Hi, can someone tell me something about this? Pointing at the runner stated in the log vs. expected runner.
Thanks, Alexander 2015-07-06 18:08 GMT-05:00 Alexander Vowinkel <vowinkel.alexan...@gmail.com> : > Hi, > > I have adopted /mnt/galaxy/galaxy-app/config/job_conf.xml: > I added a destination with following param: > <param id="nativeSpecification">-N1 --cpus-per-task 1 > --mem-per-cpu=4G</param> > > Galaxy service was restarted after chaning this. > Now I get the error "Unable to run job due to a misconfiguration of the > Galaxy job running system. Please contact a site administrator." when I > try to run a job. > Looking in the log gives: > > galaxy.jobs.runners.drmaa DEBUG 2015-07-06 22:50:40,187 (493) submitting file > /mnt/galaxy/tmp/job_working_directory/000/493/galaxy_493.sh >> galaxy.jobs.runners.drmaa DEBUG 2015-07-06 22:50:40,187 (493) native >> specification is: -N1 --cpus-per-task 1 --mem-per-cpu=4G >> galaxy.jobs.runners.drmaa ERROR 2015-07-06 22:50:40,187 (493) >> drmaa.Session.runJob() failed unconditionally >> Traceback (most recent call last): >> [...] >> InvalidAttributeValueException: code 14: Invalid native specification: -N1 >> --cpus-per-task 1 --mem-per-cpu=4G > > > Well. running this as galaxy user in the console with > > $ srun -N1 --cpus-per-task 1 --mem-per-cpu=4G >> /mnt/galaxy/tmp/job_working_directory/000/494/galaxy_494.sh > > > , it actually runs good. > > I was wondering if this is connected with the fact that the log states " > galaxy.jobs.runners.drmaa" and not something like galaxy.jobs.runners.slurm, > like defined in the job_conf.xml: <plugin id="slurm" type="runner" > load="galaxy.jobs.runners.slurm:SlurmJobRunner" /> > > So - What is going wrong here? Am I working on the wrong job_conf.xml? What > does galaxy do here? > > Thanks for help!Alexander > >
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