SPPARKS

SPPARKS stands for Stochastic Parallel PARticle Kinetic Simulator.

SPPARKS is a kinetic Monte Carlo (KMC) code designed to run efficiently on parallel computers using both KMC and Metropolis Monte Carlo algorithms. It was developed at Sandia National Laboratories, a US Department of Energy facility, with funding from the DOE. It is an open-source code, distributed freely under the terms of the GNU Public License (GPL).

Steps to run SPPARKS

Once you log into Cheaha, set up your environment for SPPARKS with the following

module load spparks/spparks

A simple script to start executing SPPARKS on an SGE scheduler

#!/bin/bash
#$ -S /bin/bash
#$ -cwd
#$ -j y
#
#$ -N spparks_test
#$ -pe mpich2 50 
#
# Job runtime max (23 hours) 
#$ -l h_rt=923:00:00,s_rt=922:55:00
#
#$ -M YOUR_EMAIL_ADDRESS
#$ -m eas
#
# Load the appropriate module file(s) for your job
. /etc/profile.d/modules.sh
module load spparks/spparks
#$ -V

# This line is mandatory for MPICH2 jobs
export MPD_CON_EXT="sge_$JOB_ID.$SGE_TASK_ID"

# The order of arguments is important. Forst global, then local options.
mpiexec -machinefile $TMPDIR/machines -n $NSLOTS ${PWD}/spk_linux < ${PWD}/in.potts

exit 0

Then submit that script with

qsub name-of-script-above

Check on it with qstat.

qstat -u $USER