summaryrefslogtreecommitdiff
blob: c4951b414c97276bc306c4bd307514c4cf168dba (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
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
263
264
265
266
267
268
269
270
271
272
273
274
275
276
277
278
279
280
281
282
283
284
285
286
287
288
289
290
291
292
293
294
295
296
297
298
299
300
301
302
303
304
305
306
307
308
309
310
311
312
313
314
315
316
317
318
319
320
321
322
323
324
325
326
327
328
329
330
331
332
333
334
335
336
337
338
339
340
341
342
343
344
345
346
# Copyright 1999-2020 Gentoo Authors
# Distributed under the terms of the GNU General Public License v2

EAPI=7

CMAKE_MAKEFILE_GENERATOR="ninja"

PYTHON_COMPAT=( python3_{6,7,8,9} )

DISTUTILS_SINGLE_IMPL=1

inherit bash-completion-r1 cmake cuda distutils-r1 eutils flag-o-matic multilib readme.gentoo-r1 toolchain-funcs xdg-utils

if [[ $PV = *9999* ]]; then
	EGIT_REPO_URI="
		https://gitlab.com/gromacs/gromacs.git
		https://github.com/gromacs/gromacs.git
		git://git.gromacs.org/gromacs.git"
	[[ $PV = 9999 ]] && EGIT_BRANCH="master" || EGIT_BRANCH="release-${PV:0:4}"
	inherit git-r3
else
	SRC_URI="
		http://ftp.gromacs.org/gromacs/${PN}-${PV/_/-}.tar.gz
		test? ( http://ftp.gromacs.org/regressiontests/regressiontests-${PV/_/-}.tar.gz )"
	KEYWORDS="~amd64 ~arm ~x86 ~amd64-linux ~x86-linux ~x64-macos ~x86-macos"
fi

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"

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 +custom-cflags +doc -double-precision +fftw +gmxapi +gmxapi-legacy +hwloc lapack +lmfit mkl mpi +offensive opencl openmp +python +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 )
	${PYTHON_DEPS}
	!sci-chemistry/gmxapi
	"
BDEPEND="${CDEPEND}
	virtual/pkgconfig
	doc? (
		app-doc/doxygen
		$(python_gen_cond_dep '
			dev-python/sphinx[${PYTHON_MULTI_USEDEP}]
		')
		media-gfx/mscgen
		media-gfx/graphviz
		dev-texlive/texlive-latex
		dev-texlive/texlive-latexextra
		media-gfx/imagemagick
	)"
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 )"

if [[ ${PV} != *9999 ]]; then
	S="${WORKDIR}/${PN}-${PV/_/-}"
fi

PATCHES=( "${FILESDIR}/${PN}-2020_beta1-pytest.patch" )

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"
}

pkg_setup() {
	python-single-r1_pkg_setup
}

src_unpack() {
	if [[ ${PV} != *9999 ]]; then
		default
	else
		git-r3_src_unpack
		if use test; then
			EGIT_REPO_URI="git://git.gromacs.org/regressiontests.git" \
			EGIT_BRANCH="${EGIT_BRANCH}" \
			EGIT_CHECKOUT_DIR="${WORKDIR}/regressiontests"\
				git-r3_src_unpack
		fi
	fi
}

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"

	# try to create policy for imagemagik
	mkdir -p ${HOME}/.config/ImageMagick
	cat >> ${HOME}/.config/ImageMagick/policy.xml <<- EOF
	<?xml version="1.0" encoding="UTF-8"?>
	<!DOCTYPE policymap [
	<!ELEMENT policymap (policy)+>
	!ATTLIST policymap xmlns CDATA #FIXED ''>
	<!ELEMENT policy EMPTY>
	<!ATTLIST policy xmlns CDATA #FIXED '' domain NMTOKEN #REQUIRED
			name NMTOKEN #IMPLIED pattern CDATA #IMPLIED rights NMTOKEN #IMPLIED
			stealth NMTOKEN #IMPLIED value CDATA #IMPLIED>
	]>
	<policymap>
		<policy domain="coder" rights="read | write" pattern="PS" />
		<policy domain="coder" rights="read | write" pattern="PS2" />
		<policy domain="coder" rights="read | write" pattern="PS3" />
		<policy domain="coder" rights="read | write" pattern="EPS" />
		<policy domain="coder" rights="read | write" pattern="PDF" />
		<policy domain="coder" rights="read | write" pattern="XPS" />
	</policymap>
	EOF
}

src_configure() {
	local mycmakeargs_pre=( ) extra fft_opts=( )

	if use custom-cflags; then
		#go from slowest to fastest acceleration
		local acce="None"
		if (use amd64 || use x86); then
		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"
		use cpu_flags_x86_avx512f && acce="AVX_512"
		elif (use arm); then
			use cpu_flags_arm_neon && acce="ARM_NEON"
		elif (use arm64); then
			use cpu_flags_arm_neon && acce="ARM_NEON_ASIMD"
		fi
	else
		strip-flags
	fi

	#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_BUILD_MANUAL=$(usex doc)
		-DGMX_HWLOC=$(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 gpu=( "-DGMX_GPU=OFF" )
		[[ ${x} = "float" ]] && use cuda && gpu=( "-DGMX_GPU=CUDA" )
		use opencl && gpu=( "-DGMX_GPU=OPENCL" )
		mycmakeargs=(
			${mycmakeargs_pre[@]} ${p}
			-DGMX_MPI=OFF
			-DGMX_THREAD_MPI=$(usex threads)
			-DGMXAPI=$(usex gmxapi)
			-DGMX_INSTALL_LEGACY_API=$(usex gmxapi-legacy)
			"${gpu[@]}"
			"$(use test && echo -DREGRESSIONTEST_PATH="${WORKDIR}/${P}_${x}/tests")"
			-DGMX_BINARY_SUFFIX="${suffix}"
			-DGMX_LIBS_SUFFIX="${suffix}"
			-DGMX_PYTHON_PACKAGE=$(usex python)
		)
		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
		if use python; then
			BUILD_DIR="${WORKDIR}/${P}_${x}"\
				cmake_src_compile	python_packaging/all
			BUILD_DIR="${WORKDIR}/${P}" \
				distutils-r1_src_compile
		fi
		# not 100% necessary for rel ebuilds as available from website
		if use doc; then
			BUILD_DIR="${WORKDIR}/${P}_${x}"\
				cmake_src_compile manual
		fi
		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 python; then
			BUILD_DIR="${WORKDIR}/${P}_${x}" \
				cmake_src_install	python_packaging/install
		fi
		if use doc; then
			newdoc "${WORKDIR}/${P}_${x}"/docs/manual/gromacs.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
}