| # Copyright 1999-2015 Gentoo Foundation |
| # Distributed under the terms of the GNU General Public License v2 |
| # $Id$ |
| |
| EAPI=5 |
| |
| CMAKE_MAKEFILE_GENERATOR="ninja" |
| |
| inherit bash-completion-r1 cmake-utils cuda eutils multilib readme.gentoo toolchain-funcs |
| |
| if [[ $PV = *9999* ]]; then |
| EGIT_REPO_URI="git://git.gromacs.org/gromacs.git |
| https://gerrit.gromacs.org/gromacs.git |
| git://github.com/gromacs/gromacs.git |
| http://repo.or.cz/r/gromacs.git" |
| [[ $PV = 9999 ]] && EGIT_BRANCH="master" || EGIT_BRANCH="release-${PV:0:1}-${PV:2:1}" |
| inherit git-r3 |
| KEYWORDS="" |
| else |
| SRC_URI="ftp://ftp.gromacs.org/pub/${PN}/${PN}-${PV/_/-}.tar.gz |
| test? ( http://gerrit.gromacs.org/download/regressiontests-${PV}.tar.gz )" |
| KEYWORDS="~alpha ~amd64 ~arm ~ppc64 ~sparc ~x86 ~amd64-linux ~x86-linux ~x64-macos ~x86-macos" |
| fi |
| |
| ACCE_IUSE="cpu_flags_x86_sse2 cpu_flags_x86_sse4_1 cpu_flags_x86_fma4 cpu_flags_x86_avx cpu_flags_x86_avx2" |
| |
| DESCRIPTION="The ultimate molecular dynamics simulation package" |
| HOMEPAGE="http://www.gromacs.org/" |
| |
| # see COPYING for details |
| # http://repo.or.cz/w/gromacs.git/blob/HEAD:/COPYING |
| # base, vmd plugins, fftpack from numpy, blas/lapck from netlib, memtestG80 library, mpi_thread lib |
| LICENSE="LGPL-2.1 UoI-NCSA !mkl? ( !fftw? ( BSD ) !blas? ( BSD ) !lapack? ( BSD ) ) cuda? ( LGPL-3 ) threads? ( BSD )" |
| SLOT="0/${PV}" |
| IUSE="X blas boost cuda +doc -double-precision +fftw lapack mkl mpi +offensive openmp +single-precision test +threads +tng ${ACCE_IUSE}" |
| |
| CDEPEND=" |
| X? ( |
| x11-libs/libX11 |
| x11-libs/libSM |
| x11-libs/libICE |
| ) |
| blas? ( virtual/blas ) |
| boost? ( >=dev-libs/boost-1.55 ) |
| cuda? ( >=dev-util/nvidia-cuda-toolkit-4.2.9-r1 ) |
| fftw? ( sci-libs/fftw:3.0 ) |
| lapack? ( virtual/lapack ) |
| mkl? ( sci-libs/mkl ) |
| mpi? ( virtual/mpi ) |
| " |
| DEPEND="${CDEPEND} |
| virtual/pkgconfig |
| doc? ( |
| app-doc/doxygen |
| dev-texlive/texlive-latex |
| dev-texlive/texlive-latexextra |
| media-gfx/imagemagick |
| )" |
| RDEPEND="${CDEPEND}" |
| |
| REQUIRED_USE=" |
| || ( single-precision double-precision ) |
| cuda? ( single-precision ) |
| mkl? ( !blas !fftw !lapack )" |
| |
| DOCS=( AUTHORS README ) |
| |
| if [[ ${PV} != *9999 ]]; then |
| S="${WORKDIR}/${PN}-${PV/_/-}" |
| fi |
| |
| 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" |
| } |
| |
| 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 |
| |
| cmake-utils_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" |
| } |
| |
| src_configure() { |
| local mycmakeargs_pre=( ) extra fft_opts=( ) |
| |
| #go from slowest to fastest acceleration |
| local acce="None" |
| 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" |
| |
| #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 |
| |
| mycmakeargs_pre+=( |
| "${fft_opts[@]}" |
| $(cmake-utils_use X GMX_X11) |
| $(cmake-utils_use blas GMX_EXTERNAL_BLAS) |
| $(cmake-utils_use lapack GMX_EXTERNAL_LAPACK) |
| $(cmake-utils_use openmp GMX_OPENMP) |
| $(cmake-utils_use offensive GMX_COOL_QUOTES) |
| $(cmake-utils_use boost GMX_EXTERNAL_BOOST) |
| $(cmake-utils_use tng GMX_USE_TNG) |
| $(cmake-utils_use doc GMX_BUILD_MANUAL) |
| -DGMX_DEFAULT_SUFFIX=off |
| -DGMX_SIMD="$acce" |
| -DGMX_LIB_INSTALL_DIR="$(get_libdir)" |
| -DGMX_VMD_PLUGIN_PATH="${EPREFIX}/usr/$(get_libdir)/vmd/plugins/*/molfile/" |
| -DGMX_X86_AVX_GCC_MASKLOAD_BUG=OFF |
| -DGMX_USE_GCC44_BUG_WORKAROUND=OFF |
| -DBUILD_TESTING=OFF |
| -DGMX_BUILD_UNITTESTS=OFF |
| ${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 cuda=( "-DGMX_GPU=OFF" ) |
| [[ ${x} = "float" ]] && use cuda && \ |
| cuda=( -DGMX_GPU=ON ) |
| mycmakeargs=( |
| ${mycmakeargs_pre[@]} ${p} |
| -DGMX_MPI=OFF |
| $(cmake-utils_use threads GMX_THREAD_MPI) |
| "${cuda[@]}" |
| -DGMX_OPENMM=OFF |
| "$(use test && echo -DREGRESSIONTEST_PATH="${WORKDIR}/${P}_${x}/tests")" |
| -DGMX_BINARY_SUFFIX="${suffix}" |
| -DGMX_LIBS_SUFFIX="${suffix}" |
| ) |
| BUILD_DIR="${WORKDIR}/${P}_${x}" cmake-utils_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 ${cuda} |
| -DGMX_OPENMM=OFF |
| -DGMX_BUILD_MDRUN_ONLY=ON |
| -DBUILD_SHARED_LIBS=OFF |
| -DGMX_BUILD_MANUAL=OFF |
| -DGMX_BINARY_SUFFIX="_mpi${suffix}" |
| -DGMX_LIBS_SUFFIX="_mpi${suffix}" |
| ) |
| BUILD_DIR="${WORKDIR}/${P}_${x}_mpi" CC="mpicc" cmake-utils_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-utils_src_compile |
| # not 100% necessary for rel ebuilds as available from website |
| if use doc; then |
| BUILD_DIR="${WORKDIR}/${P}_${x}"\ |
| cmake-utils_src_compile manual |
| fi |
| use mpi || continue |
| einfo "Compiling for ${x} precision with mpi" |
| BUILD_DIR="${WORKDIR}/${P}_${x}_mpi"\ |
| cmake-utils_src_compile |
| done |
| } |
| |
| src_test() { |
| for x in ${GMX_DIRS}; do |
| BUILD_DIR="${WORKDIR}/${P}_${x}"\ |
| cmake-utils_src_make check |
| done |
| } |
| |
| src_install() { |
| for x in ${GMX_DIRS}; do |
| BUILD_DIR="${WORKDIR}/${P}_${x}" \ |
| cmake-utils_src_install |
| 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-utils_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 "http://dx.doi.org/10.1021/ct700301q" |
| einfo |
| readme.gentoo_print_elog |
| } |