diff options
author | Alexey Shvetsov <alexxy@gentoo.org> | 2013-12-06 13:34:20 +0400 |
---|---|---|
committer | Alexey Shvetsov <alexxy@gentoo.org> | 2013-12-06 13:34:20 +0400 |
commit | 48ddd384fe8e96a4e904b8ccb1da1fc86087b1e3 (patch) | |
tree | e2caf908ab30974b6c744ad5c69edd3a9bac2fe4 /sci-chemistry/gromacs | |
parent | app-doc/root-docs: version bump (diff) | |
download | sci-48ddd384fe8e96a4e904b8ccb1da1fc86087b1e3.tar.gz sci-48ddd384fe8e96a4e904b8ccb1da1fc86087b1e3.tar.bz2 sci-48ddd384fe8e96a4e904b8ccb1da1fc86087b1e3.zip |
Add 5.0-beta1 release
Package-Manager: portage-2.2.7
Diffstat (limited to 'sci-chemistry/gromacs')
-rw-r--r-- | sci-chemistry/gromacs/ChangeLog | 6 | ||||
-rw-r--r-- | sci-chemistry/gromacs/Manifest | 2 | ||||
-rw-r--r-- | sci-chemistry/gromacs/gromacs-5.0_beta1.ebuild | 258 | ||||
-rw-r--r-- | sci-chemistry/gromacs/gromacs-9999.ebuild | 13 |
4 files changed, 271 insertions, 8 deletions
diff --git a/sci-chemistry/gromacs/ChangeLog b/sci-chemistry/gromacs/ChangeLog index 781b35426..4c5ac13af 100644 --- a/sci-chemistry/gromacs/ChangeLog +++ b/sci-chemistry/gromacs/ChangeLog @@ -2,6 +2,12 @@ # Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ +*gromacs-5.0_beta1 (06 Dec 2013) + + 06 Dec 2013; Alexey Shvetsov <alexxy@gentoo.org> +gromacs-5.0_beta1.ebuild, + gromacs-9999.ebuild: + Add 5.0-beta1 release + 05 Dec 2013; Alexey Shvetsov <alexxy@gentoo.org> gromacs-9999.ebuild: Make gromacs 9999 build manual again diff --git a/sci-chemistry/gromacs/Manifest b/sci-chemistry/gromacs/Manifest new file mode 100644 index 000000000..a076f19ae --- /dev/null +++ b/sci-chemistry/gromacs/Manifest @@ -0,0 +1,2 @@ +DIST gromacs-5.0-beta1.tar.gz 18849424 SHA256 c663d570302e7cc91cf732b356fbaa4b39fd8a527927ca4ca13f35797f1ee88b SHA512 86ad4a9169ddb78308f3036c880281ccb0e53f459226d4b66d1175d4e5deb05da772988b981baae2cc3e6468afbc31b5a9bff54b2bd0a3ce326a61f360a01e5c WHIRLPOOL 364c45ef77868b2fd13a1c4b49c287cdb5d4883077b63a70de23f82e178a688ed3aa6cf95d4c4fa2fd7d283c8f03dc04a9442dc28663fd170d044933c4b54128 +DIST regressiontests-5.0-beta1.tar.gz 44826977 SHA256 da629f5fbdf0c1a72c964d1af7709895ce243bb5563b64a34664c6c9006ff2ae SHA512 cd69a4fc78291f6ae21a19e3ff20bac74f79d4b4b78831a6cad6868f9974120739fa3f34b7d3d8f99b93464e19705b45727719cd8aa59f60eb2d86b39c1d5990 WHIRLPOOL 557c71de47c7a4507ba33f198c7954f77460995f4f62e737de6f376a859a7819289ae227434e0cd7501873a5bd4b35f76aa7a7e24fc966d957c727e848743f17 diff --git a/sci-chemistry/gromacs/gromacs-5.0_beta1.ebuild b/sci-chemistry/gromacs/gromacs-5.0_beta1.ebuild new file mode 100644 index 000000000..81ed0ccde --- /dev/null +++ b/sci-chemistry/gromacs/gromacs-5.0_beta1.ebuild @@ -0,0 +1,258 @@ +# Copyright 1999-2013 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Header: $ + +EAPI=5 + +TEST_PV="5.0-beta1" + +CMAKE_MAKEFILE_GENERATOR="ninja" + +inherit bash-completion-r1 cmake-utils cuda eutils multilib readme.gentoo toolchain-funcs + +if [[ $PV = *9999* ]]; then + EGIT_REPO_URI="git://git.gromacs.org/gromacs.git + https://gerrit.gromacs.org/gromacs.git + git://github.com/gromacs/gromacs.git + http://repo.or.cz/r/gromacs.git" + EGIT_BRANCH="master" + inherit git-2 +else + SRC_URI="ftp://ftp.gromacs.org/pub/${PN}/${PN}-${PV/_/-}.tar.gz + test? ( http://${PN}.googlecode.com/files/regressiontests-${TEST_PV}.tar.gz )" +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 openmp +single-precision test +threads zsh-completion ${ACCE_IUSE}" + +CDEPEND=" + X? ( + x11-libs/libX11 + x11-libs/libSM + x11-libs/libICE + ) + blas? ( virtual/blas ) + cuda? ( >=dev-util/nvidia-cuda-toolkit-4.2.9-r1 ) + fftw? ( sci-libs/fftw:3.0 ) + gsl? ( sci-libs/gsl ) + lapack? ( virtual/lapack ) + mkl? ( sci-libs/mkl ) + mpi? ( virtual/mpi ) + " +DEPEND="${CDEPEND} + virtual/pkgconfig + doc? ( + 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 [[ ${PV} != *9999 ]]; then + default + else + git-2_src_unpack + if use test; then + EGIT_REPO_URI="git://git.gromacs.org/regressiontests.git" \ + EGIT_BRANCH="master" EGIT_NOUNPACK="yes" EGIT_COMMIT="master" \ + EGIT_SOURCEDIR="${WORKDIR}/regressiontests"\ + git-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) + $(cmake-utils_use doc GMX_BUILD_MANUAL) + -DGMX_DEFAULT_SUFFIX=off + -DGMX_ACCELERATION="$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 + -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 + use mpi || continue + einfo "Configuring for ${x} precision with mpi" + mycmakeargs=( + ${mycmakeargs_pre[@]} ${p} + -DGMX_THREAD_MPI=OFF + -DGMX_MPI=ON ${cuda} + -DGMX_OPENMM=OFF + -DGMX_BUILD_MDRUN_ONLY=ON + -DGMX_BUILD_MANUAL=OFF + -DGMX_BINARY_SUFFIX="_mpi${suffix}" + -DGMX_LIBS_SUFFIX="_mpi${suffix}" + ) + BUILD_DIR="${WORKDIR}/${P}_${x}_mpi" CC="mpicc" cmake-utils_src_configure + done +} + +src_compile() { + for x in ${GMX_DIRS}; do + einfo "Compiling for ${x} precision" + BUILD_DIR="${WORKDIR}/${P}_${x}"\ + cmake-utils_src_compile + 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-${PV}.pdf" + fi + use mpi || continue + BUILD_DIR="${WORKDIR}/${P}_${x}_mpi" \ + cmake-utils_src_install + done + + 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 -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" + einfo + readme.gentoo_print_elog +} diff --git a/sci-chemistry/gromacs/gromacs-9999.ebuild b/sci-chemistry/gromacs/gromacs-9999.ebuild index 20a16c65c..81ed0ccde 100644 --- a/sci-chemistry/gromacs/gromacs-9999.ebuild +++ b/sci-chemistry/gromacs/gromacs-9999.ebuild @@ -5,7 +5,6 @@ EAPI=5 TEST_PV="5.0-beta1" -MANUAL_PV="5.0-beta1" CMAKE_MAKEFILE_GENERATOR="ninja" @@ -19,8 +18,7 @@ if [[ $PV = *9999* ]]; then EGIT_BRANCH="master" inherit git-2 else - SRC_URI="ftp://ftp.gromacs.org/pub/${PN}/${P}.tar.gz - doc? ( ftp://ftp.gromacs.org/pub/manual/manual-${MANUAL_PV}.pdf -> ${PN}-manual-${MANUAL_PV}.pdf ) + SRC_URI="ftp://ftp.gromacs.org/pub/${PN}/${PN}-${PV/_/-}.tar.gz test? ( http://${PN}.googlecode.com/files/regressiontests-${TEST_PV}.tar.gz )" fi @@ -67,6 +65,10 @@ REQUIRED_USE=" 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 && \ @@ -251,11 +253,6 @@ pkg_postinst() { 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 } |