diff options
author | Justin Lecher <jlec@gentoo.org> | 2015-03-06 09:42:32 +0000 |
---|---|---|
committer | Justin Lecher <jlec@gentoo.org> | 2015-03-06 09:42:32 +0000 |
commit | 16bbcf1f9b93294b6a975a0865cfc6b06aefc8aa (patch) | |
tree | 2c9fd528fa0936cca20f5310044575e920ee75a1 /sci-chemistry | |
parent | amd64 stable wrt bug #541048 (diff) | |
download | historical-16bbcf1f9b93294b6a975a0865cfc6b06aefc8aa.tar.gz historical-16bbcf1f9b93294b6a975a0865cfc6b06aefc8aa.tar.bz2 historical-16bbcf1f9b93294b6a975a0865cfc6b06aefc8aa.zip |
Install missing header
Package-Manager: portage-2.2.18/cvs/Linux x86_64
Manifest-Sign-Key: 0xB9D4F231BD1558AB!
Diffstat (limited to 'sci-chemistry')
-rw-r--r-- | sci-chemistry/gromacs/ChangeLog | 8 | ||||
-rw-r--r-- | sci-chemistry/gromacs/Manifest | 27 | ||||
-rw-r--r-- | sci-chemistry/gromacs/gromacs-5.0.4-r1.ebuild | 284 | ||||
-rw-r--r-- | sci-chemistry/gromacs/metadata.xml | 8 |
4 files changed, 315 insertions, 12 deletions
diff --git a/sci-chemistry/gromacs/ChangeLog b/sci-chemistry/gromacs/ChangeLog index f427475736e9..c415376982ed 100644 --- a/sci-chemistry/gromacs/ChangeLog +++ b/sci-chemistry/gromacs/ChangeLog @@ -1,6 +1,12 @@ # 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 1.155 2015/02/26 19:04:02 maekke Exp $ +# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/gromacs/ChangeLog,v 1.156 2015/03/06 09:42:31 jlec Exp $ + +*gromacs-5.0.4-r1 (06 Mar 2015) + + 06 Mar 2015; Justin Lecher <jlec@gentoo.org> +gromacs-5.0.4-r1.ebuild, + metadata.xml: + Install missing header 26 Feb 2015; Markus Meier <maekke@gentoo.org> gromacs-5.0.4.ebuild: arm stable, bug #538370 diff --git a/sci-chemistry/gromacs/Manifest b/sci-chemistry/gromacs/Manifest index 013d3aa1fa74..1cd2ec0a3175 100644 --- a/sci-chemistry/gromacs/Manifest +++ b/sci-chemistry/gromacs/Manifest @@ -1,5 +1,5 @@ -----BEGIN PGP SIGNED MESSAGE----- -Hash: SHA256 +Hash: SHA512 DIST gromacs-4.6.5.tar.gz 10991576 SHA256 a7242f315963a111e87fd28795696b1e818ac97479788356c4f73a04e9cdef09 SHA512 6ebb3ef74cf9ef2a749bdad6ce7c2deca607ef3b04cab3ce0be25ac1e7c69b3716761a66b5214642b82a96571e488d8a7bffda651840e56d95c14ba099cc1e0c WHIRLPOOL e639f0d1256173dafe8ba1231d46596f23a29b5ab97883600673b078e2927492dd473834398cd9fd864eb3d529ef853c2592d0b2c5ebb18ebb25ca171568aa72 DIST gromacs-4.6.7.tar.gz 11031209 SHA256 6afb1837e363192043de34b188ca3cf83db6bd189601f2001a1fc5b0b2a214d9 SHA512 8472aa06e2050b469dac4c3a0b039014fa45055cdc550226605d90abec6956830ad2a1b634d10529fbf2e55e686a497e689dd165333bef7fe89b193227fa98e5 WHIRLPOOL 221b3d4e5ce6505edb5badc0e14391e6861cb7efad108b8b6eeaed435df6df15bc3580e52f18007c98e987b02a7d003381400d8adca246dc47c680954dcfe25a @@ -11,13 +11,26 @@ DIST regressiontests-4.6.7.tar.gz 44036109 SHA256 afe433fb40860392970851d9c317e6 DIST regressiontests-5.0.4.tar.gz 65193251 SHA256 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License v2 +# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/gromacs/gromacs-5.0.4-r1.ebuild,v 1.1 2015/03/06 09:42:31 jlec 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}_${x}_mpi" \ + cmake-utils_src_install + done + + if use tng; then + insinto /usr/include/tng + doins src/external/tng_io/include/tng/*h + fi + # drop unneeded stuff + rm "${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 +} diff --git a/sci-chemistry/gromacs/metadata.xml b/sci-chemistry/gromacs/metadata.xml index 8a5c7453f0ad..264aca065256 100644 --- a/sci-chemistry/gromacs/metadata.xml +++ b/sci-chemistry/gromacs/metadata.xml @@ -9,10 +9,10 @@ <use> <flag name="cuda">Enable cuda non-bonded kernels</flag> <flag name="double-precision">More precise calculations at the expense of speed</flag> - <flag name="single-precision">Single precision version of gromacs (default)</flag> - <flag name="boost">Enable external boost library</flag> - <flag name="tng">Enable new trajectory format - tng</flag> - <flag name="make-symlinks">Create symbolic links for pre-5.0 binary names</flag> + <flag name="single-precision">Single precision version of gromacs (default)</flag> + <flag name="boost">Enable external boost library</flag> + <flag name="tng">Enable new trajectory format - tng</flag> + <flag name="make-symlinks">Create symbolic links for pre-5.0 binary names</flag> <!-- acceleration optimization flags --> <flag name="offensive">Enable gromacs partly offensive quotes</flag> <flag name="openmm">Add acceleration through <pkg>sci-libs/openmm</pkg></flag> |