[galaxy-dev] drmaa on univa grid engine

13 Apr 2017

      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-...

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

Sitz der Gesellschaft/Registered Office: Leipzig
Registergericht/Registration Office: Amtsgericht Leipzig
Handelsregister Nr./Trade Register Nr.: B 4703
Vorsitzender des Aufsichtsrats/Chairman of the Supervisory Board: 
MinDirig Wilfried Kraus
Wissenschaftlicher Geschäftsführer/Scientific Managing Director:
Prof. Dr. Dr. h.c. Georg Teutsch
Administrative Geschäftsführerin/ Administrative Managing Director:
Prof. Dr. Heike Graßmann
-------------------------------------------