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Diffstat (limited to 'sci-chemistry/gromacs/gromacs-4.5.9999.ebuild')
| -rw-r--r-- | sci-chemistry/gromacs/gromacs-4.5.9999.ebuild | 242 |
1 files changed, 242 insertions, 0 deletions
diff --git a/sci-chemistry/gromacs/gromacs-4.5.9999.ebuild b/sci-chemistry/gromacs/gromacs-4.5.9999.ebuild new file mode 100644 index 000000000..b5ed08545 --- /dev/null +++ b/sci-chemistry/gromacs/gromacs-4.5.9999.ebuild @@ -0,0 +1,242 @@ +# 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" +} |