Attention

WARNING: From 9am on 19th August until 5pm on 2nd September there will be no access to the Stanage HPC cluster.

We will send an email to notify you when Stanage is back online and available for job submission.

Attention

The ShARC HPC cluster was decommissioned on the 30th of November 2023 at 17:00. It is no longer possible for users to access that cluster.

Repast HPC

The Repast Suite is a family of advanced, free, and open source agent-based modeling and simulation platforms that have collectively been under continuous development for over 15 years: Repast for High Performance Computing 2.2.0, released on 30 September 2016, is a lean and expert-focused C++-based modeling system that is designed for use on large computing clusters and supercomputers.

Usage

Repast HPC 2.2.0 can be activated using the module file:

module load apps/repast_hpc/2.2.0/gcc-mpich-3.1.4
module load apps/repast_hpc/2.2.0/gcc-6.2-openmpi-2.1.1

Note that the above module files also loads GCC 6.2.0 compiler and either MPICH-3.1.4 or Open MPI 2.1.1.

Batch jobs

Users are encouraged to write their own batch submission scripts. The following is an example batch submission script, my_job.sh, to run the zombie_model example in parallel and which is submitted to the queue by typing qsub my_job.sh.

#!/bin/bash
#$ -cwd
#$ -l h_rt=06:00:00
#$ -l rmem=2G
#$ -pe mpi 4

module load apps/repast_hpc/2.2.0/gcc-mpich-3.1.4

export repastroot=/usr/local/packages/apps/repast_hpc/2.2.0/gcc-6.2-mpich-3.1.4

cp $repastroot/bin/zombie/* .

mpirun ./zombie_model config.props model.props

The script requests four CPU cores using the MPI parallel environment mpi with 2 GB of real memory per CPU core. The requested runtime is 6 hours.

Installation notes

Repast HPC 2.2.0 was installed using the install_repast_hpc.sh installation script. The module file is /usr/local/modulefiles/apps/repast_hpc/2.2.0/gcc-6.2-mpich-3.1.4.

Third-party software required by Repast HPC 2.2.0 (Curl 7.42.1, NetCDF 4.2.1.1, NetCDF-CXX 4.2 and Boost 1.61.0) were installed in /usr/local/packages/apps/repast_hpc/2.2.0/third-party-mpich-3.1.4 using the GCC 6.2.0 compiler with MPICH-3.1.4.

The installation of Repast HPC 2.2.0 was tested by running the example batch submission script (above).