SPPARKS

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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).

Project website:http://www.sandia.gov/~sjplimp/

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