#!/bin/bash
#
# Script Name : psub
# Purpose : PBS batch job submission with command line input executables
#           generated with default compiler. On our system, gcc is the 
#           system default compiler. User may use "module" to choose
#           the default compiler. ( a companion psubi is written 
#           specifically for executables created with Intel compiler;
#           if intel compiler is chosen as default compiler via "module",
#           psub and psubi would be fully equivalent)
#           The problem with directly submitting a batch job thru PBS qsub
#           is the fact that qsub does not accept command line input other
#           than a run script. As a result, unless you always run the same
#           executable with same runtime and same number of processors, you
#           will inevitably have to create many runscripts to cater to 
#           different situations.
#           This script circumvent that by acting as an interface. Running of
#           this script, which accepts command line input, such as exec name,
#           number of processors, etc., and generate a temp script that 
#           include all those command line input into the script and submit 
#           it via qsub. This temp script is called "psub.USERID", where USERID
#           is the user's own ID.
# Usage:
# cootie % psub exec-name numprocs [-l walltime=xx:xx:xx ...]
#
# Examples: (examples below override the script's default of
#            30 mins walltime and per processor node ppn=1)
# cootie % psub ../../a.out 4 "-l walltime=00:45:00"
# cootie % psub ../../a.out 4 "-l walltime=00:45:00 -l nodes=2:ppn=2"
#
# The output files from using this script are:
# 1) psub.USERID -- the temp script 
# 2) psub.USERID.ennnnn -- PBS error file
# 3) psub.USERID.onnnnn -- PBS output file
# 4) psub.JOBID.out -- stdout file (output to "terminal")
#
# Author : Kadin Tseng, SCV, Boston University
# Date   : April 23, 2005

if [ $# -ge 2 ] 
then
script="psub.${USER}"
echo "#!/bin/bash" > $script
echo '#' >> $script
echo '# All lines starting with "#PBS" are PBS commands' >> $script
echo '#' >> $script
echo "# Request $2 nodes with 1 processor per node" >> $script
echo '#' >> $script
echo "#PBS -l nodes=$2:ppn=1" >> $script
echo '#' >> $script
echo '# Set wall clock time to 0 hours, 30 minutes and 0 seconds' >> $script
echo '#PBS -l walltime=00:30:00' >> $script
echo '#' >> $script
echo 'GMCONF=`/usr/local/pbs/util/mknodes`' >> $script
echo "cd \$PBS_O_WORKDIR" >> $script
echo "#PBS $3" >> $script
MPIRUN="/usr/local/IT/mpichgm-1.2.6..14b/gcc/bin/mpirun"
if [ -f mystdin ]
then
echo "$MPIRUN -machinefile \$GMCONF -np $2 $1 < mystdin > psubi.\$PBS_JOBID.out" >> $script
else
echo "$MPIRUN -machinefile \$GMCONF -np $2 $1 > psubi.\$PBS_JOBID.out" >> $script
fi
echo "exit 0" >> $script
chmod +x $script
qsub $script $3
else
  echo "Usage: psub a.out num-procs ['optional PBS parameters']"
fi