LAMMPS

Introduction

LAMMPS is a Molecular Dynamics Simulator.

Web Page

Official website

Job Scripts

The value of $SLURM_NTASKS is worked out by SLURM and so changing the value of –nodes is reflected automatically. This script sends to the compute partition.

This script assumes a 10 hour run time, but adapt as required.

#!/bin/bash -l
#SBATCH --time=10:00:00
#SBATCH --job-name={some_lammps_job}
#SBATCH --account={replace_this_with_your_project_account}
#SBATCH --partition=compute

module purge
module load lammps/version/flavour
mpirun -np $SLURM_NTASKS lmp_mpi < {some_input_file}

Where version is replaced by a version name, e.g. 17Nov16 and a flavour with a flavour version, e.g. 2.

and submit with

sbatch --partition=compute --ntasks={some_number} myjob.sh

where {some_number} is the required level of parallelism. SLURM will select the number of nodes required for the job based on the number of cores asked for (1 rank to 1 core) and the number of cores on the nodes in that partition.

Versions

17Nov16

Flavours

1

Architecture

x86_64

Group
module load site-local
Build Details

MPI build, lmp_mpi.

Compiled with:

Usage
module load lammps/17Nov16/1

NB set

OMP_NUM_THREADS=1

to avoid mixed-mode parallelism.

Example Job Scripts

None yet.

Status

Untested.

2

Architecture

x86_64

Group
module load site-local
Build Details

This uses an outdated MLNX_OFED and should not be used.

MPI build, lmp_mpi.

Compiled with:

Compiled with the following additional libaries:

  • asphere
  • body
  • class2
  • colloid
  • coreshell
  • dipole
  • granular
  • kokkos
  • kspace
  • manybody
  • mc
  • misc
  • molecule
  • mpiio
  • peri
  • qeq
  • replica
  • rigid
  • shock
  • snap
  • srd
  • user-cg-cmm
  • user-diffraction
  • user-dpd
  • user-drude
  • user-eff
  • user-fep
  • user-intel
  • user-lb
  • user-manifold
  • user-mgpt
  • user-molfile
  • user-nc-dump
  • user-phonon
  • user-qtb
  • user-reaxc
  • user-smtbq
  • user-sph
  • user-tally
Usage
module load lammps/17Nov16/2

NB: set

OMP_NUM_THREADS=1

to avoid mixed-mode parallelism.

Example Job Scripts

None yet.

Status

Passes most of the test cases that are relevant to the above packages and for which the data is available.

5

Architecture

x86_64

Group
module load site-local

This is strictly experimental.

Build Details

MPI build, lmp_mpi.

Compiled with:

Compiled with the following additional libaries:

  • asphere
  • body
  • class2
  • colloid
  • coreshell
  • dipole
  • granular
  • kokkos
  • kspace
  • manybody
  • mc
  • misc
  • molecule
  • mpiio
  • peri
  • qeq
  • replica
  • rigid
  • shock
  • snap
  • srd
  • user-cg-cmm
  • user-diffraction
  • user-dpd
  • user-drude
  • user-eff
  • user-fep
  • user-intel
  • user-lb
  • user-manifold
  • user-mgpt
  • user-molfile
  • user-nc-dump
  • user-phonon
  • user-qtb
  • user-reaxc
  • user-smtbq
  • user-sph
  • user-tally
Usage
module load lammps/17Nov16/5

NB: to avoid mixed mode parallelism set

export OMP_NUM_THREADS=1
Example Job Scripts

None yet.

Status

Untested.