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commit: 85353117bd877ef8ee97f3754cc0ab85d5a586d5 |
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Author: Alexey Shvetsov <alexxy <AT> gentoo <DOT> org> |
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AuthorDate: Mon Jan 27 22:11:17 2020 +0000 |
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Commit: Alexey Shvetsov <alexxy <AT> gentoo <DOT> org> |
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CommitDate: Mon Jan 27 22:11:17 2020 +0000 |
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URL: https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=85353117 |
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|
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sci-chemistry/gromacs: Drop old version |
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|
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Package-Manager: Portage-2.3.85, 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 | 2 - |
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sci-chemistry/gromacs/gromacs-2019.2.ebuild | 312 ---------------------------- |
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2 files changed, 314 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 68cba940949..e5351904160 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-2018.8.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-2019.5.tar.gz 33445791 BLAKE2B 1e2e2764b0c8774c878abf4f32c2fa7ddd9b46f464cf1256deb48335433d92ef1b315f5534cdec9f766ae928a71361b5a4dd4a4def638269eb260ff98dbbe8bb SHA512 fdd177e4dfd29629b72bfbb4d61ff7bcdb37279f534883a9df8fd57569212fe1e9f8b8c9cec347fcc607539f31412d604d11ee3c0eb797251960435962b1bec6 |
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DIST gromacs-2020.tar.gz 28928068 BLAKE2B 72d4ff8f6b383284e61df9d3b2b53c51300f6961d4c19810670c8ee9ba2f1864d2a325e2774093b9338db785cb91a94461bf93f16cdf4caf0f690298a672d51c SHA512 15f0d58cd8d217eab39ef8e3535dec34127708797eaf6575fb340292cbee2303cd25deb84b3d4417a787076f4ae7be9e4958ec3a347a3aa9aed52ef337a4587c |
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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-2019.5.tar.gz 67643634 BLAKE2B c4d9535d9a8a650869d67544ad5f367324f45e55325bb5074ece9b010f232f2f0dd97c9af97924d3f2368ed63015ca7330baff1cc681310e1439ec330b70ee8d SHA512 7c0917b76e7db35ab4e3271d523d268e0e2d858091e68ead863bfe6d1e56b381e30fdbf44f479f6e065c029e2eb27cfa0dbaa1b243f185144321aaf5084c55ce |
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DIST regressiontests-2020.tar.gz 48536146 BLAKE2B 9511db78b5d6a5ea431fdb73782f28dde4b94655139886c0ad519888ef3e435fe81807f158d66c1a4284cb88fe730f62d039ac23549f17d0ce5984764ef35f10 SHA512 5a35aaf6fe2f3b146c7045e9c967dc1c8bf754748cc1f2a7300193ae3f206a9f5058329380ae7b03b181410303bcd434584571e6161a75f99e52bd48f8ba1821 |
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|
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diff --git a/sci-chemistry/gromacs/gromacs-2019.2.ebuild b/sci-chemistry/gromacs/gromacs-2019.2.ebuild |
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deleted file mode 100644 |
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index 58d733d2c33..00000000000 |
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--- a/sci-chemistry/gromacs/gromacs-2019.2.ebuild |
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+++ /dev/null |
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@@ -1,312 +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)" |
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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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- if use lmfit; then |
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- local lmfit_opts=( -DGMX_USE_LMFIT=EXTERNAL ) |
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- else |
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- local lmfit_opts=( -DGMX_USE_LMFIT=INTERNAL ) |
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- fi |
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- |
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- mycmakeargs_pre+=( |
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- "${fft_opts[@]}" |
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- "${lmfit_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=$(usex test) |
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- -DPYTHON_EXECUTABLE="${EPREFIX}/usr/bin/${EPYTHON}" |
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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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- -DGMXAPI=$(usex gmxapi) |
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- "${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="${suffix}" |
265 |
- ) |
266 |
- BUILD_DIR="${WORKDIR}/${P}_${x}" cmake-utils_src_configure |
267 |
- [[ ${CHOST} != *-darwin* ]] || \ |
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- sed -i '/SET(CMAKE_INSTALL_NAME_DIR/s/^/#/' "${WORKDIR}/${P}_${x}/gentoo_rules.cmake" || die |
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- use mpi || continue |
270 |
- einfo "Configuring for ${x} precision with mpi" |
271 |
- mycmakeargs=( |
272 |
- ${mycmakeargs_pre[@]} ${p} |
273 |
- -DGMX_THREAD_MPI=OFF |
274 |
- -DGMX_MPI=ON ${cuda} |
275 |
- -DGMX_OPENMM=OFF |
276 |
- -DGMXAPI=OFF |
277 |
- -DGMX_BUILD_MDRUN_ONLY=ON |
278 |
- -DBUILD_SHARED_LIBS=OFF |
279 |
- -DGMX_BUILD_MANUAL=OFF |
280 |
- -DGMX_BINARY_SUFFIX="_mpi${suffix}" |
281 |
- -DGMX_LIBS_SUFFIX="_mpi${suffix}" |
282 |
- ) |
283 |
- BUILD_DIR="${WORKDIR}/${P}_${x}_mpi" CC="mpicc" cmake-utils_src_configure |
284 |
- [[ ${CHOST} != *-darwin* ]] || \ |
285 |
- sed -i '/SET(CMAKE_INSTALL_NAME_DIR/s/^/#/' "${WORKDIR}/${P}_${x}_mpi/gentoo_rules.cmake" || die |
286 |
- done |
287 |
-} |
288 |
- |
289 |
-src_compile() { |
290 |
- for x in ${GMX_DIRS}; do |
291 |
- einfo "Compiling for ${x} precision" |
292 |
- BUILD_DIR="${WORKDIR}/${P}_${x}"\ |
293 |
- cmake-utils_src_compile |
294 |
- # not 100% necessary for rel ebuilds as available from website |
295 |
- if use doc; then |
296 |
- BUILD_DIR="${WORKDIR}/${P}_${x}"\ |
297 |
- cmake-utils_src_compile manual |
298 |
- fi |
299 |
- use mpi || continue |
300 |
- einfo "Compiling for ${x} precision with mpi" |
301 |
- BUILD_DIR="${WORKDIR}/${P}_${x}_mpi"\ |
302 |
- cmake-utils_src_compile |
303 |
- done |
304 |
-} |
305 |
- |
306 |
-src_test() { |
307 |
- for x in ${GMX_DIRS}; do |
308 |
- BUILD_DIR="${WORKDIR}/${P}_${x}"\ |
309 |
- cmake-utils_src_make check |
310 |
- done |
311 |
-} |
312 |
- |
313 |
-src_install() { |
314 |
- for x in ${GMX_DIRS}; do |
315 |
- BUILD_DIR="${WORKDIR}/${P}_${x}" \ |
316 |
- cmake-utils_src_install |
317 |
- if use doc; then |
318 |
- newdoc "${WORKDIR}/${P}_${x}"/docs/manual/gromacs.pdf "${PN}-manual-${PV}.pdf" |
319 |
- fi |
320 |
- use mpi || continue |
321 |
- BUILD_DIR="${WORKDIR}/${P}_${x}_mpi" \ |
322 |
- cmake-utils_src_install |
323 |
- done |
324 |
- |
325 |
- if use tng; then |
326 |
- insinto /usr/include/tng |
327 |
- doins src/external/tng_io/include/tng/*h |
328 |
- fi |
329 |
- # drop unneeded stuff |
330 |
- rm "${ED}"usr/bin/GMXRC* || die |
331 |
- for x in "${ED}"usr/bin/gmx-completion-*.bash ; do |
332 |
- local n=${x##*/gmx-completion-} |
333 |
- n="${n%.bash}" |
334 |
- cat "${ED}"usr/bin/gmx-completion.bash "$x" > "${T}/${n}" || die |
335 |
- newbashcomp "${T}"/"${n}" "${n}" |
336 |
- done |
337 |
- rm "${ED}"usr/bin/gmx-completion*.bash || die |
338 |
- readme.gentoo_create_doc |
339 |
-} |
340 |
- |
341 |
-pkg_postinst() { |
342 |
- einfo |
343 |
- einfo "Please read and cite:" |
344 |
- einfo "Gromacs 4, J. Chem. Theory Comput. 4, 435 (2008). " |
345 |
- einfo "https://dx.doi.org/10.1021/ct700301q" |
346 |
- einfo |
347 |
- readme.gentoo_print_elog |
348 |
-} |