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