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).

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

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

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

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

exit 0

Then submit that script with qsub name-of-script-above

Check on it with qstat. qstat -u $USER