lammps

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:

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