ottxor 14/12/21 23:12:47 Modified: ChangeLog Added: gromacs-5.0.4.ebuild Log: version bump (Portage version: 2.2.14/cvs/Linux x86_64, signed Manifest commit with key C2000586)
Revision Changes Path 1.149 sci-chemistry/gromacs/ChangeLog file : http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-chemistry/gromacs/ChangeLog?rev=1.149&view=markup plain: http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-chemistry/gromacs/ChangeLog?rev=1.149&content-type=text/plain diff : http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-chemistry/gromacs/ChangeLog?r1=1.148&r2=1.149 Index: ChangeLog =================================================================== RCS file: /var/cvsroot/gentoo-x86/sci-chemistry/gromacs/ChangeLog,v retrieving revision 1.148 retrieving revision 1.149 diff -u -r1.148 -r1.149 --- ChangeLog 25 Nov 2014 16:04:38 -0000 1.148 +++ ChangeLog 21 Dec 2014 23:12:47 -0000 1.149 @@ -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 1.148 2014/11/25 16:04:38 ottxor Exp $ +# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/gromacs/ChangeLog,v 1.149 2014/12/21 23:12:47 ottxor Exp $ + +*gromacs-5.0.4 (21 Dec 2014) + + 21 Dec 2014; Christoph Junghans <ott...@gentoo.org> +gromacs-5.0.4.ebuild: + version bump 25 Nov 2014; Christoph Junghans <ott...@gentoo.org> gromacs-4.6.5.ebuild, gromacs-4.6.6.ebuild, gromacs-4.6.7.ebuild, gromacs-5.0.1.ebuild, 1.1 sci-chemistry/gromacs/gromacs-5.0.4.ebuild file : http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-chemistry/gromacs/gromacs-5.0.4.ebuild?rev=1.1&view=markup plain: http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-chemistry/gromacs/gromacs-5.0.4.ebuild?rev=1.1&content-type=text/plain Index: gromacs-5.0.4.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-5.0.4.ebuild,v 1.1 2014/12/21 23:12:47 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-${PV}.tar.gz )" KEYWORDS="~alpha ~amd64 ~arm ~ppc64 ~sparc ~x86 ~amd64-linux ~x86-linux ~x64-macos ~x86-macos" fi ACCE_IUSE="sse2 sse4_1 avx_128_fma avx_256 avx2_256" DESCRIPTION="The ultimate molecular dynamics simulation package" HOMEPAGE="http://www.gromacs.org/"; # see COPYING for details # http://repo.or.cz/w/gromacs.git/blob/HEAD:/COPYING # base, vmd plugins, fftpack from numpy, blas/lapck from netlib, memtestG80 library, mpi_thread lib LICENSE="LGPL-2.1 UoI-NCSA !mkl? ( !fftw? ( BSD ) !blas? ( BSD ) !lapack? ( BSD ) ) cuda? ( LGPL-3 ) threads? ( BSD )" SLOT="0/${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 sse2 && acce="SSE2" use sse4_1 && acce="SSE4.1" use avx_128_fma && acce="AVX_128_FMA" use avx_256 && acce="AVX_256" use avx2_256 && 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 gmx bashcomp_alias gmx mdrun rm "${ED}"usr/bin/gmx-completion{,?*}.bash || die if use double-precision && use single-precision; then bashcomp_alias gmx gmx_d bashcomp_alias gmx mdrun_d fi 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 }
