add lammps

apps/lammps/install_lammps.sh

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+#!/bin/bash
+sudo yum install -y epel-release
+sudo yum install -y lammps
+

apps/lammps/readme.md

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+## Install and run LAMMPS Benchmarks
+
+## Prerequisites
+
+Cluster is built with the desired configuration for networking, storage, compute etc. You can see the tutorial or examples folder in this repo for how to set this up.
+
+Dependencies for binary version:
+
+* None
+
+NOTE: Update the path to the lammps installer storageendpoint, sasurl and license server in $azhpc_dir/apps/lammps/install_lammps.sh
+
+First copy the apps directory to the cluster in a shared directory.  The `azhpc-scp` can be used to do this:
+
+```
+azhpc-scp -u hpcuser -r $azhpc_dir/apps/. hpcuser@headnode:/apps
+```
+
+> Alternatively you can checkout the azurehpc repository but you will need to update the paths according to where you put it.
+
+## Installation
+
+```
+azhpc-run -u hpcuser -n "headnode compute" /apps/lammps/install_lammps.sh  
+
+```
+
+## Connect to the headnode
+
+```
+azhpc-connect -u hpcuser headnode
+```
+
+## Running
+
+NOTE: Update the path to the lammps benchmark storageendpoint, saskey and license server in $azhpc_dir/apps/lammps/run_lammps_intelmpi.sh
+
+Now, you can run as follows:
+
+```
+qsub -l select=2:ncpus=15:mpiprocs=15,place=scatter:excl /apps/lammps/run_lammps_intelmpi.sh
+
+```

apps/lammps/run_lammps_intelmpi.sh

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+#!/bin/bash
+DATA_DIR=/data
+CORES=`cat $PBS_NODEFILE | wc -l`
+PPN=`cat $PBS_NODEFILE | uniq -c | head -1 | awk '{ print $1 }'`
+MPI_HOSTFILE=$PBS_NODEFILE
+
+export lammps_case=in.lj
+echo "downloading case ${lammps_case}..."
+
+wget  "https://lammps.sandia.gov/inputs/${lammps_case}.txt" -O ${DATA_DIR}/${lammps_case}
+
+source /opt/intel/impi/*/bin64/mpivars.sh
+export MPI_ROOT=$I_MPI_ROOT
+export I_MPI_FABRICS=shm:dapl
+export I_MPI_DAPL_PROVIDER=ofa-v2-ib0
+export I_MPI_DYNAMIC_CONNECTION=0
+export I_MPI_FALLBACK_DEVICE=0
+export OMP_NUM_THREADS=$CORES
+
+echo "Running LAMMPS Benchmark case : [${lammps_case}] on ${CORES} cores"
+mpirun -np $CORES -hostfile $MPI_HOSTFILE -ppn $PPN lmp -in ${DATA_DIR}/${lammps_case}