wiki.chpc.ac.za

This is an old revision of the document!

---

LIGGGHTS and lammps at the CHPC

The molecular dynamics code lammps and the related LIGGGHTS descreet element method code are now installed at the CHPC, although only limited support is available for them at this point. Lammps is installed at /opt/gridware/non-supported/lammps, and LIGGGHTS is at /opt/gridware/non-supported/LIGGGHTS .

In either case, the directory contains a file named lammps_env or liggghts_env. This should be sourced from your submit script before running the executable, for which a symbolic link is provided in the same directory. An example script for lights, parallelized across three nodes (select = 3) with 12 processors per node (ncpus =12:mpiprocs=12) is shown below:

#!/bin/bash 
#PBS -l select=3:ncpus=12:mpiprocs=12:mem=4GB:jobtype=dell,place=free:group=nodetype
#PBS -q workq
#PBS -l walltime=01:00:00
#PBS -o /export/home/username/scratch5/liggghtsJobs/job01/stdout
#PBS -e /export/home/username/scratch5/liggghts>Jobs/job01/stderr
#PBS -m abe
#PBS -M username@email.co.za
### Source the LIGGGHTS environment:
. /opt/gridware/non-supported/LIGGGHTS/liggghts_env
##### Running commands
# The -d option used with moab no longer works.  Set this environment variable explicitly.
export PBS_JOBDIR=/export/home/username/scratch5/liggghtsJobs/job01
# Explicitly change to the job directory
cd $PBS_JOBDIR
nproc=`cat $PBS_NODEFILE | wc -l`
mpirun -np $nproc liggghts < in.lj