid
return errmsg not in e
return errmsg not in result.runtime.stderr

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