I finally found out that this native specification is NOT about the native parameters of slurm. It comes from the DRMA-"wrapper" of slurm: http://apps.man.poznan.pl/trac/slurm-drmaa/wiki/WikiStart#Nativespecification And this does not support mem-per-cpu. Which is a huge restriction.
The logger seems to print drmaa because it is the base class of the SlurmRunner. Anybody stumbled upon this before? A way would be to have a slurm runner that uses native calls instead of drmaa. Pros/Cons? Any opinions on this topic? Or solutions to get the mem-per-cpu option? I read, that this is criticised by some people from the slurm-drmaa community too. Patches are available, but not included in a release. Best, Alexander 2015-07-31 11:38 GMT-05:00 Alexander Vowinkel <vowinkel.alexan...@gmail.com> : > 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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