Contents


Deprecated: please see new documentation site.



Introduction

LAMMPS stands for Large-scale Atomic/Molecular Massively Parallel Simulator. LAMMPS has potentials for soft materials (biomolecules, polymers) and solid-state materials (metals, semiconductors) and coarse-grained or mesoscopic systems. It can be used to model atoms or, more generically, as a parallel particle simulator at the atomic, meso, or continuum scale.

Version and availability

Version "4 May 2011" is available on all Dell Linux x86 Cluster and LSU HPC machines Tezpur and Pandora.

Usage

Before running a LAMMPS job, you need to add '+lammps-4May11-intel-11.1-mvapich-1.1' (Pandora add '+lammps-4May11') to your .soft file and resoft ( '+mvapich-1.1-intel-11.1' is also required and needs to appear before any other keywords in your .soft file). For more information on the .soft file and the resoft command, please refer to Managing the Environment with SoftEnv.

To run LAMMPS through PBS, you need a script like the one below. In this example, LAMMPS runs with 8 processors and the input file is in.flow.couette that can be found in the examples directory.

 #!/bin/bash
 #PBS -A your_allocation
 #PBS -q checkpt
 #PBS -l nodes=1:ppn=8
 #PBS -l walltime=12:00:00
 #PBS -V
 #PBS -j oe
 #PBS -N lammps-couette
   
 export EXEC=lmp_linux
 export EXEC_DIR=/usr/local/packages/lammps/4May11/intel-11.1-mvapich-1.1/bin
 export WORKDIR=$PBS_O_WORKDIR
 export NPROCS=`wc -l $PBS_NODEFILE |gawk '//{print $1}'`
   
 cd $WORKDIR
 mpirun -machinefile $PBS_NODEFILE -np $NPROCS $EXEC_DIR/$EXEC \
        < in.flow.couette 

Then submit it to run (assuming that the script above is named runlammps.pbs)

qsub runlammps.pbs

References

A LAMMPS User Manual is available on-line.


Users may direct questions to sys-help@loni.org.

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