aboutsummaryrefslogtreecommitdiff
blob: 40d7fadd0f482e32566e66986f26c97d2b07248d (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
347
348
349
350
351
352
353
354
355
356
357
358
359
360
361
362
363
364
365
366
367
368
369
370
371
372
373
374
375
376
377
378
379
380
381
382
383
384
385
386
387
388
389
390
# Copyright 1999-2015 Gentoo Foundation
# Distributed under the terms of the GNU General Public License v2
# $Header: $

EAPI=5

PYTHON_COMPAT=( python{2_5,2_6,2_7} )

inherit autotools-utils eutils flag-o-matic fortran-2 multilib python-single-r1 toolchain-funcs

DESCRIPTION="Find total energy, charge density and electronic structure using density functional theory"
HOMEPAGE="http://www.abinit.org/"
SRC_URI="http://ftp.abinit.org/${P}.tar.gz"

LICENSE="GPL-2"
SLOT="0"
KEYWORDS="~amd64 ~x86"
IUSE="atompaw bigdft cuda cuda-double -debug +etsf_io +fftw fftw-mpi +fftw-threads +fox gsl +hdf5 levmar -libabinit libxc -lotf mpi +netcdf openmp python scalapack scripts -test +threads wannier"

REQUIRED_USE="${PYTHON_REQUIRED_USE}"
#"			scalapack? ( !bigdft )"

RDEPEND="virtual/blas
	virtual/lapack
	${PYTHON_DEPS}
	dev-python/numpy
	atompaw? ( >=sci-physics/atompaw-4.0.0.10[libxc?] )
	bigdft? ( >=sci-physics/bigdft-1.7.0.93[scalapack?]
		<sci-physics/bigdft-1.7.5 )
	cuda? ( dev-util/nvidia-cuda-sdk )
	etsf_io? ( >=sci-libs/etsf_io-1.0.4 )
	fftw? (
		sci-libs/fftw:3.0
		fftw-threads? (
			openmp? ( sci-libs/fftw:3.0[openmp] )
			!openmp? ( sci-libs/fftw:3.0[threads] )
			)
		fftw-mpi? (
			sci-libs/fftw:3.0[mpi]
			openmp? ( sci-libs/fftw:3.0[openmp] )
			!openmp? ( sci-libs/fftw:3.0[threads] )
			)
		)
	fox? ( >=sci-libs/fox-4.1.2-r2[sax] )
	gsl? ( sci-libs/gsl )
	hdf5? ( sci-libs/hdf5[fortran] )
	levmar? ( sci-libs/levmar )
	libxc? ( >=sci-libs/libxc-2.0.3[fortran]
			<sci-libs/libxc-2.2 )
	netcdf? (
		sci-libs/netcdf[hdf5?]
		|| (
			sci-libs/netcdf[fortran]
			sci-libs/netcdf-fortran
			)
		)
	mpi? ( virtual/mpi )
	scalapack? ( virtual/scalapack )
	scripts? ( dev-python/PyQt4 )
	wannier? ( >=sci-libs/wannier90-1.2-r1 )"
DEPEND="${RDEPEND}
	virtual/pkgconfig
	dev-perl/Text-Markdown"

S=${WORKDIR}/${P%[a-z]}

DOCS=( AUTHORS ChangeLog COPYING INSTALL KNOWN_PROBLEMS NEWS PACKAGING
	README README.ChangeLog README.GPU README.xlf RELNOTES THANKS )

FORTRAN_STANDARD=90

pkg_setup() {
	# Doesn't compile with gcc-4.0, only >=4.1
	if [[ $(tc-getFC) == *gfortran ]]; then
		if [[ $(gcc-major-version) -eq 4 ]] \
			&& [[ $(gcc-minor-version) -lt 1  ]]; then
				die "Requires gcc-4.1 or newer"
		fi
	fi

	# fortran-2.eclass does not handle mpi wrappers
	if use mpi; then
		export FC="mpif90"
		export F77="mpif77"
		export CC="mpicc"
		export CXX="mpic++"
	else
		tc-export FC F77 CC CXX
	fi

	# Preprocesor macross can make some lines really long
	append-fflags -ffree-line-length-none

	# This should be correct:
	#   It is gcc-centric because toolchain-funcs.eclass is gcc-centric.
	#   Should a bug be filed against toolchain-funcs.eclass?
	# if use openmp; then
	#         tc-has-openmp || \
	#                 die "Please select an openmp capable compiler like gcc[openmp]"
	# fi
	#
	# This is completely wrong:
	#   If other compilers than Gnu Compiler Collection can be used by portage,
	#   their support of OpenMP should be properly tested. This code limits the test
	#   to gcc, and blindly supposes that other compilers do support OpenMP.
	# if use openmp && [[ $(tc-getCC)$ == *gcc* ]] &&	! tc-has-openmp; then
	# 	die "Please select an openmp capable compiler like gcc[openmp]"
	# fi
	#
	# Luckily Abinit is a fortran package.
	#   fortran-2.eclass has its own test for OpenMP support,
	#   more general than toolchain-funcs.eclass
	#   The test itself proceeds inside fortran-2_pkg_setup
	if use openmp; then FORTRAN_NEED_OPENMP=1; fi

	fortran-2_pkg_setup

	if use openmp; then
		# based on _fortran-has-openmp() of fortran-2.eclass
		local code=ebuild-openmp-flags
		local ret
		local openmp

		pushd "${T}"
		cat <<- EOF > "${code}.c"
		# include <omp.h>
		main () {
			int nthreads;
			nthreads=omp_get_num_threads();
		}
		EOF

		for openmp in -fopenmp -xopenmp -openmp -mp -omp -qsmp=omp; do
			${CC} ${openmp} "${code}.c" -o "${code}.o" &>> "${T}"/_c_compile_test.log
			ret=$?
			(( ${ret} )) || break
		done

		rm -f "${code}.*"
		popd

		if (( ${ret} )); then
			die "Please switch to an openmp compatible C compiler"
		else
			export CC="${CC} ${openmp}"
			export CXX="${CXX} ${openmp}"
		fi

		pushd "${T}"
		cat <<- EOF > "${code}.f"
		1     call omp_get_num_threads
		2     end
		EOF

		for openmp in -fopenmp -xopenmp -openmp -mp -omp -qsmp=omp; do
			${FC} ${openmp} "${code}.f" -o "${code}.o" &>> "${T}"/_f_compile_test.log
			ret=$?
			(( ${ret} )) || break
		done

		rm -f "${code}.*"
		popd

		if (( ${ret} )); then
			die "Please switch to an openmp compatible fortran compiler."
		else
			export FC="${FC} ${openmp}"
			export F77="${F77} ${openmp}"
		fi
	fi

	# Sort out some USE options
	if use fftw-threads && ! use fftw; then
		ewarn "fftw-threads set but fftw not used, ignored."
	fi
	if use fftw-mpi; then
		if ! use fftw; then
			ewarn "fftw-mpi set but fftw not used, ignored."
		elif ! use mpi; then
			ewarn "fftw-mpi set but mpi not used, ignored."
		elif ! use fftw-threads; then
			ewarn "fftw-mpi set but fftw-threads not. Will use a threaded fftw nevertheless, required with MPI."
		fi
	fi
	if use cuda-double && ! use cuda; then
		ewarn "cuda-double set but cuda not used, ignored"
	fi

	python-single-r1_pkg_setup

}

src_prepare() {
	epatch \
		"${FILESDIR}"/6.2.2-change-default-directories.patch \
		"${FILESDIR}"/6.12.1-autoconf.patch \
		"${FILESDIR}"/6.12.1-xmalloc.patch \
		"${FILESDIR}"/7.10.4-libabinit_options.patch \
		"${FILESDIR}"/7.4.2-levmar_diag_scaling.patch \
		"${FILESDIR}"/7.4.2-cuda_link_stdc++.patch \
		"${FILESDIR}"/7.6.4-cuda_header.patch \
		"${FILESDIR}"/7.10.4-syntax.patch
	eautoreconf
	sed -e"s/\(grep '\^-\)\(\[LloW\]\)'/\1\\\(\2\\\|pthread\\\)'/g" -i configure || ewarn "sed on configure failed"
	python_fix_shebang "${S}"
}

src_configure() {
	local modules="$(FoX-config --sax --fcflags)"
	local FoX_libs="$(FoX-config --sax --libs)"

	local trio_flavor=""
	use etsf_io && trio_flavor="${trio_flavor}+etsf_io"
	use fox && trio_flavor="${trio_flavor}+fox"
	use netcdf && trio_flavor="${trio_flavor}+netcdf"
	test "no${trio_flavor}" = "no" && trio_flavor="none"

	local netcdff_libs="-lnetcdff"
	use hdf5 && netcdff_libs="${netcdff_libs} -lhdf5_fortran"

#	local linalg_flavor="atlas"
	local linalg_flavor="custom"
	local mylapack="lapack"
	use scalapack && mylapack="scalapack" && linalg_flavor="${linalg_flavor}+scalapack"

	local dft_flavor=""
	use atompaw && dft_flavor="${dft_flavor}+atompaw"
	use bigdft && dft_flavor="${dft_flavor}+bigdft"
	use libxc && dft_flavor="${dft_flavor}+libxc"
	use wannier && dft_flavor="${dft_flavor}+wannier90"
	test "no${dft_flavor}" = "no" && dft_flavor="none"

	local fft_flavor="fftw3"
	local fft_libs=""
	# The fftw threads support is protected by black magick.
	# Anybody removes it, dies.
	# New USE flag "fftw-threads" was added to control usage
	# of the threaded fftw variant. Since fftw-3.3 has expanded
	# the paralel options by MPI and OpenMP support, analogical
	# USE flags should be added to select them in future;
	# unusable with previous FFTW versions, they are postponed
	# for now.
	if use mpi && use fftw-mpi; then
		fft_flavor="fftw3-mpi"
		fft_libs+="$($(tc-getPKG_CONFIG) --libs fftw3_mpi)"
		fft_libs+="$($(tc-getPKG_CONFIG) --libs fftw3f_mpi)"
		if use openmp; then
			fft_libs+="$($(tc-getPKG_CONFIG) --libs fftw3_omp)"
			fft_libs+="$($(tc-getPKG_CONFIG) --libs fftw3f_omp)"
		else
			fft_libs+="$($(tc-getPKG_CONFIG) --libs fftw3_threads)"
			fft_libs+="$($(tc-getPKG_CONFIG) --libs fftw3f_threads)"
		fi
	elif use fftw-threads; then
		fft_flavor="fftw3-threads"
		if use openmp; then
			fft_libs+="$($(tc-getPKG_CONFIG) --libs fftw3_omp)"
			fft_libs+="$($(tc-getPKG_CONFIG) --libs fftw3f_omp)"
		else
			fft_libs+="$($(tc-getPKG_CONFIG) --libs fftw3_threads)"
			fft_libs+="$($(tc-getPKG_CONFIG) --libs fftw3f_threads)"
		fi
	else
		fft_libs+="$($(tc-getPKG_CONFIG) --libs fftw3)"
		fft_libs+="$($(tc-getPKG_CONFIG) --libs fftw3f)"
	fi

	local gpu_flavor="none"
	if use cuda; then
		gpu_flavor="cuda-single"
		if use cuda-double; then
			gpu_flavor="cuda-double"
		fi
	fi

	local myeconfargs=(
		--enable-clib
		--enable-exports
		$(use_enable debug debug enhanced)
		$(use_enable mpi)
		$(use_enable mpi mpi-io)
		$(use_enable openmp)
		$(use_enable lotf)
		$(use_enable cuda gpu)
		"$(use cuda && echo "--with-gpu-flavor=${gpu_flavor}")"
		"$(use cuda && echo "--with-gpu-prefix=/opt/cuda/")"
		"$(use gsl && echo "--with-math-flavor=gsl")"
		"$(use gsl && echo "--with-math-incs=$($(tc-getPKG_CONFIG) --cflags gsl)")"
		"$(use gsl && echo "--with-math-libs=$($(tc-getPKG_CONFIG) --libs gsl)")"
		"$(use levmar && echo "--with-algo-flavor=levmar")"
		"$(use levmar && echo "--with-algo-libs=-llevmar")"
		--with-linalg-flavor="${linalg_flavor}"
		--with-linalg-libs="$($(tc-getPKG_CONFIG) --libs "${mylapack}")"
		--with-trio-flavor="${trio_flavor}"
		"$(use netcdf && echo "--with-netcdf-incs=-I/usr/include")"
		"$(use netcdf && echo "--with-netcdf-libs=$($(tc-getPKG_CONFIG) --libs netcdf) ${netcdff_libs}")"
		"$(use fox && echo "--with-fox-incs=${modules}")"
		"$(use fox && echo "--with-fox-libs=${FoX_libs}")"
		"$(use etsf_io && echo "--with-etsf-io-incs=${modules}")"
		"$(use etsf_io && echo "--with-etsf-io-libs=-letsf_io -letsf_io_utils -letsf_io_low_level")"
		--with-dft-flavor="${dft_flavor}"
		"$(use atompaw && echo "--with-atompaw-incs=${modules}")"
		"$(use atompaw && echo "--with-atompaw-libs=-latompaw")"
		"$(use bigdft && echo "--with-bigdft-incs=${modules}")"
		"$(use bigdft && echo "--with-bigdft-libs=$($(tc-getPKG_CONFIG) --libs bigdft)")"
		"$(use libxc && echo "--with-libxc-incs=${modules}")"
		"$(use libxc && echo "--with-libxc-libs=$($(tc-getPKG_CONFIG) --libs libxc)")"
		"$(use wannier && echo "--with-wannier90-bins=/usr/bin")"
		"$(use wannier && echo "--with-wannier90-incs=${modules}")"
		"$(use wannier && echo "--with-wannier90-libs=-lwannier $($(tc-getPKG_CONFIG) --libs blas lapack)")"
		"$(use fftw && echo "--with-fft-flavor=${fft_flavor}")"
		"$(use fftw && echo "--with-fft-incs=-I/usr/include")"
		"$(use fftw && echo "--with-fft-libs=${fft_libs}")"
		--with-timer-flavor="abinit"
		LD="$(tc-getLD)"
		FCFLAGS="${FCFLAGS:- ${FFLAGS:- -O2}} ${modules} -I/usr/include"
		)

	MARKDOWN=Markdown.pl autotools-utils_src_configure
}

src_compile() {
	autotools-utils_src_compile

	# Apparently libabinit.a is not built by default
	# Used by BigDFT. Should probably be built separately,
	# as a package of its own: BigDFT used by Abinit.
	# Does libabinit.a depend on BigDFT, if used?
	# Can Abinit use external libabinit.a?
	use libabinit && autotools-utils_src_compile libabinit.a

	sed -i -e's/libatlas/lapack/' "${AUTOTOOLS_BUILD_DIR}"/config.pc || ewarn "sed on config.pc failed"
}

src_test() {
	einfo "The complete tests take quite a while, easily several hours or even days."
	# autotools-utils_src_test expanded and modified
	_check_build_dir
	pushd "${BUILD_DIR}" > /dev/null || die

	einfo "Running the internal tests."
	emake tests_in || ewarn 'The internal tests failed.'

	einfo "Running the thorough tests. Be patient, please."
	"${S}"/tests/runtests.py || ewarn "The package has not passed the thorough tests."

	popd > /dev/null || die
}

src_install() {
	#autotools-utils_src_install() expanded
	_check_build_dir
	pushd "${AUTOTOOLS_BUILD_DIR}" > /dev/null
	emake DESTDIR="${D}" install || die "make install failed"

	use libabinit && dolib libabinit.a

	if use test; then
		for dc in results.tar.gz results.txt suite_report.html; do
			test -e Test_suite/"${dc}" && dodoc Test_suite/"${dc}" || ewarn "Copying tests results ${dc} failed"
		done
	fi

	popd > /dev/null

	# XXX: support installing them from builddir as well!!!
	if [[ ${DOCS} ]]; then
		dodoc "${DOCS[@]}" || die "dodoc failed"
	else
		local f
		# same list as in PMS
		for f in README* ChangeLog AUTHORS NEWS TODO CHANGES \
				THANKS BUGS FAQ CREDITS CHANGELOG; do
			if [[ -s ${f} ]]; then
				dodoc "${f}" || ewarn "(default) dodoc ${f} failed"
			fi
		done
	fi
	if [[ ${HTML_DOCS} ]]; then
		dohtml -r "${HTML_DOCS[@]}" || ewarn "dohtml failed"
	fi

	if use scripts; then
		insinto /usr/share/"${P}"
		doins -r scripts
	fi

	# Remove libtool files and unnecessary static libs
	prune_libtool_files
}