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251 lines
7.7 KiB
251 lines
7.7 KiB
# Copyright 1999-2012 Gentoo Foundation
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# Distributed under the terms of the GNU General Public License v2
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# $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 $
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EAPI="4"
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TEST_PV="4.0.4"
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MANUAL_PV="4.5.4"
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#to find external blas/lapack
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CMAKE_MIN_VERSION="2.8.5-r2"
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inherit bash-completion-r1 cmake-utils eutils fortran-2 multilib toolchain-funcs
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if [ "${PV%9999}" != "${PV}" ]; then
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EGIT_REPO_URI="git://git.gromacs.org/gromacs"
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EGIT_BRANCH="release-4-5-patches"
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inherit git-2
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else
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SRC_URI="${SRC_URI} ftp://ftp.gromacs.org/pub/${PN}/${P}.tar.gz"
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fi
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DESCRIPTION="The ultimate molecular dynamics simulation package"
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HOMEPAGE="http://www.gromacs.org/"
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SRC_URI="${SRC_URI}
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sse2? ( http://dev.gentoo.org/~alexxy/gromacs/0001-Make-stack-non-executable-for-GAS-assembly.patch.gz )
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sse2? ( http://dev.gentoo.org/~alexxy/gromacs/0002-Make-stack-non-executable-for-ATT-assembly.patch.gz )
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doc? ( ftp://ftp.gromacs.org/pub/manual/manual-${MANUAL_PV}.pdf -> gromacs-manual-${MANUAL_PV}.pdf )
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test? ( ftp://ftp.gromacs.org/pub/tests/gmxtest-${TEST_PV}.tgz )"
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LICENSE="GPL-2"
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SLOT="0"
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KEYWORDS="amd64 ppc64 x86 ~amd64-linux ~x86-linux ~x86-macos"
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IUSE="X altivec blas doc -double-precision +fftw fkernels gsl lapack
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mpi +single-precision sse2 test +threads xml zsh-completion"
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REQUIRED_USE="fkernels? ( !threads )"
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CDEPEND="
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X? (
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x11-libs/libX11
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x11-libs/libSM
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x11-libs/libICE
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)
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blas? ( virtual/blas )
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fftw? ( sci-libs/fftw:3.0 )
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fkernels? ( virtual/fortran )
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gsl? ( sci-libs/gsl )
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lapack? ( virtual/lapack )
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mpi? ( virtual/mpi )
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xml? ( dev-libs/libxml2:2 )"
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DEPEND="${CDEPEND}
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virtual/pkgconfig"
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RDEPEND="${CDEPEND}
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app-shells/tcsh"
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RESTRICT="test"
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pkg_setup() {
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use fkernels && fortran-2_pkg_setup
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}
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src_prepare() {
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#add user patches from /etc/portage/patches/sci-chemistry/gromacs
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epatch_user
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if use mpi && use threads; then
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elog "mdrun uses only threads OR mpi, and gromacs favours the"
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elog "use of mpi over threads, so a mpi-version of mdrun will"
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elog "be compiled. If you want to run mdrun on shared memory"
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elog "machines only, you can safely disable mpi"
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fi
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if use sse2; then
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# Add patches for non-exec stack - qa issue
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epatch "${WORKDIR}/0001-Make-stack-non-executable-for-GAS-assembly.patch"
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epatch "${WORKDIR}/0002-Make-stack-non-executable-for-ATT-assembly.patch"
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#alexxy patches, renamve kernel from .s to .S
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epatch "${FILESDIR}/${P}-cmake-cpp-asm.patch"
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epatch "${FILESDIR}/${P}-enable-see.patch"
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fi
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GMX_DIRS=""
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use single-precision && GMX_DIRS+=" float"
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use double-precision && GMX_DIRS+=" double"
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#if neither single-precision nor double-precision is enabled
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#build at least default (single)
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[ -z "$GMX_DIRS" ] && GMX_DIRS+=" float"
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for x in ${GMX_DIRS}; do
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mkdir -p "${WORKDIR}/${P}_${x}" || die
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use test && cp -r "${WORKDIR}"/gmxtest "${WORKDIR}/${P}_${x}"
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done
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}
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src_configure() {
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local mycmakeargs_pre=( )
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#from gromacs configure
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if use fftw; then
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mycmakeargs_pre+=("-DGMX_FFT_LIBRARY=fftw3")
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else
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mycmakeargs_pre+=("-DGMX_FFT_LIBRARY=fftpack")
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ewarn "WARNING: The built-in FFTPACK routines are slow."
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ewarn "Are you sure you don\'t want to use FFTW?"
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ewarn "It is free and much faster..."
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fi
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if [[ $(gcc-version) == "4.1" ]]; then
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eerror "gcc 4.1 is not supported by gromacs"
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eerror "please run test suite"
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die
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fi
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#note for gentoo-PREFIX on apple: use --enable-apple-64bit
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#note for gentoo-PREFIX on aix, fortran (xlf) is still much faster
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if use fkernels; then
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ewarn "Fortran kernels are usually not faster than C kernels and assembly"
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ewarn "I hope, you know what are you doing..."
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fi
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if use double-precision ; then
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#from gromacs manual
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elog
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elog "For most simulations single precision is accurate enough. In some"
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elog "cases double precision is required to get reasonable results:"
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elog
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elog "-normal mode analysis, for the conjugate gradient or l-bfgs minimization"
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elog " and the calculation and diagonalization of the Hessian "
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elog "-calculation of the constraint force between two large groups of atoms"
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elog "-energy conservation: this can only be done without temperature coupling and"
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elog " without cutoffs"
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elog
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fi
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if use mpi ; then
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elog "You have enabled mpi, only mdrun will make use of mpi, that is why"
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elog "we configure/compile gromacs twice (with and without mpi) and only"
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elog "install mdrun with mpi support. In addtion you will get libgmx and"
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elog "libmd with and without mpi support."
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fi
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#go from slowest to fasterest acceleration
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local acce="none"
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use fkernels && acce="fortran"
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use altivec && acce="altivec"
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use ia64 && acce="ia64"
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use sse2 && acce="sse"
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mycmakeargs_pre+=(
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$(cmake-utils_use X GMX_X11)
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$(cmake-utils_use blas GMX_EXTERNAL_BLAS)
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$(cmake-utils_use gsl GMX_GSL)
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$(cmake-utils_use lapack GMX_EXTERNAL_LAPACK)
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$(cmake-utils_use threads GMX_THREADS)
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$(cmake-utils_use xml GMX_XML)
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-DGMX_DEFAULT_SUFFIX=off
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-DGMX_ACCELERATION="$acce"
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-DGMXLIB="$(get_libdir)"
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)
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for x in ${GMX_DIRS}; do
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einfo "Configuring for ${x} precision"
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local suffix=""
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#if we build single and double - double is suffixed
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use double-precision && use single-precision && \
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[ "${x}" = "double" ] && suffix="_d"
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local p
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[ "${x}" = "double" ] && p="-DGMX_DOUBLE=ON" || p="-DGMX_DOUBLE=OFF"
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mycmakeargs=( ${mycmakeargs_pre[@]} ${p} -DGMX_MPI=OFF
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-DGMX_BINARY_SUFFIX="${suffix}" -DGMX_LIBS_SUFFIX="${suffix}" )
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CMAKE_BUILD_DIR="${WORKDIR}/${P}_${x}" cmake-utils_src_configure
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use mpi || continue
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einfo "Configuring for ${x} precision with mpi"
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mycmakeargs=( ${mycmakeargs_pre[@]} ${p} -DGMX_MPI=ON
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-DGMX_BINARY_SUFFIX="_mpi${suffix}" -DGMX_LIBS_SUFFIX="_mpi${suffix}" )
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CMAKE_BUILD_DIR="${WORKDIR}/${P}_${x}_mpi" cmake-utils_src_configure
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done
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}
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src_compile() {
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for x in ${GMX_DIRS}; do
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einfo "Compiling for ${x} precision"
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CMAKE_BUILD_DIR="${WORKDIR}/${P}_${x}"\
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cmake-utils_src_compile
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use mpi || continue
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einfo "Compiling for ${x} precision with mpi"
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CMAKE_BUILD_DIR="${WORKDIR}/${P}_${x}_mpi"\
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cmake-utils_src_compile mdrun
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done
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}
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src_test() {
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for x in ${GMX_DIRS}; do
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local oldpath="${PATH}"
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export PATH="${WORKDIR}/${P}_${x}/src/kernel:${S}-{x}/src/tools:${PATH}"
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cd "${WORKDIR}/${P}_${x}"
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emake -j1 tests || die "${x} Precision test failed"
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export PATH="${oldpath}"
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done
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}
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src_install() {
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for x in ${GMX_DIRS}; do
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CMAKE_BUILD_DIR="${WORKDIR}/${P}_${x}" \
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cmake-utils_src_install
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use mpi || continue
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#cmake-utils_src_install does not support args
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#using cmake-utils_src_compile instead
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CMAKE_BUILD_DIR="${WORKDIR}/${P}_${x}_mpi" \
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cmake-utils_src_make install-mdrun DESTDIR="${D}"
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done
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sed -n -e '/^GMXBIN/,/^GMXDATA/p' "${ED}"/usr/bin/GMXRC.bash > "${T}/80gromacs"
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echo "VMD_PLUGIN_PATH=${EPREFIX}/usr/$(get_libdir)/vmd/plugins/*/molfile/" >> "${T}/80gromacs"
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doenvd "${T}/80gromacs"
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rm -f "${ED}"/usr/bin/GMXRC*
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newbashcomp "${ED}"/usr/bin/completion.bash ${PN}
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if use zsh-completion ; then
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insinto /usr/share/zsh/site-functions
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newins "${ED}"/usr/bin/completion.zsh _${PN}
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fi
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rm -f "${ED}"/usr/bin/completion.*
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# Fix typos in a couple of files.
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sed -e "s:+0f:-f:" -i "${ED}"usr/share/gromacs/tutor/gmxdemo/demo \
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|| die "Failed to fixup demo script."
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cd "${S}"
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dodoc AUTHORS INSTALL* README*
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if use doc; then
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newdoc "${DISTDIR}/gromacs-manual-${MANUAL_PV}.pdf" "manual-${MANUAL_PV}.pdf"
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dohtml -r "${ED}usr/share/gromacs/html/"
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fi
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rm -rf "${ED}usr/share/gromacs/html/"
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}
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pkg_postinst() {
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einfo
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einfo "Please read and cite:"
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einfo "Gromacs 4, J. Chem. Theory Comput. 4, 435 (2008). "
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einfo "http://dx.doi.org/10.1021/ct700301q"
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einfo
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einfo $(g_luck)
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einfo "For more Gromacs cool quotes (gcq) add g_luck to your .bashrc"
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einfo
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elog "Gromacs can use sci-chemistry/vmd to read additional file formats"
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}
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