sci-chemistry/gromacs: added live ebuilds for old, stable, experimental branch

(Portage version: 2.1.6.13/git/Linux i686)
 (Signed Manifest commit)

1 files changed, 233 insertions, 0 deletions

diff --git a/sci-chemistry/gromacs/gromacs-9999.ebuild b/sci-chemistry/gromacs/gromacs-9999.ebuild
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+# Copyright 1999-2009 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: $
+
+EAPI="2"
+
+LIBTOOLIZE="true"
+TEST_PV="4.0.4"
+
+inherit autotools bash-completion eutils fortran git multilib
+
+DESCRIPTION="The ultimate molecular dynamics simulation package"
+HOMEPAGE="http://www.gromacs.org/"
+SRC_URI="test? ( ftp://ftp.gromacs.org/pub/tests/gmxtest-${TEST_PV}.tgz )
+		doc? ( ftp://ftp.gromacs.org/pub/manual/manual-4.0.pdf )"
+
+LICENSE="GPL-2"
+SLOT="0"
+KEYWORDS="~alpha ~amd64 ~ppc64 ~sparc ~x86"
+IUSE="X blas dmalloc doc -double-precision +fftw fkernels gsl lapack mpi +single-precision static test +xml zsh-completion"
+
+DEPEND="app-shells/tcsh
+	X? ( x11-libs/libX11 )
+	dmalloc? ( dev-libs/dmalloc )
+	blas? ( virtual/blas )
+	fftw? ( sci-libs/fftw:3.0 )
+	gsl? ( sci-libs/gsl )
+	lapack? ( virtual/lapack )
+	mpi? ( virtual/mpi )
+	xml? ( dev-libs/libxml2 )"
+
+RDEPEND="${DEPEND}"
+
+RESTRICT="test"
+
+EGIT_REPO_URI="git://git.gromacs.org/gromacs"
+
+src_prepare() {
+	# Fix typos in a couple of files.
+	sed -e "s:+0f:-f:" -i share/tutor/gmxdemo/demo \
+		|| die "Failed to fixup demo script."
+
+	# Fix a sandbox violation that occurs when re-emerging with mpi.
+	sed "/libdir=\"\$(libdir)\"/ a\	temp_libdir=\"${D}usr/$( get_libdir )\" ; \\\\" \
+	-i src/tools/Makefile.am \
+	|| die "sed tools/Makefile.am failed"
+
+	sed -e "s:\$\$libdir:\$temp_libdir:" \
+	-i src/tools/Makefile.am \
+	|| die "sed tools/Makefile.am failed"
+
+	sed "/libdir=\"\$(libdir)\"/ a\ temp_libdir=\"${D}usr/$( get_libdir )\" ; \\\\" \
+	-i src/tools/Makefile.am \
+	|| die "sed tools/Makefile.am failed"
+
+	sed -e "s:\$\$libdir:\$\$temp_libdir:" \
+	-i src/tools/Makefile.am \
+	|| die "sed tools/Makefile.am failed"
+
+	use fkernels && epatch "${FILESDIR}/${PN}-4.0.4-configure-gfortran.patch"
+
+	eautoreconf
+
+	cd "${WORKDIR}"
+
+	use test && mv gmxtest "${P}"
+	mv "${P}" "${P}-single"
+	if ( use double-precision ) ; then
+		einfo "Moving sources for Multiprecision Build"
+		cp -prP "${P}-single" "${P}-double"
+	fi
+}
+
+src_configure() {
+	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="${myconf} --disable-fortran"
+	fi
+
+	# if we need external blas
+	if use blas; then
+		export LIBS="${LIBS} -lblas"
+		myconf="${myconf} $(use_with blas external-blas)"
+	fi
+
+	# if we need external lapack
+	if use lapack; then
+		export LIBS="${LIBS} -llapack"
+		myconf="${myconf} $(use_with lapack external-lapack)"
+	fi
+
+	myconf="--datadir=/usr/share \
+			--bindir=/usr/bin \
+			--libdir=/usr/$(get_libdir) \
+			--docdir=/usr/share/doc/"${PF}" \
+			$(use_with dmalloc) \
+			$(use_with fftw fft fftw3) \
+			$(use_with gsl) \
+			$(use_enable mpi) \
+			$(use_with X x) \
+			$(use_with xml) \
+			$(use_enable static all-static) \
+			${myconf}"
+
+	#if we build both double is suffixed
+	if ( use double-precision && use single-precision ); then
+		suffix_d="_d"
+	else
+		suffix_d=""
+	fi
+
+	if use double-precision ; then
+		#from gromacs manual
+		elog
+		elog "For most simulations single precision is accurate enough. In some"
+		elog "cases double precision is required	to get reasonable results:"
+		elog
+		elog "-normal mode analysis, for the conjugate gradient or l-bfgs minimization"
+		elog " and the calculation and diagonalization of the Hessian "
+		elog "-calculation of the constraint force between two large groups of	atoms"
+		elog "-energy conservation: this can only be done without temperature coupling and"
+		elog " without cutoffs"
+		elog
+		einfo "Configuring Double Precison Gromacs"
+		cd "${WORKDIR}"/"${P}"-double
+		myconf_d="${myconf} --enable-double --program-suffix='${suffix_d}'"
+		econf ${myconf_d} || die "Double Precision econf failed"
+	fi
+
+	if use single-precision ; then
+		einfo "Configuring Single Precison Gromacs"
+		cd "${WORKDIR}"/"${P}"-single
+		myconf_s="${myconf} --enable-float --program-suffix=''"
+		econf ${myconf_s} || die "configure failed"
+	fi
+}
+
+src_compile() {
+	if use double-precision ; then
+		einfo "Building Double Precison Gromacs"
+		cd "${WORKDIR}"/"${P}"-double
+		emake || die "Double Precision emake failed"
+	fi
+
+	if use single-precision ; then
+		einfo "Building Single Precison Gromacs"
+		cd "${WORKDIR}"/"${P}"-single
+		emake || die "Single Precision emake failed"
+	fi
+}
+
+src_test() {
+	if use single-precision ; then
+		export PATH="${WORKDIR}/${P}-single/src/kernel:${WORKDIR}/${P}-single/src/tools:$PATH"
+		cd "${WORKDIR}"/"${P}"-single
+		emake -j1 tests || 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}"/"${P}"-double
+		emake -j1 tests || die "Double Precision test failed"
+	fi
+}
+
+src_install() {
+	if use single-precision ; then
+		einfo "Installing Single Precision"
+		cd "${WORKDIR}"/"${P}"-single
+		emake DESTDIR="${D}" install || die "Installing Single Precision failed"
+	fi
+
+	if use double-precision ; then
+		einfo "Installing Double 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
+	use doc && dodoc "${DISTDIR}"/manual-4.0.pdf
+}
+
+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
+}