From 0d7b0c9507cf23e6aa3f40da5df1c32b0f83a47c Mon Sep 17 00:00:00 2001 From: mathiasg Date: Tue, 4 Sep 2018 15:28:24 -0400 Subject: [PATCH 1/2] FIX: catch exception if jobid not found in squeue call --- nipype/pipeline/plugins/slurm.py | 18 +++++++++++------- 1 file changed, 11 insertions(+), 7 deletions(-) diff --git a/nipype/pipeline/plugins/slurm.py b/nipype/pipeline/plugins/slurm.py index 285d2d6584..b916d82848 100644 --- a/nipype/pipeline/plugins/slurm.py +++ b/nipype/pipeline/plugins/slurm.py @@ -62,13 +62,17 @@ def __init__(self, **kwargs): super(SLURMPlugin, self).__init__(self._template, **kwargs) def _is_pending(self, taskid): - # subprocess.Popen requires taskid to be a string - res = CommandLine( - 'squeue', - args=' '.join(['-j', '%s' % taskid]), - resource_monitor=False, - terminal_output='allatonce').run() - return res.runtime.stdout.find(str(taskid)) > -1 + try: + res = CommandLine( + 'squeue', + args=' '.join(['-j', '%s' % taskid]), + resource_monitor=False, + terminal_output='allatonce').run() + return res.runtime.stdout.find(str(taskid)) > -1 + except Exception as e: + if 'Invalid job id' not in str(e): + raise(e) + return False def _submit_batchtask(self, scriptfile, node): """ From 5653828fd20b373a7f969ee3f031469945aabcec Mon Sep 17 00:00:00 2001 From: mathiasg Date: Fri, 14 Sep 2018 11:00:31 -0400 Subject: [PATCH 2/2] FIX: make exception explicit --- nipype/pipeline/plugins/slurm.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/nipype/pipeline/plugins/slurm.py b/nipype/pipeline/plugins/slurm.py index b916d82848..e27c05be04 100644 --- a/nipype/pipeline/plugins/slurm.py +++ b/nipype/pipeline/plugins/slurm.py @@ -69,7 +69,7 @@ def _is_pending(self, taskid): resource_monitor=False, terminal_output='allatonce').run() return res.runtime.stdout.find(str(taskid)) > -1 - except Exception as e: + except RuntimeError as e: if 'Invalid job id' not in str(e): raise(e) return False