LAMMPS Guide

LAMMPS Molecular Dynamics Simulator
Author	Sandia National Labs and Temple University
Website	http://lammps.sandia.gov
Source	Git
Category	Commandline utility
Help	manual mailing list workshops

From the LAMMPS README file:

LAMMPS is a classical molecular dynamics simulation code designed to run efficiently on parallel computers. It was developed at Sandia National Laboratories, a US Department of Energy facility, with funding from the DOE. It is an open-source code, distributed freely under the terms of the GNU Public License (GPL).

Loading the LAMMPS module

Best practise is to specify the module with the version number for programs to run consistently. To see the versions of modules on the cluster, use the module avail command:

module avail lammps

Now we can load the latest available LAMMPS module, which at the time of writing is 28Jun14:

module load lammps/28Jun14

One can avoid loading the module at each log in, by using module initadd:

$ module initadd lammps/28Jun14

Running LAMMPS

If possible, you should always first run your code in your local machine just to ensure that your code is correct. You can do it on a small dataset and a small configuration (single processor, etc.). This way you would be able to catch any errors not related to the cluster even before submitting your job.

Below we show a step by step example on how to run a simple LAMMPS simulation in the cluster. We have used one of the examples bundled with LAMMPS distribution, namely flow.

Copy your code and data to the cluster

We are assuming that you are using the terminal to copy your data. If you are using a GUI client such as [1] you should be able to do it in a visual way.

Open a terminal to connect to the cluster and create a directory for the experiment.

$ mkdir lammpstest && ls
lammpstest

Our code / data is located in the directory ~/Downloads/lammps-10Aug15/examples/flow in the local machine.

$ ls ~/Downloads/lammps-10Aug15/examples/flow
in.flow.couette  log.15May15.flow.couette.g++.1  log.15May15.flow.pois.g++.1
in.flow.pois     log.15May15.flow.couette.g++.4  log.15May15.flow.pois.g++.4

Let us copy everything in this folder to the cluster using the [2] command. Because we are using secure protocol you will be asked for your the password of your cluster account. In the snippet below remember to replace the word hronetuser with your actual account name.

$ cd ~/Downloads/lammps-10Aug15/examples
$ ls | grep flow
flow
$ scp -r flow user@login3.storrs.hpc.uconn.edu:~/lammpstest/flow
in.flow.pois                                  100% 1503     1.5KB/s   00:00    
in.flow.couette                               100% 1505     1.5KB/s   00:00    
log.15May15.flow.couette.g++.1                100% 4559     4.5KB/s   00:00    
log.15May15.flow.pois.g++.4                   100% 4561     4.5KB/s   00:00    
log.15May15.flow.pois.g++.1                   100% 4559     4.5KB/s   00:00    
log.15May15.flow.couette.g++.4                100% 4560     4.5KB/s   00:00 

The -r switch tells the scp command to copy everything recursively. You can of course selectively copy the files you need by omitting this switch. See the manual for scp for details.

Now let's make sure our files are copied to the cluster. For this we switch back to the cluster's terminal and do the following:

$ ls ~/lammpstest
flow
$ cd ~/lammpstest/flow && ls
in.flow.couette  log.15May15.flow.couette.g++.1  log.15May15.flow.pois.g++.1
in.flow.pois     log.15May15.flow.couette.g++.4  log.15May15.flow.pois.g++.4

SLURM script

SLURM is the scheduler program for our cluster. In the cluster we need to create a simple script which would tell SLURM how to run your job. For details see the SLURM Guide.

You can either create this script in the terminal using any editor such as nano, or you can create it in your local machine and use the scp command to copy it into the cluster. We can put this script in the lammpstest directory, and it would contain the following lines:

$ cd ~/lammpstest
$ cat lammps_job.sh

#!/bin/bash
#SBATCH -n 48
#SBATCH -o lammps_sim_out-%J.txt
#SBATCH -e lammps_sim_out-%J.txt
#SBATCH --mail-type=ALL
#SBATCH --mail-user=user@engr.uconn.edu
mpiexec lammps < flow/in.flow.couette

This script is telling how many processors we need as well as which files the output (and errors) should be written to. Basically, the lines starting with #SBATCH provide the switches for the [3] command, which submits a job to SLURM. Note that we have told SLURM to email us at every event for this job such as begin / queued / end / error etc.

The last line is the command that would be run as the job. It invokes the lammps module with the input ~/lammpstest/flow/in.flow.couette.

Extra Note: If you are using mpirun in your submission scripts, it is recommended to use the following command syntax:

mpirun lammps -in inputfile

The lammps documentation site mentioned this note if mpirun is being used with the < operator:

"The redirection operator “<” will not always work when running in parallel with mpirun; for those systems the -in form is required."

Submitting your job

Before you submit your job make sure that the LAMMPS module is loaded, as described at the first part of this guide. When you are ready, simple do the following:

$ sbatch < lammps_job.sh
Submitted batch job 24703

Checking output

When the job is done we would get email notifications. You can also check your job status using the sjobs command. We can check on the lammps output itself using tail:

$ tail -f lammps_sim_out.txt