# Copyright 1999-2012 Gentoo Foundation # Distributed under the terms of the GNU General Public License v2 # $Header: /var/cvsroot/gentoo-x86/sci-chemistry/gromacs/gromacs-4.6_beta3-r1.ebuild,v 1.2 2012/12/29 23:00:35 ottxor Exp $ EAPI=5 TEST_PV="4.0.4" MANUAL_PV="4.6-beta1" CMAKE_MAKEFILE_GENERATOR="ninja" inherit bash-completion-r1 cmake-utils eutils multilib toolchain-funcs SRC_URI="test? ( ftp://ftp.gromacs.org/pub/tests/gmxtest-${TEST_PV}.tgz )" if [[ $PV = *9999* ]]; then EGIT_REPO_URI="git://git.gromacs.org/gromacs.git https://gerrit.gromacs.org/gromacs.git git://github.com/gromacs/gromacs.git http://repo.or.cz/r/gromacs.git" EGIT_BRANCH="release-4-6" inherit git-2 PDEPEND="doc? ( ~app-doc/${PN}-manual-${PV} )" else S="${WORKDIR}/${P//_/-}" SRC_URI="${SRC_URI} ftp://ftp.gromacs.org/pub/${PN}/${P//_/-}.tar.gz doc? ( ftp://ftp.gromacs.org/pub/manual/${PN}-manual-${MANUAL_PV}.pdf )" fi ACCE_IUSE="sse2 sse41 avx128fma avx256" DESCRIPTION="The ultimate molecular dynamics simulation package" HOMEPAGE="http://www.gromacs.org/" LICENSE="GPL-2" SLOT="0" KEYWORDS="~alpha ~amd64 ~ppc64 ~sparc ~x86 ~amd64-linux ~x86-linux ~x86-macos" IUSE="X blas cuda doc -double-precision +fftw gsl lapack mkl mpi +offensive openmm openmp +single-precision test +threads zsh-completion ${ACCE_IUSE}" CDEPEND=" X? ( x11-libs/libX11 x11-libs/libSM x11-libs/libICE ) blas? ( virtual/blas ) cuda? ( dev-util/nvidia-cuda-toolkit ) fftw? ( sci-libs/fftw:3.0 ) gsl? ( sci-libs/gsl ) lapack? ( virtual/lapack ) mkl? ( sci-libs/mkl ) mpi? ( virtual/mpi ) openmm? ( dev-util/nvidia-cuda-toolkit sci-libs/openmm[cuda,opencl] )" DEPEND="${CDEPEND} virtual/pkgconfig" RDEPEND="${CDEPEND}" RESTRICT="test" REQUIRED_USE=" || ( single-precision double-precision ) cuda? ( single-precision ) openmm? ( single-precision ) mkl? ( !blas !fftw !lapack )" 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_prepare() { #notes/todos # -on apple: there is framework support #add user patches from /etc/portage/patches/sci-chemistry/gromacs epatch_user GMX_DIRS="" use single-precision && GMX_DIRS+=" float" use double-precision && GMX_DIRS+=" double" for x in ${GMX_DIRS}; do mkdir -p "${WORKDIR}/${P}_${x}" || die use test && cp -r "${WORKDIR}"/gmxtest "${WORKDIR}/${P}_${x}" done } src_configure() { local mycmakeargs_pre=( ) extra fft_opts=( ) #go from slowest to fastest acceleration local acce="None" use sse2 && acce="SSE2" use sse41 && acce="SSE4.1" use avx128fma && acce="AVX_128_FMA" use avx256 && acce="AVX_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 gsl GMX_GSL) $(cmake-utils_use lapack GMX_EXTERNAL_LAPACK) $(cmake-utils_use openmp GMX_OPENMP) $(cmake-utils_use !offensive GMX_NO_QUOTES) -DGMX_DEFAULT_SUFFIX=off -DGMX_ACCELERATION="$acce" -DGMXLIB="$(get_libdir)" -DGMX_VMD_PLUGIN_PATH="${EPREFIX}/usr/$(get_libdir)/vmd/plugins/*/molfile/" ${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 [[ ${x} = "double" ]] && p="-DGMX_DOUBLE=ON" || p="-DGMX_DOUBLE=OFF" local cuda=$(cmake-utils_use cuda GMX_GPU) [[ ${x} = "double" ]] && use cuda && cuda="-DGMX_GPU=OFF" mycmakeargs=( ${mycmakeargs_pre[@]} ${p} -DGMX_MPI=OFF $(cmake-utils_use threads GMX_THREAD_MPI) ${cuda} -DGMX_BINARY_SUFFIX="${suffix}" -DGMX_LIBS_SUFFIX="${suffix}" ) BUILD_DIR="${WORKDIR}/${P}_${x}" cmake-utils_src_configure if [[ ${x} = float ]] && use openmm; then einfo "Configuring for openmm build" mycmakeargs=( ${mycmakeargs_pre[@]} ${p} -DGMX_MPI=OFF -DGMX_THREAD_MPI=OFF -DGMX_GPU=OFF -DGMX_OPENMM=ON -DGMX_BINARY_SUFFIX="_openmm" -DGMX_LIBS_SUFFIX="_openmm" ) BUILD_DIR="${WORKDIR}/${P}_openmm" \ OPENMM_ROOT_DIR="${EPREFIX}/usr" cmake-utils_src_configure fi use mpi || continue einfo "Configuring for ${x} precision with mpi" mycmakeargs=( ${mycmakeargs_pre[@]} ${p} -DGMX_THREAD_MPI=OFF -DGMX_MPI=ON ${cuda} -DGMX_BINARY_SUFFIX="_mpi${suffix}" -DGMX_LIBS_SUFFIX="_mpi${suffix}" ) BUILD_DIR="${WORKDIR}/${P}_${x}_mpi" CC="mpicc" cmake-utils_src_configure done } src_compile() { for x in ${GMX_DIRS}; do einfo "Compiling for ${x} precision" BUILD_DIR="${WORKDIR}/${P}_${x}"\ cmake-utils_src_compile if [[ ${x} = float ]] && use openmm; then einfo "Compiling for openmm build" BUILD_DIR="${WORKDIR}/${P}_openmm"\ cmake-utils_src_compile mdrun fi use mpi || continue einfo "Compiling for ${x} precision with mpi" BUILD_DIR="${WORKDIR}/${P}_${x}_mpi"\ cmake-utils_src_compile mdrun done } src_test() { for x in ${GMX_DIRS}; do local oldpath="${PATH}" export PATH="${WORKDIR}/${P}_${x}/src/kernel:${S}-{x}/src/tools:${PATH}" cd "${WORKDIR}/${P}_${x}" emake -j1 tests || die "${x} Precision test failed" export PATH="${oldpath}" done } src_install() { for x in ${GMX_DIRS}; do BUILD_DIR="${WORKDIR}/${P}_${x}" \ cmake-utils_src_install if [[ ${x} = float ]] && use openmm; then BUILD_DIR="${WORKDIR}/${P}_openmm" \ DESTDIR="${D}" cmake-utils_src_make install-mdrun fi use mpi || continue BUILD_DIR="${WORKDIR}/${P}_${x}_mpi" \ DESTDIR="${D}" cmake-utils_src_make install-mdrun done rm -f "${ED}"/usr/bin/GMXRC* newbashcomp "${ED}"/usr/bin/completion.bash ${PN} if use zsh-completion ; then insinto /usr/share/zsh/site-functions newins "${ED}"/usr/bin/completion.zsh _${PN} fi rm -f "${ED}"/usr/bin/completion.* cd "${S}" dodoc AUTHORS INSTALL* README* if use doc; then dohtml -r "${ED}usr/share/gromacs/html/" if [[ $PV = *9999* ]]; then insinto /usr/share/gromacs doins "admin/programs.txt" ls -1 "${ED}"/usr/bin | sed -e '/_d$/d' > "${T}"/programs.list doins "${T}"/programs.list else dodoc "${DISTDIR}/${PN}-manual-${MANUAL_PV}.pdf" fi fi rm -rf "${ED}usr/share/gromacs/html/" } 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" if use offensive; then einfo einfo $(g_luck) einfo "For more Gromacs cool quotes (gcq) add g_luck to your .bashrc" fi einfo elog "Gromacs can use sci-chemistry/vmd to read additional file formats" }