sge-mdrun

#!/bin/bash

###############################
# Job name and log/err output #
###############################
#$ -S /bin/bash
#$ -V
#$ -N c8ntf2.qlsmd.min.8
#$ -r n
#$ -e $JOB_ID.err
#$ -o $JOB_ID.log
#$ -q UI-HM
#$ -cwd

#########################
# Important run details #
#########################
###$ -m abe
###$ -M ryan-p-daly@uiowa.edu
#$ -pe 24cpn 24
###$ -l 
###$ -ckpt user
###$ -l h_rt=8:00:00

########################
# Load modules and set #
# up the environment   #
########################
source ~/.bash_profile intel-composer_xe_2015.3.187

# Tell everyone what nodes are being used
if [ -f "${PE_HOSTFILE}" ]; then
    echo "Nodes:"
    cat "${PE_HOSTFILE}"
else
    echo "WARNING: No host file found."
fi

idx="8"
jobid="${JOB_ID}"
jobidin=""
while getopts "i:j:k:h" opt; do
    case ${opt} in
        h)
            echo "Usage: $(basename $0) [-h] [-i index] [-j jobid] [-k jobid_in]"
            exit 0
            ;;
        i)
            idx="${OPTARG}"
            ;;
        j)
            jobid="${OPTARG}"
            ;;
        k)
            jobidin="${OPTARG}"
            ;;
        ?|*)
            echo "No such option available."
            ;;
    esac
done
pref="${idx:+${idx}_}"
suff="${jobid:+_${jobid}}"
suffin="${jobidin:+_${jobidin}}"

# Check for presence of all required files
if [ ! -f ${pref}topol.top ]; then
    exit 127 # Unsigned byte => -1
fi
if [ ! -f ${pref}step.mdp ]; then
    exit 126 # Unsigned byte => -2
fi
if [ ! -f ${pref}confin.gro ]; then
    exit 125 # Unsigned byte => -3
fi

# Identify locations of binaries needed
GMXBIN="/opt/gromacs/4.6.5/bin"
GROMPP="${GMXBIN}/grompp_d"
MDRUN="${GMXBIN}/mdrun_d"

# Set the call string
MPIRUN_GROMPP=""
MPIARGS_GROMPP=""
EXENAME_GROMPP="${GROMPP}"
EXEARGS_GROMPP="-o ${pref}topol${suff}.tpr \
    -p ${pref}topol${suffin}.top \
    -f ${pref}step${suffin}.mdp \
    -c ${pref}confin${suffin}.gro \
    -po ${pref}mdout${suff}.mdp \
    -pp ${pref}processed${suff}.top \
    -maxwarn 100"
if [ -f "${pref}trajin${suffin}.trr" ]; then
    EXEARGS_GROMPP="${EXEARGS_GROMPP} -t ${pref}trajin${suffin}.trr"
fi
if [ -f "${pref}index${suffin}.ndx" ]; then
    EXEARGS_GROMPP="${EXEARGS_GROMPP} -n ${pref}index${suffin}.ndx"
fi

# Copy files to suffix them with ${JOB_ID}
for name in topol.top step.mdp confin.gro index.ndx trajin.trr
do
    srce="${pref}${name}"
    srcf="${srce}${suffin}"
    if [ -f "${srcf}" ]; then
        targ="$(echo "${srce}" | sed 's/\(^.*\)\.\([^\.\t]\+\)/\1'${suff}'\.\2/g')"
        echo "Copying $(printf "%16s" ${srcf}) => $(printf "%16s" ${targ})" >&2
        cp "${srcf}" "${targ}"
    fi
done

# Set the call string for first step
CALL_STRING_GROMPP="${MPIRUN_GROMPP} ${MPIARGS_GROMPP} ${EXENAME_GROMPP} ${EXEARGS_GROMPP}"

# Output start and finish times
echo "Running in $(pwd)"
echo "Calling:"
echo ${CALL_STRING_GROMPP}
echo "Started at $(date)"
eval ${CALL_STRING_GROMPP}
echo "Finished ${EXENAME_GROMPP} at $(date)"

# Set up location of mpirun
MPIRUN_MDRUN=""
MPIARGS_MDRUN=""
EXENAME_MDRUN="${MDRUN}"
EXEARGS_MDRUN="-v -c ${pref}confout${suff}.gro \
   -e ${pref}ener${suff}.edr \
   -g ${pref}md${suff}.log \
   -s ${pref}topol${suff}.tpr \
   -o ${pref}traj${suff}.trr \
   -x ${pref}traj${suff}.xtc \
   -cpo ${pref}state${suff}.cpt \
   -mtx ${pref}nm${suff}.mtx"

# If an index file of the appropriate index and jobid shows up
# then you can at least load it
if [ -f "${pref}index${suff}.ndx" ]; then
    EXEARGS_MDRUN="${EXEARGS_MDRUN} -n ${pref}index${suff}.ndx"
fi

# Important if using -ckpt in SGE or equivalent in any other queue
# Variable RESTARTED is available for SGE as far as I know; no guarantee
# for any other queue manager; writes a checkpoint every 5 minutes here
if [ $RESTARTED -eq 1 ] && [ -f "${pref}state${suff}.cpt" ]; then
    EXEARGS_MDRUN="${EXEARGS_MDRUN} -cpi state.cpt -cpt 5 -append"
fi

# Set the call string
CALL_STRING_MDRUN="${MPIRUN_MDRUN} ${MPIARGS_MDRUN} ${EXENAME_MDRUN} ${EXEARGS_MDRUN}"

# Output start and finish times
echo "Running in $(pwd)"
echo "Calling:"
echo ${CALL_STRING_MDRUN}
echo "Started at $(date)"
eval ${CALL_STRING_MDRUN}
echo "Finished ${EXENAME_MDRUN} at $(date)"

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