LAMMPS¶

LAMMPS is a large scale classical molecular dynamics code, and stands for Large-scale Atomic/Molecular Massively Parallel Simulator. LAMMPS has potentials for soft materials (biomolecules, polymers), solid-state materials (metals, semiconductors) and coarse-grained or mesoscopic systems. It can be used to model atoms or, more generically, as a parallel particle simulator at the atomic, meso, or continuum scale.

How to Access LAMMPS¶

NERSC uses modules to manage access to software. To use the default version of LAMMPS, type:

module load lammps

Using LAMMPS on Cori¶

There are two ways of running LAMMPS on Cori: submitting a batch job, or running interactively in an interactive batch session.

#!/bin/bash
#SBATCH -J test_lammps
#SBATCH -C haswell
#SBATCH -q debug
#SBATCH -N 2
#SBATCH -t 30:00
#SBATCH -o test_lammps.o%j

module load lammps

# LAMMPS supports 2 different ways of reading inputs files

srun -n 64 -c 2 --cpu-bind=cores lmp_cori < test.in
srun -n 64 -c 2 --cpu-bind=cores lmp_cori -in test.in

#!/bin/bash
#SBATCH -J test_lammps
#SBATCH -C knl
#SBATCH -q debug
#SBATCH -N 2
#SBATCH -t 30:00
#SBATCH -o test_lammps.o%j

module load lammps

# LAMMPS supports 2 different ways of reading inputs files

srun -n 136 -c 2 --cpu-bind=cores lmp_cori < test.in
srun -n 136 -c 2 --cpu-bind=cores lmp_cori -in test.in

These job scripts request two nodes in the debug partition, and run for up to 30 minutes. The first example runs 64 MPI processes across 64 cores on 2 nodes of Cori Haswell. The second example runs 136 MPI processes across 136 cores on 2 nodes of Cori KNL.

Then submit the job script using the sbatch command, e.g., assuming the job script name is test_lammps.slurm:

sbatch test_lammps.slurm

Official LAMMPS documentation and support¶

• LAMMPS Online Manual