LAMMPS
Useful links
LAMMPS Web page
LAMMPS Documentation
Access
LAMMPS is open source software distributed under the GNU GPL. All HECToR users have access to the LAMMPS binaries.
Running
To run LAMMPS you need to add the correct module to your environment. The default build of LAMMPS is currently 25 Sep 2011 so
module add lammps
will give you access to LAMMPS 25/09/2011 build.
An example job submission script is shown below.
#!/bin/bash --login #PBS -N lammps #PBS -l mppwidth=1024 #PBS -l mppnppn=32 #PBS -l walltime=00:05:00 #PBS -A z01 # Move to directory that script was submitted from export PBS_O_WORKDIR=$(readlink -f $PBS_O_WORKDIR) cd $PBS_O_WORKDIR # Set the number of threads to 1 # This prevents any system libraries from automatically # using threading. export OMP_NUM_THREADS=1 module load lammps # cd to /work file system so that job runs on the lustre filesystem cd /work/z01/z01/fiona/lammps_test_modules # Copy test data across cp $LAMMPS_BENCH/data.rhodo . cp $LAMMPS_BENCH/in.rhodo . # Run LAMMPS aprun -n 1024 -N 32 lmp_hector -in in.rhodo > rhodopsin.out