{"action":"created","issue":{"url":"https://api.github.com/repos/bioconda/bioconda-recipes/issues/7535","repository_url":"https://api.github.com/repos/bioconda/bioconda-recipes","labels_url":"https://api.github.com/repos/bioconda/bioconda-recipes/issues/7535/labels{/name}","comments_url":"https://api.github.com/repos/bioconda/bioconda-recipes/issues/7535/comments","events_url":"https://api.github.com/repos/bioconda/bioconda-recipes/issues/7535/events","html_url":"https://github.com/bioconda/bioconda-recipes/pull/7535","id":294822341,"number":7535,"title":"Update to gromacs 2018","user":{"login":"stain","id":253413,"avatar_url":"https://avatars0.githubusercontent.com/u/253413?v=4","gravatar_id":"","url":"https://api.github.com/users/stain","html_url":"https://github.com/stain","followers_url":"https://api.github.com/users/stain/followers","following_url":"https://api.github.com/users/stain/following{/other_user}","gists_url":"https://api.github.com/users/stain/gists{/gist_id}","starred_url":"https://api.github.com/users/stain/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/stain/subscriptions","organizations_url":"https://api.github.com/users/stain/orgs","repos_url":"https://api.github.com/users/stain/repos","events_url":"https://api.github.com/users/stain/events{/privacy}","received_events_url":"https://api.github.com/users/stain/received_events","type":"User","site_admin":false},"labels":[],"state":"closed","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":12,"created_at":"2018-02-06T16:23:48Z","updated_at":"2018-02-17T10:57:30Z","closed_at":"2018-02-11T09:12:20Z","author_association":"MEMBER","pull_request":{"url":"https://api.github.com/repos/bioconda/bioconda-recipes/pulls/7535","html_url":"https://github.com/bioconda/bioconda-recipes/pull/7535","diff_url":"https://github.com/bioconda/bioconda-recipes/pull/7535.diff","patch_url":"https://github.com/bioconda/bioconda-recipes/pull/7535.patch"},"body":"* [x] I have read the [guidelines for bioconda recipes](https://bioconda.github.io/guidelines.html).\r\n* [ ] This PR adds a new recipe.\r\n* [x] AFAIK, this recipe **is directly relevant to the biological sciences** (otherwise, please submit to the more general purpose [conda-forge channel](https://conda-forge.org/docs/)).\r\n* [x] This PR updates an existing recipe.\r\n* [ ] This PR does something else (explain below).\r\n\r\nNote that this updates to the latest gromacs 2018.\r\n\r\nIt might be that this can be optimized better, enabling openmp, gpu and hwloc.\r\n\r\n```\r\nGROMACS version:    2018\r\nPrecision:          single\r\nMemory model:       64 bit\r\nMPI library:        thread_mpi\r\nOpenMP support:     disabled\r\nGPU support:        disabled\r\nSIMD instructions:  AVX_256\r\nFFT library:        fftw-3.3.5-fma-sse2-avx-avx2-avx2_128\r\nRDTSCP usage:       enabled\r\nTNG support:        enabled\r\nHwloc support:      disabled\r\nTracing support:    disabled\r\nBuilt on:           2018-02-06 15:38:42\r\nBuilt by:           stain@biggie [CMAKE]\r\nBuild OS/arch:      Linux 4.13.0-26-generic x86_64\r\nBuild CPU vendor:   Intel\r\nBuild CPU brand:    Intel(R) Core(TM) i7-3520M CPU @ 2.90GHz\r\nBuild CPU family:   6   Model: 58   Stepping: 9\r\nBuild CPU features: aes apic avx clfsh cmov cx8 cx16 f16c htt intel lahf\r\nmmx msr nonstop_tsc pcid pclmuldq pdcm popcnt pse rdrnd rdtscp sse2 sse3\r\nsse4.1 sse4.2 ssse3 tdt x2apic\r\nC compiler:\r\n/tmp/miniconda/conda-bld/gromacs_1517931402329/_t_env/bin/cc GNU 4.8.5\r\nC compiler flags:    -mavx    -Wno-unknown-pragmas  -O3 -DNDEBUG\r\n-funroll-all-loops -fexcess-precision=fast\r\nC++ compiler:\r\n/tmp/miniconda/conda-bld/gromacs_1517931402329/_t_env/bin/c++ GNU 4.8.5\r\nC++ compiler flags:  -mavx    -std=c++11  -Wno-unknown-pragmas  -O3\r\n-DNDEBUG -funroll-all-loops -fexcess-precision=fast\r\n```\r\n"},"comment":{"url":"https://api.github.com/repos/bioconda/bioconda-recipes/issues/comments/366433501","html_url":"https://github.com/bioconda/bioconda-recipes/pull/7535#issuecomment-366433501","issue_url":"https://api.github.com/repos/bioconda/bioconda-recipes/issues/7535","id":366433501,"user":{"login":"bgruening","id":469983,"avatar_url":"https://avatars2.githubusercontent.com/u/469983?v=4","gravatar_id":"","url":"https://api.github.com/users/bgruening","html_url":"https://github.com/bgruening","followers_url":"https://api.github.com/users/bgruening/followers","following_url":"https://api.github.com/users/bgruening/following{/other_user}","gists_url":"https://api.github.com/users/bgruening/gists{/gist_id}","starred_url":"https://api.github.com/users/bgruening/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/bgruening/subscriptions","organizations_url":"https://api.github.com/users/bgruening/orgs","repos_url":"https://api.github.com/users/bgruening/repos","events_url":"https://api.github.com/users/bgruening/events{/privacy}","received_events_url":"https://api.github.com/users/bgruening/received_events","type":"User","site_admin":false},"created_at":"2018-02-17T10:57:30Z","updated_at":"2018-02-17T10:57:30Z","author_association":"CONTRIBUTOR","body":"@mbargull are you under OSX?\r\nThis package works for me:\r\n\r\n```\r\n(gromacs) bag@bag:~/projects/code/galaxytools/tools/sklearn$ gmx -version\r\n                          :-) GROMACS - gmx, 2018 (-:\r\n\r\n                            GROMACS is written by:\r\n     Emile Apol      Rossen Apostolov  Herman J.C. Berendsen    Par Bjelkmar   \r\n Aldert van Buuren   Rudi van Drunen     Anton Feenstra    Gerrit Groenhof  \r\n Christoph Junghans   Anca Hamuraru    Vincent Hindriksen Dimitrios Karkoulis\r\n    Peter Kasson        Jiri Kraus      Carsten Kutzner      Per Larsson    \r\n  Justin A. Lemkul    Viveca Lindahl    Magnus Lundborg   Pieter Meulenhoff \r\n   Erik Marklund      Teemu Murtola       Szilard Pall       Sander Pronk   \r\n   Roland Schulz     Alexey Shvetsov     Michael Shirts     Alfons Sijbers  \r\n   Peter Tieleman    Teemu Virolainen  Christian Wennberg    Maarten Wolf   \r\n                           and the project leaders:\r\n        Mark Abraham, Berk Hess, Erik Lindahl, and David van der Spoel\r\n\r\nCopyright (c) 1991-2000, University of Groningen, The Netherlands.\r\nCopyright (c) 2001-2017, The GROMACS development team at\r\nUppsala University, Stockholm University and\r\nthe Royal Institute of Technology, Sweden.\r\ncheck out http://www.gromacs.org for more information.\r\n\r\nGROMACS is free software; you can redistribute it and/or modify it\r\nunder the terms of the GNU Lesser General Public License\r\nas published by the Free Software Foundation; either version 2.1\r\nof the License, or (at your option) any later version.\r\n\r\nGROMACS:      gmx, version 2018\r\nExecutable:   /home/bag/miniconda3/envs/gromacs/bin/gmx\r\nData prefix:  /home/bag/miniconda3/envs/gromacs\r\nWorking dir:  /home/bag/projects/code/galaxytools/tools/sklearn\r\nCommand line:\r\n  gmx -version\r\n\r\nGROMACS version:    2018\r\nPrecision:          single\r\nMemory model:       64 bit\r\nMPI library:        thread_mpi\r\nOpenMP support:     enabled (GMX_OPENMP_MAX_THREADS = 64)\r\nGPU support:        OpenCL\r\nSIMD instructions:  AVX2_256\r\nFFT library:        fftw-3.3.7-sse2-avx\r\nRDTSCP usage:       enabled\r\nTNG support:        enabled\r\nHwloc support:      hwloc-1.11.0\r\nTracing support:    disabled\r\nBuilt on:           2018-02-11 09:16:43\r\nBuilt by:           root@prealloc-bwcms7lf-4e53d87d-eec9-494f-8a45-abc0a48dc5c8 [CMAKE]\r\nBuild OS/arch:      Linux 4.4.0-96-generic x86_64\r\nBuild CPU vendor:   Intel\r\nBuild CPU brand:    Intel(R) Xeon(R) CPU @ 2.30GHz\r\nBuild CPU family:   6   Model: 63   Stepping: 0\r\nBuild CPU features: aes apic avx avx2 clfsh cmov cx8 cx16 f16c fma htt intel lahf mmx msr nonstop_tsc pcid pclmuldq pdpe1gb popcnt pse rdrnd rdtscp sse2 sse3 sse4.1 sse4.2 ssse3 x2apic\r\nC compiler:         /home/bag/miniconda3/envs/gromacs/bin/cc GNU 4.8.5\r\nC compiler flags:    -march=core-avx2     -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast  \r\nC++ compiler:       /home/bag/miniconda3/envs/gromacs/bin/c++ GNU 4.8.5\r\nC++ compiler flags:  -march=core-avx2    -std=c++11   -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast  \r\nOpenCL include dir: /home/bag/miniconda3/envs/gromacs/include\r\nOpenCL library:     /home/bag/miniconda3/envs/gromacs/lib/libOpenCL.so\r\nOpenCL version:     2.\r\n```\r\n\r\n`ocl-icd` is also a conda-forge package?\r\n"}}
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