On Fri, Apr 17, 2015 at 3:26 PM, Beginner TI <ruiwang.sz(a)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">(a)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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