Attachment #188807 for bug #260995

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# Copyright 1999-2009 Gentoo Foundation
# Distributed under the terms of the GNU General Public License v2
# $Header: $

EAPI="1"

LIBTOOLIZE="true"

inherit autotools bash-completion eutils fortran multilib

DESCRIPTION="The ultimate molecular dynamics simulation package"
HOMEPAGE="http://www.gromacs.org/"
SRC_URI="ftp://ftp.gromacs.org/pub/${PN}/${P}.tar.gz
		test? ( ftp://ftp.gromacs.org/pub/tests/gmxtest-${PV}.tgz )
		doc? ( ftp://ftp.gromacs.org/pub/manual/manual-4.0.pdf )"

LICENSE="GPL-2"
SLOT="0"
KEYWORDS="~alpha ~amd64 ~ppc64 ~sparc ~x86"
IUSE="X blas dmalloc doc -double-precision fftw fkernels gsl lapack mpi +single-precision static test +xml zsh-completion"

DEPEND="app-shells/tcsh
	X? ( x11-libs/libX11 )
	dmalloc? ( dev-libs/dmalloc )

DEPEND=">=sci-libs/fftw-3.0.1
	app-shells/tcsh
	X? ( x11-libs/libX11
		x11-libs/libXt
		x11-libs/libXp
		x11-libs/libXext
		x11-proto/xproto
		x11-libs/openmotif )
	blas? ( virtual/blas )
	fftw? ( >=sci-libs/fftw-3.0.1 )
	gsl? ( sci-libs/gsl )
	lapack? ( virtual/lapack )
	mpi? ( virtual/mpi )


RDEPEND="${DEPEND}"

FORTRAN="g77 gfortran ifc"

src_unpack() {

	unpack ${A}
	cd "${S}"
	# Fix typos in a couple of files.

	-i src/tools/Makefile.am \
	|| die "sed tools/Makefile.am failed"

	use fkernels && epatch "${FILESDIR}/${P}-configure-gfortran.patch"

	eautoreconf

	cd "${WORKDIR}"

}

src_compile() {

	# static should work but something's broken.
	# gcc spec file may be screwed up.
	# Static linking should try -lgcc instead of -lgcc_s.
	# For more info:
	# http://lists.debian.org/debian-gcc/2002/debian-gcc-200201/msg00150.html

	# We will compile single precision by default, and suffix double-precision with _d.
	# Sparc is the only arch I can test on that needs to use fortran.
	local myconf ;
	local myconf_s ;
	local myconf_d ;
	local suffix_d ;

	#leave all assembly options enabled mdrun is smart enough to deside itself
	#there so no gentoo on bluegene!
	myconf="${myconf} --disable-bluegene"

	#from gromacs configure
	if ! use fftw; then
		ewarn "WARNING: The built-in FFTPACK routines are slow."
		ewarn "Are you sure you don\'t want to use FFTW?"
		ewarn "It is free and much faster..."
	fi

	if [[ $(gcc-version) == "4.1" ]]; then
		ewarn "gcc 4.1 is not supported by gromacs"
		ewarn "please run test suite"
	fi

	#fortran will gone in gromacs 4.1 anyway
	#note for gentoo-PREFIX on aix, fortran (xlf) is still much faster
	if use fkernels; then
		ewarn "Fortran kernels are usually not faster than C kernels and assembly"
		ewarn "I hope, you know what are you doing..."
		FORTRAN="g77 gfortran ifc"
		myconf="${myconf} --enable-fortran" && fortran_pkg_setup
	else
		myconf="${myconf} --disable-fortran"
	fi
			else
				if ! has_version "=sys-devel/gcc-3*" ; then
					die "If you must run gromacs without sse (not recommended) gfortran will not work."
				else
					myconf="${myconf} --enable-fortran" && fortran_pkg_setup
				fi
			fi
			;;

		ia64)
			myconf="$myconf --enable-ia64-asm --disable-fortran"
			;;

		alpha)
			if ! has_version "=sys-devel/gcc-3*" ; then
				die "If you must run gromacs without sse (not recommended) gfortran will not work."
			else
				myconf="$myconf --enable-fortran" && fortran_pkg_setup
			fi
			;;

		sparc)
			if ! has_version "=sys-devel/gcc-3*" ; then
				die "If you must run gromacs without sse (not recommended) gfortran will not work."
			else
				myconf="${myconf} --enable-fortran" && fortran_pkg_setup
			fi
			;;
	esac

	# if we need external blas
	if use blas; then

	myconf="--datadir=/usr/share \
			--bindir=/usr/bin \
			--libdir=/usr/$(get_libdir) \
			$(use_with dmalloc) \
			$(use_with fftw fft fftw3) \
			$(use_with gsl) \
			$(use_enable mpi) \
			$(use_with X x) \

			$(use_enable static all-static) \
			${myconf}"

	#if we build both double is suffixed
	if ( use double-precision && use single-precision ); then
		suffix_d="_d"	
	else
		suffix_d=""
	fi
		emake || die "Single Precision emake failed"

		einfo "Building Double Precision Gromacs"
		cd "${WORKDIR}"/"${P}"-double
		myconf_d="${myconf} --enable-double --disable-float --program-suffix=_d"
		econf ${myconf_d} || die "Double Precision econf failed"
		emake || die "Double Precision emake failed"

	if use double-precision ; then
		#from gromacs manual
		elog 
		elog For most simulations single precision is accurate enough. In some
		elog cases double precision is required	to get reasonable results:
		elog
		elog -normal mode analysis, for the conjugate gradient or l-bfgs minimization
		elog  and the calculation and diagonalization of the Hessian 
		elog -calculation of the constraint force between two large groups of atoms
		elog -energy conservation: this can only be done without temperature coupling and
		elog  without cutoffs
		elog
		einfo "Building Double Precison Gromacs"
		cd "${WORKDIR}"/"${P}"-double
		myconf_d="${myconf} --enable-double --program-suffix='${suffix_d}'"
		econf ${myconf_d} || die "Double Precision econf failed"
		emake || die "Double Precision emake failed"
	fi

	if use single-precision ; then
		einfo "Building Single Precison Gromacs"
		cd "${WORKDIR}"/"${P}"-single
		myconf_s="${myconf} --enable-float --program-suffix=''"
		econf ${myconf_s} || die "configure failed"
		emake || die "Single Precision emake failed"
	fi
}

src_test() {
	if use single-precision ; then
		export PATH="${WORKDIR}/${P}-single/src/kernel:${WORKDIR}/${P}-single/src/tools:$PATH"
		cd "${WORKDIR}/gmxtest"
		#test is broken, only do simple tests
		./gmxtest.pl simple || die "Single Precision test failed"
	fi

	if use double-precision ; then
		export PATH="${WORKDIR}/${P}-double/src/kernel:${WORKDIR}/${P}-double/src/tools:$PATH"
		cd "${WORKDIR}/gmxtest"
		use single-precision && ./gmxtest.pl clean
		#test is broken, only do simple tests
		./gmxtest.pl -double simple || die "Double Precision test failed"	
	fi
}

src_install() {
	if use single-precision ; then
		einfo "Installing Single Precision"

		cd "${WORKDIR}"/"${P}"-double
		emake DESTDIR="${D}" install || die "Installing Double Precision failed"
	fi
	
	sed -n -e '/^GMXBIN/,/^GMXDATA/p' ${D}/usr/bin/GMXRC.bash > "${T}/80gromacs"
	doenvd "${T}/80gromacs"
	rm -f ${D}/usr/bin/GMXRC*
	
	dobashcompletion ${D}/usr/bin/completion.bash ${PN}
	if use zsh-completion ; then
		insinto /usr/share/zsh/site-functions
		newins ${D}/usr/bin/completion.zsh _${PN}
	fi
	rm -r ${D}/usr/bin/completion.*

	dodoc AUTHORS INSTALL README
	if use doc; then
		# Move html and leave examples and templates under /usr/share/gromacs.
		mv "${D}"/usr/share/"${PN}"/html "${D}"/usr/share/doc/"${PF}"/
		dodoc "${DISTDIR}"/manual-4.0.pdf
	fi
}

pkg_postinst() {
	env-update && source /etc/profile
	elog
	elog Please read and cite:
	elog Gromacs 4, J. Chem. Theory Comput. 4, 435 \(2008\). 
	elog http://dx.doi.org/10.1021/ct700301q
	elog
	bash-completion_pkg_postinst
	elog
	elog $(luck)
	elog For more Gromacs cool quotes \(gcq\)  add luck to your .bashrc
	elog
}

Return to bug 260995

Lines 1-35 Link Here

(-)gromacs-4.0.3.ebuild (-102 / +110 lines)
1	# Copyright 1999-2009 Gentoo Foundation	1	# Copyright 1999-2009 Gentoo Foundation
2	# Distributed under the terms of the GNU General Public License v2	2	# Distributed under the terms of the GNU General Public License v2
3	# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/gromacs/gromacs-4.0.3.ebuild,v 1.2 2009/03/08 19:50:46 maekke Exp $	3	# $Header: $
4		4
5	EAPI="1"	5	EAPI="1"
6		6
7	LIBTOOLIZE="true"	7	LIBTOOLIZE="true"
8		8
9	inherit autotools eutils flag-o-matic fortran multilib	9	inherit autotools bash-completion eutils fortran multilib
10		10
11	DESCRIPTION="The ultimate molecular dynamics simulation package"	11	DESCRIPTION="The ultimate molecular dynamics simulation package"
12	HOMEPAGE="http://www.gromacs.org/"	12	HOMEPAGE="http://www.gromacs.org/"
13	SRC_URI="ftp://ftp.gromacs.org/pub/${PN}/${P}.tar.gz"	13	SRC_URI="ftp://ftp.gromacs.org/pub/${PN}/${P}.tar.gz
		14	test? ( ftp://ftp.gromacs.org/pub/tests/gmxtest-${PV}.tgz )
		15	doc? ( ftp://ftp.gromacs.org/pub/manual/manual-4.0.pdf )"
14		16
15	LICENSE="GPL-2"	17	LICENSE="GPL-2"
16	SLOT="0"	18	SLOT="0"
17	KEYWORDS="~alpha amd64 ~ppc64 ~sparc x86"	19	KEYWORDS="~alpha ~amd64 ~ppc64 ~sparc ~x86"
18	IUSE="3dnow X altivec blas double-precision gsl lapack mpi +single-precision sse sse2 static xml"	20	IUSE="X blas dmalloc doc -double-precision fftw fkernels gsl lapack mpi +single-precision static test +xml zsh-completion"
19		21
20	# mopac7 qm/mm is broken until we can get files from	22	DEPEND="app-shells/tcsh
21	# http://md.chem.rug.nl/~groenhof/qmmm.html	23	X? ( x11-libs/libX11 )
22	# or somewhere else...	24	dmalloc? ( dev-libs/dmalloc )
23
24	DEPEND=">=sci-libs/fftw-3.0.1
25	app-shells/tcsh
26	X? ( x11-libs/libX11
27	x11-libs/libXt
28	x11-libs/libXp
29	x11-libs/libXext
30	x11-proto/xproto
31	x11-libs/openmotif )
32	blas? ( virtual/blas )	25	blas? ( virtual/blas )
		26	fftw? ( >=sci-libs/fftw-3.0.1 )
33	gsl? ( sci-libs/gsl )	27	gsl? ( sci-libs/gsl )
34	lapack? ( virtual/lapack )	28	lapack? ( virtual/lapack )
35	mpi? ( virtual/mpi )	29	mpi? ( virtual/mpi )
Lines 37-46 Link Here
37		31
38	RDEPEND="${DEPEND}"	32	RDEPEND="${DEPEND}"
39		33
40	FORTRAN="g77 gfortran ifc"
41
42	src_unpack() {	34	src_unpack() {
43
44	unpack ${A}	35	unpack ${A}
45	cd "${S}"	36	cd "${S}"
46	# Fix typos in a couple of files.	37	# Fix typos in a couple of files.
Lines 64-69 Link Here
64	-i src/tools/Makefile.am \	55	-i src/tools/Makefile.am \
65	\|\| die "sed tools/Makefile.am failed"	56	\|\| die "sed tools/Makefile.am failed"
66		57
		58	use fkernels && epatch "${FILESDIR}/${P}-configure-gfortran.patch"
		59
67	eautoreconf	60	eautoreconf
68		61
69	cd "${WORKDIR}"	62	cd "${WORKDIR}"
Lines 75-148 Link Here
75	}	68	}
76		69
77	src_compile() {	70	src_compile() {
78
79	# static should work but something's broken.
80	# gcc spec file may be screwed up.
81	# Static linking should try -lgcc instead of -lgcc_s.
82	# For more info:
83	# http://lists.debian.org/debian-gcc/2002/debian-gcc-200201/msg00150.html
84
85	# We will compile single precision by default, and suffix double-precision with _d.
86	# Sparc is the only arch I can test on that needs to use fortran.
87	local myconf ;	71	local myconf ;
88	local myconf_s ;	72	local myconf_s ;
89	local myconf_d ;	73	local myconf_d ;
		74	local suffix_d ;
90		75
91	case "${ARCH}" in	76	#leave all assembly options enabled mdrun is smart enough to deside itself
92		77	#there so no gentoo on bluegene!
93	x86)	78	myconf="${myconf} --disable-bluegene"
94	if ( use sse \|\| use sse2 ) ; then	79
95	myconf="${myconf} --enable-ia32-sse"	80	#from gromacs configure
96	fi	81	if ! use fftw; then
97	myconf="$myconf $(use_enable 3dnow ia32-3dnow)"	82	ewarn "WARNING: The built-in FFTPACK routines are slow."
98		83	ewarn "Are you sure you don\'t want to use FFTW?"
99	if ( ! use sse && ! use sse2 && ! use 3dnow ) ; then	84	ewarn "It is free and much faster..."
100	if ! has_version "=sys-devel/gcc-3*" ; then	85	fi
101	die "If you must run gromacs without sse (not recommended) gfortran will not work."	86
102	else	87	if [[ $(gcc-version) == "4.1" ]]; then
103	myconf="${myconf} --enable-fortran" && fortran_pkg_setup	88	ewarn "gcc 4.1 is not supported by gromacs"
104	fi	89	ewarn "please run test suite"
105	else	90	fi
106	myconf="${myconf} --disable-fortran"	91
107	fi	92	#fortran will gone in gromacs 4.1 anyway
108	;;	93	#note for gentoo-PREFIX on aix, fortran (xlf) is still much faster
109		94	if use fkernels; then
110	amd64)	95	ewarn "Fortran kernels are usually not faster than C kernels and assembly"
111	myconf="$myconf --enable-x86-64-sse --disable-fortran"	96	ewarn "I hope, you know what are you doing..."
112	;;	97	FORTRAN="g77 gfortran ifc"
113		98	myconf="${myconf} --enable-fortran" && fortran_pkg_setup
114	ppc*)	99	else
115	if use altivec ; then	100	myconf="${myconf} --disable-fortran"
116	myconf="${myconf} --enable-ppc-altivec --disable-fortran"	101	fi
117	else
118	if ! has_version "=sys-devel/gcc-3*" ; then
119	die "If you must run gromacs without sse (not recommended) gfortran will not work."
120	else
121	myconf="${myconf} --enable-fortran" && fortran_pkg_setup
122	fi
123	fi
124	;;
125
126	ia64)
127	myconf="$myconf --enable-ia64-asm --disable-fortran"
128	;;
129
130	alpha)
131	if ! has_version "=sys-devel/gcc-3*" ; then
132	die "If you must run gromacs without sse (not recommended) gfortran will not work."
133	else
134	myconf="$myconf --enable-fortran" && fortran_pkg_setup
135	fi
136	;;
137
138	sparc)
139	if ! has_version "=sys-devel/gcc-3*" ; then
140	die "If you must run gromacs without sse (not recommended) gfortran will not work."
141	else
142	myconf="${myconf} --enable-fortran" && fortran_pkg_setup
143	fi
144	;;
145	esac
146		102
147	# if we need external blas	103	# if we need external blas
148	if use blas; then	104	if use blas; then
Lines 159-165 Link Here
159	myconf="--datadir=/usr/share \	115	myconf="--datadir=/usr/share \
160	--bindir=/usr/bin \	116	--bindir=/usr/bin \
161	--libdir=/usr/$(get_libdir) \	117	--libdir=/usr/$(get_libdir) \
162	--with-fft=fftw3 \	118	$(use_with dmalloc) \
		119	$(use_with fftw fft fftw3) \
163	$(use_with gsl) \	120	$(use_with gsl) \
164	$(use_enable mpi) \	121	$(use_enable mpi) \
165	$(use_with X x) \	122	$(use_with X x) \
Lines 167-201 Link Here
167	$(use_enable static all-static) \	124	$(use_enable static all-static) \
168	${myconf}"	125	${myconf}"
169		126
		127	#if we build both double is suffixed
170	if ( use double-precision && use single-precision ); then	128	if ( use double-precision && use single-precision ); then
171	einfo "Building Single Precison Gromacs"	129	suffix_d="_d"
172	cd "${WORKDIR}"/"${P}"-single	130	else
173	myconf_s="${myconf} --enable-float --disable-double --program-suffix=''"	131	suffix_d=""
174	econf ${myconf_s} \|\| die "Single Precision econf failed"	132	fi
175	emake \|\| die "Single Precision emake failed"
176
177	einfo "Building Double Precision Gromacs"
178	cd "${WORKDIR}"/"${P}"-double
179	myconf_d="${myconf} --enable-double --disable-float --program-suffix=_d"
180	econf ${myconf_d} \|\| die "Double Precision econf failed"
181	emake \|\| die "Double Precision emake failed"
182		133
183	elif use double-precision ; then	134	if use double-precision ; then
		135	#from gromacs manual
		136	elog
		137	elog For most simulations single precision is accurate enough. In some
		138	elog cases double precision is required to get reasonable results:
		139	elog
		140	elog -normal mode analysis, for the conjugate gradient or l-bfgs minimization
		141	elog and the calculation and diagonalization of the Hessian
		142	elog -calculation of the constraint force between two large groups of atoms
		143	elog -energy conservation: this can only be done without temperature coupling and
		144	elog without cutoffs
		145	elog
184	einfo "Building Double Precison Gromacs"	146	einfo "Building Double Precison Gromacs"
185	cd "${WORKDIR}"/"${P}"-double	147	cd "${WORKDIR}"/"${P}"-double
186	myconf_d="${myconf} --enable-double --disable-float --program-suffix=''"	148	myconf_d="${myconf} --enable-double --program-suffix='${suffix_d}'"
187	econf ${myconf_d} \|\| die "Double Precision econf failed"	149	econf ${myconf_d} \|\| die "Double Precision econf failed"
188	emake \|\| die "Double Precision emake failed"	150	emake \|\| die "Double Precision emake failed"
		151	fi
189		152
190	elif use single-precision ; then	153	if use single-precision ; then
191	einfo "Building Single Precison Gromacs"	154	einfo "Building Single Precison Gromacs"
192	cd "${WORKDIR}"/"${P}"-single	155	cd "${WORKDIR}"/"${P}"-single
193	myconf_s="${myconf} --enable-float --disable-double --program-suffix=''"	156	myconf_s="${myconf} --enable-float --program-suffix=''"
194	econf ${myconf_s} \|\| die "configure failed"	157	econf ${myconf_s} \|\| die "configure failed"
195	emake \|\| die "Single Precision emake failed"	158	emake \|\| die "Single Precision emake failed"
196	fi	159	fi
197	}	160	}
198		161
		162	src_test() {
		163	if use single-precision ; then
		164	export PATH="${WORKDIR}/${P}-single/src/kernel:${WORKDIR}/${P}-single/src/tools:$PATH"
		165	cd "${WORKDIR}/gmxtest"
		166	#test is broken, only do simple tests
		167	./gmxtest.pl simple \|\| die "Single Precision test failed"
		168	fi
		169
		170	if use double-precision ; then
		171	export PATH="${WORKDIR}/${P}-double/src/kernel:${WORKDIR}/${P}-double/src/tools:$PATH"
		172	cd "${WORKDIR}/gmxtest"
		173	use single-precision && ./gmxtest.pl clean
		174	#test is broken, only do simple tests
		175	./gmxtest.pl -double simple \|\| die "Double Precision test failed"
		176	fi
		177	}
		178
199	src_install() {	179	src_install() {
200	if use single-precision ; then	180	if use single-precision ; then
201	einfo "Installing Single Precision"	181	einfo "Installing Single Precision"
Lines 208-215 Link Here
208	cd "${WORKDIR}"/"${P}"-double	188	cd "${WORKDIR}"/"${P}"-double
209	emake DESTDIR="${D}" install \|\| die "Installing Double Precision failed"	189	emake DESTDIR="${D}" install \|\| die "Installing Double Precision failed"
210	fi	190	fi
		191
		192	sed -n -e '/^GMXBIN/,/^GMXDATA/p' ${D}/usr/bin/GMXRC.bash > "${T}/80gromacs"
		193	doenvd "${T}/80gromacs"
		194	rm -f ${D}/usr/bin/GMXRC*
		195
		196	dobashcompletion ${D}/usr/bin/completion.bash ${PN}
		197	if use zsh-completion ; then
		198	insinto /usr/share/zsh/site-functions
		199	newins ${D}/usr/bin/completion.zsh _${PN}
		200	fi
		201	rm -r ${D}/usr/bin/completion.*
211		202
212	dodoc AUTHORS INSTALL README	203	dodoc AUTHORS INSTALL README
213	# Move html and leave examples and templates under /usr/share/gromacs.	204	if use doc; then
214	mv "${D}"/usr/share/"${PN}"/html "${D}"/usr/share/doc/"${PF}"/	205	# Move html and leave examples and templates under /usr/share/gromacs.
		206	mv "${D}"/usr/share/"${PN}"/html "${D}"/usr/share/doc/"${PF}"/
		207	dodoc "${DISTDIR}"/manual-4.0.pdf
		208	fi
		209	}
		210
		211	pkg_postinst() {
		212	env-update && source /etc/profile
		213	elog
		214	elog Please read and cite:
		215	elog Gromacs 4, J. Chem. Theory Comput. 4, 435 \(2008\).
		216	elog http://dx.doi.org/10.1021/ct700301q
		217	elog
		218	bash-completion_pkg_postinst
		219	elog
		220	elog $(luck)
		221	elog For more Gromacs cool quotes \(gcq\) add luck to your .bashrc
		222	elog
215	}	223	}