On Fri, Apr 17, 2015 at 3:26 PM, Beginner TI <ruiwang.sz@gmail.com> wrote:
Hi,
I'm trying to enable the capability to submit jobs to a pbs cluster, however I am quite confused by the documentation. I don't know where I could specify the pbs server. I saw the following on the page:
https://wiki.galaxyproject.org/Admin/Config/Performance/Cluster
1 <plugins> 2 <plugin id="pbs" type="runner" load="galaxy.jobs.runners.pbs:PBSJobRunner"/> 3 </plugins> 4 <destinations default="pbs_default"> 5 <destination id="pbs_default" runner="pbs"/> 6 <destination id="other_cluster" runner="pbs"> 7 <param id="destination">@other.cluster</param> 8 </destination> 9 <destination id="long_jobs" runner="pbs"> 10 <param id="Resource_List">walltime=72:00:00,nodes=1:ppn=8</param> 11 <param id="-p">128</param> 12 </destination> 13 </destinations>
is this <param id="destination"> the place you specify where your pbs/torque server? and the syntax is to prepend a '@' to the server name? for example, should a most basic config look like:
<plugins> <plugin id="pbs" type="runner" load="galaxy.jobs.runners.pbs:PBSJobRunner"> </plugins> <destinations default="pbs"> <destination id="pbs" runner="pbs" > <param id="destination">@pbs_server_full_name</param> <param id="Resource_List">walltime=72:00:00,nodes=1:ppn=8</param> <param id="-q">myqueue</param> </destination> <destinations>
I searched online and to my surprise I didn't find any useful information, or any working sample...please give me a hand guys!
I think destination just maps to the qsub -q parameter - so whatever you would fill in there on the command line you can just place in the destination argument. I really am unsure if the @ is needed - but can you try to experiment on the command line and find the right target with qsub and then just fill that value into job_conf.xml? -John
Thanks! Rui
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