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.
Sample Batch Script to Run LAMMPS on Cori Haswell
#!/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
Sample Batch Script to Run LAMMPS on Cori KNL
#!/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¶
Tip
If after the checking the above you believe there is an issue with the NERSC module file a ticket with our help desk