2013-08-08 22:58 GMT+08:00 Nate Coraor <nate@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"?>
> 
> <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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