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 <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!
> Galaxy team
> 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 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 email@example.com
>> 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"
>> load="galaxy.jobs.runners.pbs:PBSJobRunner" workers="2"/>
>> <handlers default="handlers">
>> <handler id="main" tags="handlers"/>
>> <destinations default="pbs">
>> <destination id="local" runner="local"/>
>> <destination id="pbs" runner="pbs" tags="mycluster">
>> <param id="-q">M30</param>
>> <tool id="main" handler="main" destination="pbs"/>
>> Thank you in advance for any help.
>> The Galaxy User list should be used for the discussion of
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> Jennifer Hillman-Jackson
> Please keep all replies on the list by using "reply all"
> in your mail client. To manage your subscriptions to this
> and other Galaxy lists, please use the interface at:
> To search Galaxy mailing lists use the unified search at:
Please keep all replies on the list by using "reply all"
in your mail client. To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
To search Galaxy mailing lists use the unified search at: