Skip to content
This repository has been archived by the owner on Feb 17, 2020. It is now read-only.

pm production run crash when job exists in slurm #195

Open
b97pla opened this issue Feb 20, 2013 · 1 comment
Open

pm production run crash when job exists in slurm #195

b97pla opened this issue Feb 20, 2013 · 1 comment

Comments

@b97pla
Copy link

b97pla commented Feb 20, 2013

If a job is running in slurm when doing pm production run, the script crashes with the following output:

'''2013-02-20 11:55 (INFO): Running analysis defined by config file /proj/a2010002/nobackup/illumina/M.Uhlen_12_06/P282_137C_index5/130213_BH07P4ADXX/P282_137C_index5-bcbb-config.yaml
2013-02-20 11:55 (INFO): job is queued and active
2013-02-20 11:55 (WARNING): job is queued and active; please terminate job before proceeding
2013-02-20 11:55 (WARNING): Not running job
2013-02-20 11:55 (INFO): Running analysis defined by config file /proj/a2010002/nobackup/illumina/M.Uhlen_12_06/P282_116B_index11/130213_BH07P4ADXX/P282_116B_index11-bcbb-config.yaml
Traceback (most recent call last):
File "/bubo/home/h27/funk_001/.virtualenvs/master/bin/pm", line 5, in
pkg_resources.run_script('scilifelab==0.3.0dev', 'pm')
File "/bubo/home/h27/funk_001/.venvburrito/lib/python/distribute-0.6.34-py2.7.egg/pkg_resources.py", line 505, in run_script
self.require(requires)[0].run_script(script_name, ns)
File "/bubo/home/h27/funk_001/.venvburrito/lib/python/distribute-0.6.34-py2.7.egg/pkg_resources.py", line 1245, in run_script
execfile(script_filename, namespace, namespace)
File "/bubo/home/h27/funk_001/.virtualenvs/master/lib/python2.7/site-packages/scilifelab-0.3.0dev-py2.7.egg/EGG-INFO/scripts/pm", line 46, in
app.run()
File "/bubo/home/h27/funk_001/.virtualenvs/master/lib/python2.7/site-packages/cement-2.0.2-py2.7.egg/cement/core/foundation.py", line 451, in run
self.controller._dispatch()
File "/bubo/home/h27/funk_001/.virtualenvs/master/lib/python2.7/site-packages/scilifelab-0.3.0dev-py2.7.egg/scilifelab/pm/core/controller.py", line 52, in _dispatch
getattr(self, func['label'])()
File "/bubo/home/h27/funk_001/.virtualenvs/master/lib/python2.7/site-packages/scilifelab-0.3.0dev-py2.7.egg/scilifelab/pm/core/bcbio.py", line 90, in run
if self.app.cmd.monitor(work_dir=os.path.dirname(run_info)):
File "/bubo/home/h27/funk_001/.virtualenvs/master/lib/python2.7/site-packages/scilifelab-0.3.0dev-py2.7.egg/scilifelab/pm/ext/ext_distributed.py", line 73, in monitor
return self._monitor_job(idfile, **{'workingDirectory':work_dir})
File "/bubo/home/h27/funk_001/.virtualenvs/master/lib/python2.7/site-packages/scilifelab-0.3.0dev-py2.7.egg/scilifelab/pm/ext/ext_distributed.py", line 98, in _monitor_job
s.initialize()
File "build/bdist.macosx-10.4-x86_64/egg/drmaa/init.py", line 274, in initialize

File "build/bdist.macosx-10.4-x86_64/egg/drmaa/wrappers.py", line 59, in init
File "build/bdist.macosx-10.4-x86_64/egg/drmaa/errors.py", line 90, in error_check
drmaa.errors.AlreadyActiveSessionException: code 11: DRMAA session already exist.'''

@percyfal
Copy link

@b97pla Well, it should fail if there is a job present, but not crash.

Sign up for free to subscribe to this conversation on GitHub. Already have an account? Sign in.
Labels
None yet
Projects
None yet
Development

No branches or pull requests

2 participants