blob: 5266a60f632d45e876414a608555635277cb02eb (
plain)
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
|
# Copyright 1999-2021 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 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-${PV/_/-}.pdf )
test? ( https://ftp.gromacs.org/regressiontests/regressiontests-${PV/_/-}.tar.gz )"
KEYWORDS="amd64 arm x86 ~amd64-linux ~x86-linux ~x64-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 +hwloc lapack mkl mpi +offensive opencl openmp +single-precision test +threads +tng ${ACCE_IUSE}"
CDEPEND="
X? (
x11-libs/libX11
x11-libs/libSM
x11-libs/libICE
)
blas? ( virtual/blas )
cuda? ( >=dev-util/nvidia-cuda-toolkit-4.2.9-r1 )
opencl? ( virtual/opencl )
fftw? ( sci-libs/fftw:3.0= )
hwloc? ( <sys-apps/hwloc-2:= )
lapack? ( virtual/lapack )
mkl? ( sci-libs/mkl )
mpi? ( virtual/mpi )
"
BDEPEND="${CDEPEND}
virtual/pkgconfig
"
RDEPEND="${CDEPEND}"
REQUIRED_USE="
|| ( single-precision double-precision )
cuda? ( single-precision )
cuda? ( !opencl )
mkl? ( !blas !fftw !lapack )"
DOCS=( AUTHORS README )
RESTRICT="!test? ( test )"
S="${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
mycmakeargs_pre+=(
"${fft_opts[@]}"
-DGMX_X11=$(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)
${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)
"${opencl[@]}"
"${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[@]} ${p}
-DGMX_THREAD_MPI=OFF
-DGMX_MPI=ON
-DGMX_OPENMM=OFF
-DGMX_BUILD_MDRUN_ONLY=ON
-DBUILD_SHARED_LIBS=OFF
-DGMX_BUILD_MANUAL=OFF
"${opencl[@]}"
"${cuda[@]}"
-DGMX_BINARY_SUFFIX="_mpi${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_compile 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
}
|
GitWeb