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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).