From 58401fa12262cbdaa3029d41d18e9615fdedba3f Mon Sep 17 00:00:00 2001 From: Alexey Shvetsov Date: Thu, 1 Feb 2024 16:06:17 +0300 Subject: sci-chemistry/gromacs: add 2024, drop 2024_rc Signed-off-by: Alexey Shvetsov --- sci-chemistry/gromacs/Manifest | 6 +- sci-chemistry/gromacs/gromacs-2024.ebuild | 335 +++++++++++++++++++++++++++ sci-chemistry/gromacs/gromacs-2024_rc.ebuild | 335 --------------------------- 3 files changed, 338 insertions(+), 338 deletions(-) create mode 100644 sci-chemistry/gromacs/gromacs-2024.ebuild delete mode 100644 sci-chemistry/gromacs/gromacs-2024_rc.ebuild (limited to 'sci-chemistry') diff --git a/sci-chemistry/gromacs/Manifest b/sci-chemistry/gromacs/Manifest index 6a26873979d3..cfcc1c3e8f72 100644 --- a/sci-chemistry/gromacs/Manifest +++ b/sci-chemistry/gromacs/Manifest @@ -8,7 +8,7 @@ DIST gromacs-2022.6.tar.gz 40330705 BLAKE2B fdafbd5b2a92d6022dec3e79e961fef220f1 DIST gromacs-2023.1.tar.gz 41934072 BLAKE2B 6d04642ba37a8563fafc10e0be83e33aab5ce25ef43ec2c9555e84328096bbe61426558a1433b086028f3c6637a5b3ae82241e67f206c0dd0b5254f5ec27ae4c SHA512 4bddbbc56f26487db9d35f371d65725289d1355dc4c295d32698499e05eb74e31d4db579fc1f665edb55a68b002bddacf37c0f05d3f970b1111c149990d434b1 DIST gromacs-2023.2.tar.gz 41930578 BLAKE2B ee115ba45711867ced4ad08cede0e87dffd7c4e7a45ff3ee0c06b2f46b0dec838e4b532e092ce3abd993e231ca7d517d9941b371fd6d9d64d581862dc67c449c SHA512 9bc17f310e6be6fd51b7c07bde0b58e8fa15085b2c073eb7bed0db917646586dee5d7cf9b4b178e9b4cedd40d4bcd967edcc4b26debaec6f4ca94399b13b9186 DIST gromacs-2023.3.tar.gz 42071770 BLAKE2B dea0f6b0ccd67bfa4fc58c06bd3eda6d17a7f4b1c6746c2743860cf00ba514884a27140b65b7830ca340c233510ace1734ecc09e393be3e9761e31b9e4abfeb6 SHA512 016181be78887b0e31bc7fd124ac7c25c923c6bab1ffe43d3b4a744ae68203bb9d9f976c4c81bce344f4ea8e9d610ebd5b631b2202fcd6cfefd8c1ad0ebfe10d -DIST gromacs-2024-rc.tar.gz 42467347 BLAKE2B ee9e8dd15f5fc4df267678689b2ee22beb1de0a16ed3c620063d25b3e9df2295415dccf03e9aac7b7834e0ccca4ca1aa9b6db68aacc63399f947ed6d40b0025d SHA512 fe2de756b5dfa4d64fd974e3ffd1af561edb6102e42f2443fe27d9c06e6c0ed3afcd31c38ecab4de253e531a1d8a546690e2231ba20a5bdd4bc204491dc1b4fc +DIST gromacs-2024.tar.gz 42455653 BLAKE2B 86446c5e95f9ddaf718126c409389730ee1642f36c3e0d844eb4b3a640c275e7979581365dacb57ac66daec296bbd94be6d5c0376f7255d3d3950f6759f8d69a SHA512 d64bf3cbe579003ce37dfd3d27c68746a04360d9d5491c638f3f2bd9af2c938504b0c9710c62e85225370ddf5418e6ebc2422033e46af5eee6e4aaa53699fed7 DIST manual-2018.8.pdf 10025023 BLAKE2B afb0a6e6a72d78df743fcb57e7c1716848589e571dd35167b957a9b407ca27978ccfb6cb9e0df9c9439b888f352501a00ba32281ed1e0b4193bd606f1d77152e SHA512 b1972f7ce965bfc9377542993c5943ea4868a8ed23a969d4203264746d6bea3a7a65c6379196ece37fd6d68ec7ec80f827bde87d1049284af7082759a124f1d5 DIST manual-2019.6.pdf 12702376 BLAKE2B c350127bc06a9eb3dee73da39037c84daeb89500e23cb131bd19a150bf60602d4dde7611e0c6f0f344af4093e96a899303dac71b4df56fd0c44c3a48a56606b7 SHA512 dfdff67c2c1c9ce1f1c236b7686c5331b0fe86951da6c98eddd6a3e748815e0be0a9653ae4318469fcdd913c4e7c355d64a997cc80b9d9fbe6282ef6d98e61eb DIST manual-2020.7.pdf 11850780 BLAKE2B 38594e87993badfbbcf47d6010a7f67d3c3426dab85e1462916b4d62be27b5764953f912cf2b71ee24877e0bfa27b3f74431da2da81b4977d58cb66b2cc795a3 SHA512 4f184f2c90e0bac01a48069cc546cd5b04fa5f543f90dd2d68c6d17be278152fd09456b6a6c5c8236f8fb85a174d6ec7a1c7b44d437b4e6fea5d0ada73cec0f6 @@ -19,7 +19,7 @@ DIST manual-2022.6.pdf 13081140 BLAKE2B e7ae3f23ddc076c295be2c464fe2177d6d6848d0 DIST manual-2023.1.pdf 13526498 BLAKE2B a9aabcb722954c9c83a8f5945c85e634b0b82ace8b9b077c3f2b9ff432ca71d3e2d5ca2dd52d6ce489d77d3d4ca7b41d75e5566205bb8855caa650fa2722e5ec SHA512 b6ca6c822ac5b3cbe3c84d8fd51d3ed465268c00bb5f96e2afa557d45f9c534b0de278f33a0fdf43080c9c619344b98cd71847e17b297a789eec4c8b42dea7b2 DIST manual-2023.2.pdf 13547562 BLAKE2B 17155c82d968003706f974e2fb513dced28987e4630c455674d4088dcb827136e2b7b66836a2bf7f9be472254c11ab4ec98cace1462e85a7a18b0f1eb1760781 SHA512 b8026422fb367bf58d6ddb727afe2f1b208c9abb4eb513d85d395a19a82a7fcf362390f4ae5718fa17b0aeb7bf2c90567f40913fdc3cfc51c63d3757ab5a4905 DIST manual-2023.3.pdf 13565055 BLAKE2B 0332b5c4de863e9f33d7ae7404741ee8f7f503ee0d2dc723e9cc42e9fd3fb8fc74313b43589cbfc7127daec24b721ba79a3c53ff509e718992ccbde14889ea2f SHA512 144220f18bfab6fefec738a7af743bd01733a896c853963ce113354da05514941862412786f0e2183de77634b31b334814d42daae87a9009ec0211118ed87685 -DIST manual-2024-rc.pdf 13645392 BLAKE2B 06456a805b7e85924c34d6b940d32e6e9eae1a117e50a02cfe2dd909e79968a69a78eca95ec765671ea30cdc74a1c6c9314dfa2cd8da50ef378f6f7c685e068f SHA512 b20eaea8d6fcd260018bbac76c33e4994f85bd470d6c111ced3b32f0ff805834c4c18020adfc643ec1cf7d10172b5a5a5f4ed404b912ddf25646d16f36e21d54 +DIST manual-2024.pdf 13644437 BLAKE2B 19d547686d5c5be5e1236aba648e8afb174b281802ab76e020466953ab5d2dd98701f21eb4736cb449b61960b5b7aadce6711b2b0309a41dd1997d7383bce09e SHA512 b00048651f1f81f9024ba5c4c02ad66d2b07eb7b816f0489568fb64859cac515b885a5cb4640c8b5bd7c3620655a7ebc5fc2e4e4cbb8e952ffb0c9b5815ae661 DIST regressiontests-2018.8.tar.gz 67855469 BLAKE2B 34c9b339f6229f483afbb5192ee6ba8b8f72d5c26907a853af9c53dfece0d88739e48f6b44b78d1c010f988f9385d077285300522164f533a5861e9dda879275 SHA512 3642389d27bd1942cd0f091c940ae97b197b94856a387fe581dc516b0d4169480f16551d4ba357f9282b3337d605c286d51dd38112ac87c826dda634904836bb DIST regressiontests-2019.6.tar.gz 67643195 BLAKE2B 1e054e24b187946f7ea28090d4f20cf8e1d79a26253f57ba07d130e0773d8541b8a1552a38023d31a68ce8bc62d8e0af1d98609234bb3e7d3e6d567307ebb386 SHA512 eacf1c55b982515a305c29459fe80a7cd558a8481e5689962aa956148af542568b1d1ce59c6784ecb0afd4768c2b664afa21e12af2d89ae2b06b1ba61ad72036 DIST regressiontests-2020.7.tar.gz 48541487 BLAKE2B 255608b52158c6c01e7c7c4dcf075128ecf22b2f26d32e8c203de8a4bc69c60ec95f49cf8ccd64abc3073c5e8dca9d6b01daed9dfb8f67bce2dd068ed01acd05 SHA512 2458582f94f3c9f4e1454824ce3940b4f5b6cb2151d06846c42e7a9448296fd2a6df4f53be9624e0d3317d2b59f89bb5348eb8b2970d7b46ac22ca989ef3458a @@ -30,4 +30,4 @@ DIST regressiontests-2022.6.tar.gz 48615697 BLAKE2B 566adafbc36d3c1faae322fca9cf DIST regressiontests-2023.1.tar.gz 48613205 BLAKE2B b64716e08e5597676794209a0a951d2a5a46aab2b05bc1615d6f4ba666d5c81a7fe9247fc90ce8d9a5da1a9d52eea73d3d3cd4a4072a8bad66b8de0e06dfa599 SHA512 c6924ec75e456950cef0809ea9718be1bf9d85fe6e9ba5553b2df86ef604b0c7f54d41476f45cbc0ccf801ee0290a829bf4f9eb8d0773586bb8385efc5242d4d DIST regressiontests-2023.2.tar.gz 48621115 BLAKE2B bc19380e7adaef5246d5620b611546fcd31e1b92129b78c6a8b9acf58bcebab8427aca1b71434b9d6f44535aeb7c2053ada941a8851435f3949aab43316ec136 SHA512 ecb275b93b72bc862c1c9f87c7c1b3abbe535c770e86c020f0f5684a60c6edeb19a193719f338d42576b9c40ec213b915f4c2b3c206dca574eccb8f9ade2c261 DIST regressiontests-2023.3.tar.gz 48620623 BLAKE2B e664bde0dab4bc27f1c8c1b6a24f4a9cba1164a7978d169be091945dc1cabfe821f983a7b7c891cd983d5b05bb3f27c07cdb180c0bfadb93751618cab57671e7 SHA512 0a5bd7a502973c2f658faca159ed0677907a1ca30eae3912a624e58e7cae9965c17c94ce65e94886d92444d34eb63b5b88a578459e6063687c43188031c0f836 -DIST regressiontests-2024-rc.tar.gz 48132900 BLAKE2B 540c04e1d34826040bc3c99e7d15aef951693c1c22210ed7b82c751af3b6ef600250c2611747e9164d3d9a2bd30937c7831c93ba5950378a8c39eb1aece3da85 SHA512 5336adb0901516bd47434964f79fcf02ae87126352ba39fdb6afe39e6c353e9e0f648f8133febc703ca022baa8cff4b7abda2b18f891594f338d1113874374b1 +DIST regressiontests-2024.tar.gz 48142685 BLAKE2B e24c29c2b534f2fe42e4abc122578ba618279f3182f83be604516e6ee2a34ff037b2604b4cda7a9b7e2ea9fce0a386b3efb7c8aa0cac378d6d8c1595be884c76 SHA512 6c4a847c379603590f618a4da7c691b51bbe180ca9dc59abf885ef8599e1b66758171eb05b7d7709d968f559b209c2fa4cfec8f15cc5d072fafe952567002c2e diff --git a/sci-chemistry/gromacs/gromacs-2024.ebuild b/sci-chemistry/gromacs/gromacs-2024.ebuild new file mode 100644 index 000000000000..a3319899d419 --- /dev/null +++ b/sci-chemistry/gromacs/gromacs-2024.ebuild @@ -0,0 +1,335 @@ +# Copyright 1999-2024 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=8 + +CMAKE_MAKEFILE_GENERATOR="ninja" + +PYTHON_COMPAT=( python3_{10..12} ) + +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 + " + [[ ${PV} = 9999 ]] && EGIT_BRANCH="master" || EGIT_BRANCH="release-${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-text/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 [[ ${PV} != *9999 ]]; then + default + else + git-r3_src_unpack + if use test; then + EGIT_REPO_URI="https://gitlab.com/gromacs/gromacs-regressiontests.git" \ + EGIT_BRANCH="${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/articles.html" + einfo + readme.gentoo_print_elog +} diff --git a/sci-chemistry/gromacs/gromacs-2024_rc.ebuild b/sci-chemistry/gromacs/gromacs-2024_rc.ebuild deleted file mode 100644 index a3319899d419..000000000000 --- a/sci-chemistry/gromacs/gromacs-2024_rc.ebuild +++ /dev/null @@ -1,335 +0,0 @@ -# Copyright 1999-2024 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=8 - -CMAKE_MAKEFILE_GENERATOR="ninja" - -PYTHON_COMPAT=( python3_{10..12} ) - -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 - " - [[ ${PV} = 9999 ]] && EGIT_BRANCH="master" || EGIT_BRANCH="release-${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-text/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 [[ ${PV} != *9999 ]]; then - default - else - git-r3_src_unpack - if use test; then - EGIT_REPO_URI="https://gitlab.com/gromacs/gromacs-regressiontests.git" \ - EGIT_BRANCH="${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/articles.html" - einfo - readme.gentoo_print_elog -} -- cgit v1.2.3-65-gdbad