{"id":21480609,"url":"https://github.com/flatironinstitute/skellysim","last_synced_at":"2025-07-15T12:32:25.921Z","repository":{"id":38689877,"uuid":"302383534","full_name":"flatironinstitute/SkellySim","owner":"flatironinstitute","description":"Hydrodynamic Cytoskeleton Simulator","archived":false,"fork":false,"pushed_at":"2024-05-13T16:05:23.000Z","size":11628,"stargazers_count":21,"open_issues_count":15,"forks_count":2,"subscribers_count":6,"default_branch":"main","last_synced_at":"2024-05-13T17:33:10.960Z","etag":null,"topics":["cpp","cytoskeleton","fast-multipole-method","fluid-dynamics","high-performance-computing","hybrid-parallelism","molecular-motors","mpi","openmp","python","simulation","trilinos"],"latest_commit_sha":null,"homepage":"https://users.flatironinstitute.org/~rblackwell/py-skellysim","language":"C++","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"apache-2.0","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/flatironinstitute.png","metadata":{"files":{"readme":"README.md","changelog":null,"contributing":null,"funding":null,"license":"LICENSE","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":"2020-10-08T15:25:04.000Z","updated_at":"2024-05-13T16:05:30.000Z","dependencies_parsed_at":"2023-10-17T01:55:03.631Z","dependency_job_id":"b8112c53-4f93-4e2f-a012-18c28b9ef6c8","html_url":"https://github.com/flatironinstitute/SkellySim","commit_stats":null,"previous_names":[],"tags_count":13,"template":false,"template_full_name":null,"repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/flatironinstitute%2FSkellySim","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/flatironinstitute%2FSkellySim/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/flatironinstitute%2FSkellySim/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/flatironinstitute%2FSkellySim/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/flatironinstitute","download_url":"https://codeload.github.com/flatironinstitute/SkellySim/tar.gz/refs/heads/main","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":226038788,"owners_count":17564047,"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","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":["cpp","cytoskeleton","fast-multipole-method","fluid-dynamics","high-performance-computing","hybrid-parallelism","molecular-motors","mpi","openmp","python","simulation","trilinos"],"created_at":"2024-11-23T12:16:53.559Z","updated_at":"2024-11-23T12:16:54.570Z","avatar_url":"https://github.com/flatironinstitute.png","language":"C++","funding_links":[],"categories":[],"sub_categories":[],"readme":"![](docs/source/images/SkellySim_Logo_RGB_Full.png)\n\nSkellySim is a simulation package for simulating cellular components such as flexible filaments, motor proteins, and arbitrary rigid bodies.\nIt's designed to be highly scalable, capable of both OpenMP and MPI style parallelism, while using the efficient STKFMM/PVFMM libraries for hydrodynamic resolution.\n\n# Documentation\nFlatiron users should read [Installation/Running at FI first](#installation-running-at-fi),\nsince users there should not have to install the `C++` portion themselves.\n\n[SkellySim documentation](https://users.flatironinstitute.org/~rblackwell/py-skellysim)\n\n# Installation/Running at FI\n## Basic setup\nThere are (currently) two components to skelly_sim, the python portion, and the actual\nbinary. The python portion is mostly for visualization, as well as generating config files and\nprecompute data. The binary (C++) portion is for actually running the simulation.\n\nTo install the python portion (in your virtual environment, conda environment, or using the `pip3 --user` option). For a virtualenv\n```bash\nmodule load python\npython3 -m venv /path/to/my/virtualenv\nsource /path/to/my/virtualenv/bin/activate\npip3 install git+https://github.com/flatironinstitute/SkellySim\n```\nor for a conda environment\n```\nconda create -n myenvname\nconda activate myenvname\npip3 install git+https://github.com/flatironinstitute/SkellySim\n```\nDue to the complex dependencies of the C++ portion, until I finish packaging things, you can use my modules. \n```bash\nmodule -q purge\n# REMOVE python module from this if you are using conda!!!!\nmodule use ~rblackwell/modules\nmodule -q load gcc/11 openmpi python trilinos pvfmm/1.3.0 intel-oneapi-mkl cuda flexiblas skelly_sim\n```\n\n## Building from source at FI (developers or externs)\n\n\n```bash\nmodule -q purge\nmodule -q load gcc/11 openmpi python cmake trilinos pvfmm stkfmm intel-oneapi-mkl cuda boost flexiblas\n\ngit clone https://github.com/flatironinstitute/SkellySim\ncd SkellySim\ngit submodule update --init --recursive\nmkdir -p build\ncd build\ncmake .. -DCMAKE_BUILD_TYPE=Release -DCMAKE_CXX_FLAGS=-march=broadwell -DCMAKE_CUDA_ARCHITECTURES=\"70;75;86;90\" -DBLA_VENDOR=FlexiBLAS\nmake -j$((2*$(nproc)))\n```\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fflatironinstitute%2Fskellysim","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fflatironinstitute%2Fskellysim","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fflatironinstitute%2Fskellysim/lists"}