SPPARKS

Stochastic Parallel PARticle Kinetic Simulator (SPPARKS)

SPPARKS is a parallel Monte Carlo code for on-lattice and off-lattice models that includes algorithms for kinetic Monte Carlo (KMC), rejection kinetic Monte Carlo (rKMC), and Metropolis Monte Carlo (MMC). It implements several KMC solvers whose serial computational complexity ranges from O(N) to O(NlogN) to O(1) in the number of events N owned by a processor. In a generic sense the solvers catalog a list of "events", each with an associated probability, choose a single event to perform, and advance time by the correct amount. Events may be chosen individually at random, or by sweeping over sites in a more ordered fashion.

A full description of the package and links to download can be found in SPPARKS webpage.

Installation on HiperGator

Untar and unzip the downloaded file in your chosen directory.

tar -xzvf ssparks.tar.gz

Build SSPARKS

Enter in src directory.

cd src

Load modules

module load gcc openmpi

Build the binary executables

make mpi

Move the executable file to the bin folder

mv spk_mpi ~/home/bin

If bin folder is not set in environment variables

Edit the bash_profile file

vi ~/.bash_profile

Add the following code at the end of this file

PATH=$PATH:$HOME/bin

Run it via HiperGator submission script

#!/bin/bash

#SBATCH --job-name=<job-name>

#SBATCH --output <Output>

#SBATCH --error <Error-output>

##SBATCH --mail-type=ALL

#SBATCH --qos=<account> ex. phillpot

##SBATCH --mail-user=<email-address>

#SBATCH --ntasks=8              # Number of MPI processes (CPUs)

#SBATCH --mem-per-cpu=2G        # Per processor memory request

#SBATCH --time=96:00:00         # Walltime in hh:mm:ss or d-hh:mm:ss

module purge

module load gcc openmpi

mpiexec <spk_mpi file postion> -in in.* > job.log # the position should be like /home/<account>/bin/spk_mpi