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 5586D138247 for ; Thu, 5 Dec 2013 03:41:27 +0000 (UTC) Received: from pigeon.gentoo.org (localhost [127.0.0.1]) by pigeon.gentoo.org (Postfix) with SMTP id E3ED0E0E42; Thu, 5 Dec 2013 03:41:26 +0000 (UTC) Received: from smtp.gentoo.org (smtp.gentoo.org [140.211.166.183]) (using TLSv1 with cipher AECDH-AES256-SHA (256/256 bits)) (No client certificate requested) by pigeon.gentoo.org (Postfix) with ESMTPS id 6D571E0E42 for ; Thu, 5 Dec 2013 03:41:26 +0000 (UTC) Received: from hornbill.gentoo.org (hornbill.gentoo.org [94.100.119.163]) (using TLSv1 with cipher AECDH-AES256-SHA (256/256 bits)) (No client certificate requested) by smtp.gentoo.org (Postfix) with ESMTPS id 48ED433F456 for ; Thu, 5 Dec 2013 03:41:25 +0000 (UTC) Received: from localhost.localdomain (localhost [127.0.0.1]) by hornbill.gentoo.org (Postfix) with ESMTP id CC54AE530A for ; Thu, 5 Dec 2013 03:41:23 +0000 (UTC) From: "Alexey Shvetsov" To: gentoo-commits@lists.gentoo.org Content-Transfer-Encoding: 8bit Content-type: text/plain; charset=UTF-8 Reply-To: gentoo-dev@lists.gentoo.org, "Alexey Shvetsov" Message-ID: <1386214867.3b3b3c81eb3f813d2d1de5ad5894121a04f04e6d.alexxy@gentoo> Subject: [gentoo-commits] proj/sci:master commit in: sci-chemistry/gromacs/ X-VCS-Repository: proj/sci X-VCS-Files: sci-chemistry/gromacs/ChangeLog sci-chemistry/gromacs/gromacs-4.5.9999.ebuild sci-chemistry/gromacs/metadata.xml X-VCS-Directories: sci-chemistry/gromacs/ X-VCS-Committer: alexxy X-VCS-Committer-Name: Alexey Shvetsov X-VCS-Revision: 3b3b3c81eb3f813d2d1de5ad5894121a04f04e6d X-VCS-Branch: master Date: Thu, 5 Dec 2013 03:41:23 +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: cb67e1cd-b28f-47f7-8fff-53328cd3b8fa X-Archives-Hash: 92cbfa0d60dc53f4a74ae777d237a550 commit: 3b3b3c81eb3f813d2d1de5ad5894121a04f04e6d Author: Alexey Shvetsov gentoo org> AuthorDate: Thu Dec 5 03:41:07 2013 +0000 Commit: Alexey Shvetsov gentoo org> CommitDate: Thu Dec 5 03:41:07 2013 +0000 URL: http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=3b3b3c81 Drop 4.5 Package-Manager: portage-2.2.7 --- sci-chemistry/gromacs/ChangeLog | 4 + sci-chemistry/gromacs/gromacs-4.5.9999.ebuild | 242 -------------------------- sci-chemistry/gromacs/metadata.xml | 1 - 3 files changed, 4 insertions(+), 243 deletions(-) diff --git a/sci-chemistry/gromacs/ChangeLog b/sci-chemistry/gromacs/ChangeLog index 732b917..996e1d9 100644 --- a/sci-chemistry/gromacs/ChangeLog +++ b/sci-chemistry/gromacs/ChangeLog @@ -2,6 +2,10 @@ # Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ + 05 Dec 2013; Alexey Shvetsov -Manifest, + -gromacs-4.5.9999.ebuild, metadata.xml: + Drop 4.5 + 05 Dec 2013; Alexey Shvetsov gromacs-9999.ebuild: Update live ebuild to current state diff --git a/sci-chemistry/gromacs/gromacs-4.5.9999.ebuild b/sci-chemistry/gromacs/gromacs-4.5.9999.ebuild deleted file mode 100644 index b5ed085..0000000 --- a/sci-chemistry/gromacs/gromacs-4.5.9999.ebuild +++ /dev/null @@ -1,242 +0,0 @@ -# Copyright 1999-2013 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 -# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/gromacs/gromacs-4.5.7.ebuild,v 1.2 2013/05/05 17:31:09 ottxor Exp $ - -EAPI="4" - -TEST_PV="4.0.4" -MANUAL_PV="4.5.6" - -FORTRAN_NEEDED=fkernels - -inherit bash-completion-r1 cmake-utils eutils fortran-2 multilib toolchain-funcs - -SRC_URI="test? ( ftp://ftp.gromacs.org/pub/tests/gmxtest-${TEST_PV}.tgz ) - doc? ( ftp://ftp.gromacs.org/pub/manual/manual-${MANUAL_PV}.pdf -> gromacs-manual-${MANUAL_PV}.pdf )" - -if [ "${PV%9999}" != "${PV}" ]; then - EGIT_REPO_URI="git://git.gromacs.org/gromacs http://repo.or.cz/r/gromacs.git" - EGIT_BRANCH="release-4-5-patches" - inherit git-2 -else - SRC_URI="${SRC_URI} ftp://ftp.gromacs.org/pub/${PN}/${P}.tar.gz - sse2? ( http://dev.gentoo.org/~alexxy/gromacs/0001-Make-stack-non-executable-for-GAS-assembly.patch.gz ) - sse2? ( http://dev.gentoo.org/~alexxy/gromacs/0002-Make-stack-non-executable-for-ATT-assembly.patch.gz )" -fi - -DESCRIPTION="The ultimate molecular dynamics simulation package" -HOMEPAGE="http://www.gromacs.org/" - -LICENSE="GPL-2" -SLOT="0" -KEYWORDS="~alpha ~amd64 ~ppc64 ~sparc ~x86 ~amd64-linux ~x86-linux ~x86-macos" -IUSE="X altivec blas doc -double-precision +fftw fkernels gsl lapack -mpi +single-precision sse2 test +threads xml zsh-completion" -REQUIRED_USE="fkernels? ( !threads )" - -CDEPEND=" - X? ( - x11-libs/libX11 - x11-libs/libSM - x11-libs/libICE - ) - blas? ( virtual/blas ) - fftw? ( sci-libs/fftw:3.0 ) - gsl? ( sci-libs/gsl ) - lapack? ( virtual/lapack ) - mpi? ( virtual/mpi ) - xml? ( dev-libs/libxml2:2 )" -DEPEND="${CDEPEND} - virtual/pkgconfig" -RDEPEND="${CDEPEND} - app-shells/tcsh" - -RESTRICT="test" - -src_prepare() { - #add user patches from /etc/portage/patches/sci-chemistry/gromacs - epatch_user - - if use mpi && use threads; then - elog "mdrun uses only threads OR mpi, and gromacs favours the" - elog "use of mpi over threads, so a mpi-version of mdrun will" - elog "be compiled. If you want to run mdrun on shared memory" - elog "machines only, you can safely disable mpi" - fi - - if [[ ${PV} != *9999 ]] && use sse2; then - # Add patches for non-exec stack - qa issue - epatch "${WORKDIR}/0001-Make-stack-non-executable-for-GAS-assembly.patch" - epatch "${WORKDIR}/0002-Make-stack-non-executable-for-ATT-assembly.patch" - #alexxy patches, renamve kernel from .s to .S - epatch "${FILESDIR}/${P}-cmake-cpp-asm.patch" - fi - - GMX_DIRS="" - use single-precision && GMX_DIRS+=" float" - use double-precision && GMX_DIRS+=" double" - #if neither single-precision nor double-precision is enabled - #build at least default (single) - [ -z "$GMX_DIRS" ] && GMX_DIRS+=" float" - - for x in ${GMX_DIRS}; do - mkdir -p "${WORKDIR}/${P}_${x}" || die - use test && cp -r "${WORKDIR}"/gmxtest "${WORKDIR}/${P}_${x}" - done -} - -src_configure() { - local mycmakeargs_pre=( ) - #from gromacs configure - if use fftw; then - mycmakeargs_pre+=("-DGMX_FFT_LIBRARY=fftw3") - else - mycmakeargs_pre+=("-DGMX_FFT_LIBRARY=fftpack") - ewarn "WARNING: The built-in FFTPACK routines are slow." - ewarn "Are you sure you don\'t want to use FFTW?" - ewarn "It is free and much faster..." - fi - - if [[ $(gcc-version) == "4.1" ]]; then - eerror "gcc 4.1 is not supported by gromacs" - eerror "please run test suite" - die - fi - - #note for gentoo-PREFIX on apple: use --enable-apple-64bit - - #note for gentoo-PREFIX on aix, fortran (xlf) is still much faster - if use fkernels; then - ewarn "Fortran kernels are usually not faster than C kernels and assembly" - ewarn "I hope, you know what are you doing..." - fi - - if use double-precision ; then - #from gromacs manual - elog - elog "For most simulations single precision is accurate enough. In some" - elog "cases double precision is required to get reasonable results:" - elog - elog "-normal mode analysis, for the conjugate gradient or l-bfgs minimization" - elog " and the calculation and diagonalization of the Hessian " - elog "-calculation of the constraint force between two large groups of atoms" - elog "-energy conservation: this can only be done without temperature coupling and" - elog " without cutoffs" - elog - fi - - if use mpi ; then - elog "You have enabled mpi, only mdrun will make use of mpi, that is why" - elog "we configure/compile gromacs twice (with and without mpi) and only" - elog "install mdrun with mpi support. In addtion you will get libgmx and" - elog "libmd with and without mpi support." - fi - - #go from slowest to fasterest acceleration - local acce="none" - use fkernels && acce="fortran" - use altivec && acce="altivec" - use ia64 && acce="ia64" - use sse2 && acce="sse" - - mycmakeargs_pre+=( - $(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 threads GMX_THREADS) - $(cmake-utils_use xml GMX_XML) - -DGMX_DEFAULT_SUFFIX=off - -DGMX_ACCELERATION="$acce" - -DGMXLIB="$(get_libdir)" - ) - - 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" - mycmakeargs=( ${mycmakeargs_pre[@]} ${p} -DGMX_MPI=OFF - -DGMX_BINARY_SUFFIX="${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[@]} ${p} -DGMX_MPI=ON - -DGMX_BINARY_SUFFIX="_mpi${suffix}" -DGMX_LIBS_SUFFIX="_mpi${suffix}" ) - BUILD_DIR="${WORKDIR}/${P}_${x}_mpi" 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 - use mpi || continue - einfo "Compiling for ${x} precision with mpi" - BUILD_DIR="${WORKDIR}/${P}_${x}_mpi"\ - cmake-utils_src_compile mdrun - done -} - -src_test() { - for x in ${GMX_DIRS}; do - local oldpath="${PATH}" - export PATH="${WORKDIR}/${P}_${x}/src/kernel:${S}-{x}/src/tools:${PATH}" - cd "${WORKDIR}/${P}_${x}" - emake -j1 tests || die "${x} Precision test failed" - export PATH="${oldpath}" - done -} - -src_install() { - for x in ${GMX_DIRS}; do - BUILD_DIR="${WORKDIR}/${P}_${x}" \ - cmake-utils_src_install - use mpi || continue - #cmake-utils_src_install does not support args - #using cmake-utils_src_compile instead - BUILD_DIR="${WORKDIR}/${P}_${x}_mpi" \ - cmake-utils_src_make install-mdrun DESTDIR="${D}" - done - - sed -n -e '/^GMXBIN/,/^GMXDATA/p' "${ED}"/usr/bin/GMXRC.bash > "${T}/80gromacs" - echo "VMD_PLUGIN_PATH=${EPREFIX}/usr/$(get_libdir)/vmd/plugins/*/molfile/" >> "${T}/80gromacs" - - doenvd "${T}/80gromacs" - rm -f "${ED}"/usr/bin/GMXRC* - - newbashcomp "${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.* - - # Fix typos in a couple of files. - sed -e "s:+0f:-f:" -i "${ED}"usr/share/gromacs/tutor/gmxdemo/demo \ - || die "Failed to fixup demo script." - - cd "${S}" - dodoc AUTHORS INSTALL* README* - if use doc; then - newdoc "${DISTDIR}/gromacs-manual-${MANUAL_PV}.pdf" "manual-${MANUAL_PV}.pdf" - dohtml -r "${ED}usr/share/gromacs/html/" - fi - rm -rf "${ED}usr/share/gromacs/html/" -} - -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 - einfo $(g_luck) - einfo "For more Gromacs cool quotes (gcq) add g_luck to your .bashrc" - einfo - elog "Gromacs can use sci-chemistry/vmd to read additional file formats" -} diff --git a/sci-chemistry/gromacs/metadata.xml b/sci-chemistry/gromacs/metadata.xml index 8a88d53..880233e 100644 --- a/sci-chemistry/gromacs/metadata.xml +++ b/sci-chemistry/gromacs/metadata.xml @@ -11,7 +11,6 @@ More precise calculations at the expense of speed Single precision version of gromacs (default) - Enable building of Fortran Kernels for platforms that dont have assembly loops Enable sse4.1 acceleration Enable 128bit avx with fma (e.g. AMD BullDozer) Enable 256bit avx (e.g. Intel Sandy Bridge)