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sci-chemistry/gromacs: Version bump
Package-Manager: Portage-2.3.67, Repoman-2.3.14 Signed-off-by: Alexey Shvetsov <alexxy@gentoo.org>
This commit is contained in:
Alexey Shvetsov
@@ -1,6 +1,8 @@
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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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307
sci-chemistry/gromacs/gromacs-2019.3.ebuild
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307
sci-chemistry/gromacs/gromacs-2019.3.ebuild
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@@ -0,0 +1,307 @@
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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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EAPI=6
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CMAKE_MAKEFILE_GENERATOR="ninja"
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PYTHON_COMPAT=( python2_7 )
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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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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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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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DESCRIPTION="The ultimate molecular dynamics simulation package"
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HOMEPAGE="http://www.gromacs.org/"
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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 ${ACCE_IUSE}"
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CDEPEND="
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X? (
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x11-libs/libX11
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x11-libs/libSM
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x11-libs/libICE
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)
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blas? ( virtual/blas )
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cuda? ( >=dev-util/nvidia-cuda-toolkit-6.5.14 )
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opencl? ( virtual/opencl )
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fftw? ( sci-libs/fftw:3.0 )
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hwloc? ( sys-apps/hwloc )
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lapack? ( virtual/lapack )
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lmfit? ( sci-libs/lmfit )
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mkl? ( sci-libs/mkl )
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mpi? ( virtual/mpi )
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"
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DEPEND="${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[${PYTHON_USEDEP}]
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media-gfx/mscgen
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dev-texlive/texlive-latex
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dev-texlive/texlive-latexextra
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media-gfx/imagemagick
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)"
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RDEPEND="${CDEPEND}"
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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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DOCS=( AUTHORS README )
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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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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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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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src_prepare() {
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#notes/todos
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# -on apple: there is framework support
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xdg_environment_reset #591952
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cmake-utils_src_prepare
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use cuda && cuda_src_prepare
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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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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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DOC_CONTENTS="Gromacs can use sci-chemistry/vmd to read additional file formats"
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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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src_configure() {
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local mycmakeargs_pre=( ) extra fft_opts=( )
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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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#to create man pages, build tree binaries are executed (bug #398437)
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[[ ${CHOST} = *-darwin* ]] && \
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extra+=" -DCMAKE_BUILD_WITH_INSTALL_RPATH=OFF"
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if use fftw; then
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fft_opts=( -DGMX_FFT_LIBRARY=fftw3 )
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elif use mkl && has_version "=sci-libs/mkl-10*"; then
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fft_opts=( -DGMX_FFT_LIBRARY=mkl
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-DMKL_INCLUDE_DIR="${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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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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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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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="${suffix}"
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)
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BUILD_DIR="${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 ${cuda}
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-DGMX_OPENMM=OFF
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-DGMXAPI=OFF
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-DGMX_BUILD_MDRUN_ONLY=ON
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-DBUILD_SHARED_LIBS=OFF
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-DGMX_BUILD_MANUAL=OFF
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-DGMX_BINARY_SUFFIX="_mpi${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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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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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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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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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
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rm "${ED}"usr/bin/GMXRC* || die
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for x in "${ED}"usr/bin/gmx-completion-*.bash ; do
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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
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newbashcomp "${T}"/"${n}" "${n}"
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done
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rm "${ED}"usr/bin/gmx-completion*.bash || die
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readme.gentoo_create_doc
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}
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pkg_postinst() {
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einfo
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einfo "Please read and cite:"
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einfo "Gromacs 4, J. Chem. Theory Comput. 4, 435 (2008). "
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einfo "https://dx.doi.org/10.1021/ct700301q"
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einfo
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readme.gentoo_print_elog
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}
|
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