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# Copyright 1999-2020 Gentoo Authors
# Distributed under the terms of the GNU General Public License v2
EAPI=7
CMAKE_MAKEFILE_GENERATOR="ninja"
inherit bash-completion-r1 cmake cuda eutils multilib readme.gentoo-r1 toolchain-funcs xdg-utils
SRC_URI="
http://ftp.gromacs.org/gromacs/${PN}-${PV/_/-}.tar.gz
doc? ( http://ftp.gromacs.org/manual/manual-${PV/_/-}.pdf )
test? ( http://ftp.gromacs.org/regressiontests/regressiontests-${PV/_/-}.tar.gz )"
KEYWORDS="~amd64 ~arm x86 ~amd64-linux ~x86-linux ~x64-macos ~x86-macos"
ACCE_IUSE="cpu_flags_x86_sse2 cpu_flags_x86_sse4_1 cpu_flags_x86_fma4 cpu_flags_x86_avx cpu_flags_x86_avx2"
DESCRIPTION="The ultimate molecular dynamics simulation package"
HOMEPAGE="http://www.gromacs.org/"
# see COPYING for details
# https://repo.or.cz/w/gromacs.git/blob/HEAD:/COPYING
# base, vmd plugins, fftpack from numpy, blas/lapck from netlib, memtestG80 library, mpi_thread lib
LICENSE="LGPL-2.1 UoI-NCSA !mkl? ( !fftw? ( BSD ) !blas? ( BSD ) !lapack? ( BSD ) ) cuda? ( LGPL-3 ) threads? ( BSD )"
SLOT="0/${PV}"
IUSE="X blas cuda +doc -double-precision +fftw +gmxapi +hwloc lapack +lmfit mkl mpi +offensive opencl openmp +single-precision test +threads +tng ${ACCE_IUSE}"
CDEPEND="
X? (
x11-libs/libX11
x11-libs/libSM
x11-libs/libICE
)
blas? ( virtual/blas )
cuda? ( >=dev-util/nvidia-cuda-toolkit-6.5.14 )
opencl? ( virtual/opencl )
fftw? ( sci-libs/fftw:3.0 )
hwloc? ( sys-apps/hwloc )
lapack? ( virtual/lapack )
lmfit? ( sci-libs/lmfit )
mkl? ( sci-libs/mkl )
mpi? ( virtual/mpi )
${PYTHON_DEPS}
"
BDEPEND="${CDEPEND}
virtual/pkgconfig
"
RDEPEND="${CDEPEND}"
REQUIRED_USE="
|| ( single-precision double-precision )
cuda? ( single-precision )
cuda? ( !opencl )
mkl? ( !blas !fftw !lapack )
${PYTHON_REQUIRED_USE}"
DOCS=( AUTHORS README )
RESTRICT="!test? ( test )"
S="${WORKDIR}/${PN}-${PV/_/-}"
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
xdg_environment_reset #591952
cmake_src_prepare
use cuda && cuda_src_prepare
GMX_DIRS=""
use single-precision && GMX_DIRS+=" float"
use double-precision && GMX_DIRS+=" double"
if use test; then
for x in ${GMX_DIRS}; do
mkdir -p "${WORKDIR}/${P}_${x}" || die
cp -al "${WORKDIR}/regressiontests"* "${WORKDIR}/${P}_${x}/tests" || die
done
fi
DOC_CONTENTS="Gromacs can use sci-chemistry/vmd to read additional file formats"
}
src_configure() {
local mycmakeargs_pre=( ) extra fft_opts=( )
#go from slowest to fastest acceleration
local acce="None"
use cpu_flags_x86_sse2 && acce="SSE2"
use cpu_flags_x86_sse4_1 && acce="SSE4.1"
use cpu_flags_x86_fma4 && acce="AVX_128_FMA"
use cpu_flags_x86_avx && acce="AVX_256"
use cpu_flags_x86_avx2 && acce="AVX2_256"
#to create man pages, build tree binaries are executed (bug #398437)
[[ ${CHOST} = *-darwin* ]] && \
extra+=" -DCMAKE_BUILD_WITH_INSTALL_RPATH=OFF"
if use fftw; then
fft_opts=( -DGMX_FFT_LIBRARY=fftw3 )
elif use mkl && has_version "=sci-libs/mkl-10*"; then
fft_opts=( -DGMX_FFT_LIBRARY=mkl
-DMKL_INCLUDE_DIR="${MKLROOT}/include"
-DMKL_LIBRARIES="$(echo /opt/intel/mkl/10.0.5.025/lib/*/libmkl.so);$(echo /opt/intel/mkl/10.0.5.025/lib/*/libiomp*.so)"
)
elif use mkl; then
local bits=$(get_libdir)
fft_opts=( -DGMX_FFT_LIBRARY=mkl
-DMKL_INCLUDE_DIR="$(echo /opt/intel/*/mkl/include)"
-DMKL_LIBRARIES="$(echo /opt/intel/*/mkl/lib/*${bits/lib}/libmkl_rt.so)"
)
else
fft_opts=( -DGMX_FFT_LIBRARY=fftpack )
fi
if use lmfit; then
local lmfit_opts=( -DGMX_USE_LMFIT=EXTERNAL )
else
local lmfit_opts=( -DGMX_USE_LMFIT=INTERNAL )
fi
mycmakeargs_pre+=(
"${fft_opts[@]}"
"${lmfit_opts[@]}"
-DGMX_X11=$(usex X)
-DGMX_EXTERNAL_BLAS=$(usex blas)
-DGMX_EXTERNAL_LAPACK=$(usex lapack)
-DGMX_OPENMP=$(usex openmp)
-DGMX_COOL_QUOTES=$(usex offensive)
-DGMX_USE_TNG=$(usex tng)
-DGMX_HWLOC=$(usex hwloc)
-DGMX_DEFAULT_SUFFIX=off
-DGMX_SIMD="$acce"
-DGMX_VMD_PLUGIN_PATH="${EPREFIX}/usr/$(get_libdir)/vmd/plugins/*/molfile/"
-DBUILD_TESTING=$(usex test)
-DGMX_BUILD_UNITTESTS=$(usex test)
-DPYTHON_EXECUTABLE="${EPREFIX}/usr/bin/${EPYTHON}"
${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=( "-DGMX_GPU=OFF" )
[[ ${x} = "float" ]] && use cuda && \
cuda=( "-DGMX_GPU=ON" )
local opencl=( "-DGMX_USE_OPENCL=OFF" )
use opencl && opencl=( "-DGMX_USE_OPENCL=ON" ) cuda=( "-DGMX_GPU=ON" )
mycmakeargs=(
${mycmakeargs_pre[@]} ${p}
-DGMX_MPI=OFF
-DGMX_THREAD_MPI=$(usex threads)
-DGMXAPI=$(usex gmxapi)
"${opencl[@]}"
"${cuda[@]}"
"$(use test && echo -DREGRESSIONTEST_PATH="${WORKDIR}/${P}_${x}/tests")"
-DGMX_BINARY_SUFFIX="${suffix}"
-DGMX_LIBS_SUFFIX="${suffix}"
)
BUILD_DIR="${WORKDIR}/${P}_${x}" cmake_src_configure
[[ ${CHOST} != *-darwin* ]] || \
sed -i '/SET(CMAKE_INSTALL_NAME_DIR/s/^/#/' "${WORKDIR}/${P}_${x}/gentoo_rules.cmake" || die
use mpi || continue
einfo "Configuring for ${x} precision with mpi"
mycmakeargs=(
${mycmakeargs_pre[@]} ${p}
-DGMX_THREAD_MPI=OFF
-DGMX_MPI=ON
-DGMX_OPENMM=OFF
-DGMXAPI=OFF
"${opencl[@]}"
"${cuda[@]}"
-DGMX_BUILD_MDRUN_ONLY=ON
-DBUILD_SHARED_LIBS=OFF
-DGMX_BUILD_MANUAL=OFF
-DGMX_BINARY_SUFFIX="_mpi${suffix}"
-DGMX_LIBS_SUFFIX="_mpi${suffix}"
)
BUILD_DIR="${WORKDIR}/${P}_${x}_mpi" CC="mpicc" cmake_src_configure
[[ ${CHOST} != *-darwin* ]] || \
sed -i '/SET(CMAKE_INSTALL_NAME_DIR/s/^/#/' "${WORKDIR}/${P}_${x}_mpi/gentoo_rules.cmake" || die
done
}
src_compile() {
for x in ${GMX_DIRS}; do
einfo "Compiling for ${x} precision"
BUILD_DIR="${WORKDIR}/${P}_${x}"\
cmake_src_compile
use mpi || continue
einfo "Compiling for ${x} precision with mpi"
BUILD_DIR="${WORKDIR}/${P}_${x}_mpi"\
cmake_src_compile
done
}
src_test() {
for x in ${GMX_DIRS}; do
BUILD_DIR="${WORKDIR}/${P}_${x}"\
cmake_src_make check
done
}
src_install() {
for x in ${GMX_DIRS}; do
BUILD_DIR="${WORKDIR}/${P}_${x}" \
cmake_src_install
if use doc; then
newdoc "${DISTDIR}/manual-${PV/_/-}.pdf" "${PN}-manual-${PV}.pdf"
fi
use mpi || continue
BUILD_DIR="${WORKDIR}/${P}_${x}_mpi" \
cmake_src_install
done
if use tng; then
insinto /usr/include/tng
doins src/external/tng_io/include/tng/*h
fi
# drop unneeded stuff
rm "${ED}"/usr/bin/GMXRC* || die
for x in "${ED}"/usr/bin/gmx-completion-*.bash ; do
local n=${x##*/gmx-completion-}
n="${n%.bash}"
cat "${ED}"/usr/bin/gmx-completion.bash "$x" > "${T}/${n}" || die
newbashcomp "${T}"/"${n}" "${n}"
done
rm "${ED}"/usr/bin/gmx-completion*.bash || die
readme.gentoo_create_doc
}
pkg_postinst() {
einfo
einfo "Please read and cite:"
einfo "Gromacs 4, J. Chem. Theory Comput. 4, 435 (2008). "
einfo "https://dx.doi.org/10.1021/ct700301q"
einfo
readme.gentoo_print_elog
}
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