[galaxy-dev] Re: Daemon mode fail job submission

28 Apr 2020

      Re,

Thanks for the correction.
Unfortunately, it was not the issue.

Luc,

##job_conf

<?xml version="1.0"?>
<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>
      </plugin>
   </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

----- Mail original -----
De: "Gildas Le Corguillé" <lecorguille@sb-roscoff.fr>
À: "Luc Cornet" <luc.cornet@uliege.be>
Cc: galaxy-dev@lists.galaxyproject.org
Envoyé: Mardi 28 Avril 2020 18:13:58
Objet: Re: [galaxy-dev] Daemon mode fail job submission

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.cornet@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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