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.alexander@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.alexander@gmail.com>:

Hi,

I have adopted /mnt/galaxy/galaxy-app/config/job_conf.xml:

I added a destination with following 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