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# Copyright 1999-2012 Gentoo Foundation
# Distributed under the terms of the GNU General Public License v2
# $Header: $
EAPI=5
TEST_PV="4.0.4"
MANUAL_PV="4.6-beta1"
#to find external blas/lapack
CMAKE_MIN_VERSION="2.8.5-r2"
CMAKE_MAKEFILE_GENERATOR="ninja"
inherit bash-completion-r1 cmake-utils eutils multilib toolchain-funcs
SRC_URI="test? ( ftp://ftp.gromacs.org/pub/tests/gmxtest-${TEST_PV}.tgz )"
if [[ $PV = *9999* ]]; then
EGIT_REPO_URI="git://git.gromacs.org/gromacs.git
https://gerrit.gromacs.org/gromacs.git
git://github.com/gromacs/gromacs.git
http://repo.or.cz/r/gromacs.git"
EGIT_BRANCH="release-4-6"
inherit git-2
PDEPEND="doc? ( ~app-doc/${PN}-manual-${PV} )"
else
S="${WORKDIR}/${P//_/-}"
SRC_URI="${SRC_URI} ftp://ftp.gromacs.org/pub/${PN}/${P//_/-}.tar.gz
doc? ( ftp://ftp.gromacs.org/pub/manual/${PN}-manual-${MANUAL_PV}.pdf )"
fi
ACCE_IUSE="sse2 sse41 avx128fma avx256"
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 blas cuda doc -double-precision +fftw gsl lapack mpi +offensive openmm openmp +single-precision test +threads zsh-completion ${ACCE_IUSE}"
CDEPEND="
X? (
x11-libs/libX11
x11-libs/libSM
x11-libs/libICE
)
blas? ( virtual/blas )
cuda? ( dev-util/nvidia-cuda-toolkit )
fftw? ( sci-libs/fftw:3.0 )
gsl? ( sci-libs/gsl )
lapack? ( virtual/lapack )
mpi? ( virtual/mpi )
openmm? ( sci-libs/openmm[cuda,opencl] )"
DEPEND="${CDEPEND}
virtual/pkgconfig"
RDEPEND="${CDEPEND}"
RESTRICT="test"
REQUIRED_USE="cuda? ( single-precision ) openmm? ( single-precision cuda )"
pkg_pretend() {
[[ $(gcc-version) == "4.1" ]] && die "gcc 4.1 is not supported by gromacs"
use openmp && ! tc-has-openmp && \
die "Please switch to an openmp compatible compiler"
}
src_prepare() {
#notes/todos
# -on apple: there is framework support
# -mkl support
#add user patches from /etc/portage/patches/sci-chemistry/gromacs
epatch_user
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=( ) extra
#go from slowest to fastest acceleration
local acce="None"
use sse2 && acce="SSE2"
use sse41 && acce="SSE4.1"
use avx128fma && acce="AVX_128_FMA"
use avx256 && acce="AVX_256"
#to create man pages, build tree binaries are executed (bug #398437)
[[ ${CHOST} = *-darwin* ]] && \
extra+=" -DCMAKE_BUILD_WITH_INSTALL_RPATH=OFF"
mycmakeargs_pre+=(
-DGMX_FFT_LIBRARY=$(usex fftw fftw3 fftwpack)
$(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 openmp GMX_OPENMP)
$(cmake-utils_use !offensive GMX_NO_QUOTES)
-DGMX_DEFAULT_SUFFIX=off
-DGMX_ACCELERATION="$acce"
-DGMXLIB="$(get_libdir)"
-DGMX_VMD_PLUGIN_PATH="${EPREFIX}/usr/$(get_libdir)/vmd/plugins/*/molfile/"
${extra}
)
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
[[ ${x} = "double" ]] && p="-DGMX_DOUBLE=ON" || p="-DGMX_DOUBLE=OFF"
local cuda=$(cmake-utils_use cuda GMX_GPU)
[[ ${x} = "double" ]] && use cuda && cuda="-DGMX_GPU=OFF"
mycmakeargs=( ${mycmakeargs_pre[@]} ${p} -DGMX_MPI=OFF
$(cmake-utils_use threads GMX_THREAD_MPI) ${cuda}
-DGMX_BINARY_SUFFIX="${suffix}" -DGMX_LIBS_SUFFIX="${suffix}" )
BUILD_DIR="${WORKDIR}/${P}_${x}" cmake-utils_src_configure
if [[ ${x} = float ]] && use openmm; then
einfo "Configuring for openmm build"
mycmakeargs=( ${mycmakeargs_pre[@]} ${p} -DGMX_MPI=OFF
-DGMX_THREAD_MPI=OFF -DGMX_GPU=OFF -DGMX_OPENMM=ON
-DGMX_BINARY_SUFFIX="openmm" -DGMX_LIBS_SUFFIX="openmm" )
BUILD_DIR="${WORKDIR}/${P}_openmm" \
OPENMM_ROOT_DIR="${EPREFIX}/usr" cmake-utils_src_configure
fi
use mpi || continue
einfo "Configuring for ${x} precision with mpi"
mycmakeargs=( ${mycmakeargs_pre[@]} ${p} -DGMX_THREAD_MPI=OFF
-DGMX_MPI=ON ${cuda}
-DGMX_BINARY_SUFFIX="_mpi${suffix}" -DGMX_LIBS_SUFFIX="_mpi${suffix}" )
BUILD_DIR="${WORKDIR}/${P}_${x}_mpi" CC="mpicc" 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
if [[ ${x} = float ]] && use openmm; then
einfo "Compiling for openmm build"
BUILD_DIR="${WORKDIR}/${P}_openmm"\
cmake-utils_src_compile mdrun
fi
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
if [[ ${x} = float ]] && use openmm; then
BUILD_DIR="${WORKDIR}/${P}_openmm" \
DESTDIR="${D}" cmake-utils_src_make install-mdrun
fi
use mpi || continue
BUILD_DIR="${WORKDIR}/${P}_${x}_mpi" \
DESTDIR="${D}" cmake-utils_src_make install-mdrun
done
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.*
cd "${S}"
dodoc AUTHORS INSTALL* README*
if use doc; then
dohtml -r "${ED}usr/share/gromacs/html/"
if [[ $PV = *9999* ]]; then
insinto /usr/share/gromacs
doins "admin/programs.txt"
ls -1 "${ED}"/usr/bin | sed -e '/_d$/d' > "${T}"/programs.list
doins "${T}"/programs.list
else
dodoc "${DISTDIR}/${PN}-manual-${MANUAL_PV}.pdf"
fi
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"
if use offensive; then
einfo
einfo $(g_luck)
einfo "For more Gromacs cool quotes (gcq) add g_luck to your .bashrc"
fi
einfo
elog "Gromacs can use sci-chemistry/vmd to read additional file formats"
}
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