Question: Setting A Queue For Torque Submission
0
Xian Su • 10 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:
<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
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modified 5.0 years ago
by
Jennifer Hillman Jackson ♦ 25k
•
written
5.0 years ago by
Xian Su • 10
