#!/bin/tcsh

# mpiBLAST SGE submission script v0.9 by Joseph Landman
# copyright 2003 Scalable Informatics LLC
# http://scalableinformatics.com
#
# This code is licensed for use under the
# Artistic license.  See http://www.perl.com/language/misc/Artistic.html
# for specific details.
#
# Usage:
#	qsub -pe mpich 8 sge_mpiblast [options for blastall]
#
# to run with 8 CPUs, use any number you would like.
#

#$ -S /bin/tcsh

#### Change these as needed

# compute node temporary directory path
setenv TMP /tmp
#
#
# output file
setenv OUT ~/$NSLOTS-way.run
#
#
# path to mpirun and mpiblast
setenv MPIRUN /opt/mpich/ethernet/gcc/bin/mpirun
setenv MPIBLAST /opt/apps/mpiblast/bin/mpiblast
#
#
# path to mpiBLAST config file
setenv MPIBLAST_CONFIG /opt/apps/mpiblast/etc/mpiblast.conf
#
#
#####  End of configuration section
#####  Ordinarily you would not have to change anything below
#####  this line, though you might need to create a stage out
#####  section at the end.


setenv WORKDIR $TMP/`hostname`/`id -u`
mkdir -p $WORKDIR
#cd $WORKDIR
# only use the above is you also stage in the data to the right directory.

echo "running with NCPUs= " $NSLOTS > $OUT
echo -n "in directory " >>  $OUT
pwd >>  $OUT
echo -n "on machine " >>  $OUT
uname -a  >>  $OUT
echo -n "run started at " >>  $OUT
date >>  $OUT 
echo "running mpiBLAST with options " $* >> $OUT
$MPIRUN -v -np $NSLOTS \
              -machinefile $TMPDIR/machines  \
              $MPIBLAST \
              --config-file=$MPIBLAST_CONFIG \
              $* >>& $OUT 
echo -n " run finished at " >> $OUT
date >> $OUT