From mboxrd@z Thu Jan 1 00:00:00 1970 Return-Path: Received: from lists.gentoo.org (pigeon.gentoo.org [208.92.234.80]) by finch.gentoo.org (Postfix) with ESMTP id 8F7651392EF for ; Mon, 30 Jun 2014 03:24:09 +0000 (UTC) Received: from pigeon.gentoo.org (localhost [127.0.0.1]) by pigeon.gentoo.org (Postfix) with SMTP id 2A33CE0983; Mon, 30 Jun 2014 03:24:08 +0000 (UTC) Received: from smtp.gentoo.org (smtp.gentoo.org [140.211.166.183]) (using TLSv1.2 with cipher AECDH-AES256-SHA (256/256 bits)) (No client certificate requested) by pigeon.gentoo.org (Postfix) with ESMTPS id 5ADC6E0983 for ; Mon, 30 Jun 2014 03:24:07 +0000 (UTC) Received: from flycatcher.gentoo.org (flycatcher.gentoo.org [81.93.255.6]) (using TLSv1.2 with cipher AECDH-AES256-SHA (256/256 bits)) (No client certificate requested) by smtp.gentoo.org (Postfix) with ESMTPS id 603993402E5 for ; Mon, 30 Jun 2014 03:24:06 +0000 (UTC) Received: by flycatcher.gentoo.org (Postfix, from userid 2234) id 2C71720036; Mon, 30 Jun 2014 03:24:05 +0000 (UTC) From: "Alexey Shvetsov (alexxy)" To: gentoo-commits@lists.gentoo.org Reply-To: gentoo-dev@lists.gentoo.org, alexxy@gentoo.org Subject: [gentoo-commits] gentoo-x86 commit in sci-chemistry/gromacs: metadata.xml gromacs-5.0.ebuild ChangeLog X-VCS-Repository: gentoo-x86 X-VCS-Files: metadata.xml gromacs-5.0.ebuild ChangeLog X-VCS-Directories: sci-chemistry/gromacs X-VCS-Committer: alexxy X-VCS-Committer-Name: Alexey Shvetsov Content-Type: text/plain; charset=utf8 Content-Transfer-Encoding: 8bit Message-Id: <20140630032405.2C71720036@flycatcher.gentoo.org> Date: Mon, 30 Jun 2014 03:24:05 +0000 (UTC) Precedence: bulk List-Post: List-Help: List-Unsubscribe: List-Subscribe: List-Id: Gentoo Linux mail X-BeenThere: gentoo-commits@lists.gentoo.org X-Archives-Salt: a861e22e-0c6f-42d4-9997-0f98e82f5fc8 X-Archives-Hash: e4f586fad61362ea20f21a7ccb89772c alexxy 14/06/30 03:24:05 Modified: metadata.xml ChangeLog Added: gromacs-5.0.ebuild Log: [sci-chemistry/gromacs] GROMACS 5.0 finaly relesed (Portage version: 2.2.10/cvs/Linux x86_64, signed Manifest commit with key F82F92E6) Revision Changes Path 1.20 sci-chemistry/gromacs/metadata.xml file : http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-chemistry/gromacs/metadata.xml?rev=1.20&view=markup plain: http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-chemistry/gromacs/metadata.xml?rev=1.20&content-type=text/plain diff : http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-chemistry/gromacs/metadata.xml?r1=1.19&r2=1.20 Index: metadata.xml =================================================================== RCS file: /var/cvsroot/gentoo-x86/sci-chemistry/gromacs/metadata.xml,v retrieving revision 1.19 retrieving revision 1.20 diff -u -r1.19 -r1.20 --- metadata.xml 31 Dec 2013 23:35:05 -0000 1.19 +++ metadata.xml 30 Jun 2014 03:24:04 -0000 1.20 @@ -1,21 +1,27 @@ - sci-chemistry - - ottxor@gentoo.org - Christoph Junghans - - - Enable cuda non-bonded kernels - More precise calculations at the expense of speed - Single precision version of gromacs (default) - - Enable sse4.1 acceleration - Enable 128bit avx with fma (e.g. AMD BullDozer) - Enable 256bit avx (e.g. Intel Sandy Bridge) - Enable gromacs partly offensive quotes - Add acceleration through sci-libs/openmm - Use sci-libs/mkl for fft, blas, lapack routines - + sci-chemistry + + ottxor@gentoo.org + Christoph Junghans + + + Enable cuda non-bonded kernels + More precise calculations at the expense of speed + Single precision version of gromacs (default) + Enable external boost library + Enable new trajectory format - tng + Create symbolic links for pre-5.0 binary names + + Enable sse4.1 acceleration + Enable 128bit avx with fma (e.g. AMD BullDozer) + Enable 128bit avx with fma (e.g. AMD BullDozer) + Enable 256bit avx (e.g. Intel Sandy Bridge) + Enable 256bit avx (e.g. Intel Sandy Bridge) + Enable 256bit avx2 (e.g. Intel Haswell) + Enable gromacs partly offensive quotes + Add acceleration through sci-libs/openmm + Use sci-libs/mkl for fft, blas, lapack routines + 1.140 sci-chemistry/gromacs/ChangeLog file : http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-chemistry/gromacs/ChangeLog?rev=1.140&view=markup plain: http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-chemistry/gromacs/ChangeLog?rev=1.140&content-type=text/plain diff : http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-chemistry/gromacs/ChangeLog?r1=1.139&r2=1.140 Index: ChangeLog =================================================================== RCS file: /var/cvsroot/gentoo-x86/sci-chemistry/gromacs/ChangeLog,v retrieving revision 1.139 retrieving revision 1.140 diff -u -r1.139 -r1.140 --- ChangeLog 26 Mar 2014 21:42:49 -0000 1.139 +++ ChangeLog 30 Jun 2014 03:24:04 -0000 1.140 @@ -1,6 +1,12 @@ # 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 1.139 2014/03/26 21:42:49 maekke Exp $ +# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/gromacs/ChangeLog,v 1.140 2014/06/30 03:24:04 alexxy Exp $ + +*gromacs-5.0 (30 Jun 2014) + + 30 Jun 2014; Alexey Shvetsov +gromacs-5.0.ebuild, + metadata.xml: + [sci-chemistry/gromacs] GROMACS 5.0 finaly relesed 26 Mar 2014; Markus Meier gromacs-4.6.5.ebuild: arm stable, bug #496632 1.1 sci-chemistry/gromacs/gromacs-5.0.ebuild file : http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-chemistry/gromacs/gromacs-5.0.ebuild?rev=1.1&view=markup plain: http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-chemistry/gromacs/gromacs-5.0.ebuild?rev=1.1&content-type=text/plain Index: gromacs-5.0.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.ebuild,v 1.1 2014/06/30 03:24:04 alexxy Exp $ EAPI=5 TEST_PV="5.0" CMAKE_MAKEFILE_GENERATOR="ninja" inherit bash-completion-r1 cmake-utils cuda eutils multilib readme.gentoo toolchain-funcs if [[ $PV = *9999* ]]; then EGIT_REPO_URI="git://git.gromacs.org/gromacs.git https://gerrit.gromacs.org/gromacs.git git://github.com/gromacs/gromacs.git http://repo.or.cz/r/gromacs.git" EGIT_BRANCH="release-5-0" inherit git-r3 else SRC_URI="ftp://ftp.gromacs.org/pub/${PN}/${PN}-${PV/_/-}.tar.gz test? ( http://gerrit.gromacs.org/download/regressiontests-${TEST_PV}.tar.gz )" fi ACCE_IUSE="sse2 sse4_1 avx_128_fma avx_256 avx2_256" DESCRIPTION="The ultimate molecular dynamics simulation package" HOMEPAGE="http://www.gromacs.org/" # see COPYING for details # http://repo.or.cz/w/gromacs.git/blob/HEAD:/COPYING # base, vmd plugins, fftpack from numpy, blas/lapck from netlib, memtestG80 library, mpi_thread lib LICENSE="LGPL-2.1 UoI-NCSA !mkl? ( !fftw? ( BSD ) !blas? ( BSD ) !lapack? ( BSD ) ) cuda? ( LGPL-3 ) threads? ( BSD )" SLOT="0/${PV}" KEYWORDS="~alpha ~amd64 ~arm ~ppc64 ~sparc ~x86 ~amd64-linux ~x86-linux ~x86-macos" 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 [[ ${PV} != *9999 ]]; then default else git-r3_src_unpack if use test; then EGIT_REPO_URI="git://git.gromacs.org/regressiontests.git" \ EGIT_BRANCH="master" EGIT_NOUNPACK="yes" EGIT_COMMIT="master" \ EGIT_SOURCEDIR="${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 && acee="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 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 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 BUILD_DIR="${WORKDIR}/${P}_${x}"\ cmake-utils_src_compile completion if use doc; then BUILD_DIR="${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-${PV}.pdf" fi newbashcomp "${WORKDIR}/${P}_${x}"/src/programs/completion/gmx-completion.bash gromacs use mpi || continue BUILD_DIR="${WORKDIR}/${P}_${x}_mpi" \ cmake-utils_src_install done # drop unneeded stuff rm -f "${ED}"usr/bin/gmx-completion* rm -f "${ED}"usr/bin/g_options* rm -f "${ED}"usr/bin/GMXRC* rm -f "${ED}"usr/$(get_libdir)/libtng*.a 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 }