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271 lines
7.6 KiB
271 lines
7.6 KiB
# Copyright 1999-2018 Gentoo Authors
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# Distributed under the terms of the GNU General Public License v2
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EAPI=6
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CMAKE_MAKEFILE_GENERATOR="ninja"
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inherit bash-completion-r1 cmake-utils cuda eutils multilib readme.gentoo-r1 toolchain-funcs xdg-utils
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if [[ $PV = *9999* ]]; then
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EGIT_REPO_URI="git://git.gromacs.org/gromacs.git
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https://gerrit.gromacs.org/gromacs.git
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https://github.com/gromacs/gromacs.git
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http://repo.or.cz/r/gromacs.git"
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[[ $PV = 9999 ]] && EGIT_BRANCH="master" || EGIT_BRANCH="release-${PV:0:4}"
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inherit git-r3
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else
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SRC_URI="ftp://ftp.gromacs.org/pub/${PN}/${PN}-${PV/_/-}.tar.gz
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test? ( http://gerrit.gromacs.org/download/regressiontests-${PV/_/-}.tar.gz )"
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KEYWORDS="~amd64 ~arm ~x86 ~amd64-linux ~x86-linux ~x64-macos ~x86-macos"
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fi
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ACCE_IUSE="cpu_flags_x86_sse2 cpu_flags_x86_sse4_1 cpu_flags_x86_fma4 cpu_flags_x86_avx cpu_flags_x86_avx2"
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DESCRIPTION="The ultimate molecular dynamics simulation package"
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HOMEPAGE="http://www.gromacs.org/"
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# see COPYING for details
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# http://repo.or.cz/w/gromacs.git/blob/HEAD:/COPYING
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# base, vmd plugins, fftpack from numpy, blas/lapck from netlib, memtestG80 library, mpi_thread lib
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LICENSE="LGPL-2.1 UoI-NCSA !mkl? ( !fftw? ( BSD ) !blas? ( BSD ) !lapack? ( BSD ) ) cuda? ( LGPL-3 ) threads? ( BSD )"
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SLOT="0/${PV}"
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IUSE="X blas cuda +doc -double-precision +fftw +hwloc lapack mkl mpi +offensive opencl openmp +single-precision test +threads +tng ${ACCE_IUSE}"
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CDEPEND="
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X? (
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x11-libs/libX11
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x11-libs/libSM
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x11-libs/libICE
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)
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blas? ( virtual/blas )
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cuda? ( >=dev-util/nvidia-cuda-toolkit-4.2.9-r1 )
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opencl? ( virtual/opencl )
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fftw? ( sci-libs/fftw:3.0 )
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hwloc? ( <sys-apps/hwloc-2 )
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lapack? ( virtual/lapack )
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mkl? ( sci-libs/mkl )
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mpi? ( virtual/mpi )
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"
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DEPEND="${CDEPEND}
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virtual/pkgconfig
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doc? (
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app-doc/doxygen
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dev-texlive/texlive-latex
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dev-texlive/texlive-latexextra
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media-gfx/imagemagick
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)"
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RDEPEND="${CDEPEND}"
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REQUIRED_USE="
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|| ( single-precision double-precision )
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cuda? ( single-precision )
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cuda? ( !opencl )
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mkl? ( !blas !fftw !lapack )"
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DOCS=( AUTHORS README )
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if [[ ${PV} != *9999 ]]; then
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S="${WORKDIR}/${PN}-${PV/_/-}"
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fi
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pkg_pretend() {
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[[ $(gcc-version) == "4.1" ]] && die "gcc 4.1 is not supported by gromacs"
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use openmp && ! tc-has-openmp && \
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die "Please switch to an openmp compatible compiler"
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}
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src_unpack() {
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if [[ ${PV} != *9999 ]]; then
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default
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else
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git-r3_src_unpack
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if use test; then
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EGIT_REPO_URI="git://git.gromacs.org/regressiontests.git" \
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EGIT_BRANCH="${EGIT_BRANCH}" \
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EGIT_CHECKOUT_DIR="${WORKDIR}/regressiontests"\
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git-r3_src_unpack
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fi
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fi
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}
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src_prepare() {
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#notes/todos
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# -on apple: there is framework support
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xdg_environment_reset #591952
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cmake-utils_src_prepare
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use cuda && cuda_src_prepare
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GMX_DIRS=""
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use single-precision && GMX_DIRS+=" float"
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use double-precision && GMX_DIRS+=" double"
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if use test; then
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for x in ${GMX_DIRS}; do
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mkdir -p "${WORKDIR}/${P}_${x}" || die
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cp -al "${WORKDIR}/regressiontests"* "${WORKDIR}/${P}_${x}/tests" || die
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done
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fi
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DOC_CONTENTS="Gromacs can use sci-chemistry/vmd to read additional file formats"
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}
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src_configure() {
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local mycmakeargs_pre=( ) extra fft_opts=( )
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#go from slowest to fastest acceleration
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local acce="None"
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use cpu_flags_x86_sse2 && acce="SSE2"
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use cpu_flags_x86_sse4_1 && acce="SSE4.1"
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use cpu_flags_x86_fma4 && acce="AVX_128_FMA"
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use cpu_flags_x86_avx && acce="AVX_256"
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use cpu_flags_x86_avx2 && acce="AVX2_256"
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#to create man pages, build tree binaries are executed (bug #398437)
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[[ ${CHOST} = *-darwin* ]] && \
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extra+=" -DCMAKE_BUILD_WITH_INSTALL_RPATH=OFF"
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if use fftw; then
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fft_opts=( -DGMX_FFT_LIBRARY=fftw3 )
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elif use mkl && has_version "=sci-libs/mkl-10*"; then
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fft_opts=( -DGMX_FFT_LIBRARY=mkl
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-DMKL_INCLUDE_DIR="${MKLROOT}/include"
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-DMKL_LIBRARIES="$(echo /opt/intel/mkl/10.0.5.025/lib/*/libmkl.so);$(echo /opt/intel/mkl/10.0.5.025/lib/*/libiomp*.so)"
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)
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elif use mkl; then
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local bits=$(get_libdir)
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fft_opts=( -DGMX_FFT_LIBRARY=mkl
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-DMKL_INCLUDE_DIR="$(echo /opt/intel/*/mkl/include)"
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-DMKL_LIBRARIES="$(echo /opt/intel/*/mkl/lib/*${bits/lib}/libmkl_rt.so)"
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)
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else
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fft_opts=( -DGMX_FFT_LIBRARY=fftpack )
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fi
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mycmakeargs_pre+=(
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"${fft_opts[@]}"
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-DGMX_X11=$(usex X)
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-DGMX_EXTERNAL_BLAS=$(usex blas)
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-DGMX_EXTERNAL_LAPACK=$(usex lapack)
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-DGMX_OPENMP=$(usex openmp)
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-DGMX_COOL_QUOTES=$(usex offensive)
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-DGMX_USE_TNG=$(usex tng)
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-DGMX_BUILD_MANUAL=$(usex doc)
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-DGMX_HWLOC=$(usex hwloc)
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-DGMX_DEFAULT_SUFFIX=off
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-DGMX_SIMD="$acce"
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-DGMX_VMD_PLUGIN_PATH="${EPREFIX}/usr/$(get_libdir)/vmd/plugins/*/molfile/"
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-DBUILD_TESTING=$(usex test)
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-DGMX_BUILD_UNITTESTS=$(usex test)
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${extra}
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)
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for x in ${GMX_DIRS}; do
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einfo "Configuring for ${x} precision"
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local suffix=""
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#if we build single and double - double is suffixed
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use double-precision && use single-precision && \
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[[ ${x} = "double" ]] && suffix="_d"
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local p
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[[ ${x} = "double" ]] && p="-DGMX_DOUBLE=ON" || p="-DGMX_DOUBLE=OFF"
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local cuda=( "-DGMX_GPU=OFF" )
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[[ ${x} = "float" ]] && use cuda && \
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cuda=( "-DGMX_GPU=ON" )
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local opencl=( "-DGMX_USE_OPENCL=OFF" )
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use opencl && opencl=( "-DGMX_USE_OPENCL=ON" ) cuda=( "-DGMX_GPU=ON" )
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mycmakeargs=(
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${mycmakeargs_pre[@]} ${p}
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-DGMX_MPI=OFF
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-DGMX_THREAD_MPI=$(usex threads)
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"${opencl[@]}"
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"${cuda[@]}"
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"$(use test && echo -DREGRESSIONTEST_PATH="${WORKDIR}/${P}_${x}/tests")"
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-DGMX_BINARY_SUFFIX="${suffix}"
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-DGMX_LIBS_SUFFIX="${suffix}"
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)
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BUILD_DIR="${WORKDIR}/${P}_${x}" cmake-utils_src_configure
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[[ ${CHOST} != *-darwin* ]] || \
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sed -i '/SET(CMAKE_INSTALL_NAME_DIR/s/^/#/' "${WORKDIR}/${P}_${x}/gentoo_rules.cmake" || die
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use mpi || continue
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einfo "Configuring for ${x} precision with mpi"
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mycmakeargs=(
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${mycmakeargs_pre[@]} ${p}
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-DGMX_THREAD_MPI=OFF
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-DGMX_MPI=ON ${cuda}
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-DGMX_OPENMM=OFF
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-DGMX_BUILD_MDRUN_ONLY=ON
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-DBUILD_SHARED_LIBS=OFF
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-DGMX_BUILD_MANUAL=OFF
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-DGMX_BINARY_SUFFIX="_mpi${suffix}"
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-DGMX_LIBS_SUFFIX="_mpi${suffix}"
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)
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BUILD_DIR="${WORKDIR}/${P}_${x}_mpi" CC="mpicc" cmake-utils_src_configure
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[[ ${CHOST} != *-darwin* ]] || \
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sed -i '/SET(CMAKE_INSTALL_NAME_DIR/s/^/#/' "${WORKDIR}/${P}_${x}_mpi/gentoo_rules.cmake" || die
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done
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}
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src_compile() {
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for x in ${GMX_DIRS}; do
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einfo "Compiling for ${x} precision"
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BUILD_DIR="${WORKDIR}/${P}_${x}"\
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cmake-utils_src_compile
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# not 100% necessary for rel ebuilds as available from website
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if use doc; then
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BUILD_DIR="${WORKDIR}/${P}_${x}"\
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cmake-utils_src_compile manual
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fi
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use mpi || continue
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einfo "Compiling for ${x} precision with mpi"
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BUILD_DIR="${WORKDIR}/${P}_${x}_mpi"\
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cmake-utils_src_compile
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done
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}
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src_test() {
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for x in ${GMX_DIRS}; do
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BUILD_DIR="${WORKDIR}/${P}_${x}"\
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cmake-utils_src_make check
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done
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}
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src_install() {
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for x in ${GMX_DIRS}; do
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BUILD_DIR="${WORKDIR}/${P}_${x}" \
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cmake-utils_src_install
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if use doc; then
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newdoc "${WORKDIR}/${P}_${x}"/docs/manual/gromacs.pdf "${PN}-manual-${PV}.pdf"
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fi
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use mpi || continue
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BUILD_DIR="${WORKDIR}/${P}_${x}_mpi" \
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cmake-utils_src_install
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done
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if use tng; then
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insinto /usr/include/tng
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doins src/external/tng_io/include/tng/*h
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fi
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# drop unneeded stuff
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rm "${ED}"usr/bin/GMXRC* || die
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for x in "${ED}"usr/bin/gmx-completion-*.bash ; do
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local n=${x##*/gmx-completion-}
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n="${n%.bash}"
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cat "${ED}"usr/bin/gmx-completion.bash "$x" > "${T}/${n}" || die
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newbashcomp "${T}"/"${n}" "${n}"
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done
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rm "${ED}"usr/bin/gmx-completion*.bash || die
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readme.gentoo_create_doc
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}
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pkg_postinst() {
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einfo
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einfo "Please read and cite:"
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einfo "Gromacs 4, J. Chem. Theory Comput. 4, 435 (2008). "
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einfo "https://dx.doi.org/10.1021/ct700301q"
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einfo
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readme.gentoo_print_elog
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}
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