Hi Nate,
>From your previous email,Job deletion in the pbs runner will be fixed in
the next stable release Galaxy.So whether this bug has been fixed in the
version of Galaxy(
https://bitbucket.org/galaxy/galaxy-dist/get/3b3365a39194.zip)?Thank you
very much for your help.

Regards,weiyan


2013-08-08 22:58 GMT+08:00 Nate Coraor <n...@bx.psu.edu>:

> On Aug 7, 2013, at 9:23 PM, shenwiyn wrote:
>
> > Yes,and I also have the same confuse about that.Actually when I set
> server:<id> in the universe_wsgi.ini as follows for a try,my Galaxy doesn't
> work with Cluster,if I remove server:<id>,it work .
>
> Hi Shenwiyn,
>
> Are you starting all of the servers that you have defined in
> universe_wsgi.ini?  If using run.sh, setting GALAXY_RUN_ALL in the
> environment will do this for you:
>
>     http://wiki.galaxyproject.org/Admin/Config/Performance/Scaling
>
> > [server:node01]
> > use = egg:Paste#http
> > port = 8080
> > host = 0.0.0.0
> > use_threadpool = true
> > threadpool_workers = 5
> > This is my job_conf.xml :
> > <?xml version="1.0"?>
> > <job_conf>
> >     <plugins workers="4">
> >         <plugin id="local" type="runner"
> load="galaxy.jobs.runners.local:LocalJobRunner" workers="4"/>
> >         <plugin id="pbs" type="runner"
> load="galaxy.jobs.runners.pbs:PBSJobRunner" workers="8"/>
> >     </plugins>
> >     <handlers default="batch">
> >         <handler id="node01" tags="batch"/>
> >         <handler id="node02" tags="batch"/>
> >     </handlers>
> >     <destinations default="regularjobs">
> >         <destination id="local" runner="local"/>
> >         <destination id="regularjobs" runner="pbs" tags="cluster">
> >             <param
> id="Resource_List">walltime=24:00:00,nodes=1:ppn=4,mem=10G</param>
> >             <param
> id="galaxy_external_runjob_script">scripts/drmaa_external_runner.py</param>
> >             <param
> id="galaxy_external_killjob_script">scripts/drmaa_external_killer.py</param>
> >             <param
> id="galaxy_external_chown_script">scripts/external_chown_script.py</param>
> >         </destination>
> >    </destinations>
> > </job_conf>
>
> The galaxy_external_* options are only supported with the drmaa plugin,
> and actually only belong in the univese_wsgi.ini for the moment, they have
> not been migrated to the new-style job configuration.  They should also
> only be used if you are attempting to set up "run jobs as the real user"
> job running capabilities.
>
> > Further more when I want to kill my jobs  by clicking
> <Catch(08-08-09-12-39).jpg> in galaxy web,the job keeps on running in my
> background.I do not know how to fix this.
> > Any help on this would be grateful.Thank you very much.
>
> Job deletion in the pbs runner was recently broken, but a fix for this bug
> will be part of the next stable release (on Monday).
>
> --nate
>
> >
> > shenwiyn
> >
> > From: Jurgens de Bruin
> > Date: 2013-08-07 19:55
> > To: galaxy-dev
> > Subject: [galaxy-dev] Help with cluster setup
> > Hi,
> >
> > This is my first Galaxy installation setup so apologies for stupid
> questions. I am setting up Galaxy on a Cluster running Torque as the
> resource manager. I am working through the documentation but I am unclear
> on some things:
> >
> > Firstly I am unable to find : start_job_runners within the
> universe_wsgi.ini and I dont want to just add this anywhere - any help on
> this would be create.
> >
> > Further more this is my job_conf.xml :
> >
> > <?xml version="1.0"?>
> > <!-- A sample job config that explicitly configures job running the way
> it is configured by default (if there is no explicit config). -->
> > <job_conf>
> >     <plugins>
> >         <plugin id="hpc" type="runner"
> load="galaxy.jobs.runners.drmaa:DRMAAJobRunner" workers="4"/>
> >     </plugins>
> >     <handlers>
> >   <!-- Additional job handlers - the id should match the name of a
> >              [server:<id>] in universe_wsgi.ini.
> >         <handler id="cn01"/>
> >         <handler id="cn02"/>
> >     </handlers>
> >     <destinations>
> >         <destination id="hpc" runner="drmaa"/>
> >     </destinations>
> > </job_conf>
> >
> >
> > Does this look meaning full, further more where to I set the additional
> server:<id>
> > in the universe_wsgi.ini.
> >
> > As background the cluster has 13 compute nodes and a shared storage
> array that can be accessed by all nodes in the cluster.
> >
> >
> > Thanks again
> >
> >
> >
> > --
> > Regards/Groete/Mit freundlichen Grüßen/recuerdos/meilleures salutations/
> > distinti saluti/siong/duì yú/привет
> >
> > Jurgens de Bruin
> > ___________________________________________________________
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>
>
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