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# Copyright 1999-2012 Gentoo Foundation
# Distributed under the terms of the GNU General Public License v2
# $Header: $
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
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"
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"
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
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"
}
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