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sci-chemistry/gromacs: add first beta for 2025 release
Signed-off-by: Alexey Shvetsov <[email protected]>
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| Original file line number | Diff line number | Diff line change |
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| # Copyright 1999-2024 Gentoo Authors | ||
| # Distributed under the terms of the GNU General Public License v2 | ||
|
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| EAPI=8 | ||
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| CMAKE_MAKEFILE_GENERATOR="ninja" | ||
|
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| PYTHON_COMPAT=( python3_{10..12} ) | ||
|
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| DISTUTILS_OPTIONAL=1 | ||
| DISTUTILS_USE_PEP517=no | ||
| DISTUTILS_SINGLE_IMPL=1 | ||
|
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| inherit bash-completion-r1 cmake cuda distutils-r1 flag-o-matic readme.gentoo-r1 toolchain-funcs xdg-utils | ||
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| 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" | ||
|
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| DESCRIPTION="The ultimate molecular dynamics simulation package" | ||
| HOMEPAGE="https://www.gromacs.org/" | ||
|
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| # 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] | ||
| sys-devel/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-libs/caffe2[cuda=,opencl=] ) | ||
| 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}" | ||
|
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||
| 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}" | ||
|
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| DOCS=( AUTHORS README ) | ||
|
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| RESTRICT="!test? ( test )" | ||
|
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||
| if [[ ${PV} != *9999 ]]; then | ||
| S="${WORKDIR}/${PN}-${PV/_/-}" | ||
| fi | ||
|
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| pkg_pretend() { | ||
| [[ ${MERGE_TYPE} != binary ]] && use openmp && tc-check-openmp | ||
| } | ||
|
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||
| pkg_setup() { | ||
| [[ ${MERGE_TYPE} != binary ]] && use openmp && tc-check-openmp | ||
| python-single-r1_pkg_setup | ||
| } | ||
|
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||
| 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="${WORKDIR}/regressiontests"\ | ||
| git-r3_src_unpack | ||
| fi | ||
| fi | ||
| } | ||
|
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| src_prepare() { | ||
| #notes/todos | ||
| # -on apple: there is framework support | ||
|
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| xdg_environment_reset #591952 | ||
|
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| # we can use clang as default | ||
| if use clang && ! tc-is-clang ; then | ||
| export CC=${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 | ||
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| cmake_src_prepare | ||
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| use cuda && cuda_src_prepare | ||
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| GMX_DIRS="" | ||
| use single-precision && GMX_DIRS+=" float" | ||
| use double-precision && GMX_DIRS+=" double" | ||
|
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| 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 | ||
|
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| 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 | ||
| <?xml version="1.0" encoding="UTF-8"?> | ||
| <!DOCTYPE policymap [ | ||
| <!ELEMENT policymap (policy)+> | ||
| !ATTLIST policymap xmlns CDATA #FIXED ''> | ||
| <!ELEMENT policy EMPTY> | ||
| <!ATTLIST policy xmlns CDATA #FIXED '' domain NMTOKEN #REQUIRED | ||
| name NMTOKEN #IMPLIED pattern CDATA #IMPLIED rights NMTOKEN #IMPLIED | ||
| stealth NMTOKEN #IMPLIED value CDATA #IMPLIED> | ||
| ]> | ||
| <policymap> | ||
| <policy domain="coder" rights="read | write" pattern="PS" /> | ||
| <policy domain="coder" rights="read | write" pattern="PS2" /> | ||
| <policy domain="coder" rights="read | write" pattern="PS3" /> | ||
| <policy domain="coder" rights="read | write" pattern="EPS" /> | ||
| <policy domain="coder" rights="read | write" pattern="PDF" /> | ||
| <policy domain="coder" rights="read | write" pattern="XPS" /> | ||
| </policymap> | ||
| EOF | ||
| fi | ||
| } | ||
|
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| src_configure() { | ||
| local mycmakeargs_pre=( ) extra fft_opts=( ) | ||
| local acce="AUTO" | ||
| local nnpot="OFF" | ||
|
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| if use nnpot; then | ||
| nnpot="TORCH" | ||
| fi | ||
|
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| 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 | ||
|
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||
| #to create man pages, build tree binaries are executed (bug #398437) | ||
| [[ ${CHOST} = *-darwin* ]] && \ | ||
| extra+=" -DCMAKE_BUILD_WITH_INSTALL_RPATH=OFF" | ||
|
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||
| if use fftw; then | ||
| fft_opts=( -DGMX_FFT_LIBRARY=fftw3 ) | ||
| elif use mkl; then | ||
| local bits=$(get_libdir) | ||
| fft_opts=( -DGMX_FFT_LIBRARY=mkl | ||
| -DMKL_INCLUDE_DIR="$(echo /opt/intel/*/mkl/include)" | ||
| -DMKL_LIBRARIES="$(echo /opt/intel/*/mkl/lib/*${bits/lib}/libmkl_rt.so)" | ||
| ) | ||
| else | ||
| fft_opts=( -DGMX_FFT_LIBRARY=fftpack ) | ||
| fi | ||
|
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||
| mycmakeargs_pre+=( | ||
| "${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=$(usex hwloc) | ||
| -DGMX_DEFAULT_SUFFIX=off | ||
| -DGMX_BUILD_HELP=on | ||
| -DGMX_SIMD="$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 | ||
| } | ||
|
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||
| 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 | ||
| } | ||
|
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| src_test() { | ||
| for x in ${GMX_DIRS}; do | ||
| BUILD_DIR="${WORKDIR}/${P}_${x}"\ | ||
| cmake_src_compile check | ||
| done | ||
| } | ||
|
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| 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 | ||
|
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| if use doc; then | ||
| if [[ ${PV} != *9999* ]]; then | ||
| newdoc "${DISTDIR}/manual-${PV/_/-}.pdf" "${PN}-manual-${PV}.pdf" | ||
| fi | ||
| fi | ||
| done | ||
|
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||
| if use tng; then | ||
| insinto /usr/include/tng | ||
| doins src/external/tng_io/include/tng/*h | ||
| fi | ||
| # drop unneeded stuff | ||
| rm "${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 | ||
| } | ||
|
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| 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 | ||
| } |
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