{"id":16413648,"url":"https://github.com/t-neumann/versalignlib","last_synced_at":"2025-04-04T14:41:49.130Z","repository":{"id":112522443,"uuid":"64342313","full_name":"t-neumann/versalignLib","owner":"t-neumann","description":"Showcase of parallelization technologies using sequence alignment algorithms","archived":false,"fork":false,"pushed_at":"2017-01-31T22:26:36.000Z","size":70181,"stargazers_count":2,"open_issues_count":3,"forks_count":0,"subscribers_count":1,"default_branch":"master","last_synced_at":"2025-02-10T00:26:23.770Z","etag":null,"topics":["alignments","amd-opencl","avx","benchmark","cmake","needleman-wunsch","opencl","openmp","openmp-support","parallel-computing","parallelization","showcase","smith-waterman","sse"],"latest_commit_sha":null,"homepage":null,"language":"C++","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"gpl-3.0","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/t-neumann.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":"2016-07-27T21:14:52.000Z","updated_at":"2020-05-08T05:56:22.000Z","dependencies_parsed_at":"2023-05-15T15:15:19.275Z","dependency_job_id":null,"html_url":"https://github.com/t-neumann/versalignLib","commit_stats":null,"previous_names":[],"tags_count":1,"template":false,"template_full_name":null,"repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/t-neumann%2FversalignLib","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/t-neumann%2FversalignLib/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/t-neumann%2FversalignLib/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/t-neumann%2FversalignLib/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/t-neumann","download_url":"https://codeload.github.com/t-neumann/versalignLib/tar.gz/refs/heads/master","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":247198406,"owners_count":20900078,"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":["alignments","amd-opencl","avx","benchmark","cmake","needleman-wunsch","opencl","openmp","openmp-support","parallel-computing","parallelization","showcase","smith-waterman","sse"],"created_at":"2024-10-11T06:52:01.729Z","updated_at":"2025-04-04T14:41:49.122Z","avatar_url":"https://github.com/t-neumann.png","language":"C++","readme":"# versalignLib\n\nAuthor: [Tobias Neumann](mailto:tobias.neumann.at@gmail.com)\n\nProgramming language: C/C++11\n\nTechnologies: [SSE2](https://en.wikipedia.org/wiki/SSE2), [AVX2](https://en.wikipedia.org/wiki/Advanced_Vector_Extensions), [OpenCL](https://www.khronos.org/opencl/), [OpenMP](http://www.openmp.org)\n\nSource: [tar](https://github.com/t-neumann/versalignLib/archive/v0.1.tar.gz), [zip](https://github.com/t-neumann/versalignLib/archive/v0.1.zip) \n\nWhat is it?\n-----------\n\n**versalignLib** is a showcasing project of parallelization technologies comprising implementations of the sequence alignment algorithms\n[Smith-Waterman](https://en.wikipedia.org/wiki/Smith%E2%80%93Waterman_algorithm)\nand [Needleman-Wunsch](https://en.wikipedia.org/wiki/Needleman%E2%80%93Wunsch_algorithm).\n\nIt builds a set of libraries, each library containing implementations utilizing a different\nparallelization technology (OpenMP, SSE2, AVX2, OpenCL). They are provided as [shared objects](https://en.wikipedia.org/wiki/Dynamic_loading)\nand can be dynamically loaded depending on available resources and can be benchmarked to one another.\n\n**For any details on usage and benchmarks of the reference implementation, please refer to the [Github wiki](https://github.com/t-neumann/versalignLib/wiki).**\n\nINSTALLATION\n============\n\nBuilding **versalignLib** requires *[cmake](http://www.cmake.org/)* (\u003e=2.8.11), *g++* and an OpenCL implementation.\n\n### Build tools\n\nTypically *cmake* and *g++* should be already available on your machine. If not, please install them.\n\n### OpenMP\n\nTo activate OpenMP parallelization, your compiler needs to have OpenMP support. Otherwise all Kernels except the OpenCL Kernel will run single-threaded. OpenMP is natively supported by *gcc* and for newer versions of *Clang*.\n\n### OpenCL\n\nTo build the OpenCL library, an OpenCL implementation must be available on your machine.\n\n#### Mac\n\nMac OS X comes natively with an [OpenCL implementation](https://developer.apple.com/opencl/). No need for further setup.\n\n#### Linux\nFor Linux, **versalignLib** utilizes the [AMD OpenCL™ APP SDK](http://developer.amd.com/appsdk). All you need to to is to make **versalignLib** aware of the AMD OpenCL™ APP SDK library by setting the following environment variables:\n\n \n```\ncd versalignLib\nexport LD_LIBRARY_PATH=\"$LD_LIBRARY_PATH:$PWD/opencl-AMD-sdk/x86_64/lib\"\nexport OPENCL_VENDOR_PATH=\"$PWD/opencl-AMD-sdk/x86_64/lib/vendors\"\n```\n\nIn case the symlink to the `libOpenCL.so.1` library is not preserved, recreate it like this:\n\n```\n(cd opencl-AMD-sdk/x86_64/lib ; rm libOpenCL.so ; ln -s libOpenCL.so.1 libOpenCL.so)\n```\n\n### AVX2\n\n*cmake* automatically checks whether AVX2 build support is available and will only produce the shared object if if detects support.\n\n**Caveat 1:** You still need to check for AVX2 instruction support during runtime, for more see the **versalignLib** example implementation!\n\n**Caveat 2:** OpenMP support for the AVX2 Kernel is currently disabled and needs more bugfixing!\n\n### Build\n\nTo build **versalignLib** simply run the following commands:\n\n```\ncd versalignLib\nmkdir build\ncd build\n\n# Release\ncmake -DCMAKE_BUILD_TYPE=Release ..\n# Debug\ncmake -DCMAKE_BUILD_TYPE=Debug ..\n\nmake\n```\n\n\nSystem requirements\n-------------------\n\n\u003cdl\u003e\n\u003ctable\u003e\n  \u003ctbody\u003e\n    \u003ctr\u003e\n      \u003ctd\u003e\u003cb\u003eCPU:\u003c/b\u003e\u003c/td\u003e\n      \u003ctd\u003e64 bit SSE2 enabled, (optional) AVX2 enabled\u003c/td\u003e\n    \u003c/tr\u003e\n    \u003ctr\u003e\n      \u003ctd\u003e\u003cb\u003eRAM:\u003c/b\u003e\u003c/td\u003e\n      \u003ctd\u003eTested on regular systems with minimum 4 GB RAM\u003c/td\u003e\n    \u003c/tr\u003e\n    \u003ctr\u003e\n      \u003ctd\u003e\u003cb\u003eOS:\u003c/b\u003e\u003c/td\u003e\n      \u003ctd\u003eLinux (Ubuntu Server 16.04, Debian 7.7), Mac OSX (10.11) \u003c/td\u003e\n    \u003c/tr\u003e\n    \u003ctr\u003e\n      \u003ctd\u003e\u003cb\u003eSoftware:\u003c/b\u003e\u003c/td\u003e\n      \u003ctd\u003e\u003ca href=\"https://cmake.org/\"\u003e\u003ci\u003ecmake\u003c/i\u003e\u003c/a\u003e (\u003e=2.8.11)\u003c/td\u003e\n    \u003c/tr\u003e\n  \u003c/tbody\u003e\n\u003c/table\u003e\n\u003c/dl\u003e\n\n\n","funding_links":[],"categories":[],"sub_categories":[],"project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Ft-neumann%2Fversalignlib","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Ft-neumann%2Fversalignlib","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Ft-neumann%2Fversalignlib/lists"}