Hi Matthias, in addition to the link you posted there is also this here that looks similar: http://dev.list.galaxyproject.org/DRMAA-options-for-SGE-td4140931.html Perhaps qsub is filling in a default queue, and drmaa is not doing that? You could try adding a queue to the nativeSpecification. Good luck, Marius On 13 April 2017 at 15:02, Matthias Bernt <m.bernt@ufz.de> wrote:
Dear list,
I'm struggling to get jobs running on our cluster (UGE).
In the galaxy log I see:
galaxy.jobs.runners.drmaa DEBUG 2017-04-13 12:24:57,799 (10) submitting file /gpfs1/data/galaxy_server/galaxy-dev/database/jobs_directory /000/10/galaxy_10.sh
galaxy.jobs.runners.drmaa DEBUG 2017-04-13 12:24:57,799 (10) native specification is: -l h_rt=60 -l h_vmem=1G -pe smp 2
and I get
galaxy.jobs.runners.drmaa WARNING 2017-04-13 12:24:57,805 (10) drmaa.Session.runJob() failed, will retry: code 17: error: no suitable queues
But manual submission works:
qsub -l h_rt=60 -l h_vmem=1G -pe smp 2 /gpfs1/data/galaxy_server/gala xy-dev/database/jobs_directory/000/10/galaxy_10.sh Your job 161150 ("galaxy_10.sh") has been submitted
So I checked if I can use the drmaa library to submit using the following python script (based on the example2 included in the library):
""" #!/usr/bin/env python
from __future__ import print_function import drmaa import os
def main(): """Submit a job. Note, need file called sleeper.sh in current directory. """ s = drmaa.Session() s.initialize() print('Creating job template') jt = s.createJobTemplate() jt.remoteCommand = os.getcwd() + '/sleeper.sh' jt.args = ['42','Simon says:'] jt.joinFiles=True jt.nativeSpecification = "-l h_rt=60 -l h_vmem=1G -pe smp 2"
jobid = s.runJob(jt) print('Your job has been submitted with id ' + jobid)
print('Cleaning up') s.deleteJobTemplate(jt) s.exit()
if __name__=='__main__': main() """
This gives me the same error:
drmaa.errors.DeniedByDrmException: code 17: error: no suitable queues
So it seems to be a problem related to the drmaa python library. Unfortunately I can not try without any native specs, since time, memory and cores need to be specifies (a suitable queue is chosen automatically).
I found an earlier post with the same error (but this seemed to be caused by colons in the file name): http://dev.list.galaxyproject. org/Galaxy-with-Univa-Grid-Engine-UGE-instead-of-SGE-tt46578 48.html#a4657952
Does anyone has suggestions for me?
Best regards, Matthias
--
------------------------------------------- Matthias Bernt Bioinformatics Service Molekulare Systembiologie (MOLSYB) Helmholtz-Zentrum für Umweltforschung GmbH - UFZ/ Helmholtz Centre for Environmental Research GmbH - UFZ Permoserstraße 15, 04318 Leipzig, Germany Phone +49 341 235 482296, m.bernt@ufz.de, www.ufz.de
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