LAMMPS
LAMMPS (Molecular Dynamics Simulator) is a classical molecular dynamics code with a focus on materials modeling. It's an acronym for Large-scale Atomic/Molecular Massively Parallel Simulator.
Using LAMMPS in SLURM batch jobs
(Command Line Interface)
Test LAMMPS
Load the modules
[user@umbrella]$ module purge
[user@umbrella]$ module load LAMMPS/2Aug2023_update2-foss-2023a-kokkos
Check commandline version of LAMMPS
[user@umbrella]$ lmp < /dev/null
LAMMPS (2 Aug 2023 - Update 2)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
using 1 OpenMP thread(s) per MPI task
Total wall time: 0:00:00
LAMMPS SLURM sbatch jobscript example using Shared Memory
#!/bin/bash
#SBATCH --job-name=test_lammps
#SBATCH --output=test_lammps-%j.log
#SBATCH --partition=tue.default.q
#SBATCH --nodes=1
#SBATCH --ntasks=1
#SBATCH --cpus-per-task=4
#SBATCH --mem-per-cpu=2gb
#SBATCH --time=00:05:00
module purge
module load LAMMPS/2Aug2023_update2-foss-2023a-kokkos
export OMP_NUM_THREADS=${SLURM_CPUS_PER_TASK}
lmp < in.friction
LAMMPS SLURM sbatch jobscript example using MPI
#!/bin/bash
#SBATCH --job-name=test_lammps
#SBATCH --output=test_lammps-%j.log
#SBATCH --partition=tue.default.q
#SBATCH --nodes=1
#SBATCH --ntasks=4
#SBATCH --cpus-per-task=1
#SBATCH --mem-per-cpu=2gb
#SBATCH --time=00:05:00
module purge
module load LAMMPS/2Aug2023_update2-foss-2023a-kokkos
mpirun lmp < in.friction
LAMMPS SLURM sbatch jobscript example using Shared Memory and MPI
#!/bin/bash
#SBATCH --job-name=test_lammps
#SBATCH --output=test_lammps-%j.log
#SBATCH --partition=tue.default.q
#SBATCH --nodes=1
#SBATCH --ntasks=4
#SBATCH --cpus-per-task=2
#SBATCH --mem-per-cpu=2gb
#SBATCH --time=00:05:00
module purge
module load LAMMPS/2Aug2023_update2-foss-2023a-kokkos
export OMP_NUM_THREADS=${SLURM_CPUS_PER_TASK}
mpirun lmp < in.friction