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 > > ___________________________________________________________ > > Please keep all replies on the list by using "reply all" > > in your mail client. To manage your subscriptions to this > > and other Galaxy lists, please use the interface at: > > http://lists.bx.psu.edu/ > > > > To search Galaxy mailing lists use the unified search at: > > http://galaxyproject.org/search/mailinglists/ > >
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