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

Ron Chen ron_chen_123 at yahoo.com
Mon Apr 11 17:28:06 BST 2005


http://blogs.sun.com/roller/page/hstsao/

The spacing/formating is messed up, but you can do
"view source" in the browser to see the intended
spacing.

 -Ron


--- Reuti <reuti at staff.uni-marburg.de> wrote:

> Hi,
> 
> in former times Schr?dinger 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 M?lndal
> >>>Pepparedsleden 1
> >>>S-431 83 M?lndal, 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...
> >>>
> >>> 
> >>>
>
>>>-------------------------------------------------------------
> >>
> >>-----------
> >>
>
>>>---------------------------------------------------------------------
> >>>To unsubscribe, e-mail:
> users-unsubscribe at gridengine.sunsource.net
> >>>For additional commands, e-mail:
> users-help at gridengine.sunsource.net
> >>> 
> >>>
> >>
> >>
>
>>---------------------------------------------------------------------
> >>To unsubscribe, e-mail:
> users-unsubscribe at gridengine.sunsource.net
> >>For additional commands, e-mail:
> users-help at gridengine.sunsource.net
> > 
> > 
> > 
> > 
> >
>
------------------------------------------------------------------------
> > 
> >
>
---------------------------------------------------------------------
> > To unsubscribe, e-mail:
> users-unsubscribe at gridengine.sunsource.net
> > For additional commands, e-mail:
> users-help at gridengine.sunsource.net
> 
> 
>
---------------------------------------------------------------------
> To unsubscribe, e-mail:
> users-unsubscribe at gridengine.sunsource.net
> For additional commands, e-mail:
> users-help at gridengine.sunsource.net
> 
=== message truncated ===



		
__________________________________ 
Do you Yahoo!? 
Yahoo! Small Business - Try our new resources site!
http://smallbusiness.yahoo.com/resources/ 

---------------------------------------------------------------------
To unsubscribe, e-mail: users-unsubscribe at gridengine.sunsource.net
For additional commands, e-mail: users-help at gridengine.sunsource.net




More information about the gridengine-users mailing list