[GE users] problem of qdel and parallel running in SGE

jenny lulh at genomics.org.cn
Fri Aug 20 10:05:46 BST 2010


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i met a problem: after reinstall the compute nodes, the jobs on the compute nodes didn't disappear.

# qstat -u "*" | grep 0-29
 127153 0.85000 yri.yh.170 a  r     08/11/2010 03:23:37 all.q at compute-0-29.local
        1
 127179 0.85000 yri.yh.194 a  r     08/11/2010 03:50:37 all.q at compute-0-29.local
        1
 215868 0.26138 chr2.sh    a   r     08/19/2010 09:08:45 all.q at compute-0-29.local
        1
 216640 0.26069 job1.sh  b       r     08/19/2010 10:54:45 all.q at compute-0-29.local
        1


2010-08-20
________________________________
???  Jenny_Lu
????
?????????
lulh at genomics.org.cn<mailto:lulh at genomics.org.cn>
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Mobile:15986782583  62583
________________________________
???? reuti
????? 2010-08-18  15:40:03
???? users
???
??? Re: [GE users] problem of qdel and parallel running in SGE
Hi,
Am 18.08.2010 um 07:05 schrieb mrostaee:
> sometimes after qdel a job, process of that job will be running. it means that qdel hasn't done completely (kill of all deleted job's processes not done).
>
> If i want diagnose this situation and solve problem automatically, how can i do it?
>
> Is there any script for this problem?
this sounds as if you don't have a so called Tight Integration of your parallel jobs into SGE:
http://gridengine.info/2005/09/19/parallel-environments-pes-loose-vs-tight-integration
There are some Howto's for most common parallel libraries which are also mentioned in the above link:
http://gridengine.sunsource.net/howto/howto.html#Tight%20Integration%20of%20Parallel%20Libraries
-- Reuti
> Thx
>
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