From b7fab46babb32314b0d33c04fb3688fd1f3cefe7 Mon Sep 17 00:00:00 2001
From: Alexey Shvetsov <alexxy@gentoo.org>
Date: Thu, 14 May 2009 16:17:39 +0000
Subject: Drop old version; Fix keywords for 4.0.5. Sorry =) (Portage version:
 2.2_rc33/cvs/Linux x86_64)

---
 sci-chemistry/gromacs/ChangeLog            |  11 +-
 sci-chemistry/gromacs/gromacs-4.0.3.ebuild | 215 --------------------------
 sci-chemistry/gromacs/gromacs-4.0.5.ebuild | 234 +++++++++++++++++++++++++++++
 3 files changed, 244 insertions(+), 216 deletions(-)
 delete mode 100644 sci-chemistry/gromacs/gromacs-4.0.3.ebuild
 create mode 100644 sci-chemistry/gromacs/gromacs-4.0.5.ebuild

(limited to 'sci-chemistry/gromacs')

diff --git a/sci-chemistry/gromacs/ChangeLog b/sci-chemistry/gromacs/ChangeLog
index 6148085d94a7..33c2db3aa059 100644
--- a/sci-chemistry/gromacs/ChangeLog
+++ b/sci-chemistry/gromacs/ChangeLog
@@ -1,6 +1,15 @@
 # ChangeLog for sci-chemistry/gromacs
 # Copyright 1999-2009 Gentoo Foundation; Distributed under the GPL v2
-# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/gromacs/ChangeLog,v 1.39 2009/05/14 08:25:06 fauli Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/gromacs/ChangeLog,v 1.40 2009/05/14 16:17:39 alexxy Exp $
+
+  14 May 2009; Alexey Shvetsov <alexxy@gentoo.org> -gromacs-4.0.3.ebuild,
+  +gromacs-4.0.5.ebuild:
+  Drop old version; Fix keywords for 4.0.5. Sorry =)
+
+*gromacs-4.0.5 (14 May 2009)
+
+  14 May 2009; Alexey Shvetsov <alexxy@gentoo.org> +gromacs-4.0.5.ebuild:
+  Bump new version with bugfixes. Bug #269754
 
   14 May 2009; Christian Faulhammer <fauli@gentoo.org> gromacs-4.0.4.ebuild:
   stable x86, bug 260995
diff --git a/sci-chemistry/gromacs/gromacs-4.0.3.ebuild b/sci-chemistry/gromacs/gromacs-4.0.3.ebuild
deleted file mode 100644
index da0a0d71669c..000000000000
--- a/sci-chemistry/gromacs/gromacs-4.0.3.ebuild
+++ /dev/null
@@ -1,215 +0,0 @@
-# Copyright 1999-2009 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/gromacs/gromacs-4.0.3.ebuild,v 1.2 2009/03/08 19:50:46 maekke Exp $
-
-EAPI="1"
-
-LIBTOOLIZE="true"
-
-inherit autotools eutils flag-o-matic 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"
-
-LICENSE="GPL-2"
-SLOT="0"
-KEYWORDS="~alpha amd64 ~ppc64 ~sparc x86"
-IUSE="3dnow X altivec blas double-precision gsl lapack mpi +single-precision sse sse2 static xml"
-
-# mopac7 qm/mm is broken until we can get files from
-# http://md.chem.rug.nl/~groenhof/qmmm.html
-# or somewhere else...
-
-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 )
-	gsl? ( sci-libs/gsl )
-	lapack? ( virtual/lapack )
-	mpi? ( virtual/mpi )
-	xml? ( dev-libs/libxml2 )"
-
-RDEPEND="${DEPEND}"
-
-FORTRAN="g77 gfortran ifc"
-
-src_unpack() {
-
-	unpack ${A}
-	cd "${S}"
-	# 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"
-
-	eautoreconf
-
-	cd "${WORKDIR}"
-	mv "${P}" "${P}-single"
-	if ( use double-precision ) ; then
-		einfo "Moving sources for Multiprecision Build"
-		cp -prP "${P}-single" "${P}-double"
-	fi
-}
-
-src_compile() {
-
-	# static should work but something's broken.
-	# gcc spec file may be screwed up.
-	# Static linking should try -lgcc instead of -lgcc_s.
-	# For more info:
-	# http://lists.debian.org/debian-gcc/2002/debian-gcc-200201/msg00150.html
-
-	# We will compile single precision by default, and suffix double-precision with _d.
-	# Sparc is the only arch I can test on that needs to use fortran.
-	local myconf ;
-	local myconf_s ;
-	local myconf_d ;
-
-	case "${ARCH}" in
-
-		x86)
-			if ( use sse || use sse2 ) ; then
-				myconf="${myconf} --enable-ia32-sse"
-			fi
-			myconf="$myconf $(use_enable 3dnow ia32-3dnow)"
-
-			if ( ! use sse && ! use sse2 && ! use 3dnow ) ; then
-				if ! has_version "=sys-devel/gcc-3*" ; then
-					die "If you must run gromacs without sse (not recommended) gfortran will not work."
-				else
-					myconf="${myconf} --enable-fortran" && fortran_pkg_setup
-				fi
-			else
-				myconf="${myconf} --disable-fortran"
-			fi
-			;;
-
-		amd64)
-			myconf="$myconf --enable-x86-64-sse --disable-fortran"
-			;;
-
-		ppc*)
-			if use altivec ; then
-				myconf="${myconf} --enable-ppc-altivec --disable-fortran"
-			else
-				if ! has_version "=sys-devel/gcc-3*" ; then
-					die "If you must run gromacs without sse (not recommended) gfortran will not work."
-				else
-					myconf="${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="${myconf} --enable-fortran" && fortran_pkg_setup
-			fi
-			;;
-	esac
-
-	# if we need external blas
-	if use blas; then
-		export LIBS="${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) \
-			--with-fft=fftw3 \
-			$(use_with gsl) \
-			$(use_enable mpi) \
-			$(use_with X x) \
-			$(use_with xml) \
-			$(use_enable static all-static) \
-			${myconf}"
-
-	if ( use double-precision && use single-precision ); then
-		einfo "Building Single Precison Gromacs"
-		cd "${WORKDIR}"/"${P}"-single
-		myconf_s="${myconf}  --enable-float --disable-double --program-suffix=''"
-		econf ${myconf_s} || die "Single Precision econf failed"
-		emake || die "Single Precision emake failed"
-
-		einfo "Building Double Precision Gromacs"
-		cd "${WORKDIR}"/"${P}"-double
-		myconf_d="${myconf} --enable-double --disable-float --program-suffix=_d"
-		econf ${myconf_d} || die "Double Precision econf failed"
-		emake || die "Double Precision emake failed"
-
-	elif use double-precision ; then
-		einfo "Building Double Precison Gromacs"
-		cd "${WORKDIR}"/"${P}"-double
-		myconf_d="${myconf} --enable-double --disable-float --program-suffix=''"
-		econf ${myconf_d} || die "Double Precision econf failed"
-		emake || die "Double Precision emake failed"
-
-	elif use single-precision ; then
-		einfo "Building Single Precison Gromacs"
-		cd "${WORKDIR}"/"${P}"-single
-		myconf_s="${myconf} --enable-float --disable-double --program-suffix=''"
-		econf ${myconf_s} || die "configure failed"
-		emake || die "Single Precision emake failed"
-	fi
-}
-
-src_install() {
-	if use single-precision ; then
-		einfo "Installing Single Precision"
-		cd "${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="${D}" install || die "Installing Double Precision failed"
-	fi
-
-	dodoc AUTHORS INSTALL README
-	# Move html and leave examples and templates under /usr/share/gromacs.
-	mv "${D}"/usr/share/"${PN}"/html "${D}"/usr/share/doc/"${PF}"/
-}
diff --git a/sci-chemistry/gromacs/gromacs-4.0.5.ebuild b/sci-chemistry/gromacs/gromacs-4.0.5.ebuild
new file mode 100644
index 000000000000..0917c8c908ce
--- /dev/null
+++ b/sci-chemistry/gromacs/gromacs-4.0.5.ebuild
@@ -0,0 +1,234 @@
+# Copyright 1999-2009 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/gromacs/gromacs-4.0.5.ebuild,v 1.1 2009/05/14 16:17:39 alexxy Exp $
+
+EAPI="2"
+
+LIBTOOLIZE="true"
+TEST_PV="4.0.4"
+
+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-${TEST_PV}.tgz )
+		doc? ( ftp://ftp.gromacs.org/pub/manual/manual-4.0.pdf )"
+
+LICENSE="GPL-2"
+SLOT="0"
+KEYWORDS="~alpha ~amd64 ~ppc64 ~sparc ~x86"
+IUSE="X blas dmalloc doc -double-precision +fftw fkernels gsl lapack mpi +single-precision static test +xml zsh-completion"
+
+DEPEND="app-shells/tcsh
+	X? ( x11-libs/libX11 )
+	dmalloc? ( dev-libs/dmalloc )
+	blas? ( virtual/blas )
+	fftw? ( sci-libs/fftw:3.0 )
+	gsl? ( sci-libs/gsl )
+	lapack? ( virtual/lapack )
+	mpi? ( virtual/mpi )
+	xml? ( dev-libs/libxml2 )"
+
+RDEPEND="${DEPEND}"
+
+RESTRICT="test"
+
+src_prepare() {
+
+	epatch "${FILESDIR}/${PN}-4.0.4-sparc-cyclecounter.patch"
+	# 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
+}
-- 
cgit v1.2.3-65-gdbad