{"id":17632702,"url":"https://github.com/sbstndb/grayscott_k","last_synced_at":"2026-05-16T01:31:55.902Z","repository":{"id":252582435,"uuid":"840853466","full_name":"sbstndb/grayscott_k","owner":"sbstndb","description":"A simple 3D GrayScott simulation using Kokkos enabling CUDA or OpenMP backend","archived":false,"fork":false,"pushed_at":"2024-08-15T13:50:54.000Z","size":66262,"stargazers_count":1,"open_issues_count":0,"forks_count":0,"subscribers_count":1,"default_branch":"main","last_synced_at":"2025-03-30T03:31:53.491Z","etag":null,"topics":["cuda","finite-difference","grayscott","grid","kokkos","laplacian","openmp","simulation","visualisation"],"latest_commit_sha":null,"homepage":"","language":"C++","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":null,"status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/sbstndb.png","metadata":{"files":{"readme":"README.md","changelog":null,"contributing":null,"funding":null,"license":null,"code_of_conduct":null,"threat_model":null,"audit":null,"citation":null,"codeowners":null,"security":null,"support":null,"governance":null,"roadmap":null,"authors":null,"dei":null,"publiccode":null,"codemeta":null}},"created_at":"2024-08-10T22:22:32.000Z","updated_at":"2024-08-15T13:50:57.000Z","dependencies_parsed_at":"2024-08-15T15:10:30.277Z","dependency_job_id":null,"html_url":"https://github.com/sbstndb/grayscott_k","commit_stats":null,"previous_names":["sbstndb/grayscott_kokkos","sbstndb/grayscott_k"],"tags_count":0,"template":false,"template_full_name":null,"purl":"pkg:github/sbstndb/grayscott_k","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/sbstndb%2Fgrayscott_k","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/sbstndb%2Fgrayscott_k/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/sbstndb%2Fgrayscott_k/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/sbstndb%2Fgrayscott_k/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/sbstndb","download_url":"https://codeload.github.com/sbstndb/grayscott_k/tar.gz/refs/heads/main","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/sbstndb%2Fgrayscott_k/sbom","scorecard":null,"host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":274969343,"owners_count":25383116,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2022-07-04T15:15:14.044Z","status":"online","status_checked_at":"2025-09-13T02:00:10.085Z","response_time":70,"last_error":null,"robots_txt_status":"success","robots_txt_updated_at":"2025-07-24T06:49:26.215Z","robots_txt_url":"https://github.com/robots.txt","online":true,"can_crawl_api":true,"host_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub","repositories_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories","repository_names_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repository_names","owners_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners"}},"keywords":["cuda","finite-difference","grayscott","grid","kokkos","laplacian","openmp","simulation","visualisation"],"created_at":"2024-10-23T01:45:10.718Z","updated_at":"2026-05-16T01:31:50.880Z","avatar_url":"https://github.com/sbstndb.png","language":"C++","funding_links":[],"categories":[],"sub_categories":[],"readme":"# Introduction\n Here is a simple 3D Gray-Scott simulator. \n The aim of this project is to have a first look at the Kokkos library.\n\n From the [Kokkos](https://github.com/kokkos) github repo : \n\u003e The Kokkos C++ Performance Portability Ecosystem is a production level solution for writing modern C++ applications in a hardware agnostic way.\nThanks to Kokkos, you can compile this code for multiple backends like OpenMP, CUDA, HIP.\n\n\n**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.\n\n# Compilation\nCompile the code with the following commands : \n```\ngit submodule update --init --recursive\nmkdir build \u0026\u0026 cd build \u0026\u0026 cmake ..\nmake -j \n```\n\n# Usage\nYou can currently launch the executable named `GS` with the following command :\n```\n./GS\n```\nThis will run the executable with the default parameters.\n## Future customization options\n\nIn 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:\n```\n./GS --dim 3D --stencil 7 --Du 0.05 --Dv 0.04 ...\n```\nAll the available parameters are given by : \n```\n./GS --help\n```\n\n# Prerequisites\nThe code use Kokkos as a performance portability library. Then, you must have it to compile the project.\nI suggest you to install it and read the documentation for further understanding. \n\nIt is possible to easily install `Kokkos` through the HPC [`spack`](https://github.com/spack) package manager. I suggest you to create a new environment : \n```\nspack env create kokkos\nspack env activate kokkos\nspack install kokkos // here you can specify your backend like OpenMP, pthread, CUDA, HIP, ... please read the doc\nspack load kokkos\n```\n\nThe python visualizer works withthe packages `h5py`, `numpy`, `pyvista` and `imageio`. You can install them with your favorite python installation : \n```\npip3 install h5py pyvista numpy imageio\n```\nThese packages enable reading HDF5 files and generating scientific visualizations using VTK through `PyVista`.\n\n# ShowCase\nThe animation above illustrates the complex evolving patterns generated by the Gray-Scott model in 3D. \n![Animation](media/GS_3D_compressed.gif)\n\nWe generate the animation with the python library `pyvista` throught the python script `clip.py`. \n\n**Disclaimer** : Please note that the generator can be very slow even with a powerful computer. \n\n# Todo \n### To-Do List\n\n- [x] Refactoring\n- [ ] Hierarchical parallelism with Kokkos\n- [ ] Shared memory kernels with scratch pads\n- [ ] Kokkos::SIMD usage\n- [x] Add periodic boundary conditions\n- [x] Python animation generator\n- [x] Set up the CMake build system\n- [x] Test the code on different backends (CUDA, OpenMP, Serial)\n- [x] Provide MVP (Minimum Viable Product)\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fsbstndb%2Fgrayscott_k","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fsbstndb%2Fgrayscott_k","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fsbstndb%2Fgrayscott_k/lists"}