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commit: 50ecd80e60a5e09e9684840980b027c029bd5e50 |
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Author: Alexey Shvetsov <alexxy <AT> gentoo <DOT> org> |
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AuthorDate: Wed Oct 2 10:07:31 2019 +0000 |
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Commit: Alexey Shvetsov <alexxy <AT> gentoo <DOT> org> |
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CommitDate: Wed Oct 2 10:07:31 2019 +0000 |
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URL: https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=50ecd80e |
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|
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sci-chemistry/gromacs: Drop old |
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|
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Package-Manager: Portage-2.3.76, Repoman-2.3.16 |
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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 | 2 - |
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sci-chemistry/gromacs/gromacs-2018.3.ebuild | 270 ---------------------------- |
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2 files changed, 272 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 275cb8fb5a1..5c5fd361564 100644 |
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--- a/sci-chemistry/gromacs/Manifest |
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+++ b/sci-chemistry/gromacs/Manifest |
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@@ -1,8 +1,6 @@ |
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-DIST gromacs-2018.3.tar.gz 29915626 BLAKE2B 6e6eeafecdd923a25b4a2a78a8e89f793639b57ffbd63f19d133d8474302f9a381041f138a509dadb42b36e25fe508729e860efb6b0c75cdbf01d924b0a8fd83 SHA512 3c4d6eb3942d7b54d01c94c6f6f5ae706e0f5d4f9901ea11a56fde4df97b1a9112007f2cb13feea0f19f30c89f57ae80ff53a8f5203b8cdff103aa903cd0dc8f |
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DIST gromacs-2018.7.tar.gz 29912662 BLAKE2B 0714b28ec2443f3201275fc2fa6db1202a059161362134d4de03a900a3a67fe9d31ba8c058d5ee971198fecd69379fcd389f03d25c61f50b8460c43ba5c564d5 SHA512 fbc3b847b70b1396f412b8f4a1b977268651f8d53a222dcf6349fe563ff6319e096484209a24351e382bc9162a949b3900591f5b469c32dd9effeb894f03c172 |
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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 regressiontests-2018.3.tar.gz 67857855 BLAKE2B acd7a05ae79d1b4eb47d0c68a3fec9ee19f028a5019f39c37a033f48cf6da2a468375180ad6ceca9ac4f685a8bead38550663a47d6427b51f84c32a5c810e5f0 SHA512 57980d49efe6dcc3b3d14b5913a30c68fc1de5b679ef986fec1a149c76f67139b0299c3ee2825451461294fab5f345c7ad4f42e90f8991b81aafe9c369f3ff0b |
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DIST regressiontests-2018.7.tar.gz 67856738 BLAKE2B 955ae8b5e74f90fec704cf41fbd00bd8c09d754f950551fe0adfcd407db6fdb4491a3815149ea37d36c747316c79d462e823b9f6b26f2376bf90d87aad95731b SHA512 c2ff390750bd99faebcd8d5dd8ad6dbf2b00113ed888bddddf985dbf95d7f347093adb67f3c396547b3e2990de330fddb7efe83ded91a72cf97c82a1dac7e826 |
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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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|
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diff --git a/sci-chemistry/gromacs/gromacs-2018.3.ebuild b/sci-chemistry/gromacs/gromacs-2018.3.ebuild |
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deleted file mode 100644 |
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index fd73db9a981..00000000000 |
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--- a/sci-chemistry/gromacs/gromacs-2018.3.ebuild |
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+++ /dev/null |
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@@ -1,270 +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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-inherit bash-completion-r1 cmake-utils cuda eutils multilib 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 +hwloc lapack mkl mpi +offensive opencl openmp +single-precision test +threads +tng ${ACCE_IUSE}" |
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- |
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-CDEPEND=" |
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- X? ( |
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- x11-libs/libX11 |
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- x11-libs/libSM |
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- x11-libs/libICE |
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- ) |
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- blas? ( virtual/blas ) |
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- cuda? ( >=dev-util/nvidia-cuda-toolkit-4.2.9-r1 ) |
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- opencl? ( virtual/opencl ) |
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- fftw? ( sci-libs/fftw:3.0 ) |
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- hwloc? ( <sys-apps/hwloc-2 ) |
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- lapack? ( virtual/lapack ) |
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- mkl? ( sci-libs/mkl ) |
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- mpi? ( virtual/mpi ) |
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- " |
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-DEPEND="${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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- cuda? ( !opencl ) |
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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 [[ ${PV} != *9999 ]]; then |
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- default |
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- else |
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- git-r3_src_unpack |
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- if use test; then |
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- EGIT_REPO_URI="git://git.gromacs.org/regressiontests.git" \ |
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- EGIT_BRANCH="${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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- |
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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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- "${fft_opts[@]}" |
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- -DGMX_X11=$(usex X) |
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- -DGMX_EXTERNAL_BLAS=$(usex blas) |
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- -DGMX_EXTERNAL_LAPACK=$(usex lapack) |
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- -DGMX_OPENMP=$(usex openmp) |
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- -DGMX_COOL_QUOTES=$(usex offensive) |
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- -DGMX_USE_TNG=$(usex tng) |
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- -DGMX_BUILD_MANUAL=$(usex doc) |
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- -DGMX_HWLOC=$(usex hwloc) |
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- -DGMX_DEFAULT_SUFFIX=off |
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- -DGMX_SIMD="$acce" |
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- -DGMX_VMD_PLUGIN_PATH="${EPREFIX}/usr/$(get_libdir)/vmd/plugins/*/molfile/" |
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- -DBUILD_TESTING=$(usex test) |
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- -DGMX_BUILD_UNITTESTS=$(usex test) |
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- ${extra} |
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- ) |
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- |
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- for x in ${GMX_DIRS}; do |
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- einfo "Configuring for ${x} precision" |
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- local suffix="" |
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- #if we build single and double - double is suffixed |
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- use double-precision && use single-precision && \ |
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- [[ ${x} = "double" ]] && suffix="_d" |
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- local p |
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- [[ ${x} = "double" ]] && p="-DGMX_DOUBLE=ON" || p="-DGMX_DOUBLE=OFF" |
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- local cuda=( "-DGMX_GPU=OFF" ) |
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- [[ ${x} = "float" ]] && use cuda && \ |
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- cuda=( "-DGMX_GPU=ON" ) |
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- local opencl=( "-DGMX_USE_OPENCL=OFF" ) |
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- use opencl && opencl=( "-DGMX_USE_OPENCL=ON" ) cuda=( "-DGMX_GPU=ON" ) |
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- mycmakeargs=( |
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- ${mycmakeargs_pre[@]} ${p} |
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- -DGMX_MPI=OFF |
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- -DGMX_THREAD_MPI=$(usex threads) |
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- "${opencl[@]}" |
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- "${cuda[@]}" |
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- "$(use test && echo -DREGRESSIONTEST_PATH="${WORKDIR}/${P}_${x}/tests")" |
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- -DGMX_BINARY_SUFFIX="${suffix}" |
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- -DGMX_LIBS_SUFFIX="${suffix}" |
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- ) |
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- BUILD_DIR="${WORKDIR}/${P}_${x}" cmake-utils_src_configure |
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- [[ ${CHOST} != *-darwin* ]] || \ |
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- sed -i '/SET(CMAKE_INSTALL_NAME_DIR/s/^/#/' "${WORKDIR}/${P}_${x}/gentoo_rules.cmake" || die |
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- use mpi || continue |
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- einfo "Configuring for ${x} precision with mpi" |
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- mycmakeargs=( |
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- ${mycmakeargs_pre[@]} ${p} |
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- -DGMX_THREAD_MPI=OFF |
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- -DGMX_MPI=ON ${cuda} |
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- -DGMX_OPENMM=OFF |
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- -DGMX_BUILD_MDRUN_ONLY=ON |
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- -DBUILD_SHARED_LIBS=OFF |
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- -DGMX_BUILD_MANUAL=OFF |
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- -DGMX_BINARY_SUFFIX="_mpi${suffix}" |
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- -DGMX_LIBS_SUFFIX="_mpi${suffix}" |
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- ) |
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- BUILD_DIR="${WORKDIR}/${P}_${x}_mpi" CC="mpicc" cmake-utils_src_configure |
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- [[ ${CHOST} != *-darwin* ]] || \ |
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- sed -i '/SET(CMAKE_INSTALL_NAME_DIR/s/^/#/' "${WORKDIR}/${P}_${x}_mpi/gentoo_rules.cmake" || die |
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- done |
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-} |
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- |
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-src_compile() { |
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- for x in ${GMX_DIRS}; do |
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- einfo "Compiling for ${x} precision" |
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- BUILD_DIR="${WORKDIR}/${P}_${x}"\ |
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- cmake-utils_src_compile |
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- # not 100% necessary for rel ebuilds as available from website |
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- if use doc; then |
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- BUILD_DIR="${WORKDIR}/${P}_${x}"\ |
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- cmake-utils_src_compile manual |
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- fi |
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- use mpi || continue |
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- einfo "Compiling for ${x} precision with mpi" |
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- BUILD_DIR="${WORKDIR}/${P}_${x}_mpi"\ |
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- cmake-utils_src_compile |
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- done |
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-} |
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- |
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-src_test() { |
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- for x in ${GMX_DIRS}; do |
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- BUILD_DIR="${WORKDIR}/${P}_${x}"\ |
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- cmake-utils_src_make check |
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- done |
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-} |
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- |
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-src_install() { |
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- for x in ${GMX_DIRS}; do |
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- BUILD_DIR="${WORKDIR}/${P}_${x}" \ |
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- cmake-utils_src_install |
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- if use doc; then |
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- newdoc "${WORKDIR}/${P}_${x}"/docs/manual/gromacs.pdf "${PN}-manual-${PV}.pdf" |
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- fi |
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- use mpi || continue |
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- BUILD_DIR="${WORKDIR}/${P}_${x}_mpi" \ |
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- cmake-utils_src_install |
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- done |
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- |
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- if use tng; then |
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- insinto /usr/include/tng |
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- doins src/external/tng_io/include/tng/*h |
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- fi |
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- # drop unneeded stuff |
288 |
- rm "${ED}"usr/bin/GMXRC* || die |
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- for x in "${ED}"usr/bin/gmx-completion-*.bash ; do |
290 |
- local n=${x##*/gmx-completion-} |
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- n="${n%.bash}" |
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- cat "${ED}"usr/bin/gmx-completion.bash "$x" > "${T}/${n}" || die |
293 |
- newbashcomp "${T}"/"${n}" "${n}" |
294 |
- done |
295 |
- rm "${ED}"usr/bin/gmx-completion*.bash || die |
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- readme.gentoo_create_doc |
297 |
-} |
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- |
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-pkg_postinst() { |
300 |
- einfo |
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- einfo "Please read and cite:" |
302 |
- einfo "Gromacs 4, J. Chem. Theory Comput. 4, 435 (2008). " |
303 |
- einfo "https://dx.doi.org/10.1021/ct700301q" |
304 |
- einfo |
305 |
- readme.gentoo_print_elog |
306 |
-} |