LAMMPS installations on Tetralith & Sigma

LAMMPS is a classical molecular dynamics code, and an acronym for Large-scale Atomic/Molecular Massively Parallel Simulator. For the features of this code and applications, please visit lammps.sandia.gov/doc/Intro_features.html and lammps.sandia.gov/pictures.html.

Official homepage: lammps.sandia.gov

LAMMPS manual and tutorials are also available from the official homepage.

Naming scheme for binaries and library packages

Note that lmp_tetralith, liblammps_tetralith.a and liblammps_tetralith.so also work on Sigma despite their names.

How to run

Load the LAMMPS module corresponding to the version you want to use, e.g.

module load LAMMPS/22Aug18-nsc1-intel-2018b-eb

It prepends the LAMMPS bin directory, with lmp and the equivalent lmp_tetralith binaries, to the PATH. It also launches two environmental variables. One, LMPEXEC, to the LAMMPS executable and one, LAMMPS_LIB, to the directory with the static and dynamic LAMMPS libraries.

LAMMPS can be built with a lot of packages and external libraries. To see what was included in the build of the loaded LAMMPS module,

lmp -h

To launch the desired binary. For example,

mpprun lmp -echo screen -in in.file

Use the LAMMPS_LIB variable to link with the LAMMPS library. For example,

LDFLAGS=-L${LAMMPS_LIB}

Example batch script

A minimum batch script for running LAMMPS:

#!/bin/bash
#SBATCH -n 64
#SBATCH -t 4:00:00
#SBATCH -J jobname
#SBATCH -A SNIC-xxx-yyy

module load LAMMPS/22Aug18-nsc1-intel-2018b-eb
mpprun lmp -log out.file -in in.file

(Note that you should at least edit the jobname, -J, and account, -A, before submitting but probably also the number of tasks (MPI ranks), -n, and requested walltime, -t.)

Remark

Due to the frequent updates of LAMMPS, we will build specific LAMMPS versions upon request. If you need any specific version, please contact NSC Support with your requirements (LAMMPS version, specific packages, external libraries, etc.).