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Diffstat (limited to 'sci-chemistry/gromacs/gromacs-4.5.5-r1.ebuild')
| -rw-r--r-- | sci-chemistry/gromacs/gromacs-4.5.5-r1.ebuild | 247 |
1 files changed, 0 insertions, 247 deletions
diff --git a/sci-chemistry/gromacs/gromacs-4.5.5-r1.ebuild b/sci-chemistry/gromacs/gromacs-4.5.5-r1.ebuild deleted file mode 100644 index 96690e3f1925..000000000000 --- a/sci-chemistry/gromacs/gromacs-4.5.5-r1.ebuild +++ /dev/null @@ -1,247 +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-4.5.5-r1.ebuild,v 1.11 2012/12/08 22:15:02 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" - -FORTRAN_NEEDED=fkernels - -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} - 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 ) - doc? ( ftp://ftp.gromacs.org/pub/manual/manual-${MANUAL_PV}.pdf -> gromacs-manual-${MANUAL_PV}.pdf ) - test? ( ftp://ftp.gromacs.org/pub/tests/gmxtest-${TEST_PV}.tgz )" - -LICENSE="GPL-2" -SLOT="0" -KEYWORDS="amd64 ppc64 x86 ~amd64-linux ~x86-linux ~x86-macos" -IUSE="X altivec blas doc -double-precision +fftw fkernels gsl lapack -mpi +single-precision sse2 test +threads xml zsh-completion" -REQUIRED_USE="fkernels? ( !threads )" - -CDEPEND=" - X? ( - x11-libs/libX11 - x11-libs/libSM - x11-libs/libICE - ) - blas? ( virtual/blas ) - fftw? ( sci-libs/fftw:3.0 ) - gsl? ( sci-libs/gsl ) - lapack? ( virtual/lapack ) - mpi? ( virtual/mpi ) - xml? ( dev-libs/libxml2:2 )" -DEPEND="${CDEPEND} - virtual/pkgconfig" -RDEPEND="${CDEPEND} - app-shells/tcsh" - -RESTRICT="test" - -src_prepare() { - #add user patches from /etc/portage/patches/sci-chemistry/gromacs - epatch_user - - if use mpi && use threads; then - elog "mdrun uses only threads OR mpi, and gromacs favours the" - elog "use of mpi over threads, so a mpi-version of mdrun will" - elog "be compiled. If you want to run mdrun on shared memory" - elog "machines only, you can safely disable mpi" - fi - - if use sse2; then - # Add patches for non-exec stack - qa issue - epatch "${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}/${P}-cmake-cpp-asm.patch" - - epatch "${FILESDIR}/${P}-enable-see.patch" - fi - - GMX_DIRS="" - use single-precision && GMX_DIRS+=" float" - use double-precision && GMX_DIRS+=" double" - #if neither single-precision nor double-precision is enabled - #build at least default (single) - [ -z "$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" -} |