Hi Ido Tamir, I have the same question too. I set "megablast" as "long_jobs" for the test,when I cancel my megablast job in Galaxy history before it finishs,it still work in my background.The drmaa_external_killer.py seems doesn't work.I don't know where is the problem,and hope someone can help me . a) In my advanced example I have:
<destination id="long_jobs" runner="pbs" tags="cluster"> <param id="Resource_List">walltime=72:00:00,nodes=2:ppn=8,mem=16G</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> <tools> <tool id="ucsc_tablebrowser" destination="regularjobs"/> <tool id="megablast_wrapper" destination="long_jobs"/> </tools>
b)In my background,I get the "qstat" result : Job id Name User Time Use S Queue ------------------------- ---------------- --------------- -------- - ----- 46.server ...n@genomics.cn galaxy 00:00:00 R batch
shenwiyn
From: Ido Tamir Date: 2013-07-23 21:53 To: galaxy-dev@lists.bx.psu.edu Subject: [galaxy-dev] job_conf.xml questions Hi, I work myself through the job_conf.xml and have a question:
a) In your advanced example you have:
<destination id="remote_cluster" runner="drmaa" tags="longjobs"/> <destination id="real_user_cluster" runner="drmaa"> <!-- TODO: The real user options should maybe not be considered runner params. --> <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>
Does this mean that remote_cluster jobs can not be killed unless I add the 3 scripts to this destination? Or does this have to do with the "run jobs as real user" that I don't need currently. I am using the galaxy user for all jobs for the moment?
To phrase this differently: Do I need these three scripts?
b) Can I set a wall time limit for only for my local runners?
like: <destination id="local" runner="local"/> <param id="Resource_List">walltime=72:00:00</param> </destination>
When I set it in limits, will it work for local runners and then I have to override it in every destination?
thank you very much, ido
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