add lammps example

docs/examples.md

@@ -82,3 +82,17 @@ The example for this app ([files
 here](https://github.com/Azure/hpcadvisor/tree/main/examples/namd/)) is based on
 installation using the binary from NAMD official website.
 
+
+## LAMMPS
+
+Large-scale Atomic/Molecular Massively Parallel Simulator (LAMMPS) is
+a molecular dynamics simulator designed to model particles in a variety of
+scientific and engineering applications. Developed by Sandia National
+Laboratories, it is highly scalable, so one can run it on single processors or
+in parallel using message-passing techniques. LAMMPS uses spatial-decomposition
+techniques to partition the simulation domain into small 3D sub-domains, one of
+which is assigned to each processor.
+
+The example for this app ([files
+here](https://github.com/Azure/hpcadvisor/tree/main/examples/lammps/)) is based
+on installation using [EESSI](https://www.eessi.io/).

examples/lammps/appsetup_lammps.sh

@@ -0,0 +1,64 @@
+#!/usr/bin/env bash
+
+set -x
+
+APP_EXE_PATH="${AZ_BATCH_NODE_MOUNTS_DIR}/data/"
+echo "APP_EXE_PATH=$APP_EXE_PATH"
+
+function setup_data {
+  echo "Downloading data for lammps"
+  wget https://www.lammps.org/inputs/in.lj.txt
+
+}
+
+function generate_run_script {
+
+  cat <<EOF >run_app.sh
+#!/bin/bash
+
+set -x
+cd \$AZ_TASKRUN_DIR
+echo "Execution directory: \$(pwd)"
+
+source /cvmfs/software.eessi.io/versions/2023.06/init/bash
+module load LAMMPS
+which mpirun
+which lmp
+
+cp ../in.lj.txt .
+
+NP=\$((\$NODES*\$PPN))
+export UCX_NET_DEVICES=mlx5_ib0:1
+
+input_file="in.lj.txt"
+
+new_x=10
+new_y=10
+new_z=10
+
+sed -i "s/variable\s\+x\s\+index\s\+[0-9]\+/variable x index \$new_x/" \$input_file
+sed -i "s/variable\s\+y\s\+index\s\+[0-9]\+/variable y index \$new_y/" \$input_file
+sed -i "s/variable\s\+z\s\+index\s\+[0-9]\+/variable z index \$new_z/" \$input_file
+
+time mpirun -np \$NP lmp -i in.lj.txt
+
+
+###
+
+log_file="log.lammps"
+
+if grep -q "Total wall time:" "\$log_file"; then
+  echo "Simulation completed successfully."
+  exit 0
+else
+  echo "Simulation did not complete successfully."
+  exit 1
+fi
+
+EOF
+  chmod +x run_app.sh
+}
+
+cd "$APP_EXE_PATH" || exit
+setup_data
+generate_run_script

examples/lammps/plotfilterlammps.json

@@ -0,0 +1,3 @@
+{
+  "appname": "lammps"
+}