# 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 1.8 2012/05/04 07:02:33 jdhore 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} 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-${TEST_PV}.tgz )" LICENSE="GPL-2" SLOT="0" KEYWORDS="amd64 ppc64 x86 ~amd64-linux ~x86-linux ~x86-macos" IUSE="X altivec blas doc -double-precision +fftw fkernels gsl lapack mpi +single-precision sse2 test +threads xml zsh-completion" REQUIRED_USE="fkernels? ( !threads )" CDEPEND=" X? ( x11-libs/libX11 x11-libs/libSM x11-libs/libICE ) blas? ( virtual/blas ) fftw? ( sci-libs/fftw:3.0 ) fkernels? ( virtual/fortran ) gsl? ( sci-libs/gsl ) lapack? ( virtual/lapack ) mpi? ( virtual/mpi ) xml? ( dev-libs/libxml2:2 )" DEPEND="${CDEPEND} virtual/pkgconfig" RDEPEND="${CDEPEND} app-shells/tcsh" RESTRICT="test" pkg_setup() { use fkernels && fortran-2_pkg_setup } src_prepare() { #add user patches from /etc/portage/patches/sci-chemistry/gromacs epatch_user if use mpi && use threads; then elog "mdrun uses only threads OR mpi, and gromacs favours the" elog "use of mpi over threads, so a mpi-version of mdrun will" elog "be compiled. If you want to run mdrun on shared memory" elog "machines only, you can safely disable mpi" fi if use sse2; then # Add patches for non-exec stack - qa issue epatch "${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="${suffix}" ) CMAKE_BUILD_DIR="${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() { 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" }