On Wed, Apr 30, 2014 at 4:20 AM, 沈维燕 <shenwiyn@gmail.com> wrote:
>
> 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

Hi Weiyan,

Yes, this fix is included in the April, 2014 stable release. However, I would strongly encourage you to use `hg clone` rather than downloading a static tarball. There have been a number of patches to the stable branch since its April release. In addition, the tarball linked would pull from the "default" branch of Galaxy, which includes unstable changesets.

--nate

>
>
>
> 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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>