diff options
| -rw-r--r-- | sci-chemistry/gromacs/Manifest | 2 | ||||
| -rw-r--r-- | sci-chemistry/gromacs/gromacs-2016.9999.ebuild | 10 | ||||
| -rw-r--r-- | sci-chemistry/gromacs/gromacs-2016_rc1.ebuild | 266 | ||||
| -rw-r--r-- | sci-chemistry/gromacs/gromacs-9999.ebuild | 10 | ||||
| -rw-r--r-- | sci-chemistry/gromacs/metadata.xml | 3 |
5 files changed, 278 insertions, 13 deletions
diff --git a/sci-chemistry/gromacs/Manifest b/sci-chemistry/gromacs/Manifest new file mode 100644 index 000000000..1fed511a1 --- /dev/null +++ b/sci-chemistry/gromacs/Manifest @@ -0,0 +1,2 @@ +DIST gromacs-2016-rc1.tar.gz 27322876 SHA256 69a307009cd9015b09af3c39ed4b193e71c59deccc3b34e758b3b9b5a34f7a47 SHA512 9c74ab718c9c894525524c0612aac93246be8aff86491f4b4854783d5e112c346b8c6bd185ec951a76aa398fdb2132abf42bb27b644440ceb6f6baeeede9c3a0 WHIRLPOOL cdb4d417770720069c6e1de2930d36f3a952ce9b2d111d1dd9a2f3b87d28cc199a17745db2c580da6606eb9dd59dfd9c4ddb5297de08202067dee0160a3a985e +DIST regressiontests-2016-rc1.tar.gz 66629314 SHA256 63fcf8fcb1371478b705dd8f44f2c284ac8c6f3e7eb8146f751f6e0e0f2db415 SHA512 8900efb605d69aa723bab398556a9b0d94da2b25d55948a3903f2d5a47c0f89306fffe3b0c7e780508b301463243bc73191a9dee6494ab288ca89831e71f741a WHIRLPOOL a205113884c65de4e9a75f0af59a1be910cf82a7fca8ba561c13815793f98ee0af342a0318044c49c757c8b25cfebb8b42299e885345e7f1af695f2e2b591297 diff --git a/sci-chemistry/gromacs/gromacs-2016.9999.ebuild b/sci-chemistry/gromacs/gromacs-2016.9999.ebuild index b30ff552e..1ca034301 100644 --- a/sci-chemistry/gromacs/gromacs-2016.9999.ebuild +++ b/sci-chemistry/gromacs/gromacs-2016.9999.ebuild @@ -18,7 +18,7 @@ if [[ $PV = *9999* ]]; then KEYWORDS="" else SRC_URI="ftp://ftp.gromacs.org/pub/${PN}/${PN}-${PV/_/-}.tar.gz - test? ( http://gerrit.gromacs.org/download/regressiontests-${PV}.tar.gz )" + test? ( http://gerrit.gromacs.org/download/regressiontests-${PV/_/-}.tar.gz )" KEYWORDS="~alpha ~amd64 ~arm ~ppc64 ~sparc ~x86 ~amd64-linux ~x86-linux ~x64-macos ~x86-macos" fi @@ -32,7 +32,7 @@ HOMEPAGE="http://www.gromacs.org/" # 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 lapack mkl mpi +offensive openmp +single-precision test +threads +tng ${ACCE_IUSE}" +IUSE="X blas cuda +doc -double-precision +fftw +hwloc lapack mkl mpi +offensive openmp +single-precision test +threads +tng ${ACCE_IUSE}" CDEPEND=" X? ( @@ -43,6 +43,7 @@ CDEPEND=" blas? ( virtual/blas ) cuda? ( >=dev-util/nvidia-cuda-toolkit-4.2.9-r1 ) fftw? ( sci-libs/fftw:3.0 ) + hwloc? ( sys-apps/hwloc ) lapack? ( virtual/lapack ) mkl? ( sci-libs/mkl ) mpi? ( virtual/mpi ) @@ -149,15 +150,13 @@ src_configure() { -DGMX_EXTERNAL_LAPACK=$(usex lapack) -DGMX_OPENMP=$(usex openmp) -DGMX_COOL_QUOTES=$(usex offensive) - -DGMX_EXTERNAL_BOOST=$(usex boost) -DGMX_USE_TNG=$(usex tng) -DGMX_BUILD_MANUAL=$(usex doc) + -DGMX_HWLOC=$(usex hwloc) -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 ${extra} @@ -179,7 +178,6 @@ src_configure() { -DGMX_MPI=OFF -DGMX_THREAD_MPI=$(usex threads) "${cuda[@]}" - -DGMX_OPENMM=OFF "$(use test && echo -DREGRESSIONTEST_PATH="${WORKDIR}/${P}_${x}/tests")" -DGMX_BINARY_SUFFIX="${suffix}" -DGMX_LIBS_SUFFIX="${suffix}" diff --git a/sci-chemistry/gromacs/gromacs-2016_rc1.ebuild b/sci-chemistry/gromacs/gromacs-2016_rc1.ebuild new file mode 100644 index 000000000..1ca034301 --- /dev/null +++ b/sci-chemistry/gromacs/gromacs-2016_rc1.ebuild @@ -0,0 +1,266 @@ +# Copyright 1999-2016 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI=6 + +CMAKE_MAKEFILE_GENERATOR="ninja" + +inherit bash-completion-r1 cmake-utils cuda eutils multilib readme.gentoo-r1 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" + [[ $PV = 9999 ]] && EGIT_BRANCH="master" || EGIT_BRANCH="release-${PV:0:1}-${PV:2:1}" + inherit git-r3 + KEYWORDS="" +else + SRC_URI="ftp://ftp.gromacs.org/pub/${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 cuda +doc -double-precision +fftw +hwloc lapack mkl mpi +offensive openmp +single-precision test +threads +tng ${ACCE_IUSE}" + +CDEPEND=" + X? ( + x11-libs/libX11 + x11-libs/libSM + x11-libs/libICE + ) + blas? ( virtual/blas ) + cuda? ( >=dev-util/nvidia-cuda-toolkit-4.2.9-r1 ) + fftw? ( sci-libs/fftw:3.0 ) + hwloc? ( sys-apps/hwloc ) + lapack? ( virtual/lapack ) + mkl? ( sci-libs/mkl ) + mpi? ( virtual/mpi ) + " +DEPEND="${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 [[ ${PV} != *9999 ]]; then + default + else + git-r3_src_unpack + if use test; then + EGIT_REPO_URI="git://git.gromacs.org/regressiontests.git" \ + EGIT_BRANCH="${EGIT_BRANCH}" \ + 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+=( + "${fft_opts[@]}" + -DGMX_X11=$(usex X) + -DGMX_EXTERNAL_BLAS=$(usex blas) + -DGMX_EXTERNAL_LAPACK=$(usex lapack) + -DGMX_OPENMP=$(usex openmp) + -DGMX_COOL_QUOTES=$(usex offensive) + -DGMX_USE_TNG=$(usex tng) + -DGMX_BUILD_MANUAL=$(usex doc) + -DGMX_HWLOC=$(usex hwloc) + -DGMX_DEFAULT_SUFFIX=off + -DGMX_SIMD="$acce" + -DGMX_LIB_INSTALL_DIR="$(get_libdir)" + -DGMX_VMD_PLUGIN_PATH="${EPREFIX}/usr/$(get_libdir)/vmd/plugins/*/molfile/" + -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[@]} ${p} + -DGMX_MPI=OFF + -DGMX_THREAD_MPI=$(usex threads) + "${cuda[@]}" + "$(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 + # 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-${PV}.pdf" + fi + use mpi || continue + BUILD_DIR="${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 "${ED}"usr/bin/GMXRC* || die + for x in "${ED}"usr/bin/gmx-completion-*.bash ; do + local n=${x##*/gmx-completion-} + n="${n%.bash}" + cat "${ED}"usr/bin/gmx-completion.bash "$x" > "${T}/${n}" || die + newbashcomp "${T}"/"${n}" "${n}" + done + rm "${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-9999.ebuild b/sci-chemistry/gromacs/gromacs-9999.ebuild index b30ff552e..1ca034301 100644 --- a/sci-chemistry/gromacs/gromacs-9999.ebuild +++ b/sci-chemistry/gromacs/gromacs-9999.ebuild @@ -18,7 +18,7 @@ if [[ $PV = *9999* ]]; then KEYWORDS="" else SRC_URI="ftp://ftp.gromacs.org/pub/${PN}/${PN}-${PV/_/-}.tar.gz - test? ( http://gerrit.gromacs.org/download/regressiontests-${PV}.tar.gz )" + test? ( http://gerrit.gromacs.org/download/regressiontests-${PV/_/-}.tar.gz )" KEYWORDS="~alpha ~amd64 ~arm ~ppc64 ~sparc ~x86 ~amd64-linux ~x86-linux ~x64-macos ~x86-macos" fi @@ -32,7 +32,7 @@ HOMEPAGE="http://www.gromacs.org/" # 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 lapack mkl mpi +offensive openmp +single-precision test +threads +tng ${ACCE_IUSE}" +IUSE="X blas cuda +doc -double-precision +fftw +hwloc lapack mkl mpi +offensive openmp +single-precision test +threads +tng ${ACCE_IUSE}" CDEPEND=" X? ( @@ -43,6 +43,7 @@ CDEPEND=" blas? ( virtual/blas ) cuda? ( >=dev-util/nvidia-cuda-toolkit-4.2.9-r1 ) fftw? ( sci-libs/fftw:3.0 ) + hwloc? ( sys-apps/hwloc ) lapack? ( virtual/lapack ) mkl? ( sci-libs/mkl ) mpi? ( virtual/mpi ) @@ -149,15 +150,13 @@ src_configure() { -DGMX_EXTERNAL_LAPACK=$(usex lapack) -DGMX_OPENMP=$(usex openmp) -DGMX_COOL_QUOTES=$(usex offensive) - -DGMX_EXTERNAL_BOOST=$(usex boost) -DGMX_USE_TNG=$(usex tng) -DGMX_BUILD_MANUAL=$(usex doc) + -DGMX_HWLOC=$(usex hwloc) -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 ${extra} @@ -179,7 +178,6 @@ src_configure() { -DGMX_MPI=OFF -DGMX_THREAD_MPI=$(usex threads) "${cuda[@]}" - -DGMX_OPENMM=OFF "$(use test && echo -DREGRESSIONTEST_PATH="${WORKDIR}/${P}_${x}/tests")" -DGMX_BINARY_SUFFIX="${suffix}" -DGMX_LIBS_SUFFIX="${suffix}" diff --git a/sci-chemistry/gromacs/metadata.xml b/sci-chemistry/gromacs/metadata.xml index 0c7b1076f..e98cd51fc 100644 --- a/sci-chemistry/gromacs/metadata.xml +++ b/sci-chemistry/gromacs/metadata.xml @@ -17,7 +17,8 @@ <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="boost">Enable external boost library</flag> + <flag name="hwloc">Enable HWLoc lib support</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 --> |