closed, moved to galaxy-dev@bx.psu.edu
On 11/14/13 6:35 AM, Xian Su wrote:
Greetings

I'm having a hard time getting job submission to work via torque. Posted below is the relevant part of my universe file and job_conf.xml.

The main cause comes from our torque server requiring a queue to be requested. I can submit jobs just fine via job .sub files via command line using qsub -q M30

Running jobs via webgui results in the following:
galaxy.jobs.runners.pbs WARNING 2013-11-14 13:54:23,722 (28) pbs_submit failed (try 5/5), PBS error 15039: Route rejected by all destinations
galaxy.jobs.runners.pbs ERROR 2013-11-14 13:54:25,724 (28) All attempts to submit job failed

On the torque server's pbs logs, I see the corresponding
11/14/2013 13:54:23;0080;PBS_Server.66159;Req;req_reject;Reject reply code=15039(No default queue specified MSG=requested queue not found), aux=0, type=QueueJob, from xians@podmt1-100-62.novalocal

In my universe_wsgi.ini, I'm currently using the settings:
start_job_runners = pbs
default_cluster_job_runner = pbs:///-q M30 -l nodes=1:ppn=12/
^I mainly have no idea how to find the correct syntax for this pbs:///

But when I comment out default_cluster_job_runner and instead uncomment the line for the following job conf, I get the same error:
<?xml version="1.0"?>
<job_conf>
    <plugins workers="4">
        <plugin id="local" type="runner" load="galaxy.jobs.runners.local:LocalJobRunner"/>
        <plugin id="pbs" type="runner" load="galaxy.jobs.runners.pbs:PBSJobRunner" workers="2"/>
    </plugins>
    <handlers default="handlers">
        <handler id="main" tags="handlers"/>
    </handlers>
    <destinations default="pbs">
        <destination id="local" runner="local"/>
        <destination id="pbs" runner="pbs" tags="mycluster">
            <param id="Resource_List">walltime=72:00:00,nodes=1:ppn=12</param>
            <param id="-q">M30</param>
        </destination>
    </destinations>
    <tools>
        <tool id="main" handler="main" destination="pbs"/>
    </tools>
    <limits>
    </limits>
</job_conf>

Thank you in advance for any help.

Regards,
Xian


___________________________________________________________
The Galaxy User list should be used for the discussion of
Galaxy analysis and other features on the public server
at usegalaxy.org.  Please keep all replies on the list by
using "reply all" in your mail client.  For discussion of
local Galaxy instances and the Galaxy source code, please
use the Galaxy Development list:

  http://lists.bx.psu.edu/listinfo/galaxy-dev

To manage your subscriptions to this and other Galaxy lists,
please use the interface at:

  http://lists.bx.psu.edu/

To search Galaxy mailing lists use the unified search at:

  http://galaxyproject.org/search/mailinglists/

-- 
Jennifer Hillman-Jackson
http://galaxyproject.org