Hi,
There is at least one issue
<plugin id="drmaa" type="runner"
load="galaxy.jobs.runners.drmaa:DRMAAJobRunner"/>
<param
id="drmaa_library_path">/media/vol1/gridengine/lib/linux-x64/libdrmaa.so</param>
<plugin id="drmaa" type="runner"
load="galaxy.jobs.runners.drmaa:DRMAAJobRunner">
<param
id="drmaa_library_path">/media/vol1/gridengine/lib/linux-x64/libdrmaa.so</param>
</plugin>
I don’t know if it’s THE issue :/
Gildas
----------------------------------------------------------------------------------------------------------------------------
Gildas Le Corguillé - Bioinformatician/Bioanalyste
Plateform ABiMS (Analyses and Bioinformatics for Marine Science):
http://abims.sb-roscoff.fr <http://abims.sb-roscoff.fr/>
Co-leader of the IFB Core Cluster:
https://www.france-bioinformatique.fr/en/cluster
<https://www.france-bioinformatique.fr/fr/cluster>
Member of the Workflow4Metabolomics project: http://workflow4metabolomics.org
<http://workflow4metabolomics.org/>
Station Biologique de Roscoff
Sorbonne Université / CNRS
Place Georges Teissier 29680 Roscoff FRANCE
tel: +33 2 98 29 23 81
----------------------------------------------------------------------------------------------------------------------------
> Le 28 avr. 2020 à 17:32, Luc Cornet <luc.cor...@uliege.be> a écrit :
>
> Hi galaxy community,
>
> I am quite new in galaxy but I would like to install a local instance on our
> cluster (SGE).
> I have a problem with DRMAA :
>
> When I activate the --daemon mode, the job don't pass in the queue system but
> with no Damon, it pass (the log below)
> The second problem is that $GALAXY_SLOTS is not define, Could it be related
> to the problem below ?
> Someone can help me, please ? (available at :
> https://help.galaxyproject.org/t/job-submission-failed-when-daemon/351)
>
> Thanks,
> Luc
>
> ## with no daemon
> galaxy.jobs.runners.drmaa DEBUG 2020-04-28 17:07:21,424 [p:32191,w:1,m:0]
> [DRMAARunner.work_thread-1] (47) submitting file
> /media/vol2/home/galaxy/galaxy/database/jobs_directory/000/47/galaxy_47.sh
> galaxy.jobs.runners.drmaa DEBUG 2020-04-28 17:07:21,425 [p:32191,w:1,m:0]
> [DRMAARunner.work_thread-1] (47) native specification is: -q cassava.q -pe
> snode 10
> galaxy.jobs.runners.drmaa INFO 2020-04-28 17:07:21,440 [p:32191,w:1,m:0]
> [DRMAARunner.work_thread-1] (47) queued as 1007701
> galaxy.jobs DEBUG 2020-04-28 17:07:21,441 [p:32191,w:1,m:0]
> [DRMAARunner.work_thread-1] (47) Persisting job destination (destination id:
> big_jobs)
> galaxy.jobs.runners.drmaa DEBUG 2020-04-28 17:07:22,042 [p:32191,w:1,m:0]
> [DRMAARunner.monitor_thread] (47/1007701) state change: job is queued and
> active
>
> ## with daemon
> galaxy.jobs.runners.drmaa DEBUG 2020-04-28 15:39:16,138 [p:26779,w:1,m:0]
> [DRMAARunner.work_thread-1] (45) submitting file
> /media/vol2/home/galaxy/galaxy/database/jobs_directory/000/45/galaxy_45.sh
> galaxy.jobs.runners.drmaa DEBUG 2020-04-28 15:39:16,138 [p:26779,w:1,m:0]
> [DRMAARunner.work_thread-1] (45) native specification is: -q cassava.q -pe
> snode 10
>
> ## job_conf
>
> <?xml version="1.0"?>
> <!-- A sample job config that explicitly configures job running the way it
> is
> configured by default (if there is no explicit config). -->
> <job_conf>
> <plugins>
> <plugin id="local" type="runner"
> load="galaxy.jobs.runners.local:LocalJobRunner" workers="4"/>
> <plugin id="drmaa" type="runner"
> load="galaxy.jobs.runners.drmaa:DRMAAJobRunner"/>
> <param
> id="drmaa_library_path">/media/vol1/gridengine/lib/linux-x64/libdrmaa.so</param>
> </plugins>
> <destinations default="local">
> <destination id="local" runner="local"/>
> <destination id="big_jobs" runner="drmaa">
> <param id="nativeSpecification">-q cassava.q -pe snode
> 10</param>
> </destination>
> </destinations>
> <tools>
> <tool id="maker" destination="big_jobs" />
> <tool id="metaspades" destination="big_jobs" />
> </tools>
> </job_conf>
>
>
>
> ------------
> Luc Cornet, PhD
> Bio-informatician
> Mycology and Aerobiology
> Sciensano
> ___________________________________________________________
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