# Copyright 1999-2021 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 EAPI=7 CMAKE_MAKEFILE_GENERATOR="ninja" PYTHON_COMPAT=( python3_{7,8,9} ) DISTUTILS_SINGLE_IMPL=1 inherit bash-completion-r1 cmake cuda distutils-r1 flag-o-matic multilib 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=" http://ftp.gromacs.org/gromacs/${PN}-${PV/_/-}.tar.gz test? ( http://ftp.gromacs.org/regressiontests/regressiontests-${PV/_/-}.tar.gz )" KEYWORDS="~amd64 ~arm ~x86 ~amd64-linux ~x86-linux ~x64-macos" fi ACCE_IUSE="cpu_flags_x86_sse2 cpu_flags_x86_sse4_1 cpu_flags_x86_fma4 cpu_flags_x86_avx cpu_flags_x86_avx2 cpu_flags_x86_avx512f cpu_flags_arm_neon" DESCRIPTION="The ultimate molecular dynamics simulation package" HOMEPAGE="http://www.gromacs.org/" # see COPYING for details # https://repo.or.cz/w/gromacs.git/blob/HEAD:/COPYING # base, vmd plugins, fftpack from numpy, blas/lapck from netlib, memtestG80 library, mpi_thread lib LICENSE="LGPL-2.1 UoI-NCSA !mkl? ( !fftw? ( BSD ) !blas? ( BSD ) !lapack? ( BSD ) ) cuda? ( LGPL-3 ) threads? ( BSD )" SLOT="0/${PV}" IUSE="X blas cuda +custom-cflags +doc double-precision +fftw +gmxapi +gmxapi-legacy +hwloc lapack +lmfit mkl mpi +offensive opencl openmp +python +single-precision test +threads +tng ${ACCE_IUSE}" CDEPEND=" X? ( x11-libs/libX11 x11-libs/libSM x11-libs/libICE ) blas? ( virtual/blas ) cuda? ( >=dev-util/nvidia-cuda-toolkit-6.5.14 ) opencl? ( virtual/opencl ) fftw? ( sci-libs/fftw:3.0 ) hwloc? ( sys-apps/hwloc ) lapack? ( virtual/lapack ) lmfit? ( sci-libs/lmfit ) mkl? ( sci-libs/mkl ) mpi? ( virtual/mpi ) ${PYTHON_DEPS} !sci-chemistry/gmxapi " BDEPEND="${CDEPEND} virtual/pkgconfig doc? ( app-doc/doxygen $(python_gen_cond_dep ' dev-python/sphinx[${PYTHON_MULTI_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 ) cuda? ( single-precision ) cuda? ( !opencl ) mkl? ( !blas !fftw !lapack ) ${PYTHON_REQUIRED_USE}" DOCS=( AUTHORS README ) RESTRICT="!test? ( test )" if [[ ${PV} != *9999 ]]; then S="${WORKDIR}/${PN}-${PV/_/-}" fi PATCHES=( "${FILESDIR}/${PN}-2020-pytest.patch" "${FILESDIR}/${PN}-2021-nblib.patch" ) pkg_pretend() { [[ $(gcc-version) == "4.1" ]] && die "gcc 4.1 is not supported by gromacs" use openmp && ! tc-has-openmp && \ die "Please switch to an openmp compatible compiler" } pkg_setup() { 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 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" # try to create policy for imagemagik mkdir -p ${HOME}/.config/ImageMagick cat >> ${HOME}/.config/ImageMagick/policy.xml <<- EOF !ATTLIST policymap xmlns CDATA #FIXED ''> ]> EOF } src_configure() { local mycmakeargs_pre=( ) extra fft_opts=( ) if use custom-cflags; then #go from slowest to fastest acceleration local 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) [[ ${CHOST} = *-darwin* ]] && \ extra+=" -DCMAKE_BUILD_WITH_INSTALL_RPATH=OFF" if use fftw; then fft_opts=( -DGMX_FFT_LIBRARY=fftw3 ) elif use mkl && has_version "=sci-libs/mkl-10*"; then fft_opts=( -DGMX_FFT_LIBRARY=mkl -DMKL_INCLUDE_DIR="${MKLROOT}/include" -DMKL_LIBRARIES="$(echo /opt/intel/mkl/10.0.5.025/lib/*/libmkl.so);$(echo /opt/intel/mkl/10.0.5.025/lib/*/libiomp*.so)" ) 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 if use lmfit; then local lmfit_opts=( -DGMX_USE_LMFIT=EXTERNAL ) else local lmfit_opts=( -DGMX_USE_LMFIT=INTERNAL ) fi mycmakeargs_pre+=( "${fft_opts[@]}" "${lmfit_opts[@]}" -DGMX_X11=$(usex X) -DGMX_EXTERNAL_BLAS=$(usex blas) -DGMX_EXTERNAL_LAPACK=$(usex lapack) -DGMX_OPENMP=$(usex openmp) -DGMX_COOL_QUOTES=$(usex offensive) -DGMX_USE_TNG=$(usex tng) -DGMX_BUILD_MANUAL=$(usex doc) -DGMX_HWLOC=$(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" ) use opencl && gpu=( "-DGMX_GPU=OPENCL" ) mycmakeargs=( ${mycmakeargs_pre[@]} ${p} -DGMX_MPI=OFF -DGMX_THREAD_MPI=$(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 use mpi || continue einfo "Configuring for ${x} precision with mpi" mycmakeargs=( ${mycmakeargs_pre[@]} ${p} -DGMX_THREAD_MPI=OFF -DGMX_MPI=ON -DGMX_OPENMM=OFF -DGMXAPI=OFF "${opencl[@]}" "${cuda[@]}" -DGMX_BUILD_MDRUN_ONLY=ON -DBUILD_SHARED_LIBS=OFF -DGMX_BUILD_MANUAL=OFF -DGMX_BINARY_SUFFIX="_mpi${suffix}" -DGMX_LIBS_SUFFIX="_mpi${suffix}" ) BUILD_DIR="${WORKDIR}/${P}_${x}_mpi" CC="mpicc" cmake_src_configure [[ ${CHOST} != *-darwin* ]] || \ sed -i '/SET(CMAKE_INSTALL_NAME_DIR/s/^/#/' "${WORKDIR}/${P}_${x}_mpi/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}/${P}" \ distutils-r1_src_compile fi # not 100% necessary for rel ebuilds as available from website if use doc; then BUILD_DIR="${WORKDIR}/${P}_${x}"\ cmake_src_compile manual fi use mpi || continue einfo "Compiling for ${x} precision with mpi" BUILD_DIR="${WORKDIR}/${P}_${x}_mpi"\ cmake_src_compile 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}_${x}" \ cmake_src_install python_packaging/install fi if use doc; then newdoc "${WORKDIR}/${P}_${x}"/docs/manual/gromacs.pdf "${PN}-manual-${PV}.pdf" fi use mpi || continue BUILD_DIR="${WORKDIR}/${P}_${x}_mpi" \ cmake_src_install done if use tng; then insinto /usr/include/tng doins src/external/tng_io/include/tng/*h fi # drop unneeded stuff rm "${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:" einfo "Gromacs 4, J. Chem. Theory Comput. 4, 435 (2008). " einfo "https://dx.doi.org/10.1021/ct700301q" einfo readme.gentoo_print_elog }