I finally found out that this native specification is NOT about the native
parameters of slurm.
It comes from the DRMA-"wrapper" of slurm:
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

Anybody stumbled upon this before?
A way would be to have a slurm runner that uses native calls instead of
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.


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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