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https://github.com/sbstndb/grayscott_k
A simple 3D GrayScott simulation using Kokkos enabling CUDA or OpenMP backend
https://github.com/sbstndb/grayscott_k
cuda finite-difference grayscott grid kokkos laplacian openmp simulation visualisation
Last synced: 4 days ago
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A simple 3D GrayScott simulation using Kokkos enabling CUDA or OpenMP backend
- Host: GitHub
- URL: https://github.com/sbstndb/grayscott_k
- Owner: sbstndb
- Created: 2024-08-10T22:22:32.000Z (6 months ago)
- Default Branch: main
- Last Pushed: 2024-08-15T13:50:54.000Z (6 months ago)
- Last Synced: 2024-12-10T22:41:23.724Z (2 months ago)
- Topics: cuda, finite-difference, grayscott, grid, kokkos, laplacian, openmp, simulation, visualisation
- Language: C++
- Homepage:
- Size: 63.2 MB
- Stars: 1
- Watchers: 1
- Forks: 0
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
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README
# 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](https://github.com/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`](https://github.com/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.
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
- [x] Refactoring
- [ ] Hierarchical parallelism with Kokkos
- [ ] Shared memory kernels with scratch pads
- [ ] Kokkos::SIMD usage
- [x] Add periodic boundary conditions
- [x] Python animation generator
- [x] Set up the CMake build system
- [x] Test the code on different backends (CUDA, OpenMP, Serial)
- [x] Provide MVP (Minimum Viable Product)