summaryrefslogtreecommitdiff
blob: de7348f6190bab12209520417a67a92113a1f8b4 (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
# Copyright 1999-2014 Gentoo Foundation
# Distributed under the terms of the GNU General Public License v2
# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/gromacs/gromacs-4.6.5.ebuild,v 1.2 2014/01/19 10:30:04 ago Exp $

EAPI=5

TEST_PV="4.6.5"
MANUAL_PV="4.6.5"

CMAKE_MAKEFILE_GENERATOR="ninja"

inherit bash-completion-r1 cmake-utils cuda eutils multilib readme.gentoo toolchain-funcs

if [[ $PV = *9999* ]]; then
	EGIT_REPO_URI="git://git.gromacs.org/gromacs.git
		https://gerrit.gromacs.org/gromacs.git
		git://github.com/gromacs/gromacs.git
		http://repo.or.cz/r/gromacs.git"
	EGIT_BRANCH="release-4-6"
	inherit git-2
	LIVE_DEPEND="doc? (
		dev-texlive/texlive-latex
		dev-texlive/texlive-latexextra
		media-gfx/imagemagick
		sys-apps/coreutils
	)"
else
	SRC_URI="ftp://ftp.gromacs.org/pub/${PN}/${P}.tar.gz
		doc? ( ftp://ftp.gromacs.org/pub/manual/manual-${MANUAL_PV}.pdf -> ${PN}-manual-${MANUAL_PV}.pdf )
		test? ( http://${PN}.googlecode.com/files/regressiontests-${TEST_PV}.tar.gz )"
	LIVE_DEPEND=""
fi

ACCE_IUSE="sse2 sse4_1 avx128fma avx256"

DESCRIPTION="The ultimate molecular dynamics simulation package"
HOMEPAGE="http://www.gromacs.org/"

# see COPYING for details
# http://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}"
KEYWORDS="~alpha ~amd64 ~arm ppc64 ~sparc ~x86 ~amd64-linux ~x86-linux ~x86-macos"
IUSE="X blas cuda doc -double-precision +fftw gsl lapack mkl 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-4.2.9-r1 )
	fftw? ( sci-libs/fftw:3.0 )
	gsl? ( sci-libs/gsl )
	lapack? ( virtual/lapack )
	mkl? ( sci-libs/mkl )
	mpi? ( virtual/mpi )
	openmm? (
		>=dev-util/nvidia-cuda-toolkit-4.2.9-r1
		sci-libs/openmm[cuda,opencl]
	)"
DEPEND="${CDEPEND}
	virtual/pkgconfig
	${LIVE_DEPEND}"
RDEPEND="${CDEPEND}"

REQUIRED_USE="
	|| ( single-precision double-precision )
	cuda? ( single-precision )
	openmm? ( single-precision )
	mkl? ( !blas !fftw !lapack )"

DOCS=( AUTHORS README )
HTML_DOCS=( "${ED}"/usr/share/gromacs/html/ )

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_unpack() {
	if [[ ${PV} != *9999 ]]; then
		default
	else
		git-2_src_unpack
		if use doc; then
			EGIT_REPO_URI="git://git.gromacs.org/manual.git" \
			EGIT_BRANCH="release-4-6" EGIT_NOUNPACK="yes" EGIT_COMMIT="release-4-6" \
			EGIT_SOURCEDIR="${WORKDIR}/manual"\
				git-2_src_unpack
		fi
		if use test; then
			EGIT_REPO_URI="git://git.gromacs.org/regressiontests.git" \
			EGIT_BRANCH="master" EGIT_NOUNPACK="yes" EGIT_COMMIT="master" \
			EGIT_SOURCEDIR="${WORKDIR}/regressiontests"\
				git-2_src_unpack
		fi
	fi
}

src_prepare() {
	#notes/todos
	# -on apple: there is framework support

	cmake-utils_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 sse2 && acce="SSE2"
	use sse4_1 && 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"

	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[@]}"
		$(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)
		$(cmake-utils_use offensive GMX_COOL_QUOTES)
		-DGMX_DEFAULT_SUFFIX=off
		-DGMX_ACCELERATION="$acce"
		-DGMXLIB="$(get_libdir)"
		-DGMX_VMD_PLUGIN_PATH="${EPREFIX}/usr/$(get_libdir)/vmd/plugins/*/molfile/"
		-DGMX_PREFIX_LIBMD=ON
		-DGMX_X86_AVX_GCC_MASKLOAD_BUG=OFF
		-DGMX_USE_GCC44_BUG_WORKAROUND=OFF
		${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 )
		mycmakeargs=( ${mycmakeargs_pre[@]} ${p} -DGMX_MPI=OFF
			$(cmake-utils_use threads GMX_THREAD_MPI) "${cuda[@]}" -DGMX_OPENMM=OFF
			"$(use test && echo -DREGRESSIONTEST_PATH="${WORKDIR}/${P}_${x}/tests")"
			-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[@]} ${p} -DGMX_MPI=OFF
				-DGMX_THREAD_MPI=OFF -DGMX_GPU=OFF -DGMX_OPENMM=ON
				-DOpenMM_PLUGIN_DIR="${EPREFIX}/usr/$(get_libdir)/plugins"
				-DGMX_BINARY_SUFFIX="_openmm" -DGMX_LIBS_SUFFIX="_openmm" )
			BUILD_DIR="${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 ${cuda} -DGMX_OPENMM=OFF
			-DGMX_BINARY_SUFFIX="_mpi${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 ${GMX_DIRS}; do
		BUILD_DIR="${WORKDIR}/${P}_${x}"\
			cmake-utils_src_make check
	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
		#manual can only be build after gromacs was installed once in image
		if use doc && [[ $PV = *9999*  && ! -d ${WORKDIR}/manual_build ]]; then
			mycmakeargs=( -DGMXBIN="${ED}"/usr/bin -DGMXSRC="${WORKDIR}/${P}" )
			BUILD_DIR="${WORKDIR}"/manual_build \
				CMAKE_USE_DIR="${WORKDIR}/manual" cmake-utils_src_configure
			[[ ${CHOST} = *-darwin* ]] && \
				export DYLD_LIBRARY_PATH="${DYLD_LIBRARY_PATH}${DYLD_LIBRARY_PATH:+:}${ED}/usr/$(get_libdir)"
			BUILD_DIR="${WORKDIR}"/manual_build cmake-utils_src_make
			[[ ${CHOST} = *-darwin* ]] && DYLD_LIBRARY_PATH="${ED}/usr/$(get_libdir)"
			newdoc "${WORKDIR}"/manual_build/gromacs.pdf "${PN}-manual-${PV}.pdf"
		fi
		use mpi || continue
		BUILD_DIR="${WORKDIR}/${P}_${x}_mpi" \
			DESTDIR="${D}" cmake-utils_src_make install-mdrun
	done

	use doc && [[ $PV != *9999* ]] && dodoc "${DISTDIR}/${PN}-manual-${MANUAL_PV}.pdf"
	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.*
	rm -rf "${ED}"usr/share/gromacs/html
	rm -f "${ED}"usr/bin/g_options*
	rm -f "${ED}"usr/bin/GMXRC*

	readme.gentoo_create_doc
}

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
	readme.gentoo_print_elog
}