# Intel MPI RUNTIME ENVIRONMENT sample script for Gromacs
if [ X"$1" = X'0' ] ; then
    eval $joboption_env_0
    eval $joboption_env_1
    export RUNTIME_PBS_NODES
    export RUNTIME_PBS_PPN
fi
if [ X"$1" = X'1' ] ; then
        . /opt/gromacs-4.0/bin/GMXRC
        . /opt/intel/cce/10.1.013/bin/iccvars.sh
        . /opt/intel/impi/3.1/bin64/mpivars.sh
        export LD_LIBRARY_PATH=/opt/intel/mkl/10.0.2.018/lib/em64t:/opt/intel/cce/10.1.013/lib:$LD_LIBRARY_PATH
        export MPD_CON_EXT="`date +%s`"
        export MACHINES="/tmp/$MPD_CON_EXT.machines"
        cat $PBS_NODEFILE | uniq > $MACHINES
        NODES="`cat $MACHINES | wc -l`"
        PROCS="`cat $PBS_NODEFILE | wc -l`"

        if [ "x$RUNTIME_PBS_PPN" == "x" ]; then
                PPN=""
        else
                PPN="-ppn $RUNTIME_PBS_PPN"
        fi

        mpdboot -n $NODES -f $MACHINES -r ssh
        echo "Booting Intel MPI ring of daemons: "
        mpdtrace

        export I_MPI_DEVICE="ssm"

        export GMX_MPIRUN="mpiexec ${PPN} -n ${PROCS} -envall"
fi

if [ X"$1" = X'2' ] ; then
        . /opt/intel/impi/3.1/bin64/mpivars.sh
        mpdallexit
fi