From 3478331a5f6f2612bbba9d91b98b098be44d4075 Mon Sep 17 00:00:00 2001 From: Alexey Shvetsov Date: Thu, 4 Dec 2025 18:30:35 +0300 Subject: [PATCH] sci-chemistry/gromacs: Add new versions of gromacs Signed-off-by: Alexey Shvetsov --- sci-chemistry/gromacs/Manifest | 6 + ...2024.9999.ebuild => gromacs-2025.4.ebuild} | 23 +- .../gromacs/gromacs-2026.9999.ebuild | 359 ++++++++++++++++++ .../gromacs/gromacs-2026_beta.ebuild | 359 ++++++++++++++++++ 4 files changed, 745 insertions(+), 2 deletions(-) rename sci-chemistry/gromacs/{gromacs-2024.9999.ebuild => gromacs-2025.4.ebuild} (92%) create mode 100644 sci-chemistry/gromacs/gromacs-2026.9999.ebuild create mode 100644 sci-chemistry/gromacs/gromacs-2026_beta.ebuild diff --git a/sci-chemistry/gromacs/Manifest b/sci-chemistry/gromacs/Manifest index e6f780ae6c94..b66082130db0 100644 --- a/sci-chemistry/gromacs/Manifest +++ b/sci-chemistry/gromacs/Manifest @@ -1,9 +1,15 @@ DIST gromacs-2023.5.tar.gz 42079310 BLAKE2B e50dbe76396230f4a886280bdebcf7b131506679240e77d2a2263c3b5dbfe7ef754c4265fc04e9acad7932c7691de7f694cc23140a25d0d5be649a4120f45b0c SHA512 f3a34cf0d379d6d4964d7494af6c6617c0c092293ea38a3a248af2dd2a90cae04696d52e68126176065efc480977942b00efa441028e526e1555c7e84551fc0c DIST gromacs-2024.6.tar.gz 42340289 BLAKE2B babba3ec83e8757d95733a51eebf780a2f0cf5da2fd3b2aa9410cdfca7901955cbd63d2ed0c61fde873b4438d85ae7769afa8f3d7ee1da26571d8989c516ecd4 SHA512 eb3d06df3e5c52d3dab801e5c2134fc05ded1bca8b1955f747e4efbb2b4cd1f50680f073592a5c5d580abff0a869ffd1c19c352bc6d9b4ab40465741ed7d001a DIST gromacs-2025.3.tar.gz 44407119 BLAKE2B 7e7385d5a83c02cb7152f789df6b86321b9ee22d7fb53e0e69fd01ba04ec197d1b725047f5c9983595ab124f23310f926e101d12a2113472f3b2aaa53f26b661 SHA512 8151bb0f72bf51d0368e40871b68d552c58ed69c0e431601afbf5c7923e7512d2458dfb22eb7fd79cc3c464434ca94a67c99a9f71c7e6b00d7d141789712c157 +DIST gromacs-2025.4.tar.gz 44406127 BLAKE2B 6a558e979574876bc0077e96733c0f7e267c39bff6afbf840ffc7ce0f2580ff0871136d43aa994f4bb44aa98ad4192cefac003d306c02b89aa026d46a47d2a84 SHA512 640bee4b499b06de7dc6a04c6448f174a0232afc2bc90a8e1a862842ea0cdc886eabe6d170d637ccfb9d8e979b74067ac0d52b760fd98c7d6dc47d32e5cd3733 +DIST gromacs-2026-beta.tar.gz 45617869 BLAKE2B 60cfee3bb818f9c0c528b5d65c9d05263755edb58a0c33fe5a48aca1e5b960cef3ae2fb11c2da18ecfc8610aaa1ca617fbf9000685aee93a4579bda90400b1a6 SHA512 ab6f68569231a0f5876381fda467b6bed670aedf633f479d78eef17d5a2e0f22db9602eefab66f3e192a192a312335ff16f192199e90ce5724576de389ae3f12 DIST manual-2023.5.pdf 13579081 BLAKE2B 42f687ebcdb79bfc77aabac4fd382940c23ba27da380b8eff342c2e9255a58fc11a0458220d1f71f3c13ab1cf6fdabad00ac1bad741781d0b787899165bea2cc SHA512 0661f166f7a8dc24b4244c0139f366832ddfc1298129df2a6e29800b5d1567318781ab547bc7e9ee54de7a62abba4996f8e3010c91d6917c248117e5711d7dbb DIST manual-2024.6.pdf 13698340 BLAKE2B 7926fe0c09ab1a6027e6e5d2692e2a590ec31c061b0f3e0dd278ffc8bffe923d6342bd9f375758fe5b0ca9c7fd43a216e486c694ba8d644acceb6467aac37425 SHA512 9130bda473ddfc475f3c7a6946890189bf225609208fb9e84c81606a72d63383199ac5e05f3620e7d7f96916ee475e19528d03b4ddc4b339772af61825beec45 DIST manual-2025.3.pdf 13822608 BLAKE2B 75ea8359a33941f1d44a6c471c03e268c707cdc4717ea43c455c25c5c60b7708e68849aba8fde7872aefa93691ef0bec531b7bd9cb0376b3ddee34c24058bdb5 SHA512 e0a3016eb6fc271d617795c1595a15e234c28a8492e2b0471b705c1f597b672ec05d0bb78ff3b977140c5f525dcc72c3b082cc74aee1e4207b9f1c2593a71bb5 +DIST manual-2025.4.pdf 13827071 BLAKE2B 8bc581f05fe80f1881efd7b3b5f87a34d153847fed92a4cb8b2d98666bd5b84ef46319f9f49f1c47b9940a5fa68b93d543fbf60318defc3884988a9942c1aeff SHA512 451360ba60f2c4fabe09851bdb1712a2273278f01b5b23b5afbf277b3822f8fed7eb64991a549fbac10878f366db15f12e3b93ae6285095fc30731761604f3fa +DIST manual-2026-beta.pdf 13856429 BLAKE2B 672c5e555eca4b19582e6e1ec6bdb49c7b73ae61342b5cc77810a5d9d4dfe8a73d21606367d49b7d0dbed55a526187b34f5e7cfcda5820ab80c9312236e320b9 SHA512 130cc86caab4d1567bdc274a5619c4527aa2c1555ed74fb6863ac713104cad46fea41d5401a7e0e0fe12a3bf1fc08df35d3583ffab76c5ddf5fdbc38b3693700 DIST regressiontests-2023.5.tar.gz 48619605 BLAKE2B f2549a34750c6866f054614a00a3360a09b82306e6bd5e5b848e18cdd3a3fabaac6203c5ca734901019403225dd47e0d662838abe9a1db7d07662f1c745b8e4f SHA512 3ccaf9db7dfba641a5e98ebff3d735cae3f679926aba443ffedec20dd6c85e67f0e9711ebad5dfa8105122d5411f5de6ded1802a7da4ddf0599657832c8c597a DIST regressiontests-2024.6.tar.gz 32776894 BLAKE2B 75dbf6a6ec5a1d0848a51335a1fb2e6777361d0b823e7f88c5145c881aa819abfc2eaaae1ae438538213c09659e9512bf77b4dc2f0ee63a28a1f213f49b5a47d SHA512 1150396a3c20b7747a4a58c22b26c0c40cf6e6f70b8daabfc71cbe00f2dce3ad1c02d89d264a7d7db3f3e7e9dd1c0b46a438d297cdeb074e50d8d6d3e916950b DIST regressiontests-2025.3.tar.gz 32653489 BLAKE2B 1396872d6ebe2756b02ca1a1d173edd29f4931d2b30280299723b24164e5576c14c59997c00d7919b262fb1a15083dc90541f9f7e48587090002fc7cca9e1332 SHA512 fb947dc148e21a69e1ef06258f6c2359156e4afb7c8bee9e659ea461f5e4e9fe3654bec86324e11fcd6624889490ec73cb213bf0111cf76ded966f43c1182a20 +DIST regressiontests-2025.4.tar.gz 32652577 BLAKE2B 7c4253499e94f5adeb17a17ebb93229b0a8dd0f6694af3b67a751d76e916d96bf461070b56774b331512cc351feb8889c6f843a386ac41e615f33af17d1baa2e SHA512 54c29741229a44e322b2e1445bb8d90ed4d790704d9b13fa392e78d6effa551f685e7c18e2c86ca613a85b34ebc3ddef512b406621d53471c6bbb0e1e8913ff0 +DIST regressiontests-2026-beta.tar.gz 16580940 BLAKE2B dbce022c5d43bacd897eb416393cf977f28b1fb731d4da35ae237cbf4a341cbbbe55c036eef59da7240d5758afd2d08c6ccef8f86d0078bad943a3eeb0a6a993 SHA512 f48e897b58706a479301fc8d6638dfaab161381da6099d5bdd8aec349a36aa56df32208b5dabf1279c0e475912975cf6fda66c6404a3910bc7f38db4b7dac933 diff --git a/sci-chemistry/gromacs/gromacs-2024.9999.ebuild b/sci-chemistry/gromacs/gromacs-2025.4.ebuild similarity index 92% rename from sci-chemistry/gromacs/gromacs-2024.9999.ebuild rename to sci-chemistry/gromacs/gromacs-2025.4.ebuild index f9fa1c810759..3ec2e6737603 100644 --- a/sci-chemistry/gromacs/gromacs-2024.9999.ebuild +++ b/sci-chemistry/gromacs/gromacs-2025.4.ebuild @@ -18,7 +18,7 @@ if [[ ${PV} = *9999* ]]; then https://gitlab.com/gromacs/gromacs.git https://github.com/gromacs/gromacs.git " - [[ ${PV} = 9999 ]] && EGIT_BRANCH="master" || EGIT_BRANCH="release-${PV:0:4}" + [[ ${PV} = 9999 ]] && EGIT_BRANCH="main" || EGIT_BRANCH="release-${PV:0:4}" inherit git-r3 else SRC_URI=" @@ -26,6 +26,7 @@ else 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) + # since 2025 x86-32 support was dropped KEYWORDS="~amd64 -arm ~arm64 ~riscv -x86 ~amd64-linux -x86-linux ~x64-macos" fi @@ -39,7 +40,7 @@ HOMEPAGE="https://www.gromacs.org/" # 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}" +IUSE="blas clang clang-cuda cuda +custom-cflags +doc build-manual double-precision +fftw +gmxapi +gmxapi-legacy +hwloc lapack mkl mpi nnpot +offensive opencl openmp +python +single-precision test +threads +tng ${ACCE_IUSE}" CDEPEND=" blas? ( virtual/blas ) @@ -54,6 +55,7 @@ CDEPEND=" lapack? ( virtual/lapack ) mkl? ( sci-libs/mkl ) mpi? ( virtual/mpi[cxx] ) + nnpot? ( sci-ml/caffe2[cuda=,opencl=] ) sci-libs/lmfit:= >=dev-cpp/muParser-2.3:= ${PYTHON_DEPS} @@ -61,6 +63,13 @@ CDEPEND=" BDEPEND="${CDEPEND} virtual/pkgconfig clang? ( >=llvm-core/clang-6:* ) + $(python_gen_cond_dep ' + dev-python/sphinx[${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}] + ') build-manual? ( app-text/doxygen $(python_gen_cond_dep ' @@ -182,6 +191,11 @@ src_prepare() { src_configure() { local mycmakeargs_pre=( ) extra fft_opts=( ) local acce="AUTO" + local nnpot="OFF" + + if use nnpot; then + nnpot="TORCH" + fi if use custom-cflags; then #go from slowest to fastest acceleration @@ -229,9 +243,12 @@ src_configure() { -DGMX_COOL_QUOTES=$(usex offensive) -DGMX_USE_TNG=$(usex tng) -DGMX_BUILD_MANUAL=$(usex build-manual) + -DGMX_USE_HDF5=off -DGMX_HWLOC=$(usex hwloc) -DGMX_DEFAULT_SUFFIX=off + -DGMX_BUILD_HELP=$(usex doc) -DGMX_SIMD="$acce" + -DGMX_NNPOT="$nnpot" -DGMX_VMD_PLUGIN_PATH="${EPREFIX}/usr/$(get_libdir)/vmd/plugins/*/molfile/" -DBUILD_TESTING=$(usex test) -DGMX_BUILD_UNITTESTS=$(usex test) @@ -274,6 +291,8 @@ src_compile() { einfo "Compiling for ${x} precision" BUILD_DIR="${WORKDIR}/${P}_${x}"\ cmake_src_compile + BUILD_DIR="${WORKDIR}/${P}_${x}"\ + cmake_src_compile man if use python; then BUILD_DIR="${WORKDIR}/${P}_${x}"\ cmake_src_compile python_packaging/all diff --git a/sci-chemistry/gromacs/gromacs-2026.9999.ebuild b/sci-chemistry/gromacs/gromacs-2026.9999.ebuild new file mode 100644 index 000000000000..39d1b28d5525 --- /dev/null +++ b/sci-chemistry/gromacs/gromacs-2026.9999.ebuild @@ -0,0 +1,359 @@ +# Copyright 1999-2025 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=8 + +CMAKE_MAKEFILE_GENERATOR="ninja" + +PYTHON_COMPAT=( python3_{11..13} ) + +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 + " + [[ ${PV} = 9999 ]] && EGIT_BRANCH="main" || EGIT_BRANCH="release-${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) + # since 2025 x86-32 support was dropped + KEYWORDS="~amd64 -arm ~arm64 ~riscv -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 hdf5 +hwloc lapack mkl mpi nnpot +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 ) + openmp? ( + sys-devel/gcc[openmp] + llvm-runtimes/clang-runtime[openmp] + ) + fftw? ( sci-libs/fftw:3.0= ) + hdf5? ( sci-libs/hdf5 ) + hwloc? ( sys-apps/hwloc:= ) + lapack? ( virtual/lapack ) + mkl? ( sci-libs/mkl ) + mpi? ( virtual/mpi[cxx] ) + nnpot? ( sci-ml/caffe2[cuda=,opencl=] ) + sci-libs/lmfit:= + >=dev-cpp/muParser-2.3:= + ${PYTHON_DEPS} + " +BDEPEND="${CDEPEND} + virtual/pkgconfig + clang? ( >=llvm-core/clang-6:* ) + $(python_gen_cond_dep ' + dev-python/sphinx[${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}] + ') + 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" + local nnpot="OFF" + + if use nnpot; then + nnpot="TORCH" + fi + + 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=$(usex build-manual) + -DGMX_USE_HDF5=$(usex hdf5) + -DGMX_HWLOC=$(usex hwloc) + -DGMX_DEFAULT_SUFFIX=off + -DGMX_BUILD_HELP=$(usex doc) + -DGMX_SIMD="$acce" + -DGMX_NNPOT="$nnpot" + -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 + BUILD_DIR="${WORKDIR}/${P}_${x}"\ + cmake_src_compile man + if use python; then + BUILD_DIR="${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-2026_beta.ebuild b/sci-chemistry/gromacs/gromacs-2026_beta.ebuild new file mode 100644 index 000000000000..39d1b28d5525 --- /dev/null +++ b/sci-chemistry/gromacs/gromacs-2026_beta.ebuild @@ -0,0 +1,359 @@ +# Copyright 1999-2025 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=8 + +CMAKE_MAKEFILE_GENERATOR="ninja" + +PYTHON_COMPAT=( python3_{11..13} ) + +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 + " + [[ ${PV} = 9999 ]] && EGIT_BRANCH="main" || EGIT_BRANCH="release-${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) + # since 2025 x86-32 support was dropped + KEYWORDS="~amd64 -arm ~arm64 ~riscv -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 hdf5 +hwloc lapack mkl mpi nnpot +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 ) + openmp? ( + sys-devel/gcc[openmp] + llvm-runtimes/clang-runtime[openmp] + ) + fftw? ( sci-libs/fftw:3.0= ) + hdf5? ( sci-libs/hdf5 ) + hwloc? ( sys-apps/hwloc:= ) + lapack? ( virtual/lapack ) + mkl? ( sci-libs/mkl ) + mpi? ( virtual/mpi[cxx] ) + nnpot? ( sci-ml/caffe2[cuda=,opencl=] ) + sci-libs/lmfit:= + >=dev-cpp/muParser-2.3:= + ${PYTHON_DEPS} + " +BDEPEND="${CDEPEND} + virtual/pkgconfig + clang? ( >=llvm-core/clang-6:* ) + $(python_gen_cond_dep ' + dev-python/sphinx[${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}] + ') + 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" + local nnpot="OFF" + + if use nnpot; then + nnpot="TORCH" + fi + + 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=$(usex build-manual) + -DGMX_USE_HDF5=$(usex hdf5) + -DGMX_HWLOC=$(usex hwloc) + -DGMX_DEFAULT_SUFFIX=off + -DGMX_BUILD_HELP=$(usex doc) + -DGMX_SIMD="$acce" + -DGMX_NNPOT="$nnpot" + -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 + BUILD_DIR="${WORKDIR}/${P}_${x}"\ + cmake_src_compile man + if use python; then + BUILD_DIR="${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 +}