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
Patches are available, but not included in a release.
2015-07-31 11:38 GMT-05:00 Alexander Vowinkel <vowinkel.alexan...@gmail.com>
> can someone tell me something about this?
> Pointing at the runner stated in the log vs. expected runner.
> 2015-07-06 18:08 GMT-05:00 Alexander Vowinkel <
>> 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
>> 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
>> , 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
Please keep all replies on the list by using "reply all"
in your mail client. To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
To search Galaxy mailing lists use the unified search at: