egs-submit.sh

#!/bin/bash

#####################################################################################
#
#  usage:
#
#  egs-submit <app> <template> [ pid ]
#  
#  app:      EGSnrc app to invoke
#  template: input file with "@" placeholders
#  pid:      optional, pid of job after which to queue
#
#####################################################################################

# base name of template file
template=$2
basename=${template%.*}

# job dependency for chaining
job=""
if [ $# -gt 2 ]; then
    job=$3
fi

# qsub parameters
app=$1
pegs="700icru"
queue="short"
batch="pbsdsh"
cores=16

# egsinp parameters (to be replaced in template)
ncase=100000
ecut=0.512

# submit loop
for pcut in 001 002 005 010 020 050 100; do

    # set egsinp file base name
    egsinp=${basename}_@${pcut}
    printf "\n$egsinp\n"

    # generate egsinp input file: 
    # process template through sed to replace parameters on the fly
    printf "generating: ${egsinp}.egsinp\n"
    ( set -x
    cat $template   | sed s/@ncase/${ncase}/g \
                    | sed s/@pcut/${pcut}/g \
                    | sed s/@ecut/${ecut}/g \
                    > ${egsinp}.egsinp
    )

    # job dependency string: start this one after $job
    if [ -n "$job" ]; then
        dependstr="-W depend=afterany:${job}"
    else
        dependstr=""
    fi

    # submit job and grab job number (for next loop)
    job=$( set -x; $HEN_HOUSE/scripts/run_user_code_batch ${app} ${egsinp} ${pegs} ${queue} batch=${batch} p=${cores} $dependstr )
    printf "submitted: $job\n"
    job=${job%%.*}

done
printf "\n"