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/galaxy-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-tt4657848.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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