ottxor 14/08/29 19:29:11 Modified: ChangeLog Added: gromacs-4.6.7.ebuild Log: version bump (Portage version: 2.2.8-r1/cvs/Linux x86_64, signed Manifest commit with key C2000586)
Revision Changes Path 1.143 sci-chemistry/gromacs/ChangeLog file : http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-chemistry/gromacs/ChangeLog?rev=1.143&view=markup plain: http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-chemistry/gromacs/ChangeLog?rev=1.143&content-type=text/plain diff : http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-chemistry/gromacs/ChangeLog?r1=1.142&r2=1.143 Index: ChangeLog =================================================================== RCS file: /var/cvsroot/gentoo-x86/sci-chemistry/gromacs/ChangeLog,v retrieving revision 1.142 retrieving revision 1.143 diff -u -r1.142 -r1.143 --- ChangeLog 7 Jul 2014 17:53:12 -0000 1.142 +++ ChangeLog 29 Aug 2014 19:29:11 -0000 1.143 @@ -1,6 +1,11 @@ # ChangeLog for sci-chemistry/gromacs # Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2 -# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/gromacs/ChangeLog,v 1.142 2014/07/07 17:53:12 ottxor Exp $ +# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/gromacs/ChangeLog,v 1.143 2014/08/29 19:29:11 ottxor Exp $ + +*gromacs-4.6.7 (29 Aug 2014) + + 29 Aug 2014; Christoph Junghans <ott...@gentoo.org> +gromacs-4.6.7.ebuild: + version bump 07 Jul 2014; Christoph Junghans <ott...@gentoo.org> -gromacs-4.6.2.ebuild: remove old 1.1 sci-chemistry/gromacs/gromacs-4.6.7.ebuild file : http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-chemistry/gromacs/gromacs-4.6.7.ebuild?rev=1.1&view=markup plain: http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-chemistry/gromacs/gromacs-4.6.7.ebuild?rev=1.1&content-type=text/plain Index: gromacs-4.6.7.ebuild =================================================================== # Copyright 1999-2014 Gentoo Foundation # Distributed under the terms of the GNU General Public License v2 # $Header: /var/cvsroot/gentoo-x86/sci-chemistry/gromacs/gromacs-4.6.7.ebuild,v 1.1 2014/08/29 19:29:11 ottxor Exp $ EAPI=5 TEST_PV="4.6.7" MANUAL_PV="4.6.7" CMAKE_MAKEFILE_GENERATOR="ninja" inherit bash-completion-r1 cmake-utils cuda eutils multilib readme.gentoo toolchain-funcs if [[ $PV = *9999* ]]; then EGIT_REPO_URI="git://git.gromacs.org/gromacs.git https://gerrit.gromacs.org/gromacs.git git://github.com/gromacs/gromacs.git http://repo.or.cz/r/gromacs.git"; EGIT_BRANCH="release-4-6" inherit git-2 LIVE_DEPEND="doc? ( app-doc/doxygen dev-texlive/texlive-latex dev-texlive/texlive-latexextra media-gfx/imagemagick sys-apps/coreutils )" KEYWORDS="" else SRC_URI="ftp://ftp.gromacs.org/pub/${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-${TEST_PV}.tar.gz )" LIVE_DEPEND="" KEYWORDS="~alpha ~amd64 ~arm ~ppc64 ~sparc ~x86 ~amd64-linux ~x86-linux ~x86-macos" fi ACCE_IUSE="sse2 sse4_1 avx128fma avx256" DESCRIPTION="The ultimate molecular dynamics simulation package" HOMEPAGE="http://www.gromacs.org/"; # see COPYING for details # http://repo.or.cz/w/gromacs.git/blob/HEAD:/COPYING # base, vmd plugins, fftpack from numpy, blas/lapck from netlib, memtestG80 library, mpi_thread lib LICENSE="LGPL-2.1 UoI-NCSA !mkl? ( !fftw? ( BSD ) !blas? ( BSD ) !lapack? ( BSD ) ) cuda? ( LGPL-3 ) threads? ( BSD )" SLOT="0/${PV}" 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 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 }
