diff options
| -rw-r--r-- | sci-chemistry/gromacs/ChangeLog | 7 | ||||
| -rw-r--r-- | sci-chemistry/gromacs/Manifest | 30 | ||||
| -rw-r--r-- | sci-chemistry/gromacs/gromacs-4.6.6.ebuild | 286 | ||||
| -rw-r--r-- | sci-chemistry/gromacs/gromacs-5.0.1.ebuild | 262 | ||||
| -rw-r--r-- | sci-chemistry/gromacs/gromacs-5.0.2-r1.ebuild | 275 | ||||
| -rw-r--r-- | sci-chemistry/gromacs/gromacs-5.0.2.ebuild | 262 | ||||
| -rw-r--r-- | sci-chemistry/gromacs/gromacs-5.0.ebuild | 266 |
7 files changed, 14 insertions, 1374 deletions
diff --git a/sci-chemistry/gromacs/ChangeLog b/sci-chemistry/gromacs/ChangeLog index 4f0f80a01b80..6ec6f1ec4e46 100644 --- a/sci-chemistry/gromacs/ChangeLog +++ b/sci-chemistry/gromacs/ChangeLog @@ -1,6 +1,11 @@ # ChangeLog for sci-chemistry/gromacs # Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 -# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/gromacs/ChangeLog,v 1.150 2015/01/31 20:23:56 ottxor Exp $ +# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/gromacs/ChangeLog,v 1.151 2015/01/31 20:31:16 ottxor Exp $ + + 31 Jan 2015; Christoph Junghans <ottxor@gentoo.org> -gromacs-4.6.6.ebuild, + -gromacs-5.0.1.ebuild, -gromacs-5.0.2-r1.ebuild, -gromacs-5.0.2.ebuild, + -gromacs-5.0.ebuild: + remove old 31 Jan 2015; Christoph Junghans <ottxor@gentoo.org> gromacs-4.6.5.ebuild, gromacs-4.6.6.ebuild, gromacs-4.6.7.ebuild, gromacs-5.0.1.ebuild, diff --git a/sci-chemistry/gromacs/Manifest b/sci-chemistry/gromacs/Manifest index 2817028444b1..ae6b0609d210 100644 --- a/sci-chemistry/gromacs/Manifest +++ b/sci-chemistry/gromacs/Manifest @@ -2,40 +2,26 @@ Hash: SHA256 DIST gromacs-4.6.5.tar.gz 10991576 SHA256 a7242f315963a111e87fd28795696b1e818ac97479788356c4f73a04e9cdef09 SHA512 6ebb3ef74cf9ef2a749bdad6ce7c2deca607ef3b04cab3ce0be25ac1e7c69b3716761a66b5214642b82a96571e488d8a7bffda651840e56d95c14ba099cc1e0c WHIRLPOOL e639f0d1256173dafe8ba1231d46596f23a29b5ab97883600673b078e2927492dd473834398cd9fd864eb3d529ef853c2592d0b2c5ebb18ebb25ca171568aa72 -DIST gromacs-4.6.6.tar.gz 10991950 SHA256 294b6e8eacf7064bd609edd6e9a6ce2ce9122876bc1abd593ddcb018a9b01bb0 SHA512 ff790db256d6759cde0eeb34e71937d63714c4efc9aa390532593c807ebcfa061036a16c8dd4e634c6f90b7ab120a0bf041daeab1e6e2a37f3ac4065213d8a70 WHIRLPOOL aba06e7a688a4bea7b0a9250b15789dc97157c583d08a13b78c76a581d41f2fcf63955a85c482679ab08564bad12ef81c95a712796193cf45f2b3d1051a089bd DIST gromacs-4.6.7.tar.gz 11031209 SHA256 6afb1837e363192043de34b188ca3cf83db6bd189601f2001a1fc5b0b2a214d9 SHA512 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http://repo.or.cz/r/gromacs.git" - EGIT_BRANCH="release-4-6" - inherit git-2 - LIVE_DEPEND="doc? ( - app-doc/doxygen - dev-texlive/texlive-latex - dev-texlive/texlive-latexextra - media-gfx/imagemagick - sys-apps/coreutils - )" - KEYWORDS="" -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://gerrit.gromacs.org/download/regressiontests-${TEST_PV}.tar.gz )" - LIVE_DEPEND="" - KEYWORDS="~alpha ~amd64 ~arm ~ppc64 ~sparc ~x86 ~amd64-linux ~x86-linux ~x86-macos" -fi - -ACCE_IUSE="cpu_flags_x86_sse2 cpu_flags_x86_sse4_1 cpu_flags_x86_fma4 cpu_flags_x86_avx" - -DESCRIPTION="The ultimate molecular dynamics simulation package" -HOMEPAGE="http://www.gromacs.org/" - -# see COPYING for details -# http://repo.or.cz/w/gromacs.git/blob/HEAD:/COPYING -# base, vmd plugins, fftpack from numpy, blas/lapck from netlib, memtestG80 library, mpi_thread lib -LICENSE="LGPL-2.1 UoI-NCSA !mkl? ( !fftw? ( BSD ) !blas? ( BSD ) !lapack? ( BSD ) ) cuda? ( LGPL-3 ) threads? ( BSD )" -SLOT="0/${PV}" -IUSE="X blas 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 - ${LIVE_DEPEND} - doc? ( app-doc/doxygen )" -RDEPEND="${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="release-4-6" \ - 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 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" - - #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 -} diff --git a/sci-chemistry/gromacs/gromacs-5.0.1.ebuild b/sci-chemistry/gromacs/gromacs-5.0.1.ebuild deleted file mode 100644 index c2b748bd257b..000000000000 --- a/sci-chemistry/gromacs/gromacs-5.0.1.ebuild +++ /dev/null @@ -1,262 +0,0 @@ -# Copyright 1999-2015 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 -# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/gromacs/gromacs-5.0.1.ebuild,v 1.3 2015/01/31 20:23:56 ottxor Exp $ - -EAPI=5 - -CMAKE_MAKEFILE_GENERATOR="ninja" - -inherit bash-completion-r1 cmake-utils cuda eutils multilib readme.gentoo toolchain-funcs - -if [[ $PV = *9999* ]]; then - EGIT_REPO_URI="git://git.gromacs.org/gromacs.git - https://gerrit.gromacs.org/gromacs.git - git://github.com/gromacs/gromacs.git - http://repo.or.cz/r/gromacs.git" - EGIT_BRANCH="release-5-0" - inherit git-r3 - KEYWORDS="" -else - SRC_URI="ftp://ftp.gromacs.org/pub/${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 +make-symlinks 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 [[ ${PV} != *9999 ]]; then - default - else - git-r3_src_unpack - if use test; then - EGIT_REPO_URI="git://git.gromacs.org/regressiontests.git" \ - EGIT_BRANCH="master" EGIT_COMMIT="master" \ - EGIT_CHECKOUT_DIR="${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) - $(cmake-utils_use make-symlinks GMX_SYMLINK_OLD_BINARY_NAMES) - -DGMX_DEFAULT_SUFFIX=off - -DGMX_SIMD="$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 - # generate bash completion - BUILD_DIR="${WORKDIR}/${P}_${x}"\ - cmake-utils_src_compile completion - if use doc; then - BUILD_DIR="${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-${PV}.pdf" - fi - newbashcomp "${WORKDIR}/${P}_${x}"/src/programs/completion/gmx-completion.bash gromacs - use mpi || continue - BUILD_DIR="${WORKDIR}/${P}_${x}_mpi" \ - cmake-utils_src_install - done - # drop unneeded stuff - rm "${ED}"usr/bin/GMXRC* || 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 -} diff --git a/sci-chemistry/gromacs/gromacs-5.0.2-r1.ebuild b/sci-chemistry/gromacs/gromacs-5.0.2-r1.ebuild deleted file mode 100644 index 9bc9dcee939a..000000000000 --- a/sci-chemistry/gromacs/gromacs-5.0.2-r1.ebuild +++ /dev/null @@ -1,275 +0,0 @@ -# Copyright 1999-2015 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 -# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/gromacs/gromacs-5.0.2-r1.ebuild,v 1.3 2015/01/31 20:23:56 ottxor Exp $ - -EAPI=5 - -CMAKE_MAKEFILE_GENERATOR="ninja" - -inherit bash-completion-r1 cmake-utils cuda eutils multilib readme.gentoo toolchain-funcs - -if [[ $PV = *9999* ]]; then - EGIT_REPO_URI="git://git.gromacs.org/gromacs.git - https://gerrit.gromacs.org/gromacs.git - git://github.com/gromacs/gromacs.git - http://repo.or.cz/r/gromacs.git" - EGIT_BRANCH="release-5-0" - inherit git-r3 - KEYWORDS="" -else - SRC_URI="ftp://ftp.gromacs.org/pub/${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 +make-symlinks 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 [[ ${PV} != *9999 ]]; then - default - else - git-r3_src_unpack - if use test; then - EGIT_REPO_URI="git://git.gromacs.org/regressiontests.git" \ - EGIT_BRANCH="master" EGIT_COMMIT="master" \ - EGIT_CHECKOUT_DIR="${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) - $(cmake-utils_use make-symlinks GMX_SYMLINK_OLD_BINARY_NAMES) - -DGMX_DEFAULT_SUFFIX=off - -DGMX_SIMD="$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 - # generate bash completion, not 100% necessary for - # rel ebuilds as bundled - BUILD_DIR="${WORKDIR}/${P}_${x}"\ - cmake-utils_src_compile completion - # not 100% necessary for rel ebuilds as available from website - if use doc; then - BUILD_DIR="${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 - #release ebuild does this automatically - if [[ $PV = *9999* ]]; then - cp "${WORKDIR}/${P}_${x}"/src/programs/completion/gmx-completion.bash "${ED}/usr/bin" || die - echo "complete -o nospace -F _gmx_compl gmx" > "${ED}/usr/bin/gmx-completion-gmx.bash" || die - fi - use mpi || continue - BUILD_DIR="${WORKDIR}/${P}_${x}_mpi" \ - cmake-utils_src_install - done - # drop unneeded stuff - rm "${ED}"usr/bin/GMXRC* || die - #concatenate all gmx-completion*, starting with gmx-completion.bash (fct defs) - #little hacckery as some gmx-completion* newlines ,so cat won't work - for x in "${ED}"usr/bin/gmx-completion{,?*}.bash ; do - echo $(<${x}) - done > "${T}"/gmx-bashcomp || die - newbashcomp "${T}"/gmx-bashcomp gromacs - 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 -} diff --git a/sci-chemistry/gromacs/gromacs-5.0.2.ebuild b/sci-chemistry/gromacs/gromacs-5.0.2.ebuild deleted file mode 100644 index d63bd4903e4e..000000000000 --- a/sci-chemistry/gromacs/gromacs-5.0.2.ebuild +++ /dev/null @@ -1,262 +0,0 @@ -# Copyright 1999-2015 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 -# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/gromacs/gromacs-5.0.2.ebuild,v 1.3 2015/01/31 20:23:56 ottxor Exp $ - -EAPI=5 - -CMAKE_MAKEFILE_GENERATOR="ninja" - -inherit bash-completion-r1 cmake-utils cuda eutils multilib readme.gentoo toolchain-funcs - -if [[ $PV = *9999* ]]; then - EGIT_REPO_URI="git://git.gromacs.org/gromacs.git - https://gerrit.gromacs.org/gromacs.git - git://github.com/gromacs/gromacs.git - http://repo.or.cz/r/gromacs.git" - EGIT_BRANCH="release-5-0" - inherit git-r3 - KEYWORDS="" -else - SRC_URI="ftp://ftp.gromacs.org/pub/${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 +make-symlinks 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 [[ ${PV} != *9999 ]]; then - default - else - git-r3_src_unpack - if use test; then - EGIT_REPO_URI="git://git.gromacs.org/regressiontests.git" \ - EGIT_BRANCH="master" EGIT_COMMIT="master" \ - EGIT_CHECKOUT_DIR="${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) - $(cmake-utils_use make-symlinks GMX_SYMLINK_OLD_BINARY_NAMES) - -DGMX_DEFAULT_SUFFIX=off - -DGMX_SIMD="$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 - # generate bash completion - BUILD_DIR="${WORKDIR}/${P}_${x}"\ - cmake-utils_src_compile completion - if use doc; then - BUILD_DIR="${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-${PV}.pdf" - fi - newbashcomp "${WORKDIR}/${P}_${x}"/src/programs/completion/gmx-completion.bash gromacs - use mpi || continue - BUILD_DIR="${WORKDIR}/${P}_${x}_mpi" \ - cmake-utils_src_install - done - # drop unneeded stuff - rm "${ED}"usr/bin/GMXRC* || 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 -} diff --git a/sci-chemistry/gromacs/gromacs-5.0.ebuild b/sci-chemistry/gromacs/gromacs-5.0.ebuild deleted file mode 100644 index 8f5dfac11044..000000000000 --- a/sci-chemistry/gromacs/gromacs-5.0.ebuild +++ /dev/null @@ -1,266 +0,0 @@ -# Copyright 1999-2015 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 -# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/gromacs/gromacs-5.0.ebuild,v 1.4 2015/01/31 20:23:56 ottxor Exp $ - -EAPI=5 - -TEST_PV="5.0" - -CMAKE_MAKEFILE_GENERATOR="ninja" - -inherit bash-completion-r1 cmake-utils cuda eutils multilib readme.gentoo toolchain-funcs - -if [[ $PV = *9999* ]]; then - EGIT_REPO_URI="git://git.gromacs.org/gromacs.git - https://gerrit.gromacs.org/gromacs.git - git://github.com/gromacs/gromacs.git - http://repo.or.cz/r/gromacs.git" - EGIT_BRANCH="release-5-0" - inherit git-r3 -else - SRC_URI="ftp://ftp.gromacs.org/pub/${PN}/${PN}-${PV/_/-}.tar.gz - test? ( http://gerrit.gromacs.org/download/regressiontests-${TEST_PV}.tar.gz )" -fi - -ACCE_IUSE="cpu_flags_x86_sse2 cpu_flags_x86_sse4_1 cpu_flags_x86_fma4 cpu_flags_x86_avx cpu_flags_x86_avx2" - -DESCRIPTION="The ultimate molecular dynamics simulation package" -HOMEPAGE="http://www.gromacs.org/" - -# see COPYING for details -# http://repo.or.cz/w/gromacs.git/blob/HEAD:/COPYING -# base, vmd plugins, fftpack from numpy, blas/lapck from netlib, memtestG80 library, mpi_thread lib -LICENSE="LGPL-2.1 UoI-NCSA !mkl? ( !fftw? ( BSD ) !blas? ( BSD ) !lapack? ( BSD ) ) cuda? ( LGPL-3 ) threads? ( BSD )" -SLOT="0/${PV}" -KEYWORDS="~alpha ~amd64 ~arm ~ppc64 ~sparc ~x86 ~amd64-linux ~x86-linux ~x64-macos ~x86-macos" -IUSE="X blas boost cuda +doc -double-precision +fftw lapack +make-symlinks 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 [[ ${PV} != *9999 ]]; then - default - else - git-r3_src_unpack - if use test; then - EGIT_REPO_URI="git://git.gromacs.org/regressiontests.git" \ - EGIT_BRANCH="master" EGIT_NOUNPACK="yes" EGIT_COMMIT="master" \ - EGIT_SOURCEDIR="${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) - $(cmake-utils_use make-symlinks GMX_SYMLINK_OLD_BINARY_NAMES) - -DGMX_DEFAULT_SUFFIX=off - -DGMX_SIMD="$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 - # generate bash completion - BUILD_DIR="${WORKDIR}/${P}_${x}"\ - cmake-utils_src_compile completion - if use doc; then - BUILD_DIR="${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}_${x}"/manual/gromacs.pdf "${PN}-manual-${PV}.pdf" - fi - newbashcomp "${WORKDIR}/${P}_${x}"/src/programs/completion/gmx-completion.bash gromacs - use mpi || continue - BUILD_DIR="${WORKDIR}/${P}_${x}_mpi" \ - cmake-utils_src_install - done - # drop unneeded stuff - rm -f "${ED}"usr/bin/gmx-completion* - rm -f "${ED}"usr/bin/g_options* - rm -f "${ED}"usr/bin/GMXRC* - rm -f "${ED}"usr/$(get_libdir)/libtng*.a - - 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 -} |