This is a demo for an Agent-based epidemiology code built using the AMReX framework.

For more information about AMReX: website: https://amrex-codes.github.io/ documentation: https://amrex-codes.github.io/amrex/docs_html/ source code: https://github.com/AMReX-Codes/amrex

Building the code

This demo uses CMake version 3.14 or higher. To build it: mkdir build cd build cmake .. make -j8

To build with GPU support, use the CMake option -DAMReX_GPU_BACKEND=CUDA on NVIDIA GPU, -DAMReX_GPU_BACKEND=SYCL on Intel GPU. On AMD GPU, both GPU backend and GPU architecture should be provided, e.g. -DAMReX_GPU_BACKEND=HIP -DAMReX_AMD_ARCH=gfx90a.

To write output as (compressed) HDF5, use the -DAMReX_HDF5=TRUE CMake option. Parallel HDF5 installation is required. On perlmutter, a conda environment is available at:

conda activate /global/common/software/m3623/exaepi

Compression level can be altered in src/IO.cpp file. The environment variable HDF5_CHUNK_SIZE controls the chunk size if compression is used. A value of around 100,000 is recommended to start.

For convenience, a script for setting up the module environment without HDF5 for Perlmutter is provided in etc/perlmutter_environment.sh. To use it, do:

source etc/perlmutter_environment.sh

A similar script for setting up the environment for Frontier can be found in etc/frontier_environment.sh.

Running the code

Navigate to build/bin and run the executable using one of the "inputs" files in "examples".

For example: cd build/bin ./agent ../../examples/inputs

On Aurora at ALCF, if compiled with SYCL be sure to add "agent.fast=1" at the end of the command line to speed up the case initialization

For example: mpirun -np 1 ./agent ../../examples/inputs.ca agent.fast=1

If reproducibility is a must, we do a quick run for 0 day to checkpoint the initial condition.

mpirun -np 1 ./agent ../../examples/inputs.ca agent.fast=1 agent.nsteps=0 agent.check_int=1

Subsequent runs will start from the checkpoint by adding "agent.restart=chk00000" to the end of the command line.

mpirun -np 1 ./agent ../../examples/inputs.ca agent.restart=chk00000

Looking at the output

Running the code succesfully will create a number of "plt?????" files. You can visualize these using the script at etc/plot.py. This will require the "yt" package to be installed:

https://yt-project.org/

Copyright Notice

ExaEpi Copyright (c) 2022, The Regents of the University of California, through Lawrence Berkeley National Laboratory (subject to receipt of any required approvals from the U.S. Dept. of Energy). All rights reserved.

If you have questions about your rights to use or distribute this software, please contact Berkeley Lab's Intellectual Property Office at [email protected].

NOTICE. This Software was developed under funding from the U.S. Department of Energy and the U.S. Government consequently retains certain rights. As such, the U.S. Government has been granted for itself and others acting on its behalf a paid-up, nonexclusive, irrevocable, worldwide license in the Software to reproduce, distribute copies to the public, prepare derivative works, and perform publicly and display publicly, and to permit others to do so.