Xian and I were able to resolve this on IRC, the problem is is that no default queue is
specified in the PBS client (intentionally) and the `-q` param was improperly handled in
the pbs job runner (it expected <param id=“destination”> instead). This has been
fixed in the stable branch in changeset 51b4282dce3a.
On Nov 14, 2013, at 4:50 PM, Jennifer Jackson <jen(a)bx.psu.edu> wrote:
Hello, I am going to move your question over to the
galaxt-dev(a)bx.psu.edu mailing list to give it better visibility to the development/local
install community. http://wiki.galaxyproject.org/MailingLists#The_lists
I didn't find it over here already, but apologies if double posted. Also, since I
don't know the best answer, will let others jump in!
On 11/14/13 6:35 AM, Xian Su wrote:
> 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
> 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
> 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"?>
> <plugins workers="4">
> <plugin id="local" type="runner"
> <plugin id="pbs" type="runner"
> <handlers default="handlers">
> <handler id="main" tags="handlers"/>
> <destinations default="pbs">
> <destination id="local" runner="local"/>
> <destination id="pbs" runner="pbs"
> <param id="-q">M30</param>
> <tool id="main" handler="main"
> Thank you in advance for any help.
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