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commit: c9bd05ccd7b4a36346953d48fddd1ab83a31245c |
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Author: Alexey Shvetsov <alexxy <AT> gentoo <DOT> org> |
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AuthorDate: Wed Dec 25 20:18:21 2019 +0000 |
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Commit: Alexey Shvetsov <alexxy <AT> gentoo <DOT> org> |
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CommitDate: Wed Dec 25 20:18:21 2019 +0000 |
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URL: https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=c9bd05cc |
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|
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sci-chemistry/gromacs: Drop redundant versions |
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|
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Package-Manager: Portage-2.3.83, Repoman-2.3.20 |
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Signed-off-by: Alexey Shvetsov <alexxy <AT> gentoo.org> |
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|
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sci-chemistry/gromacs/Manifest | 4 - |
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sci-chemistry/gromacs/gromacs-2019.3.ebuild | 314 ---------------------------- |
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sci-chemistry/gromacs/gromacs-2019.4.ebuild | 314 ---------------------------- |
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3 files changed, 632 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 d00891752c0..1262c124478 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 +1,10 @@ |
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DIST gromacs-2018.7.tar.gz 29912662 BLAKE2B 0714b28ec2443f3201275fc2fa6db1202a059161362134d4de03a900a3a67fe9d31ba8c058d5ee971198fecd69379fcd389f03d25c61f50b8460c43ba5c564d5 SHA512 fbc3b847b70b1396f412b8f4a1b977268651f8d53a222dcf6349fe563ff6319e096484209a24351e382bc9162a949b3900591f5b469c32dd9effeb894f03c172 |
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DIST gromacs-2018.8.tar.gz 29913703 BLAKE2B 8780032305928067fbfe1559efe9eedc4d47e27ab2f6ab54d6dba39edfcbeefbee4673d8910009048a850620b5a08ba8feb622db652c439cfa50a149ec5f0015 SHA512 6717895942f2ab7b54019511ed2aebadadde8e96d3c4b7414bb9168ffe418432d2dee330192e199f7b9d2f665c71f5d4f1ef0911aa7243d525a2ca182ef5b122 |
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DIST gromacs-2019.2.tar.gz 33437869 BLAKE2B bebe4942688dace148856d4491b687b8e0fd2c86d7fbd9eecdb46824d316a0fc3854464ecafa79d8db92327ee8467be204b050c11f1e71132184efd812c3bf09 SHA512 da7ff24e8485774e22d1c2464fbe64675c3305ef0e21a3d17e363201031952e5d4a9b81f572d5284fb6f2596ed99daf62fe78d653387d9d714274f46bc750183 |
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-DIST gromacs-2019.3.tar.gz 33441419 BLAKE2B 79319dd23982c65c7c4d8e5f633cef0c7fd99a38a4e0cc9030a3ffb0fdfc07a4fbfbcfa942896f23a143b747e044fae645498a3e6992497d1f1a7d966f80b2b0 SHA512 de9f54d095b45ea7efd1043f83a40f6c778a6e3e2067a01f48d1ce843d68d226061933ca28a3edb635b795a8ddd5ef9deb8ed1114aa3235bc8039db8ff7d0218 |
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-DIST gromacs-2019.4.tar.gz 33444527 BLAKE2B 5a01ed0e38faade037de701b72e8d52fd5a947a23228f0b5170a170dc963b00068a6b6880dd9a3f6f2a73140a3787952741dcbcc862bc357a8be8bf5640faa16 SHA512 adc6dea187b7f3a3c13fcd39445ae45248d46d56b0102fda47b1850b83ff1fb77a3fec99d4a4124b01ed04646dab6ab67749eae1bec36d1ba6f2205855cd29f8 |
28 |
DIST gromacs-2019.5.tar.gz 33445791 BLAKE2B 1e2e2764b0c8774c878abf4f32c2fa7ddd9b46f464cf1256deb48335433d92ef1b315f5534cdec9f766ae928a71361b5a4dd4a4def638269eb260ff98dbbe8bb SHA512 fdd177e4dfd29629b72bfbb4d61ff7bcdb37279f534883a9df8fd57569212fe1e9f8b8c9cec347fcc607539f31412d604d11ee3c0eb797251960435962b1bec6 |
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DIST gromacs-2020-rc1.tar.gz 29077110 BLAKE2B 5d5e6e63bd6b4dd03b688913b2da923547daddb270bca1a7d6ab8e625c26fb1031eea65330bd2e772f958e72e5a096c662633fbc71e7ee32ad83d99dcfb09170 SHA512 9dac945c5de9be2dc79bdde4d5f4afa3f2818334437ef8b4d1c57e46bdb80a0623ed7b16e1a8100395820b7eec367ea14195d420d3564f0f4eef0c88c52e78f9 |
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DIST regressiontests-2018.7.tar.gz 67856738 BLAKE2B 955ae8b5e74f90fec704cf41fbd00bd8c09d754f950551fe0adfcd407db6fdb4491a3815149ea37d36c747316c79d462e823b9f6b26f2376bf90d87aad95731b SHA512 c2ff390750bd99faebcd8d5dd8ad6dbf2b00113ed888bddddf985dbf95d7f347093adb67f3c396547b3e2990de330fddb7efe83ded91a72cf97c82a1dac7e826 |
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DIST regressiontests-2018.8.tar.gz 67855469 BLAKE2B 34c9b339f6229f483afbb5192ee6ba8b8f72d5c26907a853af9c53dfece0d88739e48f6b44b78d1c010f988f9385d077285300522164f533a5861e9dda879275 SHA512 3642389d27bd1942cd0f091c940ae97b197b94856a387fe581dc516b0d4169480f16551d4ba357f9282b3337d605c286d51dd38112ac87c826dda634904836bb |
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DIST regressiontests-2019.2.tar.gz 67643003 BLAKE2B 4178de5d62f194a81f97e442c10f123dc59c5e63f2078f7f07135709f3f6e530e0d237bf40264b285c084519d5ace75dfcbcddc16dc740c4f17233dc33542e45 SHA512 c1f25bc770d3f0a873c887d5563c1cd88179e81211b70ce6f5015696e6fa0b6931a8da7a449f2b223f3105b9e2e7eca67248e96fbfc2a7fd5fb360ba616f22ff |
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-DIST regressiontests-2019.3.tar.gz 67640462 BLAKE2B ed6c176a144e0407be66585be5d6090c31c047498bc5f48f59685108de91f2f9ddb2d22b291a15e6ffa1db848aae19b94a79c8c3d34b1067680f759a179953dd SHA512 822e905fb488ce308eb9324d93f78106da5252c773c7941d49c6162e73bdff109aeca1f0d57216c6dd6536a4c41d80013fa1cee2f5206b0c4160a3e5b4a31315 |
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-DIST regressiontests-2019.4.tar.gz 67639728 BLAKE2B aba912863669a4a6a6a74e385f9b0974d0c0aa30d3aea7834d77c8bb3f4f59effcbe10a480e74e7aa31fe32d64ba6628d67703ca1894839ce7ddfc8da93902dc SHA512 45de03d368da4e6e5c647f3fea61d64defe6d1cbc1c4219eeac2db27559e3cea7f15f9acb3e56ab934b44ca3ae4ce199b4e4969f704776bb9f0b23f1a34ff56d |
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DIST regressiontests-2019.5.tar.gz 67643634 BLAKE2B c4d9535d9a8a650869d67544ad5f367324f45e55325bb5074ece9b010f232f2f0dd97c9af97924d3f2368ed63015ca7330baff1cc681310e1439ec330b70ee8d SHA512 7c0917b76e7db35ab4e3271d523d268e0e2d858091e68ead863bfe6d1e56b381e30fdbf44f479f6e065c029e2eb27cfa0dbaa1b243f185144321aaf5084c55ce |
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DIST regressiontests-2020-rc1.tar.gz 48537816 BLAKE2B f9f4cde7a29691459d36e5f3fac91e75f4ebc6d95302c760722f4731a63a5e0695c8bc5106d38bb7b7266f6bac19bcb988496b572dca3f500f6c323c72615c60 SHA512 fb082479a3f3e03aaac4653682680ba8409f42a47f6e64e2a67e497467fce28e013b4fed8f9d3a1ce2db52237eb0e92e6e5c8de9be33beb7324d855de20b6ec7 |
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|
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diff --git a/sci-chemistry/gromacs/gromacs-2019.3.ebuild b/sci-chemistry/gromacs/gromacs-2019.3.ebuild |
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deleted file mode 100644 |
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index 5254b1f3f38..00000000000 |
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--- a/sci-chemistry/gromacs/gromacs-2019.3.ebuild |
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+++ /dev/null |
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@@ -1,314 +0,0 @@ |
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-# Copyright 1999-2019 Gentoo Authors |
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-# Distributed under the terms of the GNU General Public License v2 |
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- |
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-EAPI=6 |
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- |
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-CMAKE_MAKEFILE_GENERATOR="ninja" |
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- |
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-PYTHON_COMPAT=( python2_7 ) |
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- |
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-inherit bash-completion-r1 cmake-utils cuda eutils multilib python-single-r1 readme.gentoo-r1 toolchain-funcs xdg-utils |
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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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- https://github.com/gromacs/gromacs.git |
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- https://repo.or.cz/r/gromacs.git" |
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- [[ $PV = 9999 ]] && EGIT_BRANCH="master" || EGIT_BRANCH="release-${PV:0:4}" |
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- inherit git-r3 |
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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="~amd64 ~arm ~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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-# https://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 cuda +doc -double-precision +fftw +gmxapi +hwloc lapack +lmfit mkl mpi +offensive opencl 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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- cuda? ( >=dev-util/nvidia-cuda-toolkit-6.5.14 ) |
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- opencl? ( virtual/opencl ) |
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- fftw? ( sci-libs/fftw:3.0 ) |
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- hwloc? ( sys-apps/hwloc ) |
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- lapack? ( virtual/lapack ) |
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- lmfit? ( sci-libs/lmfit ) |
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- mkl? ( sci-libs/mkl ) |
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- mpi? ( virtual/mpi ) |
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- ${PYTHON_DEPS} |
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- " |
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-DEPEND="${CDEPEND} |
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- virtual/pkgconfig |
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- doc? ( |
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- app-doc/doxygen |
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- dev-python/sphinx[${PYTHON_USEDEP}] |
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- media-gfx/mscgen |
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- media-gfx/graphviz |
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- dev-texlive/texlive-latex |
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- dev-texlive/texlive-latexextra |
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- media-gfx/imagemagick |
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- )" |
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-RDEPEND="${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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- cuda? ( !opencl ) |
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- mkl? ( !blas !fftw !lapack ) |
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- ${PYTHON_REQUIRED_USE}" |
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- |
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-DOCS=( AUTHORS README ) |
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- |
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-RESTRICT="!test? ( test )" |
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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 [[ ${PV} != *9999 ]]; then |
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- default |
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- else |
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- git-r3_src_unpack |
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- if use test; then |
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- EGIT_REPO_URI="git://git.gromacs.org/regressiontests.git" \ |
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- EGIT_BRANCH="${EGIT_BRANCH}" \ |
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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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- xdg_environment_reset #591952 |
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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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- # try to create policy for imagemagik |
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- mkdir -p ${HOME}/.config/ImageMagick |
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- cat >> ${HOME}/.config/ImageMagick/policy.xml <<- EOF |
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- <?xml version="1.0" encoding="UTF-8"?> |
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- <!DOCTYPE policymap [ |
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- <!ELEMENT policymap (policy)+> |
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- !ATTLIST policymap xmlns CDATA #FIXED ''> |
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- <!ELEMENT policy EMPTY> |
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- <!ATTLIST policy xmlns CDATA #FIXED '' domain NMTOKEN #REQUIRED |
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- name NMTOKEN #IMPLIED pattern CDATA #IMPLIED rights NMTOKEN #IMPLIED |
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- stealth NMTOKEN #IMPLIED value CDATA #IMPLIED> |
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- ]> |
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- <policymap> |
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- <policy domain="coder" rights="read | write" pattern="PS" /> |
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- <policy domain="coder" rights="read | write" pattern="PS2" /> |
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- <policy domain="coder" rights="read | write" pattern="PS3" /> |
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- <policy domain="coder" rights="read | write" pattern="EPS" /> |
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- <policy domain="coder" rights="read | write" pattern="PDF" /> |
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- <policy domain="coder" rights="read | write" pattern="XPS" /> |
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- </policymap> |
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- EOF |
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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)" |
212 |
- ) |
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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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- |
223 |
- if use lmfit; then |
224 |
- local lmfit_opts=( -DGMX_USE_LMFIT=EXTERNAL ) |
225 |
- else |
226 |
- local lmfit_opts=( -DGMX_USE_LMFIT=INTERNAL ) |
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- fi |
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- |
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- mycmakeargs_pre+=( |
230 |
- "${fft_opts[@]}" |
231 |
- "${lmfit_opts[@]}" |
232 |
- -DGMX_X11=$(usex X) |
233 |
- -DGMX_EXTERNAL_BLAS=$(usex blas) |
234 |
- -DGMX_EXTERNAL_LAPACK=$(usex lapack) |
235 |
- -DGMX_OPENMP=$(usex openmp) |
236 |
- -DGMX_COOL_QUOTES=$(usex offensive) |
237 |
- -DGMX_USE_TNG=$(usex tng) |
238 |
- -DGMX_BUILD_MANUAL=$(usex doc) |
239 |
- -DGMX_HWLOC=$(usex hwloc) |
240 |
- -DGMX_DEFAULT_SUFFIX=off |
241 |
- -DGMX_SIMD="$acce" |
242 |
- -DGMX_VMD_PLUGIN_PATH="${EPREFIX}/usr/$(get_libdir)/vmd/plugins/*/molfile/" |
243 |
- -DBUILD_TESTING=$(usex test) |
244 |
- -DGMX_BUILD_UNITTESTS=$(usex test) |
245 |
- -DPYTHON_EXECUTABLE="${EPREFIX}/usr/bin/${EPYTHON}" |
246 |
- ${extra} |
247 |
- ) |
248 |
- |
249 |
- for x in ${GMX_DIRS}; do |
250 |
- einfo "Configuring for ${x} precision" |
251 |
- local suffix="" |
252 |
- #if we build single and double - double is suffixed |
253 |
- use double-precision && use single-precision && \ |
254 |
- [[ ${x} = "double" ]] && suffix="_d" |
255 |
- local p |
256 |
- [[ ${x} = "double" ]] && p="-DGMX_DOUBLE=ON" || p="-DGMX_DOUBLE=OFF" |
257 |
- local cuda=( "-DGMX_GPU=OFF" ) |
258 |
- [[ ${x} = "float" ]] && use cuda && \ |
259 |
- cuda=( "-DGMX_GPU=ON" ) |
260 |
- local opencl=( "-DGMX_USE_OPENCL=OFF" ) |
261 |
- use opencl && opencl=( "-DGMX_USE_OPENCL=ON" ) cuda=( "-DGMX_GPU=ON" ) |
262 |
- mycmakeargs=( |
263 |
- ${mycmakeargs_pre[@]} ${p} |
264 |
- -DGMX_MPI=OFF |
265 |
- -DGMX_THREAD_MPI=$(usex threads) |
266 |
- -DGMXAPI=$(usex gmxapi) |
267 |
- "${opencl[@]}" |
268 |
- "${cuda[@]}" |
269 |
- "$(use test && echo -DREGRESSIONTEST_PATH="${WORKDIR}/${P}_${x}/tests")" |
270 |
- -DGMX_BINARY_SUFFIX="${suffix}" |
271 |
- -DGMX_LIBS_SUFFIX="${suffix}" |
272 |
- ) |
273 |
- BUILD_DIR="${WORKDIR}/${P}_${x}" cmake-utils_src_configure |
274 |
- [[ ${CHOST} != *-darwin* ]] || \ |
275 |
- sed -i '/SET(CMAKE_INSTALL_NAME_DIR/s/^/#/' "${WORKDIR}/${P}_${x}/gentoo_rules.cmake" || die |
276 |
- use mpi || continue |
277 |
- einfo "Configuring for ${x} precision with mpi" |
278 |
- mycmakeargs=( |
279 |
- ${mycmakeargs_pre[@]} ${p} |
280 |
- -DGMX_THREAD_MPI=OFF |
281 |
- -DGMX_MPI=ON |
282 |
- -DGMX_OPENMM=OFF |
283 |
- -DGMXAPI=OFF |
284 |
- "${opencl[@]}" |
285 |
- "${cuda[@]}" |
286 |
- -DGMX_BUILD_MDRUN_ONLY=ON |
287 |
- -DBUILD_SHARED_LIBS=OFF |
288 |
- -DGMX_BUILD_MANUAL=OFF |
289 |
- -DGMX_BINARY_SUFFIX="_mpi${suffix}" |
290 |
- -DGMX_LIBS_SUFFIX="_mpi${suffix}" |
291 |
- ) |
292 |
- BUILD_DIR="${WORKDIR}/${P}_${x}_mpi" CC="mpicc" cmake-utils_src_configure |
293 |
- [[ ${CHOST} != *-darwin* ]] || \ |
294 |
- sed -i '/SET(CMAKE_INSTALL_NAME_DIR/s/^/#/' "${WORKDIR}/${P}_${x}_mpi/gentoo_rules.cmake" || die |
295 |
- done |
296 |
-} |
297 |
- |
298 |
-src_compile() { |
299 |
- for x in ${GMX_DIRS}; do |
300 |
- einfo "Compiling for ${x} precision" |
301 |
- BUILD_DIR="${WORKDIR}/${P}_${x}"\ |
302 |
- cmake-utils_src_compile |
303 |
- # not 100% necessary for rel ebuilds as available from website |
304 |
- if use doc; then |
305 |
- BUILD_DIR="${WORKDIR}/${P}_${x}"\ |
306 |
- cmake-utils_src_compile manual |
307 |
- fi |
308 |
- use mpi || continue |
309 |
- einfo "Compiling for ${x} precision with mpi" |
310 |
- BUILD_DIR="${WORKDIR}/${P}_${x}_mpi"\ |
311 |
- cmake-utils_src_compile |
312 |
- done |
313 |
-} |
314 |
- |
315 |
-src_test() { |
316 |
- for x in ${GMX_DIRS}; do |
317 |
- BUILD_DIR="${WORKDIR}/${P}_${x}"\ |
318 |
- cmake-utils_src_make check |
319 |
- done |
320 |
-} |
321 |
- |
322 |
-src_install() { |
323 |
- for x in ${GMX_DIRS}; do |
324 |
- BUILD_DIR="${WORKDIR}/${P}_${x}" \ |
325 |
- cmake-utils_src_install |
326 |
- if use doc; then |
327 |
- newdoc "${WORKDIR}/${P}_${x}"/docs/manual/gromacs.pdf "${PN}-manual-${PV}.pdf" |
328 |
- fi |
329 |
- use mpi || continue |
330 |
- BUILD_DIR="${WORKDIR}/${P}_${x}_mpi" \ |
331 |
- cmake-utils_src_install |
332 |
- done |
333 |
- |
334 |
- if use tng; then |
335 |
- insinto /usr/include/tng |
336 |
- doins src/external/tng_io/include/tng/*h |
337 |
- fi |
338 |
- # drop unneeded stuff |
339 |
- rm "${ED}"usr/bin/GMXRC* || die |
340 |
- for x in "${ED}"usr/bin/gmx-completion-*.bash ; do |
341 |
- local n=${x##*/gmx-completion-} |
342 |
- n="${n%.bash}" |
343 |
- cat "${ED}"usr/bin/gmx-completion.bash "$x" > "${T}/${n}" || die |
344 |
- newbashcomp "${T}"/"${n}" "${n}" |
345 |
- done |
346 |
- rm "${ED}"usr/bin/gmx-completion*.bash || die |
347 |
- readme.gentoo_create_doc |
348 |
-} |
349 |
- |
350 |
-pkg_postinst() { |
351 |
- einfo |
352 |
- einfo "Please read and cite:" |
353 |
- einfo "Gromacs 4, J. Chem. Theory Comput. 4, 435 (2008). " |
354 |
- einfo "https://dx.doi.org/10.1021/ct700301q" |
355 |
- einfo |
356 |
- readme.gentoo_print_elog |
357 |
-} |
358 |
|
359 |
diff --git a/sci-chemistry/gromacs/gromacs-2019.4.ebuild b/sci-chemistry/gromacs/gromacs-2019.4.ebuild |
360 |
deleted file mode 100644 |
361 |
index a08d3ecc902..00000000000 |
362 |
--- a/sci-chemistry/gromacs/gromacs-2019.4.ebuild |
363 |
+++ /dev/null |
364 |
@@ -1,314 +0,0 @@ |
365 |
-# Copyright 1999-2019 Gentoo Authors |
366 |
-# Distributed under the terms of the GNU General Public License v2 |
367 |
- |
368 |
-EAPI=7 |
369 |
- |
370 |
-CMAKE_MAKEFILE_GENERATOR="ninja" |
371 |
- |
372 |
-PYTHON_COMPAT=( python2_7 ) |
373 |
- |
374 |
-inherit bash-completion-r1 cmake-utils cuda eutils multilib python-single-r1 readme.gentoo-r1 toolchain-funcs xdg-utils |
375 |
- |
376 |
-if [[ $PV = *9999* ]]; then |
377 |
- EGIT_REPO_URI="git://git.gromacs.org/gromacs.git |
378 |
- https://gerrit.gromacs.org/gromacs.git |
379 |
- https://github.com/gromacs/gromacs.git |
380 |
- https://repo.or.cz/r/gromacs.git" |
381 |
- [[ $PV = 9999 ]] && EGIT_BRANCH="master" || EGIT_BRANCH="release-${PV:0:4}" |
382 |
- inherit git-r3 |
383 |
-else |
384 |
- SRC_URI="ftp://ftp.gromacs.org/pub/${PN}/${PN}-${PV/_/-}.tar.gz |
385 |
- test? ( http://gerrit.gromacs.org/download/regressiontests-${PV/_/-}.tar.gz )" |
386 |
- KEYWORDS="~amd64 ~arm ~x86 ~amd64-linux ~x86-linux ~x64-macos ~x86-macos" |
387 |
-fi |
388 |
- |
389 |
-ACCE_IUSE="cpu_flags_x86_sse2 cpu_flags_x86_sse4_1 cpu_flags_x86_fma4 cpu_flags_x86_avx cpu_flags_x86_avx2" |
390 |
- |
391 |
-DESCRIPTION="The ultimate molecular dynamics simulation package" |
392 |
-HOMEPAGE="http://www.gromacs.org/" |
393 |
- |
394 |
-# see COPYING for details |
395 |
-# https://repo.or.cz/w/gromacs.git/blob/HEAD:/COPYING |
396 |
-# base, vmd plugins, fftpack from numpy, blas/lapck from netlib, memtestG80 library, mpi_thread lib |
397 |
-LICENSE="LGPL-2.1 UoI-NCSA !mkl? ( !fftw? ( BSD ) !blas? ( BSD ) !lapack? ( BSD ) ) cuda? ( LGPL-3 ) threads? ( BSD )" |
398 |
-SLOT="0/${PV}" |
399 |
-IUSE="X blas cuda +doc -double-precision +fftw +gmxapi +hwloc lapack +lmfit mkl mpi +offensive opencl openmp +single-precision test +threads +tng ${ACCE_IUSE}" |
400 |
- |
401 |
-CDEPEND=" |
402 |
- X? ( |
403 |
- x11-libs/libX11 |
404 |
- x11-libs/libSM |
405 |
- x11-libs/libICE |
406 |
- ) |
407 |
- blas? ( virtual/blas ) |
408 |
- cuda? ( >=dev-util/nvidia-cuda-toolkit-6.5.14 ) |
409 |
- opencl? ( virtual/opencl ) |
410 |
- fftw? ( sci-libs/fftw:3.0 ) |
411 |
- hwloc? ( sys-apps/hwloc ) |
412 |
- lapack? ( virtual/lapack ) |
413 |
- lmfit? ( sci-libs/lmfit ) |
414 |
- mkl? ( sci-libs/mkl ) |
415 |
- mpi? ( virtual/mpi ) |
416 |
- ${PYTHON_DEPS} |
417 |
- " |
418 |
-BDEPEND="${CDEPEND} |
419 |
- virtual/pkgconfig |
420 |
- doc? ( |
421 |
- app-doc/doxygen |
422 |
- dev-python/sphinx[${PYTHON_USEDEP}] |
423 |
- media-gfx/mscgen |
424 |
- media-gfx/graphviz |
425 |
- dev-texlive/texlive-latex |
426 |
- dev-texlive/texlive-latexextra |
427 |
- media-gfx/imagemagick |
428 |
- )" |
429 |
-RDEPEND="${CDEPEND}" |
430 |
- |
431 |
-REQUIRED_USE=" |
432 |
- || ( single-precision double-precision ) |
433 |
- cuda? ( single-precision ) |
434 |
- cuda? ( !opencl ) |
435 |
- mkl? ( !blas !fftw !lapack ) |
436 |
- ${PYTHON_REQUIRED_USE}" |
437 |
- |
438 |
-DOCS=( AUTHORS README ) |
439 |
- |
440 |
-RESTRICT="!test? ( test )" |
441 |
- |
442 |
-if [[ ${PV} != *9999 ]]; then |
443 |
- S="${WORKDIR}/${PN}-${PV/_/-}" |
444 |
-fi |
445 |
- |
446 |
-pkg_pretend() { |
447 |
- [[ $(gcc-version) == "4.1" ]] && die "gcc 4.1 is not supported by gromacs" |
448 |
- use openmp && ! tc-has-openmp && \ |
449 |
- die "Please switch to an openmp compatible compiler" |
450 |
-} |
451 |
- |
452 |
-src_unpack() { |
453 |
- if [[ ${PV} != *9999 ]]; then |
454 |
- default |
455 |
- else |
456 |
- git-r3_src_unpack |
457 |
- if use test; then |
458 |
- EGIT_REPO_URI="git://git.gromacs.org/regressiontests.git" \ |
459 |
- EGIT_BRANCH="${EGIT_BRANCH}" \ |
460 |
- EGIT_CHECKOUT_DIR="${WORKDIR}/regressiontests"\ |
461 |
- git-r3_src_unpack |
462 |
- fi |
463 |
- fi |
464 |
-} |
465 |
- |
466 |
-src_prepare() { |
467 |
- #notes/todos |
468 |
- # -on apple: there is framework support |
469 |
- |
470 |
- xdg_environment_reset #591952 |
471 |
- |
472 |
- cmake-utils_src_prepare |
473 |
- |
474 |
- use cuda && cuda_src_prepare |
475 |
- |
476 |
- GMX_DIRS="" |
477 |
- use single-precision && GMX_DIRS+=" float" |
478 |
- use double-precision && GMX_DIRS+=" double" |
479 |
- |
480 |
- if use test; then |
481 |
- for x in ${GMX_DIRS}; do |
482 |
- mkdir -p "${WORKDIR}/${P}_${x}" || die |
483 |
- cp -al "${WORKDIR}/regressiontests"* "${WORKDIR}/${P}_${x}/tests" || die |
484 |
- done |
485 |
- fi |
486 |
- |
487 |
- DOC_CONTENTS="Gromacs can use sci-chemistry/vmd to read additional file formats" |
488 |
- |
489 |
- # try to create policy for imagemagik |
490 |
- mkdir -p ${HOME}/.config/ImageMagick |
491 |
- cat >> ${HOME}/.config/ImageMagick/policy.xml <<- EOF |
492 |
- <?xml version="1.0" encoding="UTF-8"?> |
493 |
- <!DOCTYPE policymap [ |
494 |
- <!ELEMENT policymap (policy)+> |
495 |
- !ATTLIST policymap xmlns CDATA #FIXED ''> |
496 |
- <!ELEMENT policy EMPTY> |
497 |
- <!ATTLIST policy xmlns CDATA #FIXED '' domain NMTOKEN #REQUIRED |
498 |
- name NMTOKEN #IMPLIED pattern CDATA #IMPLIED rights NMTOKEN #IMPLIED |
499 |
- stealth NMTOKEN #IMPLIED value CDATA #IMPLIED> |
500 |
- ]> |
501 |
- <policymap> |
502 |
- <policy domain="coder" rights="read | write" pattern="PS" /> |
503 |
- <policy domain="coder" rights="read | write" pattern="PS2" /> |
504 |
- <policy domain="coder" rights="read | write" pattern="PS3" /> |
505 |
- <policy domain="coder" rights="read | write" pattern="EPS" /> |
506 |
- <policy domain="coder" rights="read | write" pattern="PDF" /> |
507 |
- <policy domain="coder" rights="read | write" pattern="XPS" /> |
508 |
- </policymap> |
509 |
- EOF |
510 |
-} |
511 |
- |
512 |
-src_configure() { |
513 |
- local mycmakeargs_pre=( ) extra fft_opts=( ) |
514 |
- |
515 |
- #go from slowest to fastest acceleration |
516 |
- local acce="None" |
517 |
- use cpu_flags_x86_sse2 && acce="SSE2" |
518 |
- use cpu_flags_x86_sse4_1 && acce="SSE4.1" |
519 |
- use cpu_flags_x86_fma4 && acce="AVX_128_FMA" |
520 |
- use cpu_flags_x86_avx && acce="AVX_256" |
521 |
- use cpu_flags_x86_avx2 && acce="AVX2_256" |
522 |
- |
523 |
- #to create man pages, build tree binaries are executed (bug #398437) |
524 |
- [[ ${CHOST} = *-darwin* ]] && \ |
525 |
- extra+=" -DCMAKE_BUILD_WITH_INSTALL_RPATH=OFF" |
526 |
- |
527 |
- if use fftw; then |
528 |
- fft_opts=( -DGMX_FFT_LIBRARY=fftw3 ) |
529 |
- elif use mkl && has_version "=sci-libs/mkl-10*"; then |
530 |
- fft_opts=( -DGMX_FFT_LIBRARY=mkl |
531 |
- -DMKL_INCLUDE_DIR="${MKLROOT}/include" |
532 |
- -DMKL_LIBRARIES="$(echo /opt/intel/mkl/10.0.5.025/lib/*/libmkl.so);$(echo /opt/intel/mkl/10.0.5.025/lib/*/libiomp*.so)" |
533 |
- ) |
534 |
- elif use mkl; then |
535 |
- local bits=$(get_libdir) |
536 |
- fft_opts=( -DGMX_FFT_LIBRARY=mkl |
537 |
- -DMKL_INCLUDE_DIR="$(echo /opt/intel/*/mkl/include)" |
538 |
- -DMKL_LIBRARIES="$(echo /opt/intel/*/mkl/lib/*${bits/lib}/libmkl_rt.so)" |
539 |
- ) |
540 |
- else |
541 |
- fft_opts=( -DGMX_FFT_LIBRARY=fftpack ) |
542 |
- fi |
543 |
- |
544 |
- if use lmfit; then |
545 |
- local lmfit_opts=( -DGMX_USE_LMFIT=EXTERNAL ) |
546 |
- else |
547 |
- local lmfit_opts=( -DGMX_USE_LMFIT=INTERNAL ) |
548 |
- fi |
549 |
- |
550 |
- mycmakeargs_pre+=( |
551 |
- "${fft_opts[@]}" |
552 |
- "${lmfit_opts[@]}" |
553 |
- -DGMX_X11=$(usex X) |
554 |
- -DGMX_EXTERNAL_BLAS=$(usex blas) |
555 |
- -DGMX_EXTERNAL_LAPACK=$(usex lapack) |
556 |
- -DGMX_OPENMP=$(usex openmp) |
557 |
- -DGMX_COOL_QUOTES=$(usex offensive) |
558 |
- -DGMX_USE_TNG=$(usex tng) |
559 |
- -DGMX_BUILD_MANUAL=$(usex doc) |
560 |
- -DGMX_HWLOC=$(usex hwloc) |
561 |
- -DGMX_DEFAULT_SUFFIX=off |
562 |
- -DGMX_SIMD="$acce" |
563 |
- -DGMX_VMD_PLUGIN_PATH="${EPREFIX}/usr/$(get_libdir)/vmd/plugins/*/molfile/" |
564 |
- -DBUILD_TESTING=$(usex test) |
565 |
- -DGMX_BUILD_UNITTESTS=$(usex test) |
566 |
- -DPYTHON_EXECUTABLE="${EPREFIX}/usr/bin/${EPYTHON}" |
567 |
- ${extra} |
568 |
- ) |
569 |
- |
570 |
- for x in ${GMX_DIRS}; do |
571 |
- einfo "Configuring for ${x} precision" |
572 |
- local suffix="" |
573 |
- #if we build single and double - double is suffixed |
574 |
- use double-precision && use single-precision && \ |
575 |
- [[ ${x} = "double" ]] && suffix="_d" |
576 |
- local p |
577 |
- [[ ${x} = "double" ]] && p="-DGMX_DOUBLE=ON" || p="-DGMX_DOUBLE=OFF" |
578 |
- local cuda=( "-DGMX_GPU=OFF" ) |
579 |
- [[ ${x} = "float" ]] && use cuda && \ |
580 |
- cuda=( "-DGMX_GPU=ON" ) |
581 |
- local opencl=( "-DGMX_USE_OPENCL=OFF" ) |
582 |
- use opencl && opencl=( "-DGMX_USE_OPENCL=ON" ) cuda=( "-DGMX_GPU=ON" ) |
583 |
- mycmakeargs=( |
584 |
- ${mycmakeargs_pre[@]} ${p} |
585 |
- -DGMX_MPI=OFF |
586 |
- -DGMX_THREAD_MPI=$(usex threads) |
587 |
- -DGMXAPI=$(usex gmxapi) |
588 |
- "${opencl[@]}" |
589 |
- "${cuda[@]}" |
590 |
- "$(use test && echo -DREGRESSIONTEST_PATH="${WORKDIR}/${P}_${x}/tests")" |
591 |
- -DGMX_BINARY_SUFFIX="${suffix}" |
592 |
- -DGMX_LIBS_SUFFIX="${suffix}" |
593 |
- ) |
594 |
- BUILD_DIR="${WORKDIR}/${P}_${x}" cmake-utils_src_configure |
595 |
- [[ ${CHOST} != *-darwin* ]] || \ |
596 |
- sed -i '/SET(CMAKE_INSTALL_NAME_DIR/s/^/#/' "${WORKDIR}/${P}_${x}/gentoo_rules.cmake" || die |
597 |
- use mpi || continue |
598 |
- einfo "Configuring for ${x} precision with mpi" |
599 |
- mycmakeargs=( |
600 |
- ${mycmakeargs_pre[@]} ${p} |
601 |
- -DGMX_THREAD_MPI=OFF |
602 |
- -DGMX_MPI=ON |
603 |
- -DGMX_OPENMM=OFF |
604 |
- -DGMXAPI=OFF |
605 |
- "${opencl[@]}" |
606 |
- "${cuda[@]}" |
607 |
- -DGMX_BUILD_MDRUN_ONLY=ON |
608 |
- -DBUILD_SHARED_LIBS=OFF |
609 |
- -DGMX_BUILD_MANUAL=OFF |
610 |
- -DGMX_BINARY_SUFFIX="_mpi${suffix}" |
611 |
- -DGMX_LIBS_SUFFIX="_mpi${suffix}" |
612 |
- ) |
613 |
- BUILD_DIR="${WORKDIR}/${P}_${x}_mpi" CC="mpicc" cmake-utils_src_configure |
614 |
- [[ ${CHOST} != *-darwin* ]] || \ |
615 |
- sed -i '/SET(CMAKE_INSTALL_NAME_DIR/s/^/#/' "${WORKDIR}/${P}_${x}_mpi/gentoo_rules.cmake" || die |
616 |
- done |
617 |
-} |
618 |
- |
619 |
-src_compile() { |
620 |
- for x in ${GMX_DIRS}; do |
621 |
- einfo "Compiling for ${x} precision" |
622 |
- BUILD_DIR="${WORKDIR}/${P}_${x}"\ |
623 |
- cmake-utils_src_compile |
624 |
- # not 100% necessary for rel ebuilds as available from website |
625 |
- if use doc; then |
626 |
- BUILD_DIR="${WORKDIR}/${P}_${x}"\ |
627 |
- cmake-utils_src_compile manual |
628 |
- fi |
629 |
- use mpi || continue |
630 |
- einfo "Compiling for ${x} precision with mpi" |
631 |
- BUILD_DIR="${WORKDIR}/${P}_${x}_mpi"\ |
632 |
- cmake-utils_src_compile |
633 |
- done |
634 |
-} |
635 |
- |
636 |
-src_test() { |
637 |
- for x in ${GMX_DIRS}; do |
638 |
- BUILD_DIR="${WORKDIR}/${P}_${x}"\ |
639 |
- cmake-utils_src_make check |
640 |
- done |
641 |
-} |
642 |
- |
643 |
-src_install() { |
644 |
- for x in ${GMX_DIRS}; do |
645 |
- BUILD_DIR="${WORKDIR}/${P}_${x}" \ |
646 |
- cmake-utils_src_install |
647 |
- if use doc; then |
648 |
- newdoc "${WORKDIR}/${P}_${x}"/docs/manual/gromacs.pdf "${PN}-manual-${PV}.pdf" |
649 |
- fi |
650 |
- use mpi || continue |
651 |
- BUILD_DIR="${WORKDIR}/${P}_${x}_mpi" \ |
652 |
- cmake-utils_src_install |
653 |
- done |
654 |
- |
655 |
- if use tng; then |
656 |
- insinto /usr/include/tng |
657 |
- doins src/external/tng_io/include/tng/*h |
658 |
- fi |
659 |
- # drop unneeded stuff |
660 |
- rm "${ED}"/usr/bin/GMXRC* || die |
661 |
- for x in "${ED}"/usr/bin/gmx-completion-*.bash ; do |
662 |
- local n=${x##*/gmx-completion-} |
663 |
- n="${n%.bash}" |
664 |
- cat "${ED}"/usr/bin/gmx-completion.bash "$x" > "${T}/${n}" || die |
665 |
- newbashcomp "${T}"/"${n}" "${n}" |
666 |
- done |
667 |
- rm "${ED}"/usr/bin/gmx-completion*.bash || die |
668 |
- readme.gentoo_create_doc |
669 |
-} |
670 |
- |
671 |
-pkg_postinst() { |
672 |
- einfo |
673 |
- einfo "Please read and cite:" |
674 |
- einfo "Gromacs 4, J. Chem. Theory Comput. 4, 435 (2008). " |
675 |
- einfo "https://dx.doi.org/10.1021/ct700301q" |
676 |
- einfo |
677 |
- readme.gentoo_print_elog |
678 |
-} |