Re: [galaxy-dev] drmaa on univa grid engine

2017-04-13 Thread Marius van den Beek 
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  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.be...@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
> ---
>
>
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[galaxy-dev] drmaa on univa grid engine

2017-04-13 Thread Matthias Bernt 

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.be...@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
---



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