We have lammps installed for your use - and, of course, you can always download and install yourself if you want.   A makefile to start with is in /sw/cnsi/lammps

To use the precompiled one, you simply need a basic script like this:

#PBS -l nodes=1:ppn=12
#PBS -l walltime=06:00:00
source /opt/intel/bin/ intel64
# Make sure that we are in the same subdirectory as where the qsub command
# is issued.
cat $PBS_NODEFILE > nodes
# Get number of nodes allocated
NO_OF_NODES=`cat $PBS_NODEFILE | egrep -v '^#'\|'^$' | wc -l | awk '{print $1}'`
# Just for kicks, see which nodes we got.
# Run the executable. *DO NOT PUT* a '&' at the end - it will not
# work.
sleep 3
(time mpirun -np $NO_OF_NODES -machinefile nodes /sw/bin/lmp_knot < in.eam )  >& log.knot
sleep 4

All you need to change is:

  • nodes= line (to however many nodes/ppn you want)
  • wallclock line (remove it if you don't know how long it will take)
  • the input file name (in.eam in this case) and the log file (log,knot here) if you want.