From: Christoph Junghans Date: Fri, 6 Jan 2012 02:21:02 +0000 (+0000) Subject: remove obsolete X-Git-Url: http://git.tremily.us/?a=commitdiff_plain;h=cad8e8488ccc9582b3b4259385026a733782c07e;p=gentoo.git remove obsolete Package-Manager: portage-2.2.0_alpha84/cvs/Linux i686 --- diff --git a/sci-chemistry/gromacs/ChangeLog b/sci-chemistry/gromacs/ChangeLog index 0a50f170f547..a0716e8c8d63 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 1.102 2012/01/06 02:16:45 ottxor Exp $ +# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/gromacs/ChangeLog,v 1.103 2012/01/06 02:21:02 ottxor Exp $ + + 06 Jan 2012; Christoph Junghans -gromacs-4.5.4-r2.ebuild, + -gromacs-4.5.5.ebuild: + remove obsolete 06 Jan 2012; Christoph Junghans gromacs-4.5.5-r1.ebuild: keyword ~x86-macos diff --git a/sci-chemistry/gromacs/Manifest b/sci-chemistry/gromacs/Manifest index d9ba9b50827d..3c594c32a881 100644 --- a/sci-chemistry/gromacs/Manifest +++ b/sci-chemistry/gromacs/Manifest @@ -10,19 +10,17 @@ DIST gromacs-4.5.4.tar.gz 10353984 RMD160 96065d1a173231f75869764a08eb4feccc1ec5 DIST gromacs-4.5.5.tar.gz 10398178 RMD160 a3d40c3ac6ec9ee3e4607bd35afca1dd4715154e SHA1 ce4b4f9a0453dd2ffea72f28ea0bc7bb7a72f479 SHA256 e0605e4810b0d552a8761fef5540c545beeaf85893f4a6e21df9905a33f871ba DIST gromacs-manual-4.5.4.pdf 2463242 RMD160 309a1d9bc5f4821076d53f668c36f1c6bfc1714f SHA1 58c0261308212af29fa0c4f4a6d1b81da6d84766 SHA256 dc14504a7072b61e7aa576c48f04df03356824f3a9d9e744dfaf51529ab46252 EBUILD gromacs-4.5.4-r1.ebuild 8120 RMD160 111791f7aff880a5622e622e41cd7a10efeb3a89 SHA1 84e6a5e0a57a8eabace6a35b7ce271f355721d37 SHA256 a26cacd6a0b51ea14ddfe10758afda7719f194c5562b05fa0f4ca18a445277c6 -EBUILD gromacs-4.5.4-r2.ebuild 7743 RMD160 611705b9c01b331991d60736cd8d53592bc94024 SHA1 f3f2d63cfe0178d2aee329429e65dcfa7c1c8683 SHA256 cd77028e836682a9f01319db5d4a57fc3b167295b1f45b4ce29f8f9355f403c8 EBUILD gromacs-4.5.5-r1.ebuild 7954 RMD160 ca8938eeccd189ab2f6798e1b1bb95ceac7bb515 SHA1 ff668e45c0746176f079469268092effb83175bb SHA256 fba66413e86c91008f8b1fe0ed67414d7423958833144970a86514eaa56a7ae2 -EBUILD gromacs-4.5.5.ebuild 7738 RMD160 69ff972202f5e921bdaa02375592f3ade9854d57 SHA1 be04c2efb384893a08c17bcd93ca19d489c1572a SHA256 c25c49db5d22cbb6be6a2719e71f4714b93318b17a1c150986cd39e2ebe46a25 -MISC ChangeLog 17538 RMD160 1af495f42690219b69b6f88b4ef0f2944541a8f5 SHA1 a0d2197621ae00941e2217a5368ed8edc5f78714 SHA256 0ff1ab5e4d615168611adb3d315301ddfa3edd7c50d5f2b70bed5ae47778b018 +MISC ChangeLog 17662 RMD160 2cabf90404e0ce7e6bfea003af64b9cbeb41f73e SHA1 e9218812d7afc0105eafed9de1274a31e5bffa68 SHA256 e23ef5e6d3a82f1d41ebcc190ee0e4fa40f14d29ea4a1bbe945e167265889ffa MISC metadata.xml 516 RMD160 64f12e7dea05c39ad349ad44408cdaa787e9129f SHA1 9eeff9fd2cdc813796f2b5f605fd3ed9e559e3a6 SHA256 25d77da0c4b789ade2778652a4fbea6aff17ce177664ce1750684b636eebbc61 -----BEGIN PGP SIGNATURE----- Version: GnuPG v2.0.17 (GNU/Linux) -iQEcBAEBAgAGBQJPBlmUAAoJEOeBhlrCAAWGYHcIAID5r7ma99MC237yR1tQnz6h -wFjGRNv3pVuBZyCQoxAC/ZaSAzohgebPNtR3aUb6tAJ1/8ikfbF4t1kY379VH14z -W0XE+brTBZUPTmvgDkMXalUaxbh8pxH4xfwujVx6VUfNTSnpvDqeLnd8XT8gEQQH -Vwo+7Xn6NL3Q/CWUTcupHagh7DAYmH0w3C3GoeKSJ1LzibknoL3JF5pNIaT6zhoj -UnejIfn+n6TLTzeiV7s4yzigrAT5k5hzOIFszdh/MyjqsfMeyIlLGh3MmL2/RbuZ -8C9mWa6Chpe7s8azsYCmFs8Wgwacz56RHsIeXomo22mc0Ded1B70U8Ff70/h/jw= -=dOXI +iQEcBAEBAgAGBQJPBlqVAAoJEOeBhlrCAAWGO9gIALCJ1Ietfnzbuc3pGvIEF7wP +4fm7PP4WaDsdC1XT7FzC4/IN2zmrzpOStkTW1SqEFTkPoM5kcEDBx8P3NDzM0kO4 +4X3URt/QLP++bxKg7RCU5XfF2jUY7TATkWRhjyviHMvI/kVtFJvTBwaOue7N6OgZ +I7TZTH48uMyW4eA1LW9HyQOYpJL4QQVWCXjHm0jQnJQ16IpO6ZavICGingsPanvZ +fjQL845dySjLS2yTsISUXEidVxyMT98jizzQIgOPK7hPz/Cjla0E5YwFrjYU6PEv +2AV+fH8TSwnHAvQcsqtROtgfSxbVY/r3/nzurm2tvUPYIUQFQWcAfXpLBzOkRXI= +=kTc0 -----END PGP SIGNATURE----- diff --git a/sci-chemistry/gromacs/gromacs-4.5.4-r2.ebuild b/sci-chemistry/gromacs/gromacs-4.5.4-r2.ebuild deleted file mode 100644 index bbcf8ae6fd31..000000000000 --- a/sci-chemistry/gromacs/gromacs-4.5.4-r2.ebuild +++ /dev/null @@ -1,245 +0,0 @@ -# Copyright 1999-2011 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-r2.ebuild,v 1.8 2011/09/10 14:47:53 ottxor Exp $ - -EAPI="4" - -TEST_PV="4.0.4" -MANUAL_PV="4.5.4" - -#to find external blas/lapack -CMAKE_MIN_VERSION="2.8.5-r2" - -inherit bash-completion-r1 cmake-utils eutils 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-${TEST_PV}.tgz )" - -LICENSE="GPL-2" -SLOT="0" -KEYWORDS="~alpha ~amd64 ~ppc64 ~sparc ~x86 ~amd64-linux ~x86-linux" -IUSE="X altivec blas doc -double-precision +fftw fkernels gsl lapack -mpi +single-precision sse2 test +threads xml zsh-completion" -REQUIRED_USE="fkernels? ( !threads )" - -CDEPEND=" - X? ( - x11-libs/libX11 - x11-libs/libSM - x11-libs/libICE - ) - blas? ( virtual/blas ) - fftw? ( sci-libs/fftw:3.0 ) - fkernels? ( virtual/fortran ) - gsl? ( sci-libs/gsl ) - lapack? ( virtual/lapack ) - mpi? ( virtual/mpi ) - xml? ( dev-libs/libxml2:2 )" -DEPEND="${CDEPEND} - dev-util/pkgconfig" -RDEPEND="${CDEPEND} - app-shells/tcsh" - -RESTRICT="test" - -pkg_setup() { - use fkernels && fortran-2_pkg_setup -} - -src_prepare() { - #add user patches from /etc/portage/patches/sci-chemistry/gromacs - epatch_user - - if use mpi && use threads; then - elog "mdrun uses only threads OR mpi, and gromacs favours the" - elog "use of mpi over threads, so a mpi-version of mdrun will" - elog "be compiled. If you want to run mdrun on shared memory" - elog "machines only, you can safely disable mpi" - fi - - # Add patches for non-exec stack - epatch "${WORKDIR}/0001-Make-stack-non-executable-for-GAS-assembly.patch" - epatch "${WORKDIR}/0002-Make-stack-non-executable-for-ATT-assembly.patch" - - GMX_DIRS="" - use single-precision && GMX_DIRS+=" float" - use double-precision && GMX_DIRS+=" double" - #if neither single-precision nor double-precision is enabled - #build at least default (single) - [ -z "$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" - -DLIB="$(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="${suffix}" ) - CMAKE_BUILD_DIR="${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${suffix}" ) - CMAKE_BUILD_DIR="${WORKDIR}/${P}_${x}_mpi" cmake-utils_src_configure - done -} - -src_compile() { - for x in ${GMX_DIRS}; do - einfo "Compiling for ${x} precision" - CMAKE_BUILD_DIR="${WORKDIR}/${P}_${x}"\ - cmake-utils_src_compile - use mpi || continue - einfo "Compiling for ${x} precision with mpi" - CMAKE_BUILD_DIR="${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 ${GMX_DIRS}; do - CMAKE_BUILD_DIR="${WORKDIR}/${P}_${x}" \ - cmake-utils_src_install - use mpi || continue - #cmake-utils_src_install does not support args - #using cmake-utils_src_compile instead - CMAKE_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() { - env-update && source /etc/profile - 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/gromacs-4.5.5.ebuild b/sci-chemistry/gromacs/gromacs-4.5.5.ebuild deleted file mode 100644 index 4a70357d3bb8..000000000000 --- a/sci-chemistry/gromacs/gromacs-4.5.5.ebuild +++ /dev/null @@ -1,245 +0,0 @@ -# Copyright 1999-2011 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 -# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/gromacs/gromacs-4.5.5.ebuild,v 1.4 2011/12/14 16:45:32 ago Exp $ - -EAPI="4" - -TEST_PV="4.0.4" -MANUAL_PV="4.5.4" - -#to find external blas/lapack -CMAKE_MIN_VERSION="2.8.5-r2" - -inherit bash-completion-r1 cmake-utils eutils 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-${TEST_PV}.tgz )" - -LICENSE="GPL-2" -SLOT="0" -KEYWORDS="~alpha amd64 ~ppc64 ~sparc x86 ~amd64-linux ~x86-linux" -IUSE="X altivec blas doc -double-precision +fftw fkernels gsl lapack -mpi +single-precision sse2 test +threads xml zsh-completion" -REQUIRED_USE="fkernels? ( !threads )" - -CDEPEND=" - X? ( - x11-libs/libX11 - x11-libs/libSM - x11-libs/libICE - ) - blas? ( virtual/blas ) - fftw? ( sci-libs/fftw:3.0 ) - fkernels? ( virtual/fortran ) - gsl? ( sci-libs/gsl ) - lapack? ( virtual/lapack ) - mpi? ( virtual/mpi ) - xml? ( dev-libs/libxml2:2 )" -DEPEND="${CDEPEND} - dev-util/pkgconfig" -RDEPEND="${CDEPEND} - app-shells/tcsh" - -RESTRICT="test" - -pkg_setup() { - use fkernels && fortran-2_pkg_setup -} - -src_prepare() { - #add user patches from /etc/portage/patches/sci-chemistry/gromacs - epatch_user - - if use mpi && use threads; then - elog "mdrun uses only threads OR mpi, and gromacs favours the" - elog "use of mpi over threads, so a mpi-version of mdrun will" - elog "be compiled. If you want to run mdrun on shared memory" - elog "machines only, you can safely disable mpi" - fi - - # Add patches for non-exec stack - epatch "${WORKDIR}/0001-Make-stack-non-executable-for-GAS-assembly.patch" - epatch "${WORKDIR}/0002-Make-stack-non-executable-for-ATT-assembly.patch" - - GMX_DIRS="" - use single-precision && GMX_DIRS+=" float" - use double-precision && GMX_DIRS+=" double" - #if neither single-precision nor double-precision is enabled - #build at least default (single) - [ -z "$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="${suffix}" ) - CMAKE_BUILD_DIR="${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${suffix}" ) - CMAKE_BUILD_DIR="${WORKDIR}/${P}_${x}_mpi" cmake-utils_src_configure - done -} - -src_compile() { - for x in ${GMX_DIRS}; do - einfo "Compiling for ${x} precision" - CMAKE_BUILD_DIR="${WORKDIR}/${P}_${x}"\ - cmake-utils_src_compile - use mpi || continue - einfo "Compiling for ${x} precision with mpi" - CMAKE_BUILD_DIR="${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 ${GMX_DIRS}; do - CMAKE_BUILD_DIR="${WORKDIR}/${P}_${x}" \ - cmake-utils_src_install - use mpi || continue - #cmake-utils_src_install does not support args - #using cmake-utils_src_compile instead - CMAKE_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() { - env-update && source /etc/profile - 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" -}