Running LAMMPS on Grex

Note: Lammps is not available yet under the new environment SBEnv.

Introduction#

LAMMPS is a classical molecular dynamics code. The name stands for Large-scale Atomic / Molecular Massively Parallel Simulator.

Modules#

As fo now, there is no LAMMPS version added to the new environment. We will add them when users request a specific version. With that said, it is possible to use LAMMPS 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 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 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`"

Related links#