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GCG and NQS

Jack Leunissen jackl at caos.kun.nl
Thu Jan 11 14:58:49 EST 1996


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...

Good luck,
Jack

     +--------------------------------------------------------------+
       Jack A.M. Leunissen, PhD | CAOS/CAMM Center
       Email: jackl at caos.kun.nl | University of Nijmegen
       Tel. : +31 24 365 22 48  | Toernooiveld 1
       Fax  : +31 24 365 29 77  | 6525 ED Nijmegen, The Netherlands
                                | URL=http://www.caos.kun.nl/
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