Over the past two weeks we have experienced Oakely login node crashes potentially caused by a Lustre bug.


The Large-scale Atomic/Molecular Massively Parallel Simulator (LAMMPS) is a classical molecular dynamics code designed for high-performance simulation of large atomistic systems.  LAMMPS generally scales well on OSC platforms, provides a variety of modeling techniques, and offers GPU accelerated computation.

Availability & Restrictions

LAMMPS is available to all OSC users without restriction.

The following versions of LAMMPS are available on OSC systems:

Version Glenn Oakley RUBY
Oct06 X    
Jul07 X    
Jan08 X    
Apr08 X    
Sep09 X    
Mar10 X    
Jun10 X    
Aug10* X    
Oct10 X    
Mar11* X    
Jun11 X    
Jan12 X    
Feb12   X  
May12   X  
Feb14   X  
Sep14   X X



To use LAMMPS, run the following command to first set up your environment:

module load lammps

To see other available versions, run the following command:

module avail

To see information on the packages and executables for a particular installation, run the module help command, for example on Oakley:

module help lammps/01Feb14


Once a module is loaded, LAMMPS can be run with the following command:

lammps < input.file

Batch Usage

Sample batch scripts and LAMMPS input files are available here:


Below is a sample batch script for the Glenn Cluster. It asks for 16 processors and 10 hours of walltime. If the job goes beyond 10 hours, the job would be terminated.

#PBS -N chain  
#PBS -l nodes=2:ppn=8  
#PBS -l walltime=10:00:00  
#PBS -S /bin/bash  
#PBS -j oe  
module load lammps  
pbsdcp chain.in $TMPDIR  
cd $TMPDIR  
lammps < chain.in  
pbsdcp -g '*' $PBS_O_WORKDIR

GPU Usage

On the Glenn and Oakley OSC clusters, LAMMPS can run on GPU's.  See the sample scripts for details.  The following text is specific to the Glenn cluster and demonstrates using GPU's to speed up certain pair_style's. This example shows how to load and run such a GPU-enabled version.  Here is a sample PBS script to run. It uses one node and two GPU's for the computation.

#PBS -N lammpsTest
#PBS -l nodes=1:ppn=8,feature=gpu
#PBS -l walltime=00:10:00
#PBS -S /bin/bash
#PBS -j oe

module switch mvapich2-1.4-gnu
module load cuda-3.0
module load fftw2-2.1.5-double-mvapich2-1.4-gnu
module load lammps-25Mar11cuda


cp lj-gpu.in $TMPDIR

mpiexec -np 2 lmp_osc < lj-gpu.in > out


Here is a sample input with the necessary modifications to use a GPU pair_style, and it uses both GPU's.

newton off

units lj
atom_style atomic
lattice fcc 0.8442
region box block 0 20 0 20 0 20
create_box 1 box
create_atoms 1 box
mass 1 1.0

velocity all create 1.44 87287 loop geom

pair_style lj/cut/gpu 2.5
pair_coeff 1 1 1.0 1.0 2.5

neighbor 0.3 bin
neigh_modify delay 0 every 20 check no

fix 0 all gpu force/neigh 0 1 1.0
fix 1 all nve

timestep 0.003
thermo 100
run 100

Please note that the you cannot run more than two threads per node. More than two threads will cause the application to hang, since there are only two GPU's per node. The LAMMPS input and the pbs script must match up with the number of GPU's being used.

Please refer to the documentation for more pair_style's that can be used in such simulations.

Further Reading