LAMMPS Molecular Dynamics Simulator
LAMMPS is a software for molecular dynamics with focus on material modelling. It can run on single or multiple nodes, in parallel taking advantage of MPI.
License
LAMMPS is a open-source software released under the license GPLv2.
Installation
LAMMPS is available on the cluster either as a module or as a Singularity container.
Singularity containers are already available at standard directory:
ls /ceph/hpc/software/containers/singularity/images/lammps-*
Output:
/ceph/hpc/software/containers/singularity/images/lammps-10Feb2020-gpu.sif
/ceph/hpc/software/containers/singularity/images/lammps-allegro-gpu.sif
/ceph/hpc/software/containers/singularity/images/lammps-allegro.sif
/ceph/hpc/software/containers/singularity/images/lammps-gpu-octp.sif
/ceph/hpc/software/containers/singularity/images/lammps-octp2.sif
/ceph/hpc/software/containers/singularity/images/lammps-octp.sif
/ceph/hpc/software/containers/singularity/images/lammps-stable-29Oct2020-all-pkg.sif
/ceph/hpc/software/containers/singularity/images/lammps-stable-29Oct2020-extra.sif
/ceph/hpc/software/containers/singularity/images/lammps-stable-29Oct2020.sif
Availaible modules:
module avail LAMMPS
...
module --ignore-cache avail LAMMPS
Output:
-------------------------------------------------------- /cvmfs/sling.si/modules/el7/modules/all --------------------------------------------------------
LAMMPS/3Mar2020-foss-2020a-Python-3.8.2-kokkos LAMMPS/23Jun2022-foss-2021b-kokkos-CUDA-11.4.1 LAMMPS/23Jun2022-foss-2021b-kokkos (D)
Slurm
Example of SBATCH script
Example via command srun
#!/bin/bash
#SBATCH --job-name LAMMPS
#SBATCH --partition=cpu
#SBATCH --time 04:00:00
#SBATCH --nodes=1
#SBATCH --ntasks=128
#SBATCH --mem-per-cpu=2000MB
#SBATCH --cpus-per-task=1
#SBATCH --error=%j.err
#SBATCH --output=%j.out
module load LAMMPS/23Jun2022-foss-2021b-kokkos
srun --mpi=pmix_v3 -n $SLURM_NTASKS lmp -in <input_file>
Example with Singularity container:
#!/bin/bash
#SBATCH --job-name LAMMPS
#SBATCH --partition=cpu
#SBATCH --time=01:00:00
#SBATCH --mem-per-cpu=2G
#SBATCH --ntasks=128
#SBATCH --nodes=1
#SBATCH --cpus-per-task=2
#SBATCH --error=%j.err
#SBATCH --output=%j.out
export PMIX_MCA_gds=hash
srun --mpi=pmix_v3 singularity exec /ceph/hpc/software/containers/singularity/images/lammps-stable-29Oct2020.sif lmp -in <input_file>