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
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