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commit: 3b2013b913db53e99b3599ce383153ad8604ddf6 |
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Author: Alexey Shvetsov <alexxy <AT> gentoo <DOT> org> |
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AuthorDate: Mon Jul 11 18:35:53 2016 +0000 |
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Commit: Alexey Shvetsov <alexxy <AT> gentoo <DOT> org> |
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CommitDate: Mon Jul 11 18:35:53 2016 +0000 |
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URL: https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=3b2013b9 |
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|
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sci-chemistry/gromacs: Clean up old version |
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|
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Package-Manager: portage-2.3.0 |
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|
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sci-chemistry/gromacs/Manifest | 8 - |
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sci-chemistry/gromacs/gromacs-5.0.4-r1.ebuild | 284 -------------------------- |
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sci-chemistry/gromacs/gromacs-5.0.5.ebuild | 284 -------------------------- |
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sci-chemistry/gromacs/gromacs-5.0.6.ebuild | 284 -------------------------- |
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sci-chemistry/gromacs/gromacs-5.1.1.ebuild | 269 ------------------------ |
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sci-chemistry/gromacs/gromacs-5.1.ebuild | 269 ------------------------ |
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6 files changed, 1398 deletions(-) |
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|
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diff --git a/sci-chemistry/gromacs/Manifest b/sci-chemistry/gromacs/Manifest |
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index 350f1c8..ae53fba 100644 |
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--- a/sci-chemistry/gromacs/Manifest |
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+++ b/sci-chemistry/gromacs/Manifest |
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@@ -1,14 +1,6 @@ |
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DIST gromacs-5.0.4.tar.gz 26342095 SHA256 78068eeccc0b950018ddb45c41280e53c8bedae4639dca48e17c940f8896b23b SHA512 bc62b623bf71dcaa948aaf7563a3d3afa973da0702062848a20323db202e862dcee413197dacd1472866ccb40fce7709e283177b1c6c49514064f23e6c46b5ee WHIRLPOOL d8458d3d563e015e830622ae0c924e896765a6329ffe4cb1a31c7aef3c804f392d29e3f1db5617051e85058403422f7d69a160a6c7cc810564696d88f9d50bd4 |
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-DIST gromacs-5.0.5.tar.gz 26343524 SHA256 952c9d14879a12d03362b2233e47c51385dc99325bdde5223a2942938739bf4e SHA512 b45b2da5de48b0aa272b6d8583fd717762512fbd291ac35b414d23c430bf7b6db470f64e641728658e94784de9ddcde04242cfba09ff47931e01b85b8ca8fd73 WHIRLPOOL cc1f5f60d70780f8694acb16c96634d2aa8a16ff3d52be5ed4572dd37f80d9591f8060a0256f3e0f4a55069247398b8b52ad05efed691a0ab8619bc77aa64f76 |
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-DIST gromacs-5.0.6.tar.gz 26351063 SHA256 e07e950c4cd6cb84b83b145b70a15c25338ad6a7d7d1a0a83cdbd51cad954952 SHA512 5bd11d2ab79cc94c1ecf10bb05c239f7a4aed426ba3da0e536076e5145ff854889f9f0808d87a8ce007d86fce8eff9b6a809ae5fb68478528ea405c335dbffb2 WHIRLPOOL e5898fa247016a4c52e7ddc77ba03f0d39df2b863607a79f4b88f7029a2467e22cd84a507c18b52b4015619341699bbede28939be485613ac145b499a7d0998d |
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DIST gromacs-5.0.7.tar.gz 26358119 SHA256 23bc5ae28e0e274965966f0a00e44ec6ffbc28c5cd2d6b64a0aa0a2bc59472ec SHA512 612dba608fe6fd3a6fd69d1edeb97ec2975361ab44ea5219990901cecafbbe542a2c8bc6acc3f89b7fdcda77ab1b0762977ddc48cc1523155f7033e4e000660f WHIRLPOOL 26292f8751c2238f4fd9a63cb64888c2d236237dc140f08b45997b87b917b096d3d7c8451e5e0633e71cd770d7e7336dbbd3056777e290d0232a902ee4018e4b |
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-DIST gromacs-5.1.1.tar.gz 26551710 SHA256 9316fd0be320e2dd8c048f905df5be115e1b230c4ca4f3a7ef5892a1fc0bc212 SHA512 52404b4134cfbc867553a6b3f968500e3fc85b103abef6a7de9d0a9bf53c12ad1b908c35f9eed9376965db4a250c87cffe44d8c67247512c04ee84e7d1e07074 WHIRLPOOL 7a82e2cf6a73d4083ed4f1105dee4e392eaeb7e60e97a054a15e6a505e8a124d396005912b6c40acda53608cdd19ef2422c37b182733b4fe412e74defd7489b2 |
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DIST gromacs-5.1.2.tar.gz 26562718 SHA256 39d6f1d7ae8ba38cea6089da40676bfa4049a49903d21551abc030992a58f304 SHA512 ddd29bba97eaf8c32f7f5daa441c1aac85222881a9cf7757f55ef7f1a15f8f45cdc600eb90059053205d71652281c85601e107ff5928425afdb0c13e8ef1de69 WHIRLPOOL 12f217e480bd04cd0cfb68c22345cfe2cd77f9417f0f873ff61aeea734aa33d61810db4e1539cd265f1ffcf2df123353592c6176aa8dce236b64de74a97a76e0 |
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-DIST gromacs-5.1.tar.gz 26546875 SHA256 996b6061971e11942252de36b67b5cf35f02ce14adf80db8a3f079fc686c2743 SHA512 9655bd387773fa3ab0b7316854552a63945255ef02c5d9d1f98b32213b6642532b6bed88b06354d46d0ed235d6dc39e57a987a6585fb463e5aba80f366268301 WHIRLPOOL e5b4e90897c82a016911291f14daef41aa846143eae1cf5e6b9d552afe9ecbd3663d7df6350f5edd4778fa3a479c18b22efcabd9d49e1f4c304a3d39e35eaac4 |
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DIST regressiontests-5.0.4.tar.gz 65193251 SHA256 89ad9bc067035ac8f340319b538c446983d937b910067e871911d7afe2ecb3f0 SHA512 747725fa28c1c9525596bdeeb8809e45268e19036c11dac67d043aa1c51748688ca37eb6014eb7e819eb927a8b9ca2631d0ace4cdff8ed491b08c316c530ab65 WHIRLPOOL e15ccab0a0beefac41aeff11e2e596e971167f1590eed159ff82c4a8e3aec1d234287be597026951904ecfe6099f30ef3bcd48f2098b9f5201bde62e15fbc4f9 |
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-DIST regressiontests-5.0.5.tar.gz 65204335 SHA256 e48b9934de89c23a63c9adc8ba9a5aa397cf5a4d1746165d833c556d5ce54833 SHA512 1a1d1a3398ba5d3cc9f68e0f401437ccbdf3265f3ea1100b3b0d314d61ccd467ce3e8492ee09a645c5aaf9c1ca0acdf5ed6213a61bbd689833f3ca002bd5c79b WHIRLPOOL 882c9d8fa45720a5a71811db898aa33b9323bfe60340e8c4f4e2ef537f02efb531c0f3a721ead0e98bdb96f1e9d71df24d1d0faae448ab3da096c694e2a9b593 |
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-DIST regressiontests-5.0.6.tar.gz 65203643 SHA256 fd0a2408250dfc088ac9b401bc8702b8ba398a81db56c214d55f68f838d7c079 SHA512 dec41fbaa93784fb6438887eeef9f523add06032ae9801b83c492f5924872cd9b6a17e07d61cd7d8f999193d46384112e4c8046f4b2a3c28eb0c08f11c1ad8c6 WHIRLPOOL e6a8e99abc3b59be0f246769de0ebdef528caa24b930999dfbe0167a58696a68a31d0b819d2503e312977f0ec4d1ee2acb60e8eb691fab45e608250f2dfde728 |
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DIST regressiontests-5.0.7.tar.gz 65204051 SHA256 831c5f52b941826842a5312e3c6cd74a6410938bc5876d3f32d53215d64fb084 SHA512 2e93c84f62772eaf6facd45db67f51f751b4fa80923c71bc4fb293b33361b1314d714020bd8d50a1d0859aeedd67ce76f593e82ef31372128cbb8555eb6446b1 WHIRLPOOL b050f80946a76e752d53ccadd378ec0869f3221706a29f87d262a46fb11941b600d27b5388a5311a4fde53d60560f907150f884212e2d49a3df4b2519d1ceb3e |
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-DIST regressiontests-5.1.1.tar.gz 66711961 SHA256 2d51c57c6d584c4a6637b4b546eaf4b1f1713df10fe694544a82cc208a88cd78 SHA512 df865f0c900d52463cecc5482fee1c76d0c6a7f2dcb6ec657e03d1acf5ef8c60292781e6bbd43b9ebf2aab5a91782f474cef122ef118043c47eb3579656f75a6 WHIRLPOOL dd0b16ffdbd2e6eab141d327ed8922b3f038c80d414823c8d9f2e5e52cb5b820b177ec9f7a07dd794a29371eaa287a602bbd1bde9c9e895abd30c8da14f14226 |
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DIST regressiontests-5.1.2.tar.gz 66704132 SHA256 3e4704308da282e2e8e2550f6acae029353bf42ede4b1eccb20b157e399f3cf7 SHA512 b53fb36d5ce00361998ca9eb2121efc0d616e628ad81bf08c7fdc2cc43929cbc2e528cdd8260036235960ad96363b496aadd345d55fc100cdf02d680b2cca996 WHIRLPOOL 0859db2e0e51d56752f17d6021c2e5f6a6b820236aff731dd18335b3bde94899985c96bbe98f62c9144d8ff88fcc7e6f3091cf78618d7734345cfe71f0f6a026 |
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-DIST regressiontests-5.1.tar.gz 66707378 SHA256 c2d751a503d5e19962198f565edb29ea2aa67f863dce02e93b82b08a02487eca SHA512 1896f967362a1a3ae1ff13b405f4633754f97ad366c01b4b3b52368a01dae70e3b71cb171bba05c7d566fe8c3c4fcf8ce6538a6ff130143606fa2302b2e714c3 WHIRLPOOL 95b77a324a26ddc97f215ab7abc60a4d72f4fe39eaa43d14431d42d70875de71bcc9a8af90cceb4deaacead7c98e744b5200f867fb3c14bd6f2c1ff725825b8b |
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|
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diff --git a/sci-chemistry/gromacs/gromacs-5.0.4-r1.ebuild b/sci-chemistry/gromacs/gromacs-5.0.4-r1.ebuild |
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deleted file mode 100644 |
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index b5d7896..0000000 |
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--- a/sci-chemistry/gromacs/gromacs-5.0.4-r1.ebuild |
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+++ /dev/null |
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@@ -1,284 +0,0 @@ |
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-# Copyright 1999-2015 Gentoo Foundation |
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-# Distributed under the terms of the GNU General Public License v2 |
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-# $Id$ |
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- |
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-EAPI=5 |
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- |
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-CMAKE_MAKEFILE_GENERATOR="ninja" |
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- |
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-inherit bash-completion-r1 cmake-utils cuda eutils multilib readme.gentoo toolchain-funcs |
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- |
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-if [[ $PV = *9999* ]]; then |
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- EGIT_REPO_URI="git://git.gromacs.org/gromacs.git |
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- https://gerrit.gromacs.org/gromacs.git |
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- git://github.com/gromacs/gromacs.git |
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- http://repo.or.cz/r/gromacs.git" |
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- EGIT_BRANCH="release-5-0" |
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- inherit git-r3 |
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- KEYWORDS="" |
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-else |
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- SRC_URI="ftp://ftp.gromacs.org/pub/${PN}/${PN}-${PV/_/-}.tar.gz |
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- test? ( http://gerrit.gromacs.org/download/regressiontests-${PV}.tar.gz )" |
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- KEYWORDS="~alpha ~amd64 ~arm ~ppc64 ~sparc ~x86 ~amd64-linux ~x86-linux ~x64-macos ~x86-macos" |
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-fi |
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- |
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-ACCE_IUSE="cpu_flags_x86_sse2 cpu_flags_x86_sse4_1 cpu_flags_x86_fma4 cpu_flags_x86_avx cpu_flags_x86_avx2" |
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- |
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-DESCRIPTION="The ultimate molecular dynamics simulation package" |
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-HOMEPAGE="http://www.gromacs.org/" |
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- |
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-# see COPYING for details |
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-# http://repo.or.cz/w/gromacs.git/blob/HEAD:/COPYING |
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-# base, vmd plugins, fftpack from numpy, blas/lapck from netlib, memtestG80 library, mpi_thread lib |
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-LICENSE="LGPL-2.1 UoI-NCSA !mkl? ( !fftw? ( BSD ) !blas? ( BSD ) !lapack? ( BSD ) ) cuda? ( LGPL-3 ) threads? ( BSD )" |
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-SLOT="0/${PV}" |
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-IUSE="X blas boost cuda +doc -double-precision +fftw lapack +make-symlinks mkl mpi +offensive openmp +single-precision test +threads +tng ${ACCE_IUSE}" |
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- |
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-CDEPEND=" |
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- X? ( |
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- x11-libs/libX11 |
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- x11-libs/libSM |
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- x11-libs/libICE |
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- ) |
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- blas? ( virtual/blas ) |
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- boost? ( >=dev-libs/boost-1.55 ) |
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- cuda? ( >=dev-util/nvidia-cuda-toolkit-4.2.9-r1 ) |
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- fftw? ( sci-libs/fftw:3.0 ) |
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- lapack? ( virtual/lapack ) |
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- mkl? ( sci-libs/mkl ) |
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- mpi? ( virtual/mpi ) |
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- " |
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-DEPEND="${CDEPEND} |
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- virtual/pkgconfig |
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- doc? ( |
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- app-doc/doxygen |
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- dev-texlive/texlive-latex |
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- dev-texlive/texlive-latexextra |
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- media-gfx/imagemagick |
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- )" |
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-RDEPEND="${CDEPEND}" |
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- |
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-REQUIRED_USE=" |
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- || ( single-precision double-precision ) |
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- cuda? ( single-precision ) |
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- mkl? ( !blas !fftw !lapack )" |
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- |
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-DOCS=( AUTHORS README ) |
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- |
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-if [[ ${PV} != *9999 ]]; then |
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- S="${WORKDIR}/${PN}-${PV/_/-}" |
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-fi |
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- |
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-pkg_pretend() { |
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- [[ $(gcc-version) == "4.1" ]] && die "gcc 4.1 is not supported by gromacs" |
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- use openmp && ! tc-has-openmp && \ |
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- die "Please switch to an openmp compatible compiler" |
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-} |
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- |
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-src_unpack() { |
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- if [[ ${PV} != *9999 ]]; then |
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- default |
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- else |
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- git-r3_src_unpack |
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- if use test; then |
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- EGIT_REPO_URI="git://git.gromacs.org/regressiontests.git" \ |
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- EGIT_BRANCH="master" EGIT_COMMIT="master" \ |
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- EGIT_CHECKOUT_DIR="${WORKDIR}/regressiontests"\ |
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- git-r3_src_unpack |
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- fi |
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- fi |
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-} |
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- |
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-src_prepare() { |
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- #notes/todos |
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- # -on apple: there is framework support |
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- |
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- cmake-utils_src_prepare |
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- |
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- use cuda && cuda_src_prepare |
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- |
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- GMX_DIRS="" |
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- use single-precision && GMX_DIRS+=" float" |
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- use double-precision && GMX_DIRS+=" double" |
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- |
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- if use test; then |
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- for x in ${GMX_DIRS}; do |
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- mkdir -p "${WORKDIR}/${P}_${x}" || die |
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- cp -al "${WORKDIR}/regressiontests"* "${WORKDIR}/${P}_${x}/tests" || die |
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- done |
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- fi |
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- |
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- DOC_CONTENTS="Gromacs can use sci-chemistry/vmd to read additional file formats" |
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-} |
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- |
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-src_configure() { |
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- local mycmakeargs_pre=( ) extra fft_opts=( ) |
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- |
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- #go from slowest to fastest acceleration |
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- local acce="None" |
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- use cpu_flags_x86_sse2 && acce="SSE2" |
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- use cpu_flags_x86_sse4_1 && acce="SSE4.1" |
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- use cpu_flags_x86_fma4 && acce="AVX_128_FMA" |
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- use cpu_flags_x86_avx && acce="AVX_256" |
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- use cpu_flags_x86_avx2 && acce="AVX2_256" |
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- |
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- #to create man pages, build tree binaries are executed (bug #398437) |
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- [[ ${CHOST} = *-darwin* ]] && \ |
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- extra+=" -DCMAKE_BUILD_WITH_INSTALL_RPATH=OFF" |
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- |
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- if use fftw; then |
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- fft_opts=( -DGMX_FFT_LIBRARY=fftw3 ) |
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- elif use mkl && has_version "=sci-libs/mkl-10*"; then |
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- fft_opts=( -DGMX_FFT_LIBRARY=mkl |
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- -DMKL_INCLUDE_DIR="${MKLROOT}/include" |
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- -DMKL_LIBRARIES="$(echo /opt/intel/mkl/10.0.5.025/lib/*/libmkl.so);$(echo /opt/intel/mkl/10.0.5.025/lib/*/libiomp*.so)" |
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- ) |
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- elif use mkl; then |
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- local bits=$(get_libdir) |
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- fft_opts=( -DGMX_FFT_LIBRARY=mkl |
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- -DMKL_INCLUDE_DIR="$(echo /opt/intel/*/mkl/include)" |
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- -DMKL_LIBRARIES="$(echo /opt/intel/*/mkl/lib/*${bits/lib}/libmkl_rt.so)" |
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- ) |
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- else |
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- fft_opts=( -DGMX_FFT_LIBRARY=fftpack ) |
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- fi |
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- |
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- mycmakeargs_pre+=( |
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- "${fft_opts[@]}" |
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- $(cmake-utils_use X GMX_X11) |
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- $(cmake-utils_use blas GMX_EXTERNAL_BLAS) |
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- $(cmake-utils_use lapack GMX_EXTERNAL_LAPACK) |
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- $(cmake-utils_use openmp GMX_OPENMP) |
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- $(cmake-utils_use offensive GMX_COOL_QUOTES) |
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- $(cmake-utils_use boost GMX_EXTERNAL_BOOST) |
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- $(cmake-utils_use tng GMX_USE_TNG) |
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- $(cmake-utils_use doc GMX_BUILD_MANUAL) |
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- $(cmake-utils_use make-symlinks GMX_SYMLINK_OLD_BINARY_NAMES) |
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- -DGMX_DEFAULT_SUFFIX=off |
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- -DGMX_SIMD="$acce" |
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- -DGMX_LIB_INSTALL_DIR="$(get_libdir)" |
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- -DGMX_VMD_PLUGIN_PATH="${EPREFIX}/usr/$(get_libdir)/vmd/plugins/*/molfile/" |
206 |
- -DGMX_X86_AVX_GCC_MASKLOAD_BUG=OFF |
207 |
- -DGMX_USE_GCC44_BUG_WORKAROUND=OFF |
208 |
- -DBUILD_TESTING=OFF |
209 |
- -DGMX_BUILD_UNITTESTS=OFF |
210 |
- ${extra} |
211 |
- ) |
212 |
- |
213 |
- for x in ${GMX_DIRS}; do |
214 |
- einfo "Configuring for ${x} precision" |
215 |
- local suffix="" |
216 |
- #if we build single and double - double is suffixed |
217 |
- use double-precision && use single-precision && \ |
218 |
- [[ ${x} = "double" ]] && suffix="_d" |
219 |
- local p |
220 |
- [[ ${x} = "double" ]] && p="-DGMX_DOUBLE=ON" || p="-DGMX_DOUBLE=OFF" |
221 |
- local cuda=( "-DGMX_GPU=OFF" ) |
222 |
- [[ ${x} = "float" ]] && use cuda && \ |
223 |
- cuda=( -DGMX_GPU=ON ) |
224 |
- mycmakeargs=( |
225 |
- ${mycmakeargs_pre[@]} ${p} |
226 |
- -DGMX_MPI=OFF |
227 |
- $(cmake-utils_use threads GMX_THREAD_MPI) |
228 |
- "${cuda[@]}" |
229 |
- -DGMX_OPENMM=OFF |
230 |
- "$(use test && echo -DREGRESSIONTEST_PATH="${WORKDIR}/${P}_${x}/tests")" |
231 |
- -DGMX_BINARY_SUFFIX="${suffix}" |
232 |
- -DGMX_LIBS_SUFFIX="${suffix}" |
233 |
- ) |
234 |
- BUILD_DIR="${WORKDIR}/${P}_${x}" cmake-utils_src_configure |
235 |
- [[ ${CHOST} != *-darwin* ]] || \ |
236 |
- sed -i '/SET(CMAKE_INSTALL_NAME_DIR/s/^/#/' "${WORKDIR}/${P}_${x}/gentoo_rules.cmake" || die |
237 |
- use mpi || continue |
238 |
- einfo "Configuring for ${x} precision with mpi" |
239 |
- mycmakeargs=( |
240 |
- ${mycmakeargs_pre[@]} ${p} |
241 |
- -DGMX_THREAD_MPI=OFF |
242 |
- -DGMX_MPI=ON ${cuda} |
243 |
- -DGMX_OPENMM=OFF |
244 |
- -DGMX_BUILD_MDRUN_ONLY=ON |
245 |
- -DBUILD_SHARED_LIBS=OFF |
246 |
- -DGMX_BUILD_MANUAL=OFF |
247 |
- -DGMX_BINARY_SUFFIX="_mpi${suffix}" |
248 |
- -DGMX_LIBS_SUFFIX="_mpi${suffix}" |
249 |
- ) |
250 |
- BUILD_DIR="${WORKDIR}/${P}_${x}_mpi" CC="mpicc" cmake-utils_src_configure |
251 |
- [[ ${CHOST} != *-darwin* ]] || \ |
252 |
- sed -i '/SET(CMAKE_INSTALL_NAME_DIR/s/^/#/' "${WORKDIR}/${P}_${x}_mpi/gentoo_rules.cmake" || die |
253 |
- done |
254 |
-} |
255 |
- |
256 |
-src_compile() { |
257 |
- for x in ${GMX_DIRS}; do |
258 |
- einfo "Compiling for ${x} precision" |
259 |
- BUILD_DIR="${WORKDIR}/${P}_${x}"\ |
260 |
- cmake-utils_src_compile |
261 |
- # generate bash completion, not 100% necessary for |
262 |
- # rel ebuilds as bundled |
263 |
- BUILD_DIR="${WORKDIR}/${P}_${x}"\ |
264 |
- cmake-utils_src_compile completion |
265 |
- # not 100% necessary for rel ebuilds as available from website |
266 |
- if use doc; then |
267 |
- BUILD_DIR="${WORKDIR}/${P}_${x}"\ |
268 |
- cmake-utils_src_compile manual |
269 |
- fi |
270 |
- use mpi || continue |
271 |
- einfo "Compiling for ${x} precision with mpi" |
272 |
- BUILD_DIR="${WORKDIR}/${P}_${x}_mpi"\ |
273 |
- cmake-utils_src_compile |
274 |
- done |
275 |
-} |
276 |
- |
277 |
-src_test() { |
278 |
- for x in ${GMX_DIRS}; do |
279 |
- BUILD_DIR="${WORKDIR}/${P}_${x}"\ |
280 |
- cmake-utils_src_make check |
281 |
- done |
282 |
-} |
283 |
- |
284 |
-src_install() { |
285 |
- for x in ${GMX_DIRS}; do |
286 |
- BUILD_DIR="${WORKDIR}/${P}_${x}" \ |
287 |
- cmake-utils_src_install |
288 |
- if use doc; then |
289 |
- newdoc "${WORKDIR}/${P}_${x}"/docs/manual/gromacs.pdf "${PN}-manual-${PV}.pdf" |
290 |
- fi |
291 |
- #release ebuild does this automatically |
292 |
- if [[ $PV = *9999* ]]; then |
293 |
- cp "${WORKDIR}/${P}_${x}"/src/programs/completion/gmx-completion.bash "${ED}/usr/bin" || die |
294 |
- echo "complete -o nospace -F _gmx_compl gmx" > "${ED}/usr/bin/gmx-completion-gmx.bash" || die |
295 |
- fi |
296 |
- use mpi || continue |
297 |
- BUILD_DIR="${WORKDIR}/${P}_${x}_mpi" \ |
298 |
- cmake-utils_src_install |
299 |
- done |
300 |
- |
301 |
- if use tng; then |
302 |
- insinto /usr/include/tng |
303 |
- doins src/external/tng_io/include/tng/*h |
304 |
- fi |
305 |
- # drop unneeded stuff |
306 |
- rm "${ED}"usr/bin/GMXRC* || die |
307 |
- #concatenate all gmx-completion*, starting with gmx-completion.bash (fct defs) |
308 |
- #little hacckery as some gmx-completion* newlines ,so cat won't work |
309 |
- for x in "${ED}"usr/bin/gmx-completion{,?*}.bash ; do |
310 |
- echo $(<${x}) |
311 |
- done > "${T}"/gmx-bashcomp || die |
312 |
- newbashcomp "${T}"/gmx-bashcomp gmx |
313 |
- bashcomp_alias gmx mdrun |
314 |
- rm "${ED}"usr/bin/gmx-completion{,?*}.bash || die |
315 |
- if use double-precision && use single-precision; then |
316 |
- bashcomp_alias gmx gmx_d |
317 |
- bashcomp_alias gmx mdrun_d |
318 |
- fi |
319 |
- readme.gentoo_create_doc |
320 |
-} |
321 |
- |
322 |
-pkg_postinst() { |
323 |
- einfo |
324 |
- einfo "Please read and cite:" |
325 |
- einfo "Gromacs 4, J. Chem. Theory Comput. 4, 435 (2008). " |
326 |
- einfo "http://dx.doi.org/10.1021/ct700301q" |
327 |
- einfo |
328 |
- readme.gentoo_print_elog |
329 |
-} |
330 |
|
331 |
diff --git a/sci-chemistry/gromacs/gromacs-5.0.5.ebuild b/sci-chemistry/gromacs/gromacs-5.0.5.ebuild |
332 |
deleted file mode 100644 |
333 |
index b5d7896..0000000 |
334 |
--- a/sci-chemistry/gromacs/gromacs-5.0.5.ebuild |
335 |
+++ /dev/null |
336 |
@@ -1,284 +0,0 @@ |
337 |
-# Copyright 1999-2015 Gentoo Foundation |
338 |
-# Distributed under the terms of the GNU General Public License v2 |
339 |
-# $Id$ |
340 |
- |
341 |
-EAPI=5 |
342 |
- |
343 |
-CMAKE_MAKEFILE_GENERATOR="ninja" |
344 |
- |
345 |
-inherit bash-completion-r1 cmake-utils cuda eutils multilib readme.gentoo toolchain-funcs |
346 |
- |
347 |
-if [[ $PV = *9999* ]]; then |
348 |
- EGIT_REPO_URI="git://git.gromacs.org/gromacs.git |
349 |
- https://gerrit.gromacs.org/gromacs.git |
350 |
- git://github.com/gromacs/gromacs.git |
351 |
- http://repo.or.cz/r/gromacs.git" |
352 |
- EGIT_BRANCH="release-5-0" |
353 |
- inherit git-r3 |
354 |
- KEYWORDS="" |
355 |
-else |
356 |
- SRC_URI="ftp://ftp.gromacs.org/pub/${PN}/${PN}-${PV/_/-}.tar.gz |
357 |
- test? ( http://gerrit.gromacs.org/download/regressiontests-${PV}.tar.gz )" |
358 |
- KEYWORDS="~alpha ~amd64 ~arm ~ppc64 ~sparc ~x86 ~amd64-linux ~x86-linux ~x64-macos ~x86-macos" |
359 |
-fi |
360 |
- |
361 |
-ACCE_IUSE="cpu_flags_x86_sse2 cpu_flags_x86_sse4_1 cpu_flags_x86_fma4 cpu_flags_x86_avx cpu_flags_x86_avx2" |
362 |
- |
363 |
-DESCRIPTION="The ultimate molecular dynamics simulation package" |
364 |
-HOMEPAGE="http://www.gromacs.org/" |
365 |
- |
366 |
-# see COPYING for details |
367 |
-# http://repo.or.cz/w/gromacs.git/blob/HEAD:/COPYING |
368 |
-# base, vmd plugins, fftpack from numpy, blas/lapck from netlib, memtestG80 library, mpi_thread lib |
369 |
-LICENSE="LGPL-2.1 UoI-NCSA !mkl? ( !fftw? ( BSD ) !blas? ( BSD ) !lapack? ( BSD ) ) cuda? ( LGPL-3 ) threads? ( BSD )" |
370 |
-SLOT="0/${PV}" |
371 |
-IUSE="X blas boost cuda +doc -double-precision +fftw lapack +make-symlinks mkl mpi +offensive openmp +single-precision test +threads +tng ${ACCE_IUSE}" |
372 |
- |
373 |
-CDEPEND=" |
374 |
- X? ( |
375 |
- x11-libs/libX11 |
376 |
- x11-libs/libSM |
377 |
- x11-libs/libICE |
378 |
- ) |
379 |
- blas? ( virtual/blas ) |
380 |
- boost? ( >=dev-libs/boost-1.55 ) |
381 |
- cuda? ( >=dev-util/nvidia-cuda-toolkit-4.2.9-r1 ) |
382 |
- fftw? ( sci-libs/fftw:3.0 ) |
383 |
- lapack? ( virtual/lapack ) |
384 |
- mkl? ( sci-libs/mkl ) |
385 |
- mpi? ( virtual/mpi ) |
386 |
- " |
387 |
-DEPEND="${CDEPEND} |
388 |
- virtual/pkgconfig |
389 |
- doc? ( |
390 |
- app-doc/doxygen |
391 |
- dev-texlive/texlive-latex |
392 |
- dev-texlive/texlive-latexextra |
393 |
- media-gfx/imagemagick |
394 |
- )" |
395 |
-RDEPEND="${CDEPEND}" |
396 |
- |
397 |
-REQUIRED_USE=" |
398 |
- || ( single-precision double-precision ) |
399 |
- cuda? ( single-precision ) |
400 |
- mkl? ( !blas !fftw !lapack )" |
401 |
- |
402 |
-DOCS=( AUTHORS README ) |
403 |
- |
404 |
-if [[ ${PV} != *9999 ]]; then |
405 |
- S="${WORKDIR}/${PN}-${PV/_/-}" |
406 |
-fi |
407 |
- |
408 |
-pkg_pretend() { |
409 |
- [[ $(gcc-version) == "4.1" ]] && die "gcc 4.1 is not supported by gromacs" |
410 |
- use openmp && ! tc-has-openmp && \ |
411 |
- die "Please switch to an openmp compatible compiler" |
412 |
-} |
413 |
- |
414 |
-src_unpack() { |
415 |
- if [[ ${PV} != *9999 ]]; then |
416 |
- default |
417 |
- else |
418 |
- git-r3_src_unpack |
419 |
- if use test; then |
420 |
- EGIT_REPO_URI="git://git.gromacs.org/regressiontests.git" \ |
421 |
- EGIT_BRANCH="master" EGIT_COMMIT="master" \ |
422 |
- EGIT_CHECKOUT_DIR="${WORKDIR}/regressiontests"\ |
423 |
- git-r3_src_unpack |
424 |
- fi |
425 |
- fi |
426 |
-} |
427 |
- |
428 |
-src_prepare() { |
429 |
- #notes/todos |
430 |
- # -on apple: there is framework support |
431 |
- |
432 |
- cmake-utils_src_prepare |
433 |
- |
434 |
- use cuda && cuda_src_prepare |
435 |
- |
436 |
- GMX_DIRS="" |
437 |
- use single-precision && GMX_DIRS+=" float" |
438 |
- use double-precision && GMX_DIRS+=" double" |
439 |
- |
440 |
- if use test; then |
441 |
- for x in ${GMX_DIRS}; do |
442 |
- mkdir -p "${WORKDIR}/${P}_${x}" || die |
443 |
- cp -al "${WORKDIR}/regressiontests"* "${WORKDIR}/${P}_${x}/tests" || die |
444 |
- done |
445 |
- fi |
446 |
- |
447 |
- DOC_CONTENTS="Gromacs can use sci-chemistry/vmd to read additional file formats" |
448 |
-} |
449 |
- |
450 |
-src_configure() { |
451 |
- local mycmakeargs_pre=( ) extra fft_opts=( ) |
452 |
- |
453 |
- #go from slowest to fastest acceleration |
454 |
- local acce="None" |
455 |
- use cpu_flags_x86_sse2 && acce="SSE2" |
456 |
- use cpu_flags_x86_sse4_1 && acce="SSE4.1" |
457 |
- use cpu_flags_x86_fma4 && acce="AVX_128_FMA" |
458 |
- use cpu_flags_x86_avx && acce="AVX_256" |
459 |
- use cpu_flags_x86_avx2 && acce="AVX2_256" |
460 |
- |
461 |
- #to create man pages, build tree binaries are executed (bug #398437) |
462 |
- [[ ${CHOST} = *-darwin* ]] && \ |
463 |
- extra+=" -DCMAKE_BUILD_WITH_INSTALL_RPATH=OFF" |
464 |
- |
465 |
- if use fftw; then |
466 |
- fft_opts=( -DGMX_FFT_LIBRARY=fftw3 ) |
467 |
- elif use mkl && has_version "=sci-libs/mkl-10*"; then |
468 |
- fft_opts=( -DGMX_FFT_LIBRARY=mkl |
469 |
- -DMKL_INCLUDE_DIR="${MKLROOT}/include" |
470 |
- -DMKL_LIBRARIES="$(echo /opt/intel/mkl/10.0.5.025/lib/*/libmkl.so);$(echo /opt/intel/mkl/10.0.5.025/lib/*/libiomp*.so)" |
471 |
- ) |
472 |
- elif use mkl; then |
473 |
- local bits=$(get_libdir) |
474 |
- fft_opts=( -DGMX_FFT_LIBRARY=mkl |
475 |
- -DMKL_INCLUDE_DIR="$(echo /opt/intel/*/mkl/include)" |
476 |
- -DMKL_LIBRARIES="$(echo /opt/intel/*/mkl/lib/*${bits/lib}/libmkl_rt.so)" |
477 |
- ) |
478 |
- else |
479 |
- fft_opts=( -DGMX_FFT_LIBRARY=fftpack ) |
480 |
- fi |
481 |
- |
482 |
- mycmakeargs_pre+=( |
483 |
- "${fft_opts[@]}" |
484 |
- $(cmake-utils_use X GMX_X11) |
485 |
- $(cmake-utils_use blas GMX_EXTERNAL_BLAS) |
486 |
- $(cmake-utils_use lapack GMX_EXTERNAL_LAPACK) |
487 |
- $(cmake-utils_use openmp GMX_OPENMP) |
488 |
- $(cmake-utils_use offensive GMX_COOL_QUOTES) |
489 |
- $(cmake-utils_use boost GMX_EXTERNAL_BOOST) |
490 |
- $(cmake-utils_use tng GMX_USE_TNG) |
491 |
- $(cmake-utils_use doc GMX_BUILD_MANUAL) |
492 |
- $(cmake-utils_use make-symlinks GMX_SYMLINK_OLD_BINARY_NAMES) |
493 |
- -DGMX_DEFAULT_SUFFIX=off |
494 |
- -DGMX_SIMD="$acce" |
495 |
- -DGMX_LIB_INSTALL_DIR="$(get_libdir)" |
496 |
- -DGMX_VMD_PLUGIN_PATH="${EPREFIX}/usr/$(get_libdir)/vmd/plugins/*/molfile/" |
497 |
- -DGMX_X86_AVX_GCC_MASKLOAD_BUG=OFF |
498 |
- -DGMX_USE_GCC44_BUG_WORKAROUND=OFF |
499 |
- -DBUILD_TESTING=OFF |
500 |
- -DGMX_BUILD_UNITTESTS=OFF |
501 |
- ${extra} |
502 |
- ) |
503 |
- |
504 |
- for x in ${GMX_DIRS}; do |
505 |
- einfo "Configuring for ${x} precision" |
506 |
- local suffix="" |
507 |
- #if we build single and double - double is suffixed |
508 |
- use double-precision && use single-precision && \ |
509 |
- [[ ${x} = "double" ]] && suffix="_d" |
510 |
- local p |
511 |
- [[ ${x} = "double" ]] && p="-DGMX_DOUBLE=ON" || p="-DGMX_DOUBLE=OFF" |
512 |
- local cuda=( "-DGMX_GPU=OFF" ) |
513 |
- [[ ${x} = "float" ]] && use cuda && \ |
514 |
- cuda=( -DGMX_GPU=ON ) |
515 |
- mycmakeargs=( |
516 |
- ${mycmakeargs_pre[@]} ${p} |
517 |
- -DGMX_MPI=OFF |
518 |
- $(cmake-utils_use threads GMX_THREAD_MPI) |
519 |
- "${cuda[@]}" |
520 |
- -DGMX_OPENMM=OFF |
521 |
- "$(use test && echo -DREGRESSIONTEST_PATH="${WORKDIR}/${P}_${x}/tests")" |
522 |
- -DGMX_BINARY_SUFFIX="${suffix}" |
523 |
- -DGMX_LIBS_SUFFIX="${suffix}" |
524 |
- ) |
525 |
- BUILD_DIR="${WORKDIR}/${P}_${x}" cmake-utils_src_configure |
526 |
- [[ ${CHOST} != *-darwin* ]] || \ |
527 |
- sed -i '/SET(CMAKE_INSTALL_NAME_DIR/s/^/#/' "${WORKDIR}/${P}_${x}/gentoo_rules.cmake" || die |
528 |
- use mpi || continue |
529 |
- einfo "Configuring for ${x} precision with mpi" |
530 |
- mycmakeargs=( |
531 |
- ${mycmakeargs_pre[@]} ${p} |
532 |
- -DGMX_THREAD_MPI=OFF |
533 |
- -DGMX_MPI=ON ${cuda} |
534 |
- -DGMX_OPENMM=OFF |
535 |
- -DGMX_BUILD_MDRUN_ONLY=ON |
536 |
- -DBUILD_SHARED_LIBS=OFF |
537 |
- -DGMX_BUILD_MANUAL=OFF |
538 |
- -DGMX_BINARY_SUFFIX="_mpi${suffix}" |
539 |
- -DGMX_LIBS_SUFFIX="_mpi${suffix}" |
540 |
- ) |
541 |
- BUILD_DIR="${WORKDIR}/${P}_${x}_mpi" CC="mpicc" cmake-utils_src_configure |
542 |
- [[ ${CHOST} != *-darwin* ]] || \ |
543 |
- sed -i '/SET(CMAKE_INSTALL_NAME_DIR/s/^/#/' "${WORKDIR}/${P}_${x}_mpi/gentoo_rules.cmake" || die |
544 |
- done |
545 |
-} |
546 |
- |
547 |
-src_compile() { |
548 |
- for x in ${GMX_DIRS}; do |
549 |
- einfo "Compiling for ${x} precision" |
550 |
- BUILD_DIR="${WORKDIR}/${P}_${x}"\ |
551 |
- cmake-utils_src_compile |
552 |
- # generate bash completion, not 100% necessary for |
553 |
- # rel ebuilds as bundled |
554 |
- BUILD_DIR="${WORKDIR}/${P}_${x}"\ |
555 |
- cmake-utils_src_compile completion |
556 |
- # not 100% necessary for rel ebuilds as available from website |
557 |
- if use doc; then |
558 |
- BUILD_DIR="${WORKDIR}/${P}_${x}"\ |
559 |
- cmake-utils_src_compile manual |
560 |
- fi |
561 |
- use mpi || continue |
562 |
- einfo "Compiling for ${x} precision with mpi" |
563 |
- BUILD_DIR="${WORKDIR}/${P}_${x}_mpi"\ |
564 |
- cmake-utils_src_compile |
565 |
- done |
566 |
-} |
567 |
- |
568 |
-src_test() { |
569 |
- for x in ${GMX_DIRS}; do |
570 |
- BUILD_DIR="${WORKDIR}/${P}_${x}"\ |
571 |
- cmake-utils_src_make check |
572 |
- done |
573 |
-} |
574 |
- |
575 |
-src_install() { |
576 |
- for x in ${GMX_DIRS}; do |
577 |
- BUILD_DIR="${WORKDIR}/${P}_${x}" \ |
578 |
- cmake-utils_src_install |
579 |
- if use doc; then |
580 |
- newdoc "${WORKDIR}/${P}_${x}"/docs/manual/gromacs.pdf "${PN}-manual-${PV}.pdf" |
581 |
- fi |
582 |
- #release ebuild does this automatically |
583 |
- if [[ $PV = *9999* ]]; then |
584 |
- cp "${WORKDIR}/${P}_${x}"/src/programs/completion/gmx-completion.bash "${ED}/usr/bin" || die |
585 |
- echo "complete -o nospace -F _gmx_compl gmx" > "${ED}/usr/bin/gmx-completion-gmx.bash" || die |
586 |
- fi |
587 |
- use mpi || continue |
588 |
- BUILD_DIR="${WORKDIR}/${P}_${x}_mpi" \ |
589 |
- cmake-utils_src_install |
590 |
- done |
591 |
- |
592 |
- if use tng; then |
593 |
- insinto /usr/include/tng |
594 |
- doins src/external/tng_io/include/tng/*h |
595 |
- fi |
596 |
- # drop unneeded stuff |
597 |
- rm "${ED}"usr/bin/GMXRC* || die |
598 |
- #concatenate all gmx-completion*, starting with gmx-completion.bash (fct defs) |
599 |
- #little hacckery as some gmx-completion* newlines ,so cat won't work |
600 |
- for x in "${ED}"usr/bin/gmx-completion{,?*}.bash ; do |
601 |
- echo $(<${x}) |
602 |
- done > "${T}"/gmx-bashcomp || die |
603 |
- newbashcomp "${T}"/gmx-bashcomp gmx |
604 |
- bashcomp_alias gmx mdrun |
605 |
- rm "${ED}"usr/bin/gmx-completion{,?*}.bash || die |
606 |
- if use double-precision && use single-precision; then |
607 |
- bashcomp_alias gmx gmx_d |
608 |
- bashcomp_alias gmx mdrun_d |
609 |
- fi |
610 |
- readme.gentoo_create_doc |
611 |
-} |
612 |
- |
613 |
-pkg_postinst() { |
614 |
- einfo |
615 |
- einfo "Please read and cite:" |
616 |
- einfo "Gromacs 4, J. Chem. Theory Comput. 4, 435 (2008). " |
617 |
- einfo "http://dx.doi.org/10.1021/ct700301q" |
618 |
- einfo |
619 |
- readme.gentoo_print_elog |
620 |
-} |
621 |
|
622 |
diff --git a/sci-chemistry/gromacs/gromacs-5.0.6.ebuild b/sci-chemistry/gromacs/gromacs-5.0.6.ebuild |
623 |
deleted file mode 100644 |
624 |
index b5d7896..0000000 |
625 |
--- a/sci-chemistry/gromacs/gromacs-5.0.6.ebuild |
626 |
+++ /dev/null |
627 |
@@ -1,284 +0,0 @@ |
628 |
-# Copyright 1999-2015 Gentoo Foundation |
629 |
-# Distributed under the terms of the GNU General Public License v2 |
630 |
-# $Id$ |
631 |
- |
632 |
-EAPI=5 |
633 |
- |
634 |
-CMAKE_MAKEFILE_GENERATOR="ninja" |
635 |
- |
636 |
-inherit bash-completion-r1 cmake-utils cuda eutils multilib readme.gentoo toolchain-funcs |
637 |
- |
638 |
-if [[ $PV = *9999* ]]; then |
639 |
- EGIT_REPO_URI="git://git.gromacs.org/gromacs.git |
640 |
- https://gerrit.gromacs.org/gromacs.git |
641 |
- git://github.com/gromacs/gromacs.git |
642 |
- http://repo.or.cz/r/gromacs.git" |
643 |
- EGIT_BRANCH="release-5-0" |
644 |
- inherit git-r3 |
645 |
- KEYWORDS="" |
646 |
-else |
647 |
- SRC_URI="ftp://ftp.gromacs.org/pub/${PN}/${PN}-${PV/_/-}.tar.gz |
648 |
- test? ( http://gerrit.gromacs.org/download/regressiontests-${PV}.tar.gz )" |
649 |
- KEYWORDS="~alpha ~amd64 ~arm ~ppc64 ~sparc ~x86 ~amd64-linux ~x86-linux ~x64-macos ~x86-macos" |
650 |
-fi |
651 |
- |
652 |
-ACCE_IUSE="cpu_flags_x86_sse2 cpu_flags_x86_sse4_1 cpu_flags_x86_fma4 cpu_flags_x86_avx cpu_flags_x86_avx2" |
653 |
- |
654 |
-DESCRIPTION="The ultimate molecular dynamics simulation package" |
655 |
-HOMEPAGE="http://www.gromacs.org/" |
656 |
- |
657 |
-# see COPYING for details |
658 |
-# http://repo.or.cz/w/gromacs.git/blob/HEAD:/COPYING |
659 |
-# base, vmd plugins, fftpack from numpy, blas/lapck from netlib, memtestG80 library, mpi_thread lib |
660 |
-LICENSE="LGPL-2.1 UoI-NCSA !mkl? ( !fftw? ( BSD ) !blas? ( BSD ) !lapack? ( BSD ) ) cuda? ( LGPL-3 ) threads? ( BSD )" |
661 |
-SLOT="0/${PV}" |
662 |
-IUSE="X blas boost cuda +doc -double-precision +fftw lapack +make-symlinks mkl mpi +offensive openmp +single-precision test +threads +tng ${ACCE_IUSE}" |
663 |
- |
664 |
-CDEPEND=" |
665 |
- X? ( |
666 |
- x11-libs/libX11 |
667 |
- x11-libs/libSM |
668 |
- x11-libs/libICE |
669 |
- ) |
670 |
- blas? ( virtual/blas ) |
671 |
- boost? ( >=dev-libs/boost-1.55 ) |
672 |
- cuda? ( >=dev-util/nvidia-cuda-toolkit-4.2.9-r1 ) |
673 |
- fftw? ( sci-libs/fftw:3.0 ) |
674 |
- lapack? ( virtual/lapack ) |
675 |
- mkl? ( sci-libs/mkl ) |
676 |
- mpi? ( virtual/mpi ) |
677 |
- " |
678 |
-DEPEND="${CDEPEND} |
679 |
- virtual/pkgconfig |
680 |
- doc? ( |
681 |
- app-doc/doxygen |
682 |
- dev-texlive/texlive-latex |
683 |
- dev-texlive/texlive-latexextra |
684 |
- media-gfx/imagemagick |
685 |
- )" |
686 |
-RDEPEND="${CDEPEND}" |
687 |
- |
688 |
-REQUIRED_USE=" |
689 |
- || ( single-precision double-precision ) |
690 |
- cuda? ( single-precision ) |
691 |
- mkl? ( !blas !fftw !lapack )" |
692 |
- |
693 |
-DOCS=( AUTHORS README ) |
694 |
- |
695 |
-if [[ ${PV} != *9999 ]]; then |
696 |
- S="${WORKDIR}/${PN}-${PV/_/-}" |
697 |
-fi |
698 |
- |
699 |
-pkg_pretend() { |
700 |
- [[ $(gcc-version) == "4.1" ]] && die "gcc 4.1 is not supported by gromacs" |
701 |
- use openmp && ! tc-has-openmp && \ |
702 |
- die "Please switch to an openmp compatible compiler" |
703 |
-} |
704 |
- |
705 |
-src_unpack() { |
706 |
- if [[ ${PV} != *9999 ]]; then |
707 |
- default |
708 |
- else |
709 |
- git-r3_src_unpack |
710 |
- if use test; then |
711 |
- EGIT_REPO_URI="git://git.gromacs.org/regressiontests.git" \ |
712 |
- EGIT_BRANCH="master" EGIT_COMMIT="master" \ |
713 |
- EGIT_CHECKOUT_DIR="${WORKDIR}/regressiontests"\ |
714 |
- git-r3_src_unpack |
715 |
- fi |
716 |
- fi |
717 |
-} |
718 |
- |
719 |
-src_prepare() { |
720 |
- #notes/todos |
721 |
- # -on apple: there is framework support |
722 |
- |
723 |
- cmake-utils_src_prepare |
724 |
- |
725 |
- use cuda && cuda_src_prepare |
726 |
- |
727 |
- GMX_DIRS="" |
728 |
- use single-precision && GMX_DIRS+=" float" |
729 |
- use double-precision && GMX_DIRS+=" double" |
730 |
- |
731 |
- if use test; then |
732 |
- for x in ${GMX_DIRS}; do |
733 |
- mkdir -p "${WORKDIR}/${P}_${x}" || die |
734 |
- cp -al "${WORKDIR}/regressiontests"* "${WORKDIR}/${P}_${x}/tests" || die |
735 |
- done |
736 |
- fi |
737 |
- |
738 |
- DOC_CONTENTS="Gromacs can use sci-chemistry/vmd to read additional file formats" |
739 |
-} |
740 |
- |
741 |
-src_configure() { |
742 |
- local mycmakeargs_pre=( ) extra fft_opts=( ) |
743 |
- |
744 |
- #go from slowest to fastest acceleration |
745 |
- local acce="None" |
746 |
- use cpu_flags_x86_sse2 && acce="SSE2" |
747 |
- use cpu_flags_x86_sse4_1 && acce="SSE4.1" |
748 |
- use cpu_flags_x86_fma4 && acce="AVX_128_FMA" |
749 |
- use cpu_flags_x86_avx && acce="AVX_256" |
750 |
- use cpu_flags_x86_avx2 && acce="AVX2_256" |
751 |
- |
752 |
- #to create man pages, build tree binaries are executed (bug #398437) |
753 |
- [[ ${CHOST} = *-darwin* ]] && \ |
754 |
- extra+=" -DCMAKE_BUILD_WITH_INSTALL_RPATH=OFF" |
755 |
- |
756 |
- if use fftw; then |
757 |
- fft_opts=( -DGMX_FFT_LIBRARY=fftw3 ) |
758 |
- elif use mkl && has_version "=sci-libs/mkl-10*"; then |
759 |
- fft_opts=( -DGMX_FFT_LIBRARY=mkl |
760 |
- -DMKL_INCLUDE_DIR="${MKLROOT}/include" |
761 |
- -DMKL_LIBRARIES="$(echo /opt/intel/mkl/10.0.5.025/lib/*/libmkl.so);$(echo /opt/intel/mkl/10.0.5.025/lib/*/libiomp*.so)" |
762 |
- ) |
763 |
- elif use mkl; then |
764 |
- local bits=$(get_libdir) |
765 |
- fft_opts=( -DGMX_FFT_LIBRARY=mkl |
766 |
- -DMKL_INCLUDE_DIR="$(echo /opt/intel/*/mkl/include)" |
767 |
- -DMKL_LIBRARIES="$(echo /opt/intel/*/mkl/lib/*${bits/lib}/libmkl_rt.so)" |
768 |
- ) |
769 |
- else |
770 |
- fft_opts=( -DGMX_FFT_LIBRARY=fftpack ) |
771 |
- fi |
772 |
- |
773 |
- mycmakeargs_pre+=( |
774 |
- "${fft_opts[@]}" |
775 |
- $(cmake-utils_use X GMX_X11) |
776 |
- $(cmake-utils_use blas GMX_EXTERNAL_BLAS) |
777 |
- $(cmake-utils_use lapack GMX_EXTERNAL_LAPACK) |
778 |
- $(cmake-utils_use openmp GMX_OPENMP) |
779 |
- $(cmake-utils_use offensive GMX_COOL_QUOTES) |
780 |
- $(cmake-utils_use boost GMX_EXTERNAL_BOOST) |
781 |
- $(cmake-utils_use tng GMX_USE_TNG) |
782 |
- $(cmake-utils_use doc GMX_BUILD_MANUAL) |
783 |
- $(cmake-utils_use make-symlinks GMX_SYMLINK_OLD_BINARY_NAMES) |
784 |
- -DGMX_DEFAULT_SUFFIX=off |
785 |
- -DGMX_SIMD="$acce" |
786 |
- -DGMX_LIB_INSTALL_DIR="$(get_libdir)" |
787 |
- -DGMX_VMD_PLUGIN_PATH="${EPREFIX}/usr/$(get_libdir)/vmd/plugins/*/molfile/" |
788 |
- -DGMX_X86_AVX_GCC_MASKLOAD_BUG=OFF |
789 |
- -DGMX_USE_GCC44_BUG_WORKAROUND=OFF |
790 |
- -DBUILD_TESTING=OFF |
791 |
- -DGMX_BUILD_UNITTESTS=OFF |
792 |
- ${extra} |
793 |
- ) |
794 |
- |
795 |
- for x in ${GMX_DIRS}; do |
796 |
- einfo "Configuring for ${x} precision" |
797 |
- local suffix="" |
798 |
- #if we build single and double - double is suffixed |
799 |
- use double-precision && use single-precision && \ |
800 |
- [[ ${x} = "double" ]] && suffix="_d" |
801 |
- local p |
802 |
- [[ ${x} = "double" ]] && p="-DGMX_DOUBLE=ON" || p="-DGMX_DOUBLE=OFF" |
803 |
- local cuda=( "-DGMX_GPU=OFF" ) |
804 |
- [[ ${x} = "float" ]] && use cuda && \ |
805 |
- cuda=( -DGMX_GPU=ON ) |
806 |
- mycmakeargs=( |
807 |
- ${mycmakeargs_pre[@]} ${p} |
808 |
- -DGMX_MPI=OFF |
809 |
- $(cmake-utils_use threads GMX_THREAD_MPI) |
810 |
- "${cuda[@]}" |
811 |
- -DGMX_OPENMM=OFF |
812 |
- "$(use test && echo -DREGRESSIONTEST_PATH="${WORKDIR}/${P}_${x}/tests")" |
813 |
- -DGMX_BINARY_SUFFIX="${suffix}" |
814 |
- -DGMX_LIBS_SUFFIX="${suffix}" |
815 |
- ) |
816 |
- BUILD_DIR="${WORKDIR}/${P}_${x}" cmake-utils_src_configure |
817 |
- [[ ${CHOST} != *-darwin* ]] || \ |
818 |
- sed -i '/SET(CMAKE_INSTALL_NAME_DIR/s/^/#/' "${WORKDIR}/${P}_${x}/gentoo_rules.cmake" || die |
819 |
- use mpi || continue |
820 |
- einfo "Configuring for ${x} precision with mpi" |
821 |
- mycmakeargs=( |
822 |
- ${mycmakeargs_pre[@]} ${p} |
823 |
- -DGMX_THREAD_MPI=OFF |
824 |
- -DGMX_MPI=ON ${cuda} |
825 |
- -DGMX_OPENMM=OFF |
826 |
- -DGMX_BUILD_MDRUN_ONLY=ON |
827 |
- -DBUILD_SHARED_LIBS=OFF |
828 |
- -DGMX_BUILD_MANUAL=OFF |
829 |
- -DGMX_BINARY_SUFFIX="_mpi${suffix}" |
830 |
- -DGMX_LIBS_SUFFIX="_mpi${suffix}" |
831 |
- ) |
832 |
- BUILD_DIR="${WORKDIR}/${P}_${x}_mpi" CC="mpicc" cmake-utils_src_configure |
833 |
- [[ ${CHOST} != *-darwin* ]] || \ |
834 |
- sed -i '/SET(CMAKE_INSTALL_NAME_DIR/s/^/#/' "${WORKDIR}/${P}_${x}_mpi/gentoo_rules.cmake" || die |
835 |
- done |
836 |
-} |
837 |
- |
838 |
-src_compile() { |
839 |
- for x in ${GMX_DIRS}; do |
840 |
- einfo "Compiling for ${x} precision" |
841 |
- BUILD_DIR="${WORKDIR}/${P}_${x}"\ |
842 |
- cmake-utils_src_compile |
843 |
- # generate bash completion, not 100% necessary for |
844 |
- # rel ebuilds as bundled |
845 |
- BUILD_DIR="${WORKDIR}/${P}_${x}"\ |
846 |
- cmake-utils_src_compile completion |
847 |
- # not 100% necessary for rel ebuilds as available from website |
848 |
- if use doc; then |
849 |
- BUILD_DIR="${WORKDIR}/${P}_${x}"\ |
850 |
- cmake-utils_src_compile manual |
851 |
- fi |
852 |
- use mpi || continue |
853 |
- einfo "Compiling for ${x} precision with mpi" |
854 |
- BUILD_DIR="${WORKDIR}/${P}_${x}_mpi"\ |
855 |
- cmake-utils_src_compile |
856 |
- done |
857 |
-} |
858 |
- |
859 |
-src_test() { |
860 |
- for x in ${GMX_DIRS}; do |
861 |
- BUILD_DIR="${WORKDIR}/${P}_${x}"\ |
862 |
- cmake-utils_src_make check |
863 |
- done |
864 |
-} |
865 |
- |
866 |
-src_install() { |
867 |
- for x in ${GMX_DIRS}; do |
868 |
- BUILD_DIR="${WORKDIR}/${P}_${x}" \ |
869 |
- cmake-utils_src_install |
870 |
- if use doc; then |
871 |
- newdoc "${WORKDIR}/${P}_${x}"/docs/manual/gromacs.pdf "${PN}-manual-${PV}.pdf" |
872 |
- fi |
873 |
- #release ebuild does this automatically |
874 |
- if [[ $PV = *9999* ]]; then |
875 |
- cp "${WORKDIR}/${P}_${x}"/src/programs/completion/gmx-completion.bash "${ED}/usr/bin" || die |
876 |
- echo "complete -o nospace -F _gmx_compl gmx" > "${ED}/usr/bin/gmx-completion-gmx.bash" || die |
877 |
- fi |
878 |
- use mpi || continue |
879 |
- BUILD_DIR="${WORKDIR}/${P}_${x}_mpi" \ |
880 |
- cmake-utils_src_install |
881 |
- done |
882 |
- |
883 |
- if use tng; then |
884 |
- insinto /usr/include/tng |
885 |
- doins src/external/tng_io/include/tng/*h |
886 |
- fi |
887 |
- # drop unneeded stuff |
888 |
- rm "${ED}"usr/bin/GMXRC* || die |
889 |
- #concatenate all gmx-completion*, starting with gmx-completion.bash (fct defs) |
890 |
- #little hacckery as some gmx-completion* newlines ,so cat won't work |
891 |
- for x in "${ED}"usr/bin/gmx-completion{,?*}.bash ; do |
892 |
- echo $(<${x}) |
893 |
- done > "${T}"/gmx-bashcomp || die |
894 |
- newbashcomp "${T}"/gmx-bashcomp gmx |
895 |
- bashcomp_alias gmx mdrun |
896 |
- rm "${ED}"usr/bin/gmx-completion{,?*}.bash || die |
897 |
- if use double-precision && use single-precision; then |
898 |
- bashcomp_alias gmx gmx_d |
899 |
- bashcomp_alias gmx mdrun_d |
900 |
- fi |
901 |
- readme.gentoo_create_doc |
902 |
-} |
903 |
- |
904 |
-pkg_postinst() { |
905 |
- einfo |
906 |
- einfo "Please read and cite:" |
907 |
- einfo "Gromacs 4, J. Chem. Theory Comput. 4, 435 (2008). " |
908 |
- einfo "http://dx.doi.org/10.1021/ct700301q" |
909 |
- einfo |
910 |
- readme.gentoo_print_elog |
911 |
-} |
912 |
|
913 |
diff --git a/sci-chemistry/gromacs/gromacs-5.1.1.ebuild b/sci-chemistry/gromacs/gromacs-5.1.1.ebuild |
914 |
deleted file mode 100644 |
915 |
index 031dfca..0000000 |
916 |
--- a/sci-chemistry/gromacs/gromacs-5.1.1.ebuild |
917 |
+++ /dev/null |
918 |
@@ -1,269 +0,0 @@ |
919 |
-# Copyright 1999-2015 Gentoo Foundation |
920 |
-# Distributed under the terms of the GNU General Public License v2 |
921 |
-# $Id$ |
922 |
- |
923 |
-EAPI=5 |
924 |
- |
925 |
-CMAKE_MAKEFILE_GENERATOR="ninja" |
926 |
- |
927 |
-inherit bash-completion-r1 cmake-utils cuda eutils multilib readme.gentoo toolchain-funcs |
928 |
- |
929 |
-if [[ $PV = *9999* ]]; then |
930 |
- EGIT_REPO_URI="git://git.gromacs.org/gromacs.git |
931 |
- https://gerrit.gromacs.org/gromacs.git |
932 |
- git://github.com/gromacs/gromacs.git |
933 |
- http://repo.or.cz/r/gromacs.git" |
934 |
- [[ $PV = 9999 ]] && EGIT_BRANCH="master" || EGIT_BRANCH="release-${PV:0:1}-${PV:2:1}" |
935 |
- inherit git-r3 |
936 |
- KEYWORDS="" |
937 |
-else |
938 |
- SRC_URI="ftp://ftp.gromacs.org/pub/${PN}/${PN}-${PV/_/-}.tar.gz |
939 |
- test? ( http://gerrit.gromacs.org/download/regressiontests-${PV}.tar.gz )" |
940 |
- KEYWORDS="~alpha ~amd64 ~arm ~ppc64 ~sparc ~x86 ~amd64-linux ~x86-linux ~x64-macos ~x86-macos" |
941 |
-fi |
942 |
- |
943 |
-ACCE_IUSE="cpu_flags_x86_sse2 cpu_flags_x86_sse4_1 cpu_flags_x86_fma4 cpu_flags_x86_avx cpu_flags_x86_avx2" |
944 |
- |
945 |
-DESCRIPTION="The ultimate molecular dynamics simulation package" |
946 |
-HOMEPAGE="http://www.gromacs.org/" |
947 |
- |
948 |
-# see COPYING for details |
949 |
-# http://repo.or.cz/w/gromacs.git/blob/HEAD:/COPYING |
950 |
-# base, vmd plugins, fftpack from numpy, blas/lapck from netlib, memtestG80 library, mpi_thread lib |
951 |
-LICENSE="LGPL-2.1 UoI-NCSA !mkl? ( !fftw? ( BSD ) !blas? ( BSD ) !lapack? ( BSD ) ) cuda? ( LGPL-3 ) threads? ( BSD )" |
952 |
-SLOT="0/${PV}" |
953 |
-IUSE="X blas boost cuda +doc -double-precision +fftw lapack mkl mpi +offensive openmp +single-precision test +threads +tng ${ACCE_IUSE}" |
954 |
- |
955 |
-CDEPEND=" |
956 |
- X? ( |
957 |
- x11-libs/libX11 |
958 |
- x11-libs/libSM |
959 |
- x11-libs/libICE |
960 |
- ) |
961 |
- blas? ( virtual/blas ) |
962 |
- boost? ( >=dev-libs/boost-1.55 ) |
963 |
- cuda? ( >=dev-util/nvidia-cuda-toolkit-4.2.9-r1 ) |
964 |
- fftw? ( sci-libs/fftw:3.0 ) |
965 |
- lapack? ( virtual/lapack ) |
966 |
- mkl? ( sci-libs/mkl ) |
967 |
- mpi? ( virtual/mpi ) |
968 |
- " |
969 |
-DEPEND="${CDEPEND} |
970 |
- virtual/pkgconfig |
971 |
- doc? ( |
972 |
- app-doc/doxygen |
973 |
- dev-texlive/texlive-latex |
974 |
- dev-texlive/texlive-latexextra |
975 |
- media-gfx/imagemagick |
976 |
- )" |
977 |
-RDEPEND="${CDEPEND}" |
978 |
- |
979 |
-REQUIRED_USE=" |
980 |
- || ( single-precision double-precision ) |
981 |
- cuda? ( single-precision ) |
982 |
- mkl? ( !blas !fftw !lapack )" |
983 |
- |
984 |
-DOCS=( AUTHORS README ) |
985 |
- |
986 |
-if [[ ${PV} != *9999 ]]; then |
987 |
- S="${WORKDIR}/${PN}-${PV/_/-}" |
988 |
-fi |
989 |
- |
990 |
-pkg_pretend() { |
991 |
- [[ $(gcc-version) == "4.1" ]] && die "gcc 4.1 is not supported by gromacs" |
992 |
- use openmp && ! tc-has-openmp && \ |
993 |
- die "Please switch to an openmp compatible compiler" |
994 |
-} |
995 |
- |
996 |
-src_unpack() { |
997 |
- if [[ ${PV} != *9999 ]]; then |
998 |
- default |
999 |
- else |
1000 |
- git-r3_src_unpack |
1001 |
- if use test; then |
1002 |
- EGIT_REPO_URI="git://git.gromacs.org/regressiontests.git" \ |
1003 |
- EGIT_BRANCH="${EGIT_BRANCH}" \ |
1004 |
- EGIT_CHECKOUT_DIR="${WORKDIR}/regressiontests"\ |
1005 |
- git-r3_src_unpack |
1006 |
- fi |
1007 |
- fi |
1008 |
-} |
1009 |
- |
1010 |
-src_prepare() { |
1011 |
- #notes/todos |
1012 |
- # -on apple: there is framework support |
1013 |
- |
1014 |
- cmake-utils_src_prepare |
1015 |
- |
1016 |
- use cuda && cuda_src_prepare |
1017 |
- |
1018 |
- GMX_DIRS="" |
1019 |
- use single-precision && GMX_DIRS+=" float" |
1020 |
- use double-precision && GMX_DIRS+=" double" |
1021 |
- |
1022 |
- if use test; then |
1023 |
- for x in ${GMX_DIRS}; do |
1024 |
- mkdir -p "${WORKDIR}/${P}_${x}" || die |
1025 |
- cp -al "${WORKDIR}/regressiontests"* "${WORKDIR}/${P}_${x}/tests" || die |
1026 |
- done |
1027 |
- fi |
1028 |
- |
1029 |
- DOC_CONTENTS="Gromacs can use sci-chemistry/vmd to read additional file formats" |
1030 |
-} |
1031 |
- |
1032 |
-src_configure() { |
1033 |
- local mycmakeargs_pre=( ) extra fft_opts=( ) |
1034 |
- |
1035 |
- #go from slowest to fastest acceleration |
1036 |
- local acce="None" |
1037 |
- use cpu_flags_x86_sse2 && acce="SSE2" |
1038 |
- use cpu_flags_x86_sse4_1 && acce="SSE4.1" |
1039 |
- use cpu_flags_x86_fma4 && acce="AVX_128_FMA" |
1040 |
- use cpu_flags_x86_avx && acce="AVX_256" |
1041 |
- use cpu_flags_x86_avx2 && acce="AVX2_256" |
1042 |
- |
1043 |
- #to create man pages, build tree binaries are executed (bug #398437) |
1044 |
- [[ ${CHOST} = *-darwin* ]] && \ |
1045 |
- extra+=" -DCMAKE_BUILD_WITH_INSTALL_RPATH=OFF" |
1046 |
- |
1047 |
- if use fftw; then |
1048 |
- fft_opts=( -DGMX_FFT_LIBRARY=fftw3 ) |
1049 |
- elif use mkl && has_version "=sci-libs/mkl-10*"; then |
1050 |
- fft_opts=( -DGMX_FFT_LIBRARY=mkl |
1051 |
- -DMKL_INCLUDE_DIR="${MKLROOT}/include" |
1052 |
- -DMKL_LIBRARIES="$(echo /opt/intel/mkl/10.0.5.025/lib/*/libmkl.so);$(echo /opt/intel/mkl/10.0.5.025/lib/*/libiomp*.so)" |
1053 |
- ) |
1054 |
- elif use mkl; then |
1055 |
- local bits=$(get_libdir) |
1056 |
- fft_opts=( -DGMX_FFT_LIBRARY=mkl |
1057 |
- -DMKL_INCLUDE_DIR="$(echo /opt/intel/*/mkl/include)" |
1058 |
- -DMKL_LIBRARIES="$(echo /opt/intel/*/mkl/lib/*${bits/lib}/libmkl_rt.so)" |
1059 |
- ) |
1060 |
- else |
1061 |
- fft_opts=( -DGMX_FFT_LIBRARY=fftpack ) |
1062 |
- fi |
1063 |
- |
1064 |
- mycmakeargs_pre+=( |
1065 |
- "${fft_opts[@]}" |
1066 |
- $(cmake-utils_use X GMX_X11) |
1067 |
- $(cmake-utils_use blas GMX_EXTERNAL_BLAS) |
1068 |
- $(cmake-utils_use lapack GMX_EXTERNAL_LAPACK) |
1069 |
- $(cmake-utils_use openmp GMX_OPENMP) |
1070 |
- $(cmake-utils_use offensive GMX_COOL_QUOTES) |
1071 |
- $(cmake-utils_use boost GMX_EXTERNAL_BOOST) |
1072 |
- $(cmake-utils_use tng GMX_USE_TNG) |
1073 |
- $(cmake-utils_use doc GMX_BUILD_MANUAL) |
1074 |
- -DGMX_DEFAULT_SUFFIX=off |
1075 |
- -DGMX_SIMD="$acce" |
1076 |
- -DGMX_LIB_INSTALL_DIR="$(get_libdir)" |
1077 |
- -DGMX_VMD_PLUGIN_PATH="${EPREFIX}/usr/$(get_libdir)/vmd/plugins/*/molfile/" |
1078 |
- -DGMX_X86_AVX_GCC_MASKLOAD_BUG=OFF |
1079 |
- -DGMX_USE_GCC44_BUG_WORKAROUND=OFF |
1080 |
- -DBUILD_TESTING=OFF |
1081 |
- -DGMX_BUILD_UNITTESTS=OFF |
1082 |
- ${extra} |
1083 |
- ) |
1084 |
- |
1085 |
- for x in ${GMX_DIRS}; do |
1086 |
- einfo "Configuring for ${x} precision" |
1087 |
- local suffix="" |
1088 |
- #if we build single and double - double is suffixed |
1089 |
- use double-precision && use single-precision && \ |
1090 |
- [[ ${x} = "double" ]] && suffix="_d" |
1091 |
- local p |
1092 |
- [[ ${x} = "double" ]] && p="-DGMX_DOUBLE=ON" || p="-DGMX_DOUBLE=OFF" |
1093 |
- local cuda=( "-DGMX_GPU=OFF" ) |
1094 |
- [[ ${x} = "float" ]] && use cuda && \ |
1095 |
- cuda=( -DGMX_GPU=ON ) |
1096 |
- mycmakeargs=( |
1097 |
- ${mycmakeargs_pre[@]} ${p} |
1098 |
- -DGMX_MPI=OFF |
1099 |
- $(cmake-utils_use threads GMX_THREAD_MPI) |
1100 |
- "${cuda[@]}" |
1101 |
- -DGMX_OPENMM=OFF |
1102 |
- "$(use test && echo -DREGRESSIONTEST_PATH="${WORKDIR}/${P}_${x}/tests")" |
1103 |
- -DGMX_BINARY_SUFFIX="${suffix}" |
1104 |
- -DGMX_LIBS_SUFFIX="${suffix}" |
1105 |
- ) |
1106 |
- BUILD_DIR="${WORKDIR}/${P}_${x}" cmake-utils_src_configure |
1107 |
- [[ ${CHOST} != *-darwin* ]] || \ |
1108 |
- sed -i '/SET(CMAKE_INSTALL_NAME_DIR/s/^/#/' "${WORKDIR}/${P}_${x}/gentoo_rules.cmake" || die |
1109 |
- use mpi || continue |
1110 |
- einfo "Configuring for ${x} precision with mpi" |
1111 |
- mycmakeargs=( |
1112 |
- ${mycmakeargs_pre[@]} ${p} |
1113 |
- -DGMX_THREAD_MPI=OFF |
1114 |
- -DGMX_MPI=ON ${cuda} |
1115 |
- -DGMX_OPENMM=OFF |
1116 |
- -DGMX_BUILD_MDRUN_ONLY=ON |
1117 |
- -DBUILD_SHARED_LIBS=OFF |
1118 |
- -DGMX_BUILD_MANUAL=OFF |
1119 |
- -DGMX_BINARY_SUFFIX="_mpi${suffix}" |
1120 |
- -DGMX_LIBS_SUFFIX="_mpi${suffix}" |
1121 |
- ) |
1122 |
- BUILD_DIR="${WORKDIR}/${P}_${x}_mpi" CC="mpicc" cmake-utils_src_configure |
1123 |
- [[ ${CHOST} != *-darwin* ]] || \ |
1124 |
- sed -i '/SET(CMAKE_INSTALL_NAME_DIR/s/^/#/' "${WORKDIR}/${P}_${x}_mpi/gentoo_rules.cmake" || die |
1125 |
- done |
1126 |
-} |
1127 |
- |
1128 |
-src_compile() { |
1129 |
- for x in ${GMX_DIRS}; do |
1130 |
- einfo "Compiling for ${x} precision" |
1131 |
- BUILD_DIR="${WORKDIR}/${P}_${x}"\ |
1132 |
- cmake-utils_src_compile |
1133 |
- # not 100% necessary for rel ebuilds as available from website |
1134 |
- if use doc; then |
1135 |
- BUILD_DIR="${WORKDIR}/${P}_${x}"\ |
1136 |
- cmake-utils_src_compile manual |
1137 |
- fi |
1138 |
- use mpi || continue |
1139 |
- einfo "Compiling for ${x} precision with mpi" |
1140 |
- BUILD_DIR="${WORKDIR}/${P}_${x}_mpi"\ |
1141 |
- cmake-utils_src_compile |
1142 |
- done |
1143 |
-} |
1144 |
- |
1145 |
-src_test() { |
1146 |
- for x in ${GMX_DIRS}; do |
1147 |
- BUILD_DIR="${WORKDIR}/${P}_${x}"\ |
1148 |
- cmake-utils_src_make check |
1149 |
- done |
1150 |
-} |
1151 |
- |
1152 |
-src_install() { |
1153 |
- for x in ${GMX_DIRS}; do |
1154 |
- BUILD_DIR="${WORKDIR}/${P}_${x}" \ |
1155 |
- cmake-utils_src_install |
1156 |
- if use doc; then |
1157 |
- newdoc "${WORKDIR}/${P}_${x}"/docs/manual/gromacs.pdf "${PN}-manual-${PV}.pdf" |
1158 |
- fi |
1159 |
- use mpi || continue |
1160 |
- BUILD_DIR="${WORKDIR}/${P}_${x}_mpi" \ |
1161 |
- cmake-utils_src_install |
1162 |
- done |
1163 |
- |
1164 |
- if use tng; then |
1165 |
- insinto /usr/include/tng |
1166 |
- doins src/external/tng_io/include/tng/*h |
1167 |
- fi |
1168 |
- # drop unneeded stuff |
1169 |
- rm "${ED}"usr/bin/GMXRC* || die |
1170 |
- for x in "${ED}"usr/bin/gmx-completion-*.bash ; do |
1171 |
- local n=${x##*/gmx-completion-} |
1172 |
- n="${n%.bash}" |
1173 |
- cat "${ED}"usr/bin/gmx-completion.bash "$x" > "${T}/${n}" || die |
1174 |
- newbashcomp "${T}"/"${n}" "${n}" |
1175 |
- done |
1176 |
- rm "${ED}"usr/bin/gmx-completion*.bash || die |
1177 |
- readme.gentoo_create_doc |
1178 |
-} |
1179 |
- |
1180 |
-pkg_postinst() { |
1181 |
- einfo |
1182 |
- einfo "Please read and cite:" |
1183 |
- einfo "Gromacs 4, J. Chem. Theory Comput. 4, 435 (2008). " |
1184 |
- einfo "http://dx.doi.org/10.1021/ct700301q" |
1185 |
- einfo |
1186 |
- readme.gentoo_print_elog |
1187 |
-} |
1188 |
|
1189 |
diff --git a/sci-chemistry/gromacs/gromacs-5.1.ebuild b/sci-chemistry/gromacs/gromacs-5.1.ebuild |
1190 |
deleted file mode 100644 |
1191 |
index 031dfca..0000000 |
1192 |
--- a/sci-chemistry/gromacs/gromacs-5.1.ebuild |
1193 |
+++ /dev/null |
1194 |
@@ -1,269 +0,0 @@ |
1195 |
-# Copyright 1999-2015 Gentoo Foundation |
1196 |
-# Distributed under the terms of the GNU General Public License v2 |
1197 |
-# $Id$ |
1198 |
- |
1199 |
-EAPI=5 |
1200 |
- |
1201 |
-CMAKE_MAKEFILE_GENERATOR="ninja" |
1202 |
- |
1203 |
-inherit bash-completion-r1 cmake-utils cuda eutils multilib readme.gentoo toolchain-funcs |
1204 |
- |
1205 |
-if [[ $PV = *9999* ]]; then |
1206 |
- EGIT_REPO_URI="git://git.gromacs.org/gromacs.git |
1207 |
- https://gerrit.gromacs.org/gromacs.git |
1208 |
- git://github.com/gromacs/gromacs.git |
1209 |
- http://repo.or.cz/r/gromacs.git" |
1210 |
- [[ $PV = 9999 ]] && EGIT_BRANCH="master" || EGIT_BRANCH="release-${PV:0:1}-${PV:2:1}" |
1211 |
- inherit git-r3 |
1212 |
- KEYWORDS="" |
1213 |
-else |
1214 |
- SRC_URI="ftp://ftp.gromacs.org/pub/${PN}/${PN}-${PV/_/-}.tar.gz |
1215 |
- test? ( http://gerrit.gromacs.org/download/regressiontests-${PV}.tar.gz )" |
1216 |
- KEYWORDS="~alpha ~amd64 ~arm ~ppc64 ~sparc ~x86 ~amd64-linux ~x86-linux ~x64-macos ~x86-macos" |
1217 |
-fi |
1218 |
- |
1219 |
-ACCE_IUSE="cpu_flags_x86_sse2 cpu_flags_x86_sse4_1 cpu_flags_x86_fma4 cpu_flags_x86_avx cpu_flags_x86_avx2" |
1220 |
- |
1221 |
-DESCRIPTION="The ultimate molecular dynamics simulation package" |
1222 |
-HOMEPAGE="http://www.gromacs.org/" |
1223 |
- |
1224 |
-# see COPYING for details |
1225 |
-# http://repo.or.cz/w/gromacs.git/blob/HEAD:/COPYING |
1226 |
-# base, vmd plugins, fftpack from numpy, blas/lapck from netlib, memtestG80 library, mpi_thread lib |
1227 |
-LICENSE="LGPL-2.1 UoI-NCSA !mkl? ( !fftw? ( BSD ) !blas? ( BSD ) !lapack? ( BSD ) ) cuda? ( LGPL-3 ) threads? ( BSD )" |
1228 |
-SLOT="0/${PV}" |
1229 |
-IUSE="X blas boost cuda +doc -double-precision +fftw lapack mkl mpi +offensive openmp +single-precision test +threads +tng ${ACCE_IUSE}" |
1230 |
- |
1231 |
-CDEPEND=" |
1232 |
- X? ( |
1233 |
- x11-libs/libX11 |
1234 |
- x11-libs/libSM |
1235 |
- x11-libs/libICE |
1236 |
- ) |
1237 |
- blas? ( virtual/blas ) |
1238 |
- boost? ( >=dev-libs/boost-1.55 ) |
1239 |
- cuda? ( >=dev-util/nvidia-cuda-toolkit-4.2.9-r1 ) |
1240 |
- fftw? ( sci-libs/fftw:3.0 ) |
1241 |
- lapack? ( virtual/lapack ) |
1242 |
- mkl? ( sci-libs/mkl ) |
1243 |
- mpi? ( virtual/mpi ) |
1244 |
- " |
1245 |
-DEPEND="${CDEPEND} |
1246 |
- virtual/pkgconfig |
1247 |
- doc? ( |
1248 |
- app-doc/doxygen |
1249 |
- dev-texlive/texlive-latex |
1250 |
- dev-texlive/texlive-latexextra |
1251 |
- media-gfx/imagemagick |
1252 |
- )" |
1253 |
-RDEPEND="${CDEPEND}" |
1254 |
- |
1255 |
-REQUIRED_USE=" |
1256 |
- || ( single-precision double-precision ) |
1257 |
- cuda? ( single-precision ) |
1258 |
- mkl? ( !blas !fftw !lapack )" |
1259 |
- |
1260 |
-DOCS=( AUTHORS README ) |
1261 |
- |
1262 |
-if [[ ${PV} != *9999 ]]; then |
1263 |
- S="${WORKDIR}/${PN}-${PV/_/-}" |
1264 |
-fi |
1265 |
- |
1266 |
-pkg_pretend() { |
1267 |
- [[ $(gcc-version) == "4.1" ]] && die "gcc 4.1 is not supported by gromacs" |
1268 |
- use openmp && ! tc-has-openmp && \ |
1269 |
- die "Please switch to an openmp compatible compiler" |
1270 |
-} |
1271 |
- |
1272 |
-src_unpack() { |
1273 |
- if [[ ${PV} != *9999 ]]; then |
1274 |
- default |
1275 |
- else |
1276 |
- git-r3_src_unpack |
1277 |
- if use test; then |
1278 |
- EGIT_REPO_URI="git://git.gromacs.org/regressiontests.git" \ |
1279 |
- EGIT_BRANCH="${EGIT_BRANCH}" \ |
1280 |
- EGIT_CHECKOUT_DIR="${WORKDIR}/regressiontests"\ |
1281 |
- git-r3_src_unpack |
1282 |
- fi |
1283 |
- fi |
1284 |
-} |
1285 |
- |
1286 |
-src_prepare() { |
1287 |
- #notes/todos |
1288 |
- # -on apple: there is framework support |
1289 |
- |
1290 |
- cmake-utils_src_prepare |
1291 |
- |
1292 |
- use cuda && cuda_src_prepare |
1293 |
- |
1294 |
- GMX_DIRS="" |
1295 |
- use single-precision && GMX_DIRS+=" float" |
1296 |
- use double-precision && GMX_DIRS+=" double" |
1297 |
- |
1298 |
- if use test; then |
1299 |
- for x in ${GMX_DIRS}; do |
1300 |
- mkdir -p "${WORKDIR}/${P}_${x}" || die |
1301 |
- cp -al "${WORKDIR}/regressiontests"* "${WORKDIR}/${P}_${x}/tests" || die |
1302 |
- done |
1303 |
- fi |
1304 |
- |
1305 |
- DOC_CONTENTS="Gromacs can use sci-chemistry/vmd to read additional file formats" |
1306 |
-} |
1307 |
- |
1308 |
-src_configure() { |
1309 |
- local mycmakeargs_pre=( ) extra fft_opts=( ) |
1310 |
- |
1311 |
- #go from slowest to fastest acceleration |
1312 |
- local acce="None" |
1313 |
- use cpu_flags_x86_sse2 && acce="SSE2" |
1314 |
- use cpu_flags_x86_sse4_1 && acce="SSE4.1" |
1315 |
- use cpu_flags_x86_fma4 && acce="AVX_128_FMA" |
1316 |
- use cpu_flags_x86_avx && acce="AVX_256" |
1317 |
- use cpu_flags_x86_avx2 && acce="AVX2_256" |
1318 |
- |
1319 |
- #to create man pages, build tree binaries are executed (bug #398437) |
1320 |
- [[ ${CHOST} = *-darwin* ]] && \ |
1321 |
- extra+=" -DCMAKE_BUILD_WITH_INSTALL_RPATH=OFF" |
1322 |
- |
1323 |
- if use fftw; then |
1324 |
- fft_opts=( -DGMX_FFT_LIBRARY=fftw3 ) |
1325 |
- elif use mkl && has_version "=sci-libs/mkl-10*"; then |
1326 |
- fft_opts=( -DGMX_FFT_LIBRARY=mkl |
1327 |
- -DMKL_INCLUDE_DIR="${MKLROOT}/include" |
1328 |
- -DMKL_LIBRARIES="$(echo /opt/intel/mkl/10.0.5.025/lib/*/libmkl.so);$(echo /opt/intel/mkl/10.0.5.025/lib/*/libiomp*.so)" |
1329 |
- ) |
1330 |
- elif use mkl; then |
1331 |
- local bits=$(get_libdir) |
1332 |
- fft_opts=( -DGMX_FFT_LIBRARY=mkl |
1333 |
- -DMKL_INCLUDE_DIR="$(echo /opt/intel/*/mkl/include)" |
1334 |
- -DMKL_LIBRARIES="$(echo /opt/intel/*/mkl/lib/*${bits/lib}/libmkl_rt.so)" |
1335 |
- ) |
1336 |
- else |
1337 |
- fft_opts=( -DGMX_FFT_LIBRARY=fftpack ) |
1338 |
- fi |
1339 |
- |
1340 |
- mycmakeargs_pre+=( |
1341 |
- "${fft_opts[@]}" |
1342 |
- $(cmake-utils_use X GMX_X11) |
1343 |
- $(cmake-utils_use blas GMX_EXTERNAL_BLAS) |
1344 |
- $(cmake-utils_use lapack GMX_EXTERNAL_LAPACK) |
1345 |
- $(cmake-utils_use openmp GMX_OPENMP) |
1346 |
- $(cmake-utils_use offensive GMX_COOL_QUOTES) |
1347 |
- $(cmake-utils_use boost GMX_EXTERNAL_BOOST) |
1348 |
- $(cmake-utils_use tng GMX_USE_TNG) |
1349 |
- $(cmake-utils_use doc GMX_BUILD_MANUAL) |
1350 |
- -DGMX_DEFAULT_SUFFIX=off |
1351 |
- -DGMX_SIMD="$acce" |
1352 |
- -DGMX_LIB_INSTALL_DIR="$(get_libdir)" |
1353 |
- -DGMX_VMD_PLUGIN_PATH="${EPREFIX}/usr/$(get_libdir)/vmd/plugins/*/molfile/" |
1354 |
- -DGMX_X86_AVX_GCC_MASKLOAD_BUG=OFF |
1355 |
- -DGMX_USE_GCC44_BUG_WORKAROUND=OFF |
1356 |
- -DBUILD_TESTING=OFF |
1357 |
- -DGMX_BUILD_UNITTESTS=OFF |
1358 |
- ${extra} |
1359 |
- ) |
1360 |
- |
1361 |
- for x in ${GMX_DIRS}; do |
1362 |
- einfo "Configuring for ${x} precision" |
1363 |
- local suffix="" |
1364 |
- #if we build single and double - double is suffixed |
1365 |
- use double-precision && use single-precision && \ |
1366 |
- [[ ${x} = "double" ]] && suffix="_d" |
1367 |
- local p |
1368 |
- [[ ${x} = "double" ]] && p="-DGMX_DOUBLE=ON" || p="-DGMX_DOUBLE=OFF" |
1369 |
- local cuda=( "-DGMX_GPU=OFF" ) |
1370 |
- [[ ${x} = "float" ]] && use cuda && \ |
1371 |
- cuda=( -DGMX_GPU=ON ) |
1372 |
- mycmakeargs=( |
1373 |
- ${mycmakeargs_pre[@]} ${p} |
1374 |
- -DGMX_MPI=OFF |
1375 |
- $(cmake-utils_use threads GMX_THREAD_MPI) |
1376 |
- "${cuda[@]}" |
1377 |
- -DGMX_OPENMM=OFF |
1378 |
- "$(use test && echo -DREGRESSIONTEST_PATH="${WORKDIR}/${P}_${x}/tests")" |
1379 |
- -DGMX_BINARY_SUFFIX="${suffix}" |
1380 |
- -DGMX_LIBS_SUFFIX="${suffix}" |
1381 |
- ) |
1382 |
- BUILD_DIR="${WORKDIR}/${P}_${x}" cmake-utils_src_configure |
1383 |
- [[ ${CHOST} != *-darwin* ]] || \ |
1384 |
- sed -i '/SET(CMAKE_INSTALL_NAME_DIR/s/^/#/' "${WORKDIR}/${P}_${x}/gentoo_rules.cmake" || die |
1385 |
- use mpi || continue |
1386 |
- einfo "Configuring for ${x} precision with mpi" |
1387 |
- mycmakeargs=( |
1388 |
- ${mycmakeargs_pre[@]} ${p} |
1389 |
- -DGMX_THREAD_MPI=OFF |
1390 |
- -DGMX_MPI=ON ${cuda} |
1391 |
- -DGMX_OPENMM=OFF |
1392 |
- -DGMX_BUILD_MDRUN_ONLY=ON |
1393 |
- -DBUILD_SHARED_LIBS=OFF |
1394 |
- -DGMX_BUILD_MANUAL=OFF |
1395 |
- -DGMX_BINARY_SUFFIX="_mpi${suffix}" |
1396 |
- -DGMX_LIBS_SUFFIX="_mpi${suffix}" |
1397 |
- ) |
1398 |
- BUILD_DIR="${WORKDIR}/${P}_${x}_mpi" CC="mpicc" cmake-utils_src_configure |
1399 |
- [[ ${CHOST} != *-darwin* ]] || \ |
1400 |
- sed -i '/SET(CMAKE_INSTALL_NAME_DIR/s/^/#/' "${WORKDIR}/${P}_${x}_mpi/gentoo_rules.cmake" || die |
1401 |
- done |
1402 |
-} |
1403 |
- |
1404 |
-src_compile() { |
1405 |
- for x in ${GMX_DIRS}; do |
1406 |
- einfo "Compiling for ${x} precision" |
1407 |
- BUILD_DIR="${WORKDIR}/${P}_${x}"\ |
1408 |
- cmake-utils_src_compile |
1409 |
- # not 100% necessary for rel ebuilds as available from website |
1410 |
- if use doc; then |
1411 |
- BUILD_DIR="${WORKDIR}/${P}_${x}"\ |
1412 |
- cmake-utils_src_compile manual |
1413 |
- fi |
1414 |
- use mpi || continue |
1415 |
- einfo "Compiling for ${x} precision with mpi" |
1416 |
- BUILD_DIR="${WORKDIR}/${P}_${x}_mpi"\ |
1417 |
- cmake-utils_src_compile |
1418 |
- done |
1419 |
-} |
1420 |
- |
1421 |
-src_test() { |
1422 |
- for x in ${GMX_DIRS}; do |
1423 |
- BUILD_DIR="${WORKDIR}/${P}_${x}"\ |
1424 |
- cmake-utils_src_make check |
1425 |
- done |
1426 |
-} |
1427 |
- |
1428 |
-src_install() { |
1429 |
- for x in ${GMX_DIRS}; do |
1430 |
- BUILD_DIR="${WORKDIR}/${P}_${x}" \ |
1431 |
- cmake-utils_src_install |
1432 |
- if use doc; then |
1433 |
- newdoc "${WORKDIR}/${P}_${x}"/docs/manual/gromacs.pdf "${PN}-manual-${PV}.pdf" |
1434 |
- fi |
1435 |
- use mpi || continue |
1436 |
- BUILD_DIR="${WORKDIR}/${P}_${x}_mpi" \ |
1437 |
- cmake-utils_src_install |
1438 |
- done |
1439 |
- |
1440 |
- if use tng; then |
1441 |
- insinto /usr/include/tng |
1442 |
- doins src/external/tng_io/include/tng/*h |
1443 |
- fi |
1444 |
- # drop unneeded stuff |
1445 |
- rm "${ED}"usr/bin/GMXRC* || die |
1446 |
- for x in "${ED}"usr/bin/gmx-completion-*.bash ; do |
1447 |
- local n=${x##*/gmx-completion-} |
1448 |
- n="${n%.bash}" |
1449 |
- cat "${ED}"usr/bin/gmx-completion.bash "$x" > "${T}/${n}" || die |
1450 |
- newbashcomp "${T}"/"${n}" "${n}" |
1451 |
- done |
1452 |
- rm "${ED}"usr/bin/gmx-completion*.bash || die |
1453 |
- readme.gentoo_create_doc |
1454 |
-} |
1455 |
- |
1456 |
-pkg_postinst() { |
1457 |
- einfo |
1458 |
- einfo "Please read and cite:" |
1459 |
- einfo "Gromacs 4, J. Chem. Theory Comput. 4, 435 (2008). " |
1460 |
- einfo "http://dx.doi.org/10.1021/ct700301q" |
1461 |
- einfo |
1462 |
- readme.gentoo_print_elog |
1463 |
-} |