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.
--nate
On Nov 14, 2013, at 4:50 PM, Jennifer Jackson j...@bx.psu.edu wrote:
Hello, I am going to move your question over to the galaxt-...@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!
Best,
Jen
Galaxy team
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_Listwalltime=72:00:00,nodes=1:ppn=12/param
param id=-qM30/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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Jennifer Hillman-Jackson
http://galaxyproject.org
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