diff options
author | Christoph Junghans <ottxor@gentoo.org> | 2012-03-09 00:59:12 +0000 |
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committer | Christoph Junghans <ottxor@gentoo.org> | 2012-03-09 00:59:12 +0000 |
commit | ed73cf8d04bebe50bd62380f9dcf3db8b7cbbcdd (patch) | |
tree | 1935af753b5a5e44e2a0c6084e02d6f51d0a7bb4 /sci-chemistry | |
parent | new snapshot, cleanup (diff) | |
download | gentoo-2-ed73cf8d04bebe50bd62380f9dcf3db8b7cbbcdd.tar.gz gentoo-2-ed73cf8d04bebe50bd62380f9dcf3db8b7cbbcdd.tar.bz2 gentoo-2-ed73cf8d04bebe50bd62380f9dcf3db8b7cbbcdd.zip |
remove old (fixes bug #392121)
(Portage version: 2.2.0_alpha90/cvs/Linux i686)
Diffstat (limited to 'sci-chemistry')
-rw-r--r-- | sci-chemistry/gromacs/ChangeLog | 6 | ||||
-rw-r--r-- | sci-chemistry/gromacs/gromacs-4.5.4-r1.ebuild | 257 | ||||
-rw-r--r-- | sci-chemistry/gromacs/metadata.xml | 1 |
3 files changed, 5 insertions, 259 deletions
diff --git a/sci-chemistry/gromacs/ChangeLog b/sci-chemistry/gromacs/ChangeLog index c4295e44c6ed..c3b053776947 100644 --- a/sci-chemistry/gromacs/ChangeLog +++ b/sci-chemistry/gromacs/ChangeLog @@ -1,6 +1,10 @@ # ChangeLog for sci-chemistry/gromacs # Copyright 1999-2012 Gentoo Foundation; Distributed under the GPL v2 -# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/gromacs/ChangeLog,v 1.106 2012/03/08 23:04:42 ranger Exp $ +# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/gromacs/ChangeLog,v 1.107 2012/03/09 00:59:11 ottxor Exp $ + + 09 Mar 2012; Christoph Junghans <ottxor@gentoo.org> -gromacs-4.5.4-r1.ebuild, + metadata.xml: + remove old (fixes bug #392121) 08 Mar 2012; Brent Baude <ranger@gentoo.org> gromacs-4.5.5-r1.ebuild: Marking gromacs-4.5.5-r1 ppc64 for bug 391147 diff --git a/sci-chemistry/gromacs/gromacs-4.5.4-r1.ebuild b/sci-chemistry/gromacs/gromacs-4.5.4-r1.ebuild deleted file mode 100644 index d68fbf406be2..000000000000 --- a/sci-chemistry/gromacs/gromacs-4.5.4-r1.ebuild +++ /dev/null @@ -1,257 +0,0 @@ -# Copyright 1999-2012 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 -# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/gromacs/gromacs-4.5.4-r1.ebuild,v 1.13 2012/02/06 03:43:24 ottxor Exp $ - -EAPI="4" - -LIBTOOLIZE="true" -TEST_PV="4.0.4" -MANUAL_PV="4.5.4" - -inherit autotools-utils bash-completion-r1 flag-o-matic fortran-2 multilib toolchain-funcs - -if [ "${PV%9999}" != "${PV}" ]; then - EGIT_REPO_URI="git://git.gromacs.org/gromacs" - EGIT_BRANCH="release-4-5-patches" - inherit git-2 -else - SRC_URI="${SRC_URI} ftp://ftp.gromacs.org/pub/${PN}/${P}.tar.gz" -fi - -DESCRIPTION="The ultimate molecular dynamics simulation package" -HOMEPAGE="http://www.gromacs.org/" -SRC_URI="${SRC_URI} - http://dev.gentoo.org/~alexxy/gromacs/0001-Make-stack-non-executable-for-GAS-assembly.patch.gz - http://dev.gentoo.org/~alexxy/gromacs/0002-Make-stack-non-executable-for-ATT-assembly.patch.gz - doc? ( ftp://ftp.gromacs.org/pub/manual/manual-${MANUAL_PV}.pdf -> gromacs-manual-${MANUAL_PV}.pdf ) - test? ( ftp://ftp.gromacs.org/pub/tests/gmxtest-${TEST_PV}.tgz )" - -LICENSE="GPL-2" -SLOT="0" -KEYWORDS="amd64 ppc64 x86 ~amd64-linux ~x86-linux" -IUSE="X altivec blas dmalloc doc -double-precision +fftw fkernels +gsl lapack -mpi +single-precision sse2 static-libs test +threads +xml zsh-completion" -REQUIRED_USE="fkernels? ( !threads )" - -CDEPEND=" - X? ( - x11-libs/libX11 - x11-libs/libSM - x11-libs/libICE - ) - dmalloc? ( dev-libs/dmalloc ) - blas? ( virtual/blas ) - fftw? ( sci-libs/fftw:3.0 ) - fkernels? ( virtual/fortran ) - gsl? ( sci-libs/gsl ) - lapack? ( virtual/lapack ) - mpi? ( virtual/mpi ) - xml? ( dev-libs/libxml2:2 )" -DEPEND="${CDEPEND} - dev-util/pkgconfig" -RDEPEND="${CDEPEND} - app-shells/tcsh" - -RESTRICT="test" - -pkg_setup() { - use fkernels && fortran-2_pkg_setup -} - -src_prepare() { - if use mpi && use threads; then - elog "mdrun uses only threads OR mpi, and gromacs favours the" - elog "use of mpi over threads, so a mpi-version of mdrun will" - elog "be compiled. If you want to run mdrun on shared memory" - elog "machines only, you can safely disable mpi" - fi - - # Add patches for non-exec stack - epatch "${WORKDIR}/0001-Make-stack-non-executable-for-GAS-assembly.patch" - epatch "${WORKDIR}/0002-Make-stack-non-executable-for-ATT-assembly.patch" - - autotools-utils_src_prepare || die - - eautoreconf || die - - GMX_DIRS="" - use single-precision && GMX_DIRS+=" float" - use double-precision && GMX_DIRS+=" double" - #if neither single-precision nor double-precision is enabled - #build at least default (single) - [ -z "$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() { - #from gromacs configure - if ! use fftw; then - 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 - - #fortran will gone in gromacs 5.0 anyway - #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 - - # if we need external blas or lapack - use blas && append-libs $(pkg-config blas --libs) - use lapack && append-libs $(pkg-config lapack --libs) - local sseflag="x86-64-sse" - use x86 && sseflag="ia32-sse" - - #missing flag in autotools (bug #339837) - use sse2 && append-flags -msse2 - - for x in ${GMX_DIRS}; do - #if we build single and double - double is suffixed - use double-precision && use single-precision && \ - [ "${x}" = "double" ] && suffix="_d" - myeconfargs=( - --bindir="${EPREFIX}"/usr/bin - --docdir="${EPREFIX}"/usr/share/doc/"${PF}" - --enable-"${x}" - $(use_with dmalloc) - $(use_with fftw fft fftw3) - $(use_with gsl) - $(use_with X x) - $(use_with xml) - $(use_enable threads) - $(use_enable altivec ppc-altivec) - $(use_enable ia64 ia64-asm) - $(use_with lapack external-lapack) - $(use_with blas external-blas) - $(use_enable fkernels fortran) - --disable-bluegene - --disable-la-files - --disable-power6 - --disable-ia32-sse - --disable-x86-64-sse - $(use_enable sse2 $sseflag) - ) - #disable ia32-sse and x86-64-sse and enable what we really need in last line - - einfo "Configuring for ${x} precision" - AUTOTOOLS_BUILD_DIR="${WORKDIR}/${P}_${x}"\ - autotools-utils_src_configure --disable-mpi --program-suffix="${suffix}" \ - CC="$(tc-getCC)" F77="$(tc-getFC)" - use mpi || continue - einfo "Configuring for ${x} precision with mpi" - AUTOTOOLS_BUILD_DIR="${WORKDIR}/${P}_${x}_mpi"\ - autotools-utils_src_configure --enable-mpi --program-suffix="_mpi${suffix}" \ - CC="$(tc-getCC)" F77="$(tc-getFC)" - done -} - -src_compile() { - for x in ${GMX_DIRS}; do - einfo "Compiling for ${x} precision" - AUTOTOOLS_BUILD_DIR="${WORKDIR}/${P}_${x}"\ - autotools-utils_src_compile - use mpi || continue - einfo "Compiling for ${x} precision with mpi" - AUTOTOOLS_BUILD_DIR="${WORKDIR}/${P}_${x}_mpi"\ - autotools-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 ${GMX_DIRS}; do - AUTOTOOLS_BUILD_DIR="${WORKDIR}/${P}_${x}" \ - autotools-utils_src_install - use mpi || continue - #autotools-utils_src_install does not support args - #using autotools-utils_src_compile instead - AUTOTOOLS_BUILD_DIR="${WORKDIR}/${P}_${x}_mpi" \ - autotools-utils_src_compile install-mdrun DESTDIR="${D}" - - #stolen from autotools-utils_src_install see comment above - local args - has static-libs ${IUSE//+} && ! use static-libs || args='none' - remove_libtool_files ${args} - done - - sed -n -e '/^GMXBIN/,/^GMXDATA/p' "${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 ac6daa0746fa..44b30a77c485 100644 --- a/sci-chemistry/gromacs/metadata.xml +++ b/sci-chemistry/gromacs/metadata.xml @@ -3,7 +3,6 @@ <pkgmetadata> <herd>sci-chemistry</herd> <use> - <flag name="dmalloc">Enable use of Debug Malloc</flag> <flag name="double-precision">More precise calculations at the expense of speed</flag> <flag name="fkernels">Enable building of Fortran Kernels for platforms that dont have assembly loops</flag> |