| 22 |
22 |
inherit git-r3
|
| 23 |
23 |
else
|
| 24 |
24 |
SRC_URI="
|
| 25 |
|
https://ftp.gromacs.org/gromacs/${PN}-${PV/_/-}.tar.gz
|
| 26 |
|
doc? ( https://ftp.gromacs.org/manual/manual-${PV/_/-}.pdf )
|
| 27 |
|
test? ( https://ftp.gromacs.org/regressiontests/regressiontests-${PV/_/-}.tar.gz )"
|
| 28 |
|
KEYWORDS="amd64 ~arm ~x86 ~amd64-linux ~x86-linux ~x64-macos"
|
|
25 |
https://ftp.gromacs.org/gromacs/${P}.tar.gz
|
|
26 |
doc? ( https://ftp.gromacs.org/manual/manual-${PV}.pdf )
|
|
27 |
test? ( https://ftp.gromacs.org/regressiontests/regressiontests-${PV}.tar.gz )"
|
|
28 |
# since 2022 arm support was dropped (but not arm64)
|
|
29 |
KEYWORDS="~amd64 -arm ~arm64 ~x86 ~amd64-linux ~x86-linux ~x64-macos"
|
| 29 |
30 |
fi
|
| 30 |
31 |
|
| 31 |
32 |
ACCE_IUSE="cpu_flags_x86_sse2 cpu_flags_x86_sse4_1 cpu_flags_x86_fma4 cpu_flags_x86_avx cpu_flags_x86_avx2 cpu_flags_x86_avx512f cpu_flags_arm_neon"
|
| ... | ... | |
| 38 |
39 |
# base, vmd plugins, fftpack from numpy, blas/lapck from netlib, memtestG80 library, mpi_thread lib
|
| 39 |
40 |
LICENSE="LGPL-2.1 UoI-NCSA !mkl? ( !fftw? ( BSD ) !blas? ( BSD ) !lapack? ( BSD ) ) cuda? ( LGPL-3 ) threads? ( BSD )"
|
| 40 |
41 |
SLOT="0/${PV}"
|
| 41 |
|
IUSE="X blas cuda +custom-cflags +doc build-manual double-precision +fftw +gmxapi +gmxapi-legacy +hwloc lapack +lmfit mkl mpi +offensive opencl openmp +python +single-precision test +threads +tng ${ACCE_IUSE}"
|
|
42 |
IUSE="blas clang clang-cuda cuda +custom-cflags +doc build-manual double-precision +fftw +gmxapi +gmxapi-legacy +hwloc lapack mkl mpi +offensive opencl openmp +python +single-precision test +threads +tng ${ACCE_IUSE}"
|
| 42 |
43 |
|
| 43 |
44 |
CDEPEND="
|
| 44 |
|
X? (
|
| 45 |
|
x11-libs/libX11
|
| 46 |
|
x11-libs/libSM
|
| 47 |
|
x11-libs/libICE
|
| 48 |
|
)
|
| 49 |
45 |
blas? ( virtual/blas )
|
| 50 |
|
cuda? ( >=dev-util/nvidia-cuda-toolkit-6.5.14:=[profiler] )
|
|
46 |
cuda? ( >=dev-util/nvidia-cuda-toolkit-11:=[profiler] )
|
| 51 |
47 |
opencl? ( virtual/opencl )
|
| 52 |
48 |
fftw? ( sci-libs/fftw:3.0= )
|
| 53 |
49 |
hwloc? ( sys-apps/hwloc:= )
|
| 54 |
50 |
lapack? ( virtual/lapack )
|
| 55 |
|
lmfit? ( sci-libs/lmfit:= )
|
| 56 |
51 |
mkl? ( sci-libs/mkl )
|
| 57 |
|
mpi? ( virtual/mpi )
|
|
52 |
mpi? ( virtual/mpi[cxx] )
|
|
53 |
sci-libs/lmfit:=
|
|
54 |
>=dev-cpp/muParser-2.3:=
|
| 58 |
55 |
${PYTHON_DEPS}
|
| 59 |
56 |
"
|
| 60 |
57 |
BDEPEND="${CDEPEND}
|
| 61 |
58 |
virtual/pkgconfig
|
|
59 |
clang? ( >=sys-devel/clang-6:* )
|
| 62 |
60 |
build-manual? (
|
| 63 |
61 |
app-doc/doxygen
|
| 64 |
62 |
$(python_gen_cond_dep '
|
| ... | ... | |
| 70 |
68 |
dev-texlive/texlive-latexextra
|
| 71 |
69 |
media-gfx/imagemagick
|
| 72 |
70 |
)"
|
| 73 |
|
RDEPEND="${CDEPEND}"
|
|
71 |
RDEPEND="${CDEPEND}
|
|
72 |
<sci-chemistry/dssp-4"
|
| 74 |
73 |
|
| 75 |
74 |
REQUIRED_USE="
|
| 76 |
75 |
|| ( single-precision double-precision )
|
| ... | ... | |
| 78 |
77 |
cuda? ( single-precision )
|
| 79 |
78 |
opencl? ( single-precision )
|
| 80 |
79 |
cuda? ( !opencl )
|
|
80 |
clang-cuda? ( clang cuda )
|
| 81 |
81 |
mkl? ( !blas !fftw !lapack )
|
| 82 |
82 |
${PYTHON_REQUIRED_USE}"
|
| 83 |
83 |
|
| ... | ... | |
| 85 |
85 |
|
| 86 |
86 |
RESTRICT="!test? ( test )"
|
| 87 |
87 |
|
| 88 |
|
PATCHES=(
|
| 89 |
|
"${FILESDIR}/${PN}-2021-musl-stdint.patch"
|
| 90 |
|
"${FILESDIR}/${PN}-2021-cuda-detection.patch"
|
| 91 |
|
)
|
| 92 |
|
|
| 93 |
88 |
if [[ ${PV} != *9999 ]]; then
|
| 94 |
89 |
S="${WORKDIR}/${PN}-${PV/_/-}"
|
| 95 |
90 |
fi
|
| ... | ... | |
| 123 |
118 |
|
| 124 |
119 |
xdg_environment_reset #591952
|
| 125 |
120 |
|
|
121 |
# we can use clang as default
|
|
122 |
if use clang && ! tc-is-clang ; then
|
|
123 |
export CC=${CHOST}-clang
|
|
124 |
export CXX=${CHOST}-clang++
|
|
125 |
else
|
|
126 |
tc-export CXX CC
|
|
127 |
fi
|
|
128 |
# clang-cuda need to filter mfpmath
|
|
129 |
if use clang-cuda ; then
|
|
130 |
filter-mfpmath sse
|
|
131 |
filter-mfpmath i386
|
|
132 |
fi
|
|
133 |
|
| 126 |
134 |
cmake_src_prepare
|
| 127 |
135 |
|
| 128 |
136 |
use cuda && cuda_src_prepare
|
| ... | ... | |
| 203 |
211 |
fft_opts=( -DGMX_FFT_LIBRARY=fftpack )
|
| 204 |
212 |
fi
|
| 205 |
213 |
|
| 206 |
|
if use lmfit; then
|
| 207 |
|
local lmfit_opts=( -DGMX_USE_LMFIT=EXTERNAL )
|
| 208 |
|
else
|
| 209 |
|
local lmfit_opts=( -DGMX_USE_LMFIT=INTERNAL )
|
| 210 |
|
fi
|
| 211 |
|
|
| 212 |
214 |
mycmakeargs_pre+=(
|
| 213 |
215 |
"${fft_opts[@]}"
|
| 214 |
216 |
"${lmfit_opts[@]}"
|
| 215 |
|
-DGMX_X11=$(usex X)
|
|
217 |
-DGMX_USE_LMFIT=EXTERNAL
|
|
218 |
-DGMX_USE_MUPARSER=EXTERNAL
|
| 216 |
219 |
-DGMX_EXTERNAL_BLAS=$(usex blas)
|
| 217 |
220 |
-DGMX_EXTERNAL_LAPACK=$(usex lapack)
|
| 218 |
221 |
-DGMX_OPENMP=$(usex openmp)
|
| ... | ... | |
| 223 |
226 |
-DGMX_DEFAULT_SUFFIX=off
|
| 224 |
227 |
-DGMX_SIMD="$acce"
|
| 225 |
228 |
-DGMX_VMD_PLUGIN_PATH="${EPREFIX}/usr/$(get_libdir)/vmd/plugins/*/molfile/"
|
|
229 |
-DGMX_DSSP_PROGRAM_PATH="${EPREFIX}/usr/bin/dssp"
|
| 226 |
230 |
-DBUILD_TESTING=$(usex test)
|
| 227 |
231 |
-DGMX_BUILD_UNITTESTS=$(usex test)
|
| 228 |
232 |
-DPYTHON_EXECUTABLE="${EPREFIX}/usr/bin/${EPYTHON}"
|
| ... | ... | |
| 239 |
243 |
[[ ${x} = "double" ]] && p="-DGMX_DOUBLE=ON" || p="-DGMX_DOUBLE=OFF"
|
| 240 |
244 |
local gpu=( "-DGMX_GPU=OFF" )
|
| 241 |
245 |
[[ ${x} = "float" ]] && use cuda && gpu=( "-DGMX_GPU=CUDA" )
|
|
246 |
[[ ${x} = "float" ]] && use clang-cuda && gpu=( "-DGMX_GPU=CUDA" "-DGMX_CLANG_CUDA=ON" )
|
| 242 |
247 |
use opencl && gpu=( "-DGMX_GPU=OPENCL" )
|
| 243 |
248 |
local mycmakeargs=(
|
| 244 |
249 |
${mycmakeargs_pre[@]} ${p}
|
| 245 |
|
-DGMX_MPI=OFF
|
|
250 |
-DGMX_MPI=$(usex mpi)
|
| 246 |
251 |
-DGMX_THREAD_MPI=$(usex threads)
|
| 247 |
252 |
-DGMXAPI=$(usex gmxapi)
|
| 248 |
253 |
-DGMX_INSTALL_LEGACY_API=$(usex gmxapi-legacy)
|
| ... | ... | |
| 255 |
260 |
BUILD_DIR="${WORKDIR}/${P}_${x}" cmake_src_configure
|
| 256 |
261 |
[[ ${CHOST} != *-darwin* ]] || \
|
| 257 |
262 |
sed -i '/SET(CMAKE_INSTALL_NAME_DIR/s/^/#/' "${WORKDIR}/${P}_${x}/gentoo_rules.cmake" || die
|
| 258 |
|
use mpi || continue
|
| 259 |
|
einfo "Configuring for ${x} precision with mpi"
|
| 260 |
|
local mycmakeargs=(
|
| 261 |
|
${mycmakeargs_pre[@]} ${p}
|
| 262 |
|
-DGMX_THREAD_MPI=OFF
|
| 263 |
|
-DGMX_MPI=ON
|
| 264 |
|
-DGMX_OPENMM=OFF
|
| 265 |
|
-DGMXAPI=OFF
|
| 266 |
|
"${opencl[@]}"
|
| 267 |
|
"${cuda[@]}"
|
| 268 |
|
-DGMX_BUILD_MDRUN_ONLY=ON
|
| 269 |
|
-DBUILD_SHARED_LIBS=OFF
|
| 270 |
|
-DGMX_BUILD_MANUAL=OFF
|
| 271 |
|
-DGMX_BINARY_SUFFIX="_mpi${suffix}"
|
| 272 |
|
-DGMX_LIBS_SUFFIX="_mpi${suffix}"
|
| 273 |
|
)
|
| 274 |
|
BUILD_DIR="${WORKDIR}/${P}_${x}_mpi" CC="mpicc" cmake_src_configure
|
| 275 |
|
[[ ${CHOST} != *-darwin* ]] || \
|
| 276 |
|
sed -i '/SET(CMAKE_INSTALL_NAME_DIR/s/^/#/' "${WORKDIR}/${P}_${x}_mpi/gentoo_rules.cmake" || die
|
| 277 |
263 |
done
|
| 278 |
264 |
}
|
| 279 |
265 |
|
| ... | ... | |
| 293 |
279 |
BUILD_DIR="${WORKDIR}/${P}_${x}"\
|
| 294 |
280 |
cmake_src_compile manual
|
| 295 |
281 |
fi
|
| 296 |
|
use mpi || continue
|
| 297 |
|
einfo "Compiling for ${x} precision with mpi"
|
| 298 |
|
BUILD_DIR="${WORKDIR}/${P}_${x}_mpi"\
|
| 299 |
|
cmake_src_compile
|
| 300 |
282 |
done
|
| 301 |
283 |
}
|
| 302 |
284 |
|
| ... | ... | |
| 324 |
306 |
newdoc "${DISTDIR}/manual-${PV}.pdf" "${PN}-manual-${PV}.pdf"
|
| 325 |
307 |
fi
|
| 326 |
308 |
fi
|
| 327 |
|
|
| 328 |
|
use mpi || continue
|
| 329 |
|
BUILD_DIR="${WORKDIR}/${P}_${x}_mpi" \
|
| 330 |
|
cmake_src_install
|
| 331 |
309 |
done
|
| 332 |
310 |
|
| 333 |
311 |
if use tng; then
|
