From mboxrd@z Thu Jan 1 00:00:00 1970 Return-Path: Received: from lists.gentoo.org (pigeon.gentoo.org [208.92.234.80]) (using TLSv1.3 with cipher TLS_AES_256_GCM_SHA384 (256/256 bits) key-exchange X25519 server-signature RSA-PSS (2048 bits)) (No client certificate requested) by finch.gentoo.org (Postfix) with ESMTPS id 7380B15811D for ; Sun, 9 Jul 2023 14:47:52 +0000 (UTC) Received: from pigeon.gentoo.org (localhost [127.0.0.1]) by pigeon.gentoo.org (Postfix) with SMTP id A8FE3E091F; Sun, 9 Jul 2023 14:47:51 +0000 (UTC) Received: from smtp.gentoo.org (smtp.gentoo.org [IPv6:2001:470:ea4a:1:5054:ff:fec7:86e4]) (using TLSv1.3 with cipher TLS_AES_256_GCM_SHA384 (256/256 bits) key-exchange X25519 server-signature RSA-PSS (4096 bits)) (No client certificate requested) by pigeon.gentoo.org (Postfix) with ESMTPS id 7D30FE091F for ; Sun, 9 Jul 2023 14:47:51 +0000 (UTC) Received: from oystercatcher.gentoo.org (oystercatcher.gentoo.org [148.251.78.52]) (using TLSv1.3 with cipher TLS_AES_256_GCM_SHA384 (256/256 bits) key-exchange X25519 server-signature RSA-PSS (4096 bits)) (No client certificate requested) by smtp.gentoo.org (Postfix) with ESMTPS id 5DF1F340E97 for ; Sun, 9 Jul 2023 14:47:50 +0000 (UTC) Received: from localhost.localdomain (localhost [IPv6:::1]) by oystercatcher.gentoo.org (Postfix) with ESMTP id F1CA9AC4 for ; Sun, 9 Jul 2023 14:47:48 +0000 (UTC) From: "Pacho Ramos" To: gentoo-commits@lists.gentoo.org Content-Transfer-Encoding: 8bit Content-type: text/plain; charset=UTF-8 Reply-To: gentoo-dev@lists.gentoo.org, "Pacho Ramos" Message-ID: <1688914054.c1395ac7948292d04e90f9c4a024fc5cedbee591.pacho@gentoo> Subject: [gentoo-commits] repo/gentoo:master commit in: sci-chemistry/gromacs/ X-VCS-Repository: repo/gentoo X-VCS-Files: sci-chemistry/gromacs/Manifest sci-chemistry/gromacs/gromacs-2022.4.ebuild sci-chemistry/gromacs/gromacs-2023.ebuild X-VCS-Directories: sci-chemistry/gromacs/ X-VCS-Committer: pacho X-VCS-Committer-Name: Pacho Ramos X-VCS-Revision: c1395ac7948292d04e90f9c4a024fc5cedbee591 X-VCS-Branch: master Date: Sun, 9 Jul 2023 14:47:48 +0000 (UTC) Precedence: bulk List-Post: List-Help: List-Unsubscribe: List-Subscribe: List-Id: Gentoo Linux mail X-BeenThere: gentoo-commits@lists.gentoo.org X-Auto-Response-Suppress: DR, RN, NRN, OOF, AutoReply X-Archives-Salt: 577ad8db-9c55-43e1-ab92-b7c6c4a18c2d X-Archives-Hash: d86e034dddbab73935e53f8f757e7141 commit: c1395ac7948292d04e90f9c4a024fc5cedbee591 Author: Pacho Ramos gentoo org> AuthorDate: Sun Jul 9 14:45:34 2023 +0000 Commit: Pacho Ramos gentoo org> CommitDate: Sun Jul 9 14:47:34 2023 +0000 URL: https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=c1395ac7 sci-chemistry/gromacs: drop 2022.4, 2023 Signed-off-by: Pacho Ramos gentoo.org> sci-chemistry/gromacs/Manifest | 6 - sci-chemistry/gromacs/gromacs-2022.4.ebuild | 333 --------------------------- sci-chemistry/gromacs/gromacs-2023.ebuild | 335 ---------------------------- 3 files changed, 674 deletions(-) diff --git a/sci-chemistry/gromacs/Manifest b/sci-chemistry/gromacs/Manifest index 6b7f77954444..978525436fff 100644 --- a/sci-chemistry/gromacs/Manifest +++ b/sci-chemistry/gromacs/Manifest @@ -3,25 +3,19 @@ DIST gromacs-2019.6.tar.gz 33446147 BLAKE2B adc21fb6b841b06d499607f8c0166a673645 DIST gromacs-2020.7.tar.gz 29175554 BLAKE2B 98f1aa415946f8eb113febc81105f0c1b0919b96fc3c55a0ab83bf3950ff509b81eade92e645adb0bc2b407df239e20cf3f19828b6e08616437c8693c1fddcc8 SHA512 1d375c44cec38445e56cea252623b5b6c565680268999d4b6c14d6dc38759a27227655b2d29efaab9f9115d3677b446cb555e11cddafa0dc10c4827caaa2477b DIST gromacs-2021.6.tar.gz 38012702 BLAKE2B 023ae37dc53643758afa050fd179cd66f3c6d6266f6afceee5eb35c890a3ae284956f2bc2409156d6e1fa03a7f23f7b04c27e1820547fd5f147b344d94da7d40 SHA512 65d7874e5cd838ce4f29d033c66304738ccc30f1987f9f8541725058b2fc4551302a399f6ce773e81ac9485963187c48feaf92c71789f4c345c82bd335f806a7 DIST gromacs-2021.7.tar.gz 38028032 BLAKE2B 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b0c97fa652cb9b972c50f29822f530fcaa2ec9acb6d6442114fc6446c54aade5eb1bfa153c69a7e8bf64b66e8b041d7f8e0d51e7f7b0516f9e03f3d9ad626193 SHA512 7cbead90aa6d62346dcf7c2249c3cfa179884b987a749624444d2f59d93e0322f7721143bf6eb44d26102635dc70a73546ef82d4647558b6320bfdd459074017 -DIST regressiontests-2022.4.tar.gz 48614599 BLAKE2B d41d59d4336455c87f3877be48ec49b2cdc989548c51ef9c8277b05bb6cf3dc05ebfa91a0248cc113c130a0ed19aae2c8316184caf37b72aa612b211fe41b144 SHA512 6495a286b201774ea2a922376ff5c0abaae7aaef1dfd28a1a61c817b5c6ac83db99300d43cc019745ca32a025e1f8a7f538342af539d9d753e494c550b429706 DIST regressiontests-2022.5.tar.gz 48615858 BLAKE2B 6655946155291eb24f76832c76e21b5c606905e94426fd057ecdaa44d74844613ba288b651f94120553ef7d7f938de345ddaac7c3738d67bdad148359b7b4500 SHA512 8dd0c8a9b30f4c047fb756dee8eee1cb667803c231fd114717e3156c5694a195dec2b57d80b50b417312949bc4cb7da90027cc98102d84fa154a93862bc69790 DIST regressiontests-2023.1.tar.gz 48613205 BLAKE2B b64716e08e5597676794209a0a951d2a5a46aab2b05bc1615d6f4ba666d5c81a7fe9247fc90ce8d9a5da1a9d52eea73d3d3cd4a4072a8bad66b8de0e06dfa599 SHA512 c6924ec75e456950cef0809ea9718be1bf9d85fe6e9ba5553b2df86ef604b0c7f54d41476f45cbc0ccf801ee0290a829bf4f9eb8d0773586bb8385efc5242d4d -DIST regressiontests-2023.tar.gz 48620353 BLAKE2B 536550976dd761a59ff5684bc4928d534f7e45e69b0a86831e661887a3ad1ea72c1ddb72ab3a27237926083a711dd0f17ea60079fec201dd0992c1aee32ebd7e SHA512 f6b62fab39c77491698822b2f5b3f66c505e801266b31ea7ddc46378f69b524461187bba31b1b23d29f06bfc35630b0cae9a921aa92c0dfba46b2f1d904ce2b6 diff --git a/sci-chemistry/gromacs/gromacs-2022.4.ebuild b/sci-chemistry/gromacs/gromacs-2022.4.ebuild deleted file mode 100644 index ca908310a723..000000000000 --- a/sci-chemistry/gromacs/gromacs-2022.4.ebuild +++ /dev/null @@ -1,333 +0,0 @@ -# Copyright 1999-2023 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=8 - -CMAKE_MAKEFILE_GENERATOR="ninja" - -PYTHON_COMPAT=( python3_{9..11} ) - -DISTUTILS_OPTIONAL=1 -DISTUTILS_USE_PEP517=no -DISTUTILS_SINGLE_IMPL=1 - -inherit bash-completion-r1 cmake cuda distutils-r1 flag-o-matic readme.gentoo-r1 toolchain-funcs xdg-utils - -if [[ ${PV} = *9999* ]]; then - EGIT_REPO_URI=" - https://gitlab.com/gromacs/gromacs.git - https://github.com/gromacs/gromacs.git - git://git.gromacs.org/gromacs.git" - [[ ${PV} = 9999 ]] && EGIT_BRANCH="master" || EGIT_BRANCH="release-${PV:0:4}" - inherit git-r3 -else - SRC_URI=" - https://ftp.gromacs.org/gromacs/${P}.tar.gz - doc? ( https://ftp.gromacs.org/manual/manual-${PV}.pdf ) - test? ( https://ftp.gromacs.org/regressiontests/regressiontests-${PV}.tar.gz )" - # since 2022 arm support was dropped (but not arm64) - KEYWORDS="~amd64 -arm ~arm64 ~x86 ~amd64-linux ~x86-linux ~x64-macos" -fi - -ACCE_IUSE="cpu_flags_x86_sse2 cpu_flags_x86_sse4_1 cpu_flags_x86_fma4 cpu_flags_x86_avx cpu_flags_x86_avx2 cpu_flags_x86_avx512f cpu_flags_arm_neon" - -DESCRIPTION="The ultimate molecular dynamics simulation package" -HOMEPAGE="https://www.gromacs.org/" - -# see COPYING for details -# https://repo.or.cz/w/gromacs.git/blob/HEAD:/COPYING -# base, vmd plugins, fftpack from numpy, blas/lapck from netlib, memtestG80 library, mpi_thread lib -LICENSE="LGPL-2.1 UoI-NCSA !mkl? ( !fftw? ( BSD ) !blas? ( BSD ) !lapack? ( BSD ) ) cuda? ( LGPL-3 ) threads? ( BSD )" -SLOT="0/${PV}" -IUSE="blas clang clang-cuda cuda +custom-cflags +doc build-manual double-precision +fftw +gmxapi +gmxapi-legacy +hwloc lapack mkl mpi +offensive opencl openmp +python +single-precision test +threads +tng ${ACCE_IUSE}" - -CDEPEND=" - blas? ( virtual/blas ) - cuda? ( >=dev-util/nvidia-cuda-toolkit-11[profiler] ) - opencl? ( virtual/opencl ) - fftw? ( sci-libs/fftw:3.0= ) - hwloc? ( sys-apps/hwloc:= ) - lapack? ( virtual/lapack ) - mkl? ( sci-libs/mkl ) - mpi? ( virtual/mpi[cxx] ) - sci-libs/lmfit:= - >=dev-cpp/muParser-2.3:= - ${PYTHON_DEPS} - " -BDEPEND="${CDEPEND} - virtual/pkgconfig - clang? ( >=sys-devel/clang-6:* ) - build-manual? ( - app-doc/doxygen - $(python_gen_cond_dep ' - dev-python/sphinx[${PYTHON_USEDEP}] - ') - media-gfx/mscgen - media-gfx/graphviz - dev-texlive/texlive-latex - dev-texlive/texlive-latexextra - media-gfx/imagemagick - )" -RDEPEND="${CDEPEND} - > ${HOME}/.config/ImageMagick/policy.xml <<- EOF - - - !ATTLIST policymap xmlns CDATA #FIXED ''> - - - ]> - - - - - - - - - EOF - fi -} - -src_configure() { - local mycmakeargs_pre=( ) extra fft_opts=( ) - local acce="AUTO" - - if use custom-cflags; then - #go from slowest to fastest acceleration - acce="None" - if (use amd64 || use x86); then - use cpu_flags_x86_sse2 && acce="SSE2" - use cpu_flags_x86_sse4_1 && acce="SSE4.1" - use cpu_flags_x86_fma4 && acce="AVX_128_FMA" - use cpu_flags_x86_avx && acce="AVX_256" - use cpu_flags_x86_avx2 && acce="AVX2_256" - use cpu_flags_x86_avx512f && acce="AVX_512" - elif (use arm); then - use cpu_flags_arm_neon && acce="ARM_NEON" - elif (use arm64); then - use cpu_flags_arm_neon && acce="ARM_NEON_ASIMD" - fi - else - strip-flags - fi - - #to create man pages, build tree binaries are executed (bug #398437) - [[ ${CHOST} = *-darwin* ]] && \ - extra+=" -DCMAKE_BUILD_WITH_INSTALL_RPATH=OFF" - - if use fftw; then - fft_opts=( -DGMX_FFT_LIBRARY=fftw3 ) - elif use mkl; then - local bits=$(get_libdir) - fft_opts=( -DGMX_FFT_LIBRARY=mkl - -DMKL_INCLUDE_DIR="$(echo /opt/intel/*/mkl/include)" - -DMKL_LIBRARIES="$(echo /opt/intel/*/mkl/lib/*${bits/lib}/libmkl_rt.so)" - ) - else - fft_opts=( -DGMX_FFT_LIBRARY=fftpack ) - fi - - mycmakeargs_pre+=( - "${fft_opts[@]}" - "${lmfit_opts[@]}" - -DGMX_USE_LMFIT=EXTERNAL - -DGMX_USE_MUPARSER=EXTERNAL - -DGMX_EXTERNAL_BLAS=$(usex blas) - -DGMX_EXTERNAL_LAPACK=$(usex lapack) - -DGMX_OPENMP=$(usex openmp) - -DGMX_COOL_QUOTES=$(usex offensive) - -DGMX_USE_TNG=$(usex tng) - -DGMX_BUILD_MANUAL=$(usex build-manual) - -DGMX_HWLOC=$(usex hwloc) - -DGMX_DEFAULT_SUFFIX=off - -DGMX_SIMD="$acce" - -DGMX_VMD_PLUGIN_PATH="${EPREFIX}/usr/$(get_libdir)/vmd/plugins/*/molfile/" - -DGMX_DSSP_PROGRAM_PATH="${EPREFIX}/usr/bin/dssp" - -DBUILD_TESTING=$(usex test) - -DGMX_BUILD_UNITTESTS=$(usex test) - -DPYTHON_EXECUTABLE="${EPREFIX}/usr/bin/${EPYTHON}" - ${extra} - ) - - for x in ${GMX_DIRS}; do - einfo "Configuring for ${x} precision" - local suffix="" - #if we build single and double - double is suffixed - use double-precision && use single-precision && \ - [[ ${x} = "double" ]] && suffix="_d" - local p - [[ ${x} = "double" ]] && p="-DGMX_DOUBLE=ON" || p="-DGMX_DOUBLE=OFF" - local gpu=( "-DGMX_GPU=OFF" ) - [[ ${x} = "float" ]] && use cuda && gpu=( "-DGMX_GPU=CUDA" ) - [[ ${x} = "float" ]] && use clang-cuda && gpu=( "-DGMX_GPU=CUDA" "-DGMX_CLANG_CUDA=ON" ) - use opencl && gpu=( "-DGMX_GPU=OPENCL" ) - local mycmakeargs=( - ${mycmakeargs_pre[@]} ${p} - -DGMX_MPI=$(usex mpi) - -DGMX_THREAD_MPI=$(usex threads) - -DGMXAPI=$(usex gmxapi) - -DGMX_INSTALL_LEGACY_API=$(usex gmxapi-legacy) - "${gpu[@]}" - "$(use test && echo -DREGRESSIONTEST_PATH="${WORKDIR}/${P}_${x}/tests")" - -DGMX_BINARY_SUFFIX="${suffix}" - -DGMX_LIBS_SUFFIX="${suffix}" - -DGMX_PYTHON_PACKAGE=$(usex python) - ) - BUILD_DIR="${WORKDIR}/${P}_${x}" cmake_src_configure - [[ ${CHOST} != *-darwin* ]] || \ - sed -i '/SET(CMAKE_INSTALL_NAME_DIR/s/^/#/' "${WORKDIR}/${P}_${x}/gentoo_rules.cmake" || die - done -} - -src_compile() { - for x in ${GMX_DIRS}; do - einfo "Compiling for ${x} precision" - BUILD_DIR="${WORKDIR}/${P}_${x}"\ - cmake_src_compile - if use python; then - BUILD_DIR="${WORKDIR}/${P}_${x}"\ - cmake_src_compile python_packaging/all - BUILD_DIR="${WORKDIR}/${P}" \ - distutils-r1_src_compile - fi - # not 100% necessary for rel ebuilds as available from website - if use build-manual; then - BUILD_DIR="${WORKDIR}/${P}_${x}"\ - cmake_src_compile manual - fi - done -} - -src_test() { - for x in ${GMX_DIRS}; do - BUILD_DIR="${WORKDIR}/${P}_${x}"\ - cmake_src_compile check - done -} - -src_install() { - for x in ${GMX_DIRS}; do - BUILD_DIR="${WORKDIR}/${P}_${x}" \ - cmake_src_install - if use python; then - BUILD_DIR="${WORKDIR}/${P}_${x}" \ - cmake_src_install python_packaging/install - fi - if use build-manual; then - newdoc "${WORKDIR}/${P}_${x}"/docs/manual/gromacs.pdf "${PN}-manual-${PV}.pdf" - fi - - if use doc; then - if [[ ${PV} != *9999* ]]; then - newdoc "${DISTDIR}/manual-${PV}.pdf" "${PN}-manual-${PV}.pdf" - fi - fi - done - - if use tng; then - insinto /usr/include/tng - doins src/external/tng_io/include/tng/*h - fi - # drop unneeded stuff - rm "${ED}"/usr/bin/GMXRC* || die - for x in "${ED}"/usr/bin/gmx-completion-*.bash ; do - local n=${x##*/gmx-completion-} - n="${n%.bash}" - cat "${ED}"/usr/bin/gmx-completion.bash "$x" > "${T}/${n}" || die - newbashcomp "${T}"/"${n}" "${n}" - done - rm "${ED}"/usr/bin/gmx-completion*.bash || die - readme.gentoo_create_doc -} - -pkg_postinst() { - einfo - einfo "Please read and cite gromacs related papers from list:" - einfo "https://www.gromacs.org/Gromacs_papers" - einfo - readme.gentoo_print_elog -} diff --git a/sci-chemistry/gromacs/gromacs-2023.ebuild b/sci-chemistry/gromacs/gromacs-2023.ebuild deleted file mode 100644 index f57ac5829eb7..000000000000 --- a/sci-chemistry/gromacs/gromacs-2023.ebuild +++ /dev/null @@ -1,335 +0,0 @@ -# Copyright 1999-2023 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=8 - -CMAKE_MAKEFILE_GENERATOR="ninja" - -PYTHON_COMPAT=( python3_{9..11} ) - -DISTUTILS_OPTIONAL=1 -DISTUTILS_USE_PEP517=no -DISTUTILS_SINGLE_IMPL=1 - -inherit bash-completion-r1 cmake cuda distutils-r1 flag-o-matic readme.gentoo-r1 toolchain-funcs xdg-utils - -if [[ ${PV} = *9999* ]]; then - EGIT_REPO_URI=" - https://gitlab.com/gromacs/gromacs.git - https://github.com/gromacs/gromacs.git - git://git.gromacs.org/gromacs.git" - [[ ${PV} = 9999 ]] && EGIT_BRANCH="master" || EGIT_BRANCH="release-${PV:0:4}" - inherit git-r3 -else - SRC_URI=" - https://ftp.gromacs.org/gromacs/${PN}-${PV/_/-}.tar.gz - doc? ( https://ftp.gromacs.org/manual/manual-${PV/_/-}.pdf ) - test? ( https://ftp.gromacs.org/regressiontests/regressiontests-${PV/_/-}.tar.gz )" - # since 2022 arm support was dropped (but not arm64) - KEYWORDS="~amd64 -arm ~arm64 ~x86 ~amd64-linux ~x86-linux ~x64-macos" -fi - -ACCE_IUSE="cpu_flags_x86_sse2 cpu_flags_x86_sse4_1 cpu_flags_x86_fma4 cpu_flags_x86_avx cpu_flags_x86_avx2 cpu_flags_x86_avx512f cpu_flags_arm_neon" - -DESCRIPTION="The ultimate molecular dynamics simulation package" -HOMEPAGE="https://www.gromacs.org/" - -# see COPYING for details -# https://repo.or.cz/w/gromacs.git/blob/HEAD:/COPYING -# base, vmd plugins, fftpack from numpy, blas/lapck from netlib, memtestG80 library, mpi_thread lib -LICENSE="LGPL-2.1 UoI-NCSA !mkl? ( !fftw? ( BSD ) !blas? ( BSD ) !lapack? ( BSD ) ) cuda? ( LGPL-3 ) threads? ( BSD )" -SLOT="0/${PV}" -IUSE="blas clang clang-cuda cuda +custom-cflags +doc build-manual double-precision +fftw +gmxapi +gmxapi-legacy +hwloc lapack mkl mpi +offensive opencl openmp +python +single-precision test +threads +tng ${ACCE_IUSE}" - -CDEPEND=" - blas? ( virtual/blas ) - cuda? ( >=dev-util/nvidia-cuda-toolkit-11[profiler] ) - opencl? ( virtual/opencl ) - fftw? ( sci-libs/fftw:3.0= ) - hwloc? ( sys-apps/hwloc:= ) - lapack? ( virtual/lapack ) - mkl? ( sci-libs/mkl ) - mpi? ( virtual/mpi[cxx] ) - sci-libs/lmfit:= - >=dev-cpp/muParser-2.3:= - ${PYTHON_DEPS} - " -BDEPEND="${CDEPEND} - virtual/pkgconfig - clang? ( >=sys-devel/clang-6:* ) - build-manual? ( - app-doc/doxygen - $(python_gen_cond_dep ' - dev-python/sphinx[${PYTHON_USEDEP}] - dev-python/sphinx-copybutton[${PYTHON_USEDEP}] - dev-python/sphinx-inline-tabs[${PYTHON_USEDEP}] - dev-python/sphinx-argparse[${PYTHON_USEDEP}] - dev-python/sphinxcontrib-autoprogram[${PYTHON_USEDEP}] - ') - media-gfx/mscgen - media-gfx/graphviz - dev-texlive/texlive-latex - dev-texlive/texlive-latexextra - media-gfx/imagemagick - )" -RDEPEND="${CDEPEND}" - -REQUIRED_USE=" - || ( single-precision double-precision ) - doc? ( !build-manual ) - cuda? ( single-precision ) - opencl? ( single-precision ) - cuda? ( !opencl ) - clang-cuda? ( clang cuda ) - mkl? ( !blas !fftw !lapack ) - ${PYTHON_REQUIRED_USE}" - -DOCS=( AUTHORS README ) - -RESTRICT="!test? ( test )" - -if [[ ${PV} != *9999 ]]; then - S="${WORKDIR}/${PN}-${PV/_/-}" -fi - -pkg_pretend() { - [[ ${MERGE_TYPE} != binary ]] && use openmp && tc-check-openmp -} - -pkg_setup() { - [[ ${MERGE_TYPE} != binary ]] && use openmp && tc-check-openmp - python-single-r1_pkg_setup -} - -src_unpack() { - if [[ ${PV} != *9999 ]]; then - default - else - git-r3_src_unpack - if use test; then - EGIT_REPO_URI="git://git.gromacs.org/regressiontests.git" \ - EGIT_BRANCH="${EGIT_BRANCH}" \ - EGIT_CHECKOUT_DIR="${WORKDIR}/regressiontests"\ - git-r3_src_unpack - fi - fi -} - -src_prepare() { - #notes/todos - # -on apple: there is framework support - - xdg_environment_reset #591952 - - # we can use clang as default - if use clang && ! tc-is-clang ; then - export CC=${CHOST}-clang - export CXX=${CHOST}-clang++ - else - tc-export CXX CC - fi - # clang-cuda need to filter mfpmath - if use clang-cuda ; then - filter-mfpmath sse - filter-mfpmath i386 - fi - - cmake_src_prepare - - use cuda && cuda_src_prepare - - GMX_DIRS="" - use single-precision && GMX_DIRS+=" float" - use double-precision && GMX_DIRS+=" double" - - if use test; then - for x in ${GMX_DIRS}; do - mkdir -p "${WORKDIR}/${P}_${x}" || die - cp -al "${WORKDIR}/regressiontests"* "${WORKDIR}/${P}_${x}/tests" || die - done - fi - - DOC_CONTENTS="Gromacs can use sci-chemistry/vmd to read additional file formats" - if use build-manual; then - # try to create policy for imagemagik - mkdir -p ${HOME}/.config/ImageMagick - cat >> ${HOME}/.config/ImageMagick/policy.xml <<- EOF - - - !ATTLIST policymap xmlns CDATA #FIXED ''> - - - ]> - - - - - - - - - EOF - fi -} - -src_configure() { - local mycmakeargs_pre=( ) extra fft_opts=( ) - local acce="AUTO" - - if use custom-cflags; then - #go from slowest to fastest acceleration - acce="None" - if (use amd64 || use x86); then - use cpu_flags_x86_sse2 && acce="SSE2" - use cpu_flags_x86_sse4_1 && acce="SSE4.1" - use cpu_flags_x86_fma4 && acce="AVX_128_FMA" - use cpu_flags_x86_avx && acce="AVX_256" - use cpu_flags_x86_avx2 && acce="AVX2_256" - use cpu_flags_x86_avx512f && acce="AVX_512" - elif (use arm); then - use cpu_flags_arm_neon && acce="ARM_NEON" - elif (use arm64); then - use cpu_flags_arm_neon && acce="ARM_NEON_ASIMD" - fi - else - strip-flags - fi - - #to create man pages, build tree binaries are executed (bug #398437) - [[ ${CHOST} = *-darwin* ]] && \ - extra+=" -DCMAKE_BUILD_WITH_INSTALL_RPATH=OFF" - - if use fftw; then - fft_opts=( -DGMX_FFT_LIBRARY=fftw3 ) - elif use mkl; then - local bits=$(get_libdir) - fft_opts=( -DGMX_FFT_LIBRARY=mkl - -DMKL_INCLUDE_DIR="$(echo /opt/intel/*/mkl/include)" - -DMKL_LIBRARIES="$(echo /opt/intel/*/mkl/lib/*${bits/lib}/libmkl_rt.so)" - ) - else - fft_opts=( -DGMX_FFT_LIBRARY=fftpack ) - fi - - mycmakeargs_pre+=( - "${fft_opts[@]}" - "${lmfit_opts[@]}" - -DGMX_USE_LMFIT=EXTERNAL - -DGMX_USE_MUPARSER=EXTERNAL - -DGMX_EXTERNAL_BLAS=$(usex blas) - -DGMX_EXTERNAL_LAPACK=$(usex lapack) - -DGMX_OPENMP=$(usex openmp) - -DGMX_COOL_QUOTES=$(usex offensive) - -DGMX_USE_TNG=$(usex tng) - -DGMX_BUILD_MANUAL=$(usex build-manual) - -DGMX_HWLOC=$(usex hwloc) - -DGMX_DEFAULT_SUFFIX=off - -DGMX_SIMD="$acce" - -DGMX_VMD_PLUGIN_PATH="${EPREFIX}/usr/$(get_libdir)/vmd/plugins/*/molfile/" - -DBUILD_TESTING=$(usex test) - -DGMX_BUILD_UNITTESTS=$(usex test) - -DPYTHON_EXECUTABLE="${EPREFIX}/usr/bin/${EPYTHON}" - ${extra} - ) - - for x in ${GMX_DIRS}; do - einfo "Configuring for ${x} precision" - local suffix="" - #if we build single and double - double is suffixed - use double-precision && use single-precision && \ - [[ ${x} = "double" ]] && suffix="_d" - local p - [[ ${x} = "double" ]] && p="-DGMX_DOUBLE=ON" || p="-DGMX_DOUBLE=OFF" - local gpu=( "-DGMX_GPU=OFF" ) - [[ ${x} = "float" ]] && use cuda && gpu=( "-DGMX_GPU=CUDA" ) - [[ ${x} = "float" ]] && use clang-cuda && gpu=( "-DGMX_GPU=CUDA" "-DGMX_CLANG_CUDA=ON" ) - use opencl && gpu=( "-DGMX_GPU=OPENCL" ) - local mycmakeargs=( - ${mycmakeargs_pre[@]} ${p} - -DGMX_MPI=$(usex mpi) - -DGMX_THREAD_MPI=$(usex threads) - -DGMXAPI=$(usex gmxapi) - -DGMX_INSTALL_LEGACY_API=$(usex gmxapi-legacy) - "${gpu[@]}" - "$(use test && echo -DREGRESSIONTEST_PATH="${WORKDIR}/${P}_${x}/tests")" - -DGMX_BINARY_SUFFIX="${suffix}" - -DGMX_LIBS_SUFFIX="${suffix}" - -DGMX_PYTHON_PACKAGE=$(usex python) - ) - BUILD_DIR="${WORKDIR}/${P}_${x}" cmake_src_configure - [[ ${CHOST} != *-darwin* ]] || \ - sed -i '/SET(CMAKE_INSTALL_NAME_DIR/s/^/#/' "${WORKDIR}/${P}_${x}/gentoo_rules.cmake" || die - done -} - -src_compile() { - for x in ${GMX_DIRS}; do - einfo "Compiling for ${x} precision" - BUILD_DIR="${WORKDIR}/${P}_${x}"\ - cmake_src_compile - if use python; then - BUILD_DIR="${WORKDIR}/${P}_${x}"\ - cmake_src_compile python_packaging/all - BUILD_DIR="${WORKDIR}/${P}" \ - distutils-r1_src_compile - fi - # not 100% necessary for rel ebuilds as available from website - if use build-manual; then - BUILD_DIR="${WORKDIR}/${P}_${x}"\ - cmake_src_compile manual - fi - done -} - -src_test() { - for x in ${GMX_DIRS}; do - BUILD_DIR="${WORKDIR}/${P}_${x}"\ - cmake_src_compile check - done -} - -src_install() { - for x in ${GMX_DIRS}; do - BUILD_DIR="${WORKDIR}/${P}_${x}" \ - cmake_src_install - if use python; then - BUILD_DIR="${WORKDIR}/${P}_${x}" \ - cmake_src_install python_packaging/install - fi - if use build-manual; then - newdoc "${WORKDIR}/${P}_${x}"/docs/manual/gromacs.pdf "${PN}-manual-${PV}.pdf" - fi - - if use doc; then - if [[ ${PV} != *9999* ]]; then - newdoc "${DISTDIR}/manual-${PV/_/-}.pdf" "${PN}-manual-${PV}.pdf" - fi - fi - done - - if use tng; then - insinto /usr/include/tng - doins src/external/tng_io/include/tng/*h - fi - # drop unneeded stuff - rm "${ED}"/usr/bin/GMXRC* || die - for x in "${ED}"/usr/bin/gmx-completion-*.bash ; do - local n=${x##*/gmx-completion-} - n="${n%.bash}" - cat "${ED}"/usr/bin/gmx-completion.bash "$x" > "${T}/${n}" || die - newbashcomp "${T}"/"${n}" "${n}" - done - rm "${ED}"/usr/bin/gmx-completion*.bash || die - readme.gentoo_create_doc -} - -pkg_postinst() { - einfo - einfo "Please read and cite gromacs related papers from list:" - einfo "https://www.gromacs.org/Gromacs_papers" - einfo - readme.gentoo_print_elog -}