From d2fe065fd215478c09e02ab9825e99ec5366e449 Mon Sep 17 00:00:00 2001 From: Alexey Shvetsov Date: Thu, 5 Dec 2013 18:10:06 +0000 Subject: Version bump =D (Portage version: 2.2.7/cvs/Linux x86_64, signed Manifest commit with key F82F92E6) --- sci-chemistry/gromacs/ChangeLog | 7 +- sci-chemistry/gromacs/gromacs-4.6.5.ebuild | 283 +++++++++++++++++++++++++++++ 2 files changed, 289 insertions(+), 1 deletion(-) create mode 100644 sci-chemistry/gromacs/gromacs-4.6.5.ebuild (limited to 'sci-chemistry') diff --git a/sci-chemistry/gromacs/ChangeLog b/sci-chemistry/gromacs/ChangeLog index 7dd53f370e59..1e995663e89b 100644 --- a/sci-chemistry/gromacs/ChangeLog +++ b/sci-chemistry/gromacs/ChangeLog @@ -1,6 +1,11 @@ # ChangeLog for sci-chemistry/gromacs # Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2 -# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/gromacs/ChangeLog,v 1.133 2013/11/13 18:17:42 ottxor Exp $ +# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/gromacs/ChangeLog,v 1.134 2013/12/05 18:10:06 alexxy Exp $ + +*gromacs-4.6.5 (05 Dec 2013) + + 05 Dec 2013; Alexey Shvetsov +gromacs-4.6.5.ebuild: + Version bump =D *gromacs-4.6.4 (13 Nov 2013) diff --git a/sci-chemistry/gromacs/gromacs-4.6.5.ebuild b/sci-chemistry/gromacs/gromacs-4.6.5.ebuild new file mode 100644 index 000000000000..a02b40beda75 --- /dev/null +++ b/sci-chemistry/gromacs/gromacs-4.6.5.ebuild @@ -0,0 +1,283 @@ +# Copyright 1999-2013 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/gromacs/gromacs-4.6.5.ebuild,v 1.1 2013/12/05 18:10:06 alexxy Exp $ + +EAPI=5 + +TEST_PV="4.6.5" +MANUAL_PV="4.6.5" + +CMAKE_MAKEFILE_GENERATOR="ninja" + +inherit bash-completion-r1 cmake-utils cuda eutils multilib readme.gentoo toolchain-funcs + +if [[ $PV = *9999* ]]; then + EGIT_REPO_URI="git://git.gromacs.org/gromacs.git + https://gerrit.gromacs.org/gromacs.git + git://github.com/gromacs/gromacs.git + http://repo.or.cz/r/gromacs.git" + EGIT_BRANCH="release-4-6" + inherit git-2 + LIVE_DEPEND="doc? ( + dev-texlive/texlive-latex + dev-texlive/texlive-latexextra + media-gfx/imagemagick + sys-apps/coreutils + )" +else + SRC_URI="ftp://ftp.gromacs.org/pub/${PN}/${P}.tar.gz + doc? ( ftp://ftp.gromacs.org/pub/manual/manual-${MANUAL_PV}.pdf -> ${PN}-manual-${MANUAL_PV}.pdf ) + test? ( http://${PN}.googlecode.com/files/regressiontests-${TEST_PV}.tar.gz )" + LIVE_DEPEND="" +fi + +ACCE_IUSE="sse2 sse4_1 avx128fma avx256" + +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}" +KEYWORDS="~alpha ~amd64 ~arm ~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 ${ACCE_IUSE}" + +CDEPEND=" + X? ( + x11-libs/libX11 + x11-libs/libSM + x11-libs/libICE + ) + blas? ( virtual/blas ) + cuda? ( >=dev-util/nvidia-cuda-toolkit-4.2.9-r1 ) + fftw? ( sci-libs/fftw:3.0 ) + gsl? ( sci-libs/gsl ) + lapack? ( virtual/lapack ) + mkl? ( sci-libs/mkl ) + mpi? ( virtual/mpi ) + openmm? ( + >=dev-util/nvidia-cuda-toolkit-4.2.9-r1 + sci-libs/openmm[cuda,opencl] + )" +DEPEND="${CDEPEND} + virtual/pkgconfig + ${LIVE_DEPEND}" +RDEPEND="${CDEPEND}" + +REQUIRED_USE=" + || ( single-precision double-precision ) + cuda? ( single-precision ) + openmm? ( single-precision ) + mkl? ( !blas !fftw !lapack )" + +DOCS=( AUTHORS README ) +HTML_DOCS=( "${ED}"/usr/share/gromacs/html/ ) + +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 [[ ${PV} != *9999 ]]; then + default + else + git-2_src_unpack + if use doc; then + EGIT_REPO_URI="git://git.gromacs.org/manual.git" \ + EGIT_BRANCH="release-4-6" EGIT_NOUNPACK="yes" EGIT_COMMIT="release-4-6" \ + EGIT_SOURCEDIR="${WORKDIR}/manual"\ + git-2_src_unpack + fi + if use test; then + EGIT_REPO_URI="git://git.gromacs.org/regressiontests.git" \ + EGIT_BRANCH="master" EGIT_NOUNPACK="yes" EGIT_COMMIT="master" \ + EGIT_SOURCEDIR="${WORKDIR}/regressiontests"\ + git-2_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 sse2 && acce="SSE2" + use sse4_1 && 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) + $(cmake-utils_use offensive GMX_COOL_QUOTES) + -DGMX_DEFAULT_SUFFIX=off + -DGMX_ACCELERATION="$acce" + -DGMXLIB="$(get_libdir)" + -DGMX_VMD_PLUGIN_PATH="${EPREFIX}/usr/$(get_libdir)/vmd/plugins/*/molfile/" + -DGMX_PREFIX_LIBMD=ON + -DGMX_X86_AVX_GCC_MASKLOAD_BUG=OFF + -DGMX_USE_GCC44_BUG_WORKAROUND=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 + if [[ ${x} = float ]] && use openmm; then + einfo "Configuring for openmm build" + mycmakeargs=( ${mycmakeargs_pre[@]} ${p} -DGMX_MPI=OFF + -DGMX_THREAD_MPI=OFF -DGMX_GPU=OFF -DGMX_OPENMM=ON + -DOpenMM_PLUGIN_DIR="${EPREFIX}/usr/$(get_libdir)/plugins" + -DGMX_BINARY_SUFFIX="_openmm" -DGMX_LIBS_SUFFIX="_openmm" ) + BUILD_DIR="${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 ${cuda} -DGMX_OPENMM=OFF + -DGMX_BINARY_SUFFIX="_mpi${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 ${GMX_DIRS}; do + BUILD_DIR="${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 [[ ${x} = float ]] && use openmm; then + BUILD_DIR="${WORKDIR}/${P}_openmm" \ + DESTDIR="${D}" cmake-utils_src_make install-mdrun + fi + #manual can only be build after gromacs was installed once in image + if use doc && [[ $PV = *9999* && ! -d ${WORKDIR}/manual_build ]]; then + mycmakeargs=( -DGMXBIN="${ED}"/usr/bin -DGMXSRC="${WORKDIR}/${P}" ) + BUILD_DIR="${WORKDIR}"/manual_build \ + CMAKE_USE_DIR="${WORKDIR}/manual" cmake-utils_src_configure + [[ ${CHOST} = *-darwin* ]] && \ + export DYLD_LIBRARY_PATH="${DYLD_LIBRARY_PATH}${DYLD_LIBRARY_PATH:+:}${ED}/usr/$(get_libdir)" + BUILD_DIR="${WORKDIR}"/manual_build cmake-utils_src_make + [[ ${CHOST} = *-darwin* ]] && DYLD_LIBRARY_PATH="${ED}/usr/$(get_libdir)" + newdoc "${WORKDIR}"/manual_build/gromacs.pdf "${PN}-manual-${PV}.pdf" + fi + use mpi || continue + BUILD_DIR="${WORKDIR}/${P}_${x}_mpi" \ + DESTDIR="${D}" cmake-utils_src_make install-mdrun + done + + use doc && [[ $PV != *9999* ]] && dodoc "${DISTDIR}/${PN}-manual-${MANUAL_PV}.pdf" + 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.* + rm -rf "${ED}"usr/share/gromacs/html + rm -f "${ED}"usr/bin/g_options* + rm -f "${ED}"usr/bin/GMXRC* + + 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" + if use offensive; then + einfo + einfo $(g_luck) + einfo "For more Gromacs cool quotes (gcq) add g_luck to your .bashrc" + fi + einfo + readme.gentoo_print_elog +} -- cgit v1.2.3-65-gdbad