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Introduction

Here is a simple 3D Gray-Scott simulator. The aim of this project is to have a first look at the Kokkos library.

From the Kokkos github repo :

The Kokkos C++ Performance Portability Ecosystem is a production level solution for writing modern C++ applications in a hardware agnostic way. Thanks to Kokkos, you can compile this code for multiple backends like OpenMP, CUDA, HIP.

Disclaimer: Please note that this project is a work in progress and may contain errors or programming oversights due to its experimental nature. Your understanding and feedback are appreciated as we continue to develop and refine this code.

Compilation

Compile the code with the following commands :

git submodule update --init --recursive
mkdir build && cd build && cmake ..
make -j

Usage

You can currently launch the executable named GS with the following command :

./GS

This will run the executable with the default parameters.

Future customization options

In a future release, you will be able to customize the parameters via the CLI. The following example demonstrates how to launch the program with specific parameters:

./GS --dim 3D --stencil 7 --Du 0.05 --Dv 0.04 ...

All the available parameters are given by :

./GS --help

Prerequisites

The code use Kokkos as a performance portability library. Then, you must have it to compile the project. I suggest you to install it and read the documentation for further understanding.

It is possible to easily install Kokkos through the HPC spack package manager. I suggest you to create a new environment :

spack env create kokkos
spack env activate kokkos
spack install kokkos // here you can specify your backend like OpenMP, pthread, CUDA, HIP, ... please read the doc
spack load kokkos

The python visualizer works withthe packages h5py, numpy, pyvista and imageio. You can install them with your favorite python installation :

pip3 install h5py pyvista numpy imageio

These packages enable reading HDF5 files and generating scientific visualizations using VTK through PyVista.

ShowCase

The animation above illustrates the complex evolving patterns generated by the Gray-Scott model in 3D. Animation

We generate the animation with the python library pyvista throught the python script clip.py.

Disclaimer : Please note that the generator can be very slow even with a powerful computer.

Todo

To-Do List

  • Refactoring
  • Hierarchical parallelism with Kokkos
  • Shared memory kernels with scratch pads
  • Kokkos::SIMD usage
  • Add periodic boundary conditions
  • Python animation generator
  • Set up the CMake build system
  • Test the code on different backends (CUDA, OpenMP, Serial)
  • Provide MVP (Minimum Viable Product)