[GE users] qsub acting up and using 99% CPU.

Reuti reuti at staff.uni-marburg.de
Mon Apr 11 16:44:54 BST 2005


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Hi,

in former times Schrödinger had their own queuing system built into 
their programs (at least I remember something for Jaguar). Is this 
para_glide also working with SGE now? I found the short explanation, 
that "-HOST test28" should be the LSF master server (besides their 
GridMP support) in para_glide.

Cheers - Reuti

Stefan.O.Nordlander at astrazeneca.com wrote:
> Ok, so it wasn't a standard issue then. dang..
> 
> 
> This is what I've done:
> 
> 1. Added an entry for my cluster in /opt/Schrodinger/schrodinger.hosts:
> name: test28
> tmpdir: /usr/tmp
> host: master
> queue: SGE
> processors: 28
> 
> 2. Configured the files in /opt/Schrodinger/queues/SGE/:
> QPATH=/opt/az/hpc/SunONEGridEngine/current/bin/lx24-x86/
> QSUB=qsub
> QDEL=qdel
> QSTAT=qstat
> 
> etc..
> 
> 3. Started the job with:
> # $SCHRODINGER/para_glide -i molsdock.inp -n 2 -HOST test28
> Which in turn calls a wrapper script called submit which ...:
> 
> # ...
> # Submit job
> $QSUB -S /bin/sh $* $script > $qsubout
> # ...
> 
> And this is the result:
> 
> # top (on on the master):
> PID   USER PRI  NI  SIZE  RSS SHARE STAT %CPU %MEM   TIME CPU COMMAND
> 31590 me   25   0  1496 1496  1264  R    96.9  0.0   0:29   0 qsub
> 
> # ps -ef | grep qsub
> me    2552  2544  0 12:47 pts/7    00:00:00 qsub -S /bin/sh
> /home/me/.schrodinger/.jobdb/master-0-425a55d7.batch
> 
> (With an strace as described below.)
> 
> If I kill off this job and resubmit it manually with:
> 
> # qsub -S /bin/sh /home/me/.schrodinger/.jobdb/master-0-425a55d7.batch
> It starts ok on a node!
> 
> I guess this is a problem with the inner workings of this application and
> not a SGE issue.
> 
> 
> /Stefan
> 
> 
>>-----Original Message-----
>>From: Stephan Grell - Sun Germany - SSG - Software Engineer
>>[mailto:stephan.grell at sun.com]
>>Sent: den 11 april 2005 11:06
>>To: users at gridengine.sunsource.net
>>Subject: Re: [GE users] qsub acting up and using 99% CPU.
>>
>>
>>Hi,
>>
>>more information would be nice. Which version of SGE? Which 
>>OS? What was
>>the qsub command?
>>
>>Stephan
>>
>>Stefan.O.Nordlander at astrazeneca.com wrote:
>>
>>
>>>Hi,
>>>
>>>I'm hoping this is a no brainer like "erum, well you forgot 
>>
>>to turn on the
>>
>>>main auxiliary power relay.."
>>>
>>>I'm trying to run para_glide through SGE and I think I have 
>>
>>everything set
>>
>>>up ok. But when I submit a job qsub starts and uses 99.9% 
>>
>>cpu. An strace
>>
>>>shows me this:
>>>
>>>select(1, [0], [0], NULL, {1, 0})       = 1 (out [0], left {1, 0})
>>>gettimeofday({1113205289, 87082}, NULL) = 0
>>>gettimeofday({1113205289, 87121}, NULL) = 0
>>>gettimeofday({1113205289, 87159}, NULL) = 0
>>>gettimeofday({1113205289, 87197}, NULL) = 0
>>>select(1, [0], [0], NULL, {1, 0})       = 1 (out [0], left {1, 0})
>>>gettimeofday({1113205289, 87547}, NULL) = 0
>>>gettimeofday({1113205289, 87585}, NULL) = 0
>>>gettimeofday({1113205289, 87624}, NULL) = 0
>>>gettimeofday({1113205289, 87662}, NULL) = 0
>>>select(1, [0], [0], NULL, {1, 0})       = 1 (out [0], left {1, 0})
>>>gettimeofday({1113205289, 88012}, NULL) = 0
>>>gettimeofday({1113205289, 88051}, NULL) = 0
>>>gettimeofday({1113205289, 88089}, NULL) = 0
>>>gettimeofday({1113205289, 88127}, NULL) = 0
>>>...
>>>...
>>>...
>>>
>>>What's going on?
>>>(More details about the job is avalible if necessary.)
>>>
>>>
>>>Stefan Nordlander - Linux System Manager
>>>________________________________________________
>>>AstraZeneca R&D Mölndal
>>>Pepparedsleden 1
>>>S-431 83 Mölndal, Sweden
>>>Phone:    +46 (0)31 706 49 14
>>>Email:    Stefan.O.Nordlander at astrazeneca.com
>>>________________________________________________
>>>Unix _is_ user friendly, its just picky about who its friends are...
>>>
>>> 
>>>
>>>-------------------------------------------------------------
>>
>>-----------
>>
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>>>
>>
>>
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> 
> 
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