Setting a queue for torque submission
Hello, I am going to move your question over to the galaxt-dev@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_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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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 <jen@bx.psu.edu> wrote:
Hello, I am going to move your question over to the galaxt-dev@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_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
___________________________________________________________ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using "reply all" in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list:
http://lists.bx.psu.edu/listinfo/galaxy-dev
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:
-- Jennifer Hillman-Jackson
http://galaxyproject.org ___________________________________________________________ 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: http://lists.bx.psu.edu/
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participants (2)
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Jennifer Jackson -
Nate Coraor