[gentoo-commits] gentoo-x86 commit in sci-chemistry/gromacs: gromacs-3.3.3.ebuild gromacs-4.0.3.ebuild ChangeLog gromacs-4.0.ebuild gromacs-3.3.1-r1.ebuild gromacs-4.0.2.ebuild

[Jeffrey Gardner (je_fro)]

je_fro      09/01/22 04:14:36

  Modified:             gromacs-3.3.3.ebuild ChangeLog gromacs-4.0.ebuild
                        gromacs-3.3.1-r1.ebuild gromacs-4.0.2.ebuild
  Added:                gromacs-4.0.3.ebuild
  Log:
  Latest release
  (Portage version: 2.1.6.7/cvs/Linux x86_64)

Revision  Changes    Path
1.2                  sci-chemistry/gromacs/gromacs-3.3.3.ebuild

file : http://sources.gentoo.org/viewcvs.py/gentoo-x86/sci-chemistry/gromacs/gromacs-3.3.3.ebuild?rev=1.2&view=markup
plain: http://sources.gentoo.org/viewcvs.py/gentoo-x86/sci-chemistry/gromacs/gromacs-3.3.3.ebuild?rev=1.2&content-type=text/plain
diff : http://sources.gentoo.org/viewcvs.py/gentoo-x86/sci-chemistry/gromacs/gromacs-3.3.3.ebuild?r1=1.1&r2=1.2

Index: gromacs-3.3.3.ebuild
===================================================================
RCS file: /var/cvsroot/gentoo-x86/sci-chemistry/gromacs/gromacs-3.3.3.ebuild,v
retrieving revision 1.1
retrieving revision 1.2
diff -u -r1.1 -r1.2
--- gromacs-3.3.3.ebuild	6 Oct 2008 02:08:34 -0000	1.1
+++ gromacs-3.3.3.ebuild	22 Jan 2009 04:14:36 -0000	1.2
@@ -1,6 +1,6 @@
-# Copyright 1999-2008 Gentoo Foundation
+# 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-3.3.3.ebuild,v 1.1 2008/10/06 02:08:34 je_fro Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/gromacs/gromacs-3.3.3.ebuild,v 1.2 2009/01/22 04:14:36 je_fro Exp $
 EAPI="1"
 LIBTOOLIZE="true"
 inherit autotools eutils flag-o-matic fortran multilib
@@ -32,6 +32,8 @@
 	mpi? ( virtual/mpi )
 	xml? ( dev-libs/libxml2 )"
 
+RDEPEND="${DEPEND}"
+
 FORTRAN="g77 gfortran ifc"
 
 src_unpack() {



1.33                 sci-chemistry/gromacs/ChangeLog

file : http://sources.gentoo.org/viewcvs.py/gentoo-x86/sci-chemistry/gromacs/ChangeLog?rev=1.33&view=markup
plain: http://sources.gentoo.org/viewcvs.py/gentoo-x86/sci-chemistry/gromacs/ChangeLog?rev=1.33&content-type=text/plain
diff : http://sources.gentoo.org/viewcvs.py/gentoo-x86/sci-chemistry/gromacs/ChangeLog?r1=1.32&r2=1.33

Index: ChangeLog
===================================================================
RCS file: /var/cvsroot/gentoo-x86/sci-chemistry/gromacs/ChangeLog,v
retrieving revision 1.32
retrieving revision 1.33
diff -u -r1.32 -r1.33
--- ChangeLog	4 Jan 2009 01:04:00 -0000	1.32
+++ ChangeLog	22 Jan 2009 04:14:36 -0000	1.33
@@ -1,6 +1,9 @@
 # ChangeLog for sci-chemistry/gromacs
 # Copyright 2002-2009 Gentoo Foundation; Distributed under the GPL v2
-# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/gromacs/ChangeLog,v 1.32 2009/01/04 01:04:00 je_fro Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/gromacs/ChangeLog,v 1.33 2009/01/22 04:14:36 je_fro Exp $
+
+  22 Jan 2009; Jeff Gardner <je_fro@g.o> +gromacs-4.0.3.ebuild:
+  Latest version.
 
 *gromacs-4.0.2 (04 Jan 2009)
 



1.2                  sci-chemistry/gromacs/gromacs-4.0.ebuild

file : http://sources.gentoo.org/viewcvs.py/gentoo-x86/sci-chemistry/gromacs/gromacs-4.0.ebuild?rev=1.2&view=markup
plain: http://sources.gentoo.org/viewcvs.py/gentoo-x86/sci-chemistry/gromacs/gromacs-4.0.ebuild?rev=1.2&content-type=text/plain
diff : http://sources.gentoo.org/viewcvs.py/gentoo-x86/sci-chemistry/gromacs/gromacs-4.0.ebuild?r1=1.1&r2=1.2

Index: gromacs-4.0.ebuild
===================================================================
RCS file: /var/cvsroot/gentoo-x86/sci-chemistry/gromacs/gromacs-4.0.ebuild,v
retrieving revision 1.1
retrieving revision 1.2
diff -u -r1.1 -r1.2
--- gromacs-4.0.ebuild	12 Oct 2008 18:55:36 -0000	1.1
+++ gromacs-4.0.ebuild	22 Jan 2009 04:14:36 -0000	1.2
@@ -1,6 +1,6 @@
-# Copyright 1999-2008 Gentoo Foundation
+# 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.ebuild,v 1.1 2008/10/12 18:55:36 je_fro Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/gromacs/gromacs-4.0.ebuild,v 1.2 2009/01/22 04:14:36 je_fro Exp $
 
 EAPI="1"
 
@@ -33,6 +33,8 @@
 	mpi? ( virtual/mpi )
 	xml? ( dev-libs/libxml2 )"
 
+RDEPEND="${DEPEND}"
+
 FORTRAN="g77 gfortran ifc"
 
 src_unpack() {



1.13                 sci-chemistry/gromacs/gromacs-3.3.1-r1.ebuild

file : http://sources.gentoo.org/viewcvs.py/gentoo-x86/sci-chemistry/gromacs/gromacs-3.3.1-r1.ebuild?rev=1.13&view=markup
plain: http://sources.gentoo.org/viewcvs.py/gentoo-x86/sci-chemistry/gromacs/gromacs-3.3.1-r1.ebuild?rev=1.13&content-type=text/plain
diff : http://sources.gentoo.org/viewcvs.py/gentoo-x86/sci-chemistry/gromacs/gromacs-3.3.1-r1.ebuild?r1=1.12&r2=1.13

Index: gromacs-3.3.1-r1.ebuild
===================================================================
RCS file: /var/cvsroot/gentoo-x86/sci-chemistry/gromacs/gromacs-3.3.1-r1.ebuild,v
retrieving revision 1.12
retrieving revision 1.13
diff -u -r1.12 -r1.13
--- gromacs-3.3.1-r1.ebuild	27 Jun 2008 10:25:34 -0000	1.12
+++ gromacs-3.3.1-r1.ebuild	22 Jan 2009 04:14:36 -0000	1.13
@@ -1,6 +1,6 @@
-# Copyright 1999-2008 Gentoo Foundation
+# 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-3.3.1-r1.ebuild,v 1.12 2008/06/27 10:25:34 ulm Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/gromacs/gromacs-3.3.1-r1.ebuild,v 1.13 2009/01/22 04:14:36 je_fro Exp $
 
 inherit eutils fortran multilib
 
@@ -29,6 +29,8 @@
 		x11-proto/xproto
 		x11-libs/openmotif )"
 
+RDEPEND="${DEPEND}"
+
 src_unpack() {
 
 	unpack ${A}



1.2                  sci-chemistry/gromacs/gromacs-4.0.2.ebuild

file : http://sources.gentoo.org/viewcvs.py/gentoo-x86/sci-chemistry/gromacs/gromacs-4.0.2.ebuild?rev=1.2&view=markup
plain: http://sources.gentoo.org/viewcvs.py/gentoo-x86/sci-chemistry/gromacs/gromacs-4.0.2.ebuild?rev=1.2&content-type=text/plain
diff : http://sources.gentoo.org/viewcvs.py/gentoo-x86/sci-chemistry/gromacs/gromacs-4.0.2.ebuild?r1=1.1&r2=1.2

Index: gromacs-4.0.2.ebuild
===================================================================
RCS file: /var/cvsroot/gentoo-x86/sci-chemistry/gromacs/gromacs-4.0.2.ebuild,v
retrieving revision 1.1
retrieving revision 1.2
diff -u -r1.1 -r1.2
--- gromacs-4.0.2.ebuild	4 Jan 2009 01:04:00 -0000	1.1
+++ gromacs-4.0.2.ebuild	22 Jan 2009 04:14:36 -0000	1.2
@@ -1,6 +1,6 @@
 # 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-4.0.2.ebuild,v 1.1 2009/01/04 01:04:00 je_fro Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/gromacs/gromacs-4.0.2.ebuild,v 1.2 2009/01/22 04:14:36 je_fro Exp $
 
 EAPI="1"
 
@@ -33,6 +33,8 @@
 	mpi? ( virtual/mpi )
 	xml? ( dev-libs/libxml2 )"
 
+RDEPEND="${DEPEND}"
+
 FORTRAN="g77 gfortran ifc"
 
 src_unpack() {



1.1                  sci-chemistry/gromacs/gromacs-4.0.3.ebuild

file : http://sources.gentoo.org/viewcvs.py/gentoo-x86/sci-chemistry/gromacs/gromacs-4.0.3.ebuild?rev=1.1&view=markup
plain: http://sources.gentoo.org/viewcvs.py/gentoo-x86/sci-chemistry/gromacs/gromacs-4.0.3.ebuild?rev=1.1&content-type=text/plain

Index: gromacs-4.0.3.ebuild
===================================================================
# 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 1.1 2009/01/22 04:14:36 je_fro 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}"/
}