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GCG and NQS

Heikki Lehv=?iso-8859-1?Q?=E4slaiho Heikki.Lehvaslaiho at csc.fi
Mon Jan 15 06:38:57 EST 1996


Jack Leunissen wrote:
> 
> Andrew Fant wrote:
> >
> > Has anyone ever configured GCG to use NQS as the batch mechanism for long
> > sequence searches and alignments under GCG?  Unix batch is pretty much useless
> > for any sort of serious load balancing and scheduling, and I am in the
> > process of setting up NQS or some decendent thereof to handle scheduling
> > on our local cluster.  I would like to use it for long GCG runs as well,
> > if anyone can make any suggestions as to how to do this.
> 
> In the file "sitequeues" I have the GCGSubmitCommand changed into:
> 
> GCGSubmitCommand "qsub -eo -r gcg -q medium"
> 
> which send the output of any "-batch" option to the medium queue, gives it
> the name "gcg", and collects both standard and error output in the same log-
> file.
> To make sure that the user can start a batch from within any subdirectory,
> i.e. to direct the batch queue to his directory, put the following line in
> the file "etc/prologue":
> 
> cd $QSUB_WORKDIR
> 
> which does a ch-dir to the directory the user submitted the job in. That's
> about all...

Andrew and Jack,

Thanks for bringing up the subject. For some time now I've been intending to 
do something to GCG batch jobs at our site. I have now NQE load balancing running 
between two IRIXs.

Setting it up went like Jack said except getting the cd command to work.
It was necessary to add an option to qsub (-la gcg) to get a tag for jobs coming 
from GCG package and then add into a system startup file (/etc/tchs.login at our 
site) the following lines:


   if ( "$CSCENVIRONMENT" == "NQSBATCH" ) then
         echo "*** NQS Batch Job ***"
         date
         if ( $?NQSATTR ) then
           if ( "$NQSATTR" == "gcg" ) then       # For GCG job submit
             cd $QSUB_WORKDIR
           endif
         endif
   endif

This is a more general way of doing things and makes it easy to use NQS/NQE in 
different programs. This was done by our system manager Kirsti Lounamaa.

       -Heikki
-- 

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    _/  _/  _/  Heikki Lehväslaiho  <Heikki.Lehvaslaiho at CSC.FI>
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