Running LAMMPS on Grex

Introduction#

LAMMPS is a classical molecular dynamics code. The name stands for Large-scale Atomic / Molecular Massively Parallel Simulator. LAMMPS is distributed by Sandia National Laboratories, a US Department of Energy laboratory.

Modules#

On the Grex’s default software stack (SBEnv), LAMMPS was built using a variety of compilers and OpenMPI 4.1

To find out which versions are available, use module spider lammps

As an example of the version 2024 Aug 29 patch 1, using GCC:

module load arch/avx512 gcc/13.2.0 openmpi/4.1.6 
module load lammps/2024-08-29p1

or, another example of an older LAMMPS version using Intel OneAPI compilers:

module load arch/avx512 intel-one/2024.1 openmpi/4.1.6 
module load lammps/2021-09-29

There is a GPU version of LAMMPS on Grex that uses the KOKKOS library for GPU interface. It is available as follows:

module load cuda/12.4.1 arch/avx2 gcc/13.2.0 openmpi/4.1.6 
module load lammps/2024-08-29p1

The above LAMMPS version should be used only on GPU-enabled partitions.

It is also possible to load modules from the Alliance software stack after load CCEnv:

module purge
module load CCEnv
module load arch/avx512 
module load StdEnv/2023
module load intel/2023.2.1  openmpi/4.1.5
module load lammps-omp/20230802

Serial version#

Script example using a module from SBEnv:

Script example for LAMMPS: Serial version
run-lammps-serial-sbenv.sh
#!/bin/bash

#SBATCH --ntasks=1 
#SBATCH --cpus-per-task=1
#SBATCH --mem=1500M
#SBATCH --time=0-3:00:00
#SBATCH --job-name=Lammps-Test

# Load the modules:

module load arch/avx512 intel-one/2024.1 openmpi/4.1.6 
module load lammps/2021-09-29

echo "Starting run at: `date`"

lmp_exec=lmp
lmp_input="lammps.in"
lmp_output="lammps_lj_output.txt"

${lmp_exec} < ${lmp_input} > ${lmp_output}

echo "Program finished with exit code $? at: `date`"

Script example using a module from CCEnv:

Script example for LAMMPS: Serial version
run-lammps-serial-cc.sh
#!/bin/bash

#SBATCH --ntasks=1 
#SBATCH --cpus-per-task=1
#SBATCH --mem=1500M
#SBATCH --time=0-3:00:00
#SBATCH --job-name=Lammps-Test

# Load the modules:

module purge
module load CCEnv
module load arch/avx512
module load StdEnv/2023
module load intel/2023.2.1  openmpi/4.1.5
module load lammps-omp/20230802

echo "Starting run at: `date`"

lmp_exec=lmp
lmp_input="lammps.in"
lmp_output="lammps_lj_output.txt"

${lmp_exec} < ${lmp_input} > ${lmp_output}

echo "Program finished with exit code $? at: `date`"

MPI version#

Script example using a module from SBEnv:

Script example for LAMMPS: MPI version
run-lammps-mpi-sbenv.sh
#!/bin/bash

#SBATCH --ntasks=16 
#SBATCH --cpus-per-task=1
#SBATCH --mem-per-cpu=1500M
#SBATCH --time=0-3:00:00
#SBATCH --job-name=Lammps-Test

# Load the modules:

module load arch/avx512 gcc/13.2.0 openmpi/4.1.6 
module load lammps/2024-08-29p1

echo "Starting run at: `date`"

lmp_exec=lmp
lmp_input="lammps.in"
lmp_output="lammps_lj_output.txt"

srun ${lmp_exec} -in ${lmp_input} -log ${lmp_output}

echo "Program finished with exit code $? at: `date`"

Script example using a module from CCEnv:

Script example for LAMMPS: MPI version
run-lammps-mpi-cc.sh
#!/bin/bash

#SBATCH --ntasks=16 
#SBATCH --cpus-per-task=1
#SBATCH --mem-per-cpu=1500M
#SBATCH --time=0-3:00:00
#SBATCH --job-name=Lammps-Test

# Load the modules:

module purge
module load CCEnv
module load arch/avx512
module load StdEnv/2023
module load intel/2023.2.1  openmpi/4.1.5
module load lammps-omp/20230802

echo "Starting run at: `date`"

lmp_exec=lmp
lmp_input="lammps.in"
lmp_output="lammps_lj_output.txt"

srun ${lmp_exec} -in ${lmp_input} -log ${lmp_output}

echo "Program finished with exit code $? at: `date`"

Script example using a GPU version using KOKKOS from SBEnv:

Script example for LAMMPS: MPI version
run-lammps-mpi-sbenv.sh
#!/bin/bash

#SBATCH --ntasks=1 --partition=gpu 
#SBATCH --cpus-per-gpu=8 --gpus=1
#SBATCH --mem=15000M
#SBATCH --time=0-3:00:00
#SBATCH --job-name=Lammps-Test-GPU

# Load the modules:

module load cuda/12.4.1 arch/avx2 gcc/13.2.0 openmpi/4.1.6 
module load lammps/2024-08-29p1

echo "Starting run at: `date`"

lmp_exec=lmp
lmp_input="lammps.in"
lmp_output="lammps_lj_output.txt"

# this example uses KOKKOS GPU module, on a single GPU

srun ${lmp_exec} -in ${lmp_input} -k on g 1 -sf kk -pk kokkos newton off neigh full -log ${lmp_output}

echo "Program finished with exit code $? at: `date`"

Related links#