Fixup for bugs 135146 118421 and 147614.

Package-Manager: portage-2.1.1-r2

5 files changed, 250 insertions, 5 deletions

diff --git a/sci-chemistry/gromacs/ChangeLog b/sci-chemistry/gromacs/ChangeLog
index beedbdb8758b..a5c6cf341039 100644
--- a/sci-chemistry/gromacs/ChangeLog
+++ b/sci-chemistry/gromacs/ChangeLog
@@ -1,6 +1,11 @@
 # ChangeLog for sci-chemistry/gromacs
 # Copyright 2002-2006 Gentoo Foundation; Distributed under the GPL v2
-# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/gromacs/ChangeLog,v 1.12 2006/09/20 05:08:59 dberkholz Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/gromacs/ChangeLog,v 1.13 2006/12/20 04:44:52 je_fro Exp $
+
+*gromacs-3.3.1-r1 (17 Dec 2006)
+
+  17 Dec 2006; Jeff Gardner <je_fro@gentoo.org> +gromacs-3.3.1-r1.ebuild:
+  Fixup to address bugs 135146 118421 and 147614.
 
   20 Sep 2006; Donnie Berkholz <dberkholz@gentoo.org>; metadata.xml:
   (#148281) Change herd to sci-chemistry from sci.
diff --git a/sci-chemistry/gromacs/Manifest b/sci-chemistry/gromacs/Manifest
index 32466b77c83a..f87d97ff5a3d 100644
--- a/sci-chemistry/gromacs/Manifest
+++ b/sci-chemistry/gromacs/Manifest
@@ -1,3 +1,7 @@
+AUX gromacs-alpha-axp_asm.patch 613 RMD160 56a617d34b9aa96f71cb84124271107d56557773 SHA1 96518a8fa20c0d597b5cb26b843f28f26d998942 SHA256 d6ae7d258e975a0c12a8b09bef11874eb0e25d4708f299b3e265c97ada69afee
+MD5 aa14e5e53e2eb5409072fd53896b4578 files/gromacs-alpha-axp_asm.patch 613
+RMD160 56a617d34b9aa96f71cb84124271107d56557773 files/gromacs-alpha-axp_asm.patch 613
+SHA256 d6ae7d258e975a0c12a8b09bef11874eb0e25d4708f299b3e265c97ada69afee files/gromacs-alpha-axp_asm.patch 613
 AUX gromacs-ppc64-altivec.patch 571 RMD160 e6bdccd29a29fb9ee85f0ca4a15f2ea229b6f52a SHA1 fe059c262d4fdbc9b918769dc88dd8a2ed177b6b SHA256 1e60a3a12cfd706af1860ca2ff36074291540f8ffa3616636eb612037f0611c3
 MD5 46d715de402fc04d726086455ba7f074 files/gromacs-ppc64-altivec.patch 571
 RMD160 e6bdccd29a29fb9ee85f0ca4a15f2ea229b6f52a files/gromacs-ppc64-altivec.patch 571
@@ -13,6 +17,10 @@ EBUILD gromacs-3.2.1.ebuild 1897 RMD160 1abe85e471969fcde5ee6a714b76d820418178f0
 MD5 5af09df5d0c864672c46c64a841c0177 gromacs-3.2.1.ebuild 1897
 RMD160 1abe85e471969fcde5ee6a714b76d820418178f0 gromacs-3.2.1.ebuild 1897
 SHA256 7785a56bace8bbef4bdec432128c9d88d2427b667645790ea78df90929074c20 gromacs-3.2.1.ebuild 1897
+EBUILD gromacs-3.3.1-r1.ebuild 5666 RMD160 60f483c934e90edd6816eeca8040b42735051261 SHA1 e79f9ab0d9cb9698520bff0a0dbfda13781ee1a5 SHA256 0e2b506523cd3ce562d8b9f48c09e860361c766f7d6ab7e6469220d7abee9afa
+MD5 7b82165b82e235365bfad859e7587f24 gromacs-3.3.1-r1.ebuild 5666
+RMD160 60f483c934e90edd6816eeca8040b42735051261 gromacs-3.3.1-r1.ebuild 5666
+SHA256 0e2b506523cd3ce562d8b9f48c09e860361c766f7d6ab7e6469220d7abee9afa gromacs-3.3.1-r1.ebuild 5666
 EBUILD gromacs-3.3.1.ebuild 2163 RMD160 b7748b8989987d6acb0562e744702e38f79acd47 SHA1 fa5febc72867f35d1cc9714f558a9a2c9ed36353 SHA256 cabc59520dd654c54b45aa9175785e57d8826d15f93868efeadd9a895a940306
 MD5 a4e8a17060ded547ec8d8288bbbc3594 gromacs-3.3.1.ebuild 2163
 RMD160 b7748b8989987d6acb0562e744702e38f79acd47 gromacs-3.3.1.ebuild 2163
@@ -21,10 +29,10 @@ EBUILD gromacs-3.3.ebuild 1956 RMD160 3ff47faef23a3860b42d2fec7c2fa0f845ccab2a S
 MD5 d963556dde12c545dc60726f29fd3128 gromacs-3.3.ebuild 1956
 RMD160 3ff47faef23a3860b42d2fec7c2fa0f845ccab2a gromacs-3.3.ebuild 1956
 SHA256 4c51f3241c5d14d8aec8037c2f07f6a17ccbbb4189684c9f67a3a55d7fe02eeb gromacs-3.3.ebuild 1956
-MISC ChangeLog 4709 RMD160 9ccbf0f0c494e82ca29b1b2738913c68d203e75b SHA1 82f63e9e7a761a94ad71ecd275f6b1e69a831088 SHA256 30ce38267b8644840c9be09c9028dbb632485fe75401a3a3cfc7bbb65c856471
-MD5 9878fd5af146ed6df4f57f2083121722 ChangeLog 4709
-RMD160 9ccbf0f0c494e82ca29b1b2738913c68d203e75b ChangeLog 4709
-SHA256 30ce38267b8644840c9be09c9028dbb632485fe75401a3a3cfc7bbb65c856471 ChangeLog 4709
+MISC ChangeLog 4864 RMD160 3f8ceb3b003b754b8ce2f031aaf92bba4862ba9a SHA1 2c85f2e337eb68d6e69acc45b04c1856c016cf16 SHA256 20041854c6c83d454f26adf5e63be3c519dec8761badc95ad83b5b8c5d667f3b
+MD5 58c2607d5c53200fa27534e66d204187 ChangeLog 4864
+RMD160 3f8ceb3b003b754b8ce2f031aaf92bba4862ba9a ChangeLog 4864
+SHA256 20041854c6c83d454f26adf5e63be3c519dec8761badc95ad83b5b8c5d667f3b ChangeLog 4864
 MISC metadata.xml 166 RMD160 4452298fd03e7c9395d1182bfe69d60a14144af6 SHA1 cb0b513473c0348f4f6f6cd9a132e4884155fddb SHA256 84c92b49702daf95eace8d2765215cbd8650da4ef776f9f700b5ce3785dec852
 MD5 43628e9f5743b5c3b018a82669a76bc7 metadata.xml 166
 RMD160 4452298fd03e7c9395d1182bfe69d60a14144af6 metadata.xml 166
@@ -41,3 +49,6 @@ SHA256 590f94df114cae1a0a53387dfead13fadd4cad00003a6b3f454f2ae1a7f3e6e9 files/di
 MD5 0ad487900dfecda21c7258f45d995525 files/digest-gromacs-3.3.1 244
 RMD160 427f90b98362a786e7d5fca69d9069742b943ebf files/digest-gromacs-3.3.1 244
 SHA256 2eaa348fdc15b37c1fb15fb5394f6a26578c22bfd21ea4e719ba6308bbab40fc files/digest-gromacs-3.3.1 244
+MD5 0ad487900dfecda21c7258f45d995525 files/digest-gromacs-3.3.1-r1 244
+RMD160 427f90b98362a786e7d5fca69d9069742b943ebf files/digest-gromacs-3.3.1-r1 244
+SHA256 2eaa348fdc15b37c1fb15fb5394f6a26578c22bfd21ea4e719ba6308bbab40fc files/digest-gromacs-3.3.1-r1 244
diff --git a/sci-chemistry/gromacs/files/digest-gromacs-3.3.1-r1 b/sci-chemistry/gromacs/files/digest-gromacs-3.3.1-r1
new file mode 100644
index 000000000000..dc4a56cb42ec
--- /dev/null
+++ b/sci-chemistry/gromacs/files/digest-gromacs-3.3.1-r1
@@ -0,0 +1,3 @@
+MD5 1af34a99950813ca7cf893253c447cd1 gromacs-3.3.1.tar.gz 7992897
+RMD160 48e6f9098ac4f5b834f4beb050846c60aea18fff gromacs-3.3.1.tar.gz 7992897
+SHA256 3df40151ff5364fab1c4d8692ec247d8245437e954882a803178cbe6b812d81f gromacs-3.3.1.tar.gz 7992897
diff --git a/sci-chemistry/gromacs/files/gromacs-alpha-axp_asm.patch b/sci-chemistry/gromacs/files/gromacs-alpha-axp_asm.patch
new file mode 100644
index 000000000000..071b11f4b3bf
--- /dev/null
+++ b/sci-chemistry/gromacs/files/gromacs-alpha-axp_asm.patch
@@ -0,0 +1,11 @@
+diff -Naur gromacs-3.2.1/src/gmxlib/Makefile.in gromacs-3.2.1-new/src/gmxlib/Makefile.in
+--- gromacs-3.2.1/src/gmxlib/Makefile.in	2004-03-01 20:49:02.000000000 +0100
++++ gromacs-3.2.1-new/src/gmxlib/Makefile.in	2006-05-30 17:40:33.000000000 +0200
+@@ -301,6 +301,7 @@
+ LTF77COMPILE = $(LIBTOOL) --mode=compile $(F77) $(AM_FFLAGS) $(FFLAGS)
+ F77LD = $(F77)
+ CCASCOMPILE = $(CCAS) $(AM_CCASFLAGS) $(CCASFLAGS)
++LTASCOMPILE = $(LIBTOOL) --mode=compile $(AS) $(AM_ASFLAGS) $(ASFLAGS)
+ LTCCASCOMPILE = $(LIBTOOL) --mode=compile $(CCAS) $(AM_CCASFLAGS) \
+ 	$(CCASFLAGS)
+ DIST_SOURCES = $(libgmx@LIBSUFFIX@_la_SOURCES) \
diff --git a/sci-chemistry/gromacs/gromacs-3.3.1-r1.ebuild b/sci-chemistry/gromacs/gromacs-3.3.1-r1.ebuild
new file mode 100644
index 000000000000..1d2d9ca51872
--- /dev/null
+++ b/sci-chemistry/gromacs/gromacs-3.3.1-r1.ebuild
@@ -0,0 +1,215 @@
+# Copyright 1999-2006 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 1.1 2006/12/20 04:44:52 je_fro Exp $
+
+inherit eutils fortran multilib
+
+IUSE="3dnow X altivec double-precision mpi sse sse2"
+
+# mopac7 qm/mm is broken until we can get files from
+# http://md.chem.rug.nl/~groenhof/qmmm.html
+# or somewhere else...
+
+DESCRIPTION="The ultimate molecular dynamics simulation package"
+SRC_URI="ftp://ftp.gromacs.org/pub/${PN}/${P}.tar.gz"
+HOMEPAGE="http://www.gromacs.org/"
+
+LICENSE="GPL-2"
+SLOT="0"
+KEYWORDS="~alpha ~amd64 ~ppc64 ~sparc ~x86"
+
+DEPEND=">=sci-libs/fftw-3.0.1
+	mpi? ( virtual/mpi )
+	>=sys-devel/binutils-2.12*
+	app-shells/tcsh
+	X? ( x11-libs/libX11
+		x11-libs/libXt
+		x11-libs/libXp
+		x11-libs/libXext
+		x11-proto/xproto
+		virtual/motif )"
+
+#	mopac7? ( sci-chemistry/mopac7 )
+
+src_unpack() {
+
+	unpack ${A}
+	if use ppc64 && use altivec ; then
+		epatch "${FILESDIR}"/${PN}-ppc64-altivec.patch
+	fi
+
+	if use alpha ; then
+		epatch ${FILESDIR}/${PN}-alpha-axp_asm.patch
+	fi
+
+	cd "${S}"
+
+# Fix a typo in a couple of files.
+	sed -e "s:_nb_kerne010_x86_64_sse2:_nb_kernel010_x86_64_sse2:" \
+		-i src/gmxlib/nonbonded/nb_kernel_x86_64_sse2/nb_kernel010_x86_64_sse2.intel_syntax.s \
+		-i src/gmxlib/nonbonded/nb_kernel_x86_64_sse2/nb_kernel010_x86_64_sse2.s \
+		|| die "Failed to fix sse2 typo."
+
+# Fix a sandbox violation that occurs when re-emerging with mpi.
+	sed "/libdir=\"\$(libdir)\"/ a\	temp_libdir=\"${D}usr/$( get_libdir )\" ; \\\\" \
+	-i src/tools/Makefile.am \
+	|| die "sed tools/Makefile.am failed"
+
+	sed -e "s:\$\$libdir:\$temp_libdir:" \
+	-i src/tools/Makefile.am \
+	|| die "sed tools/Makefile.am failed"
+
+	cd "${WORKDIR}" && mv ${P} ${P}-single ;
+
+	use double-precision && cp -prP ${P}-single ${P}-double ;
+
+	if use mpi ; then
+		cp -prP ${P}-single ${P}-single-mpi
+		use double-precision && cp -prP ${P}-double ${P}-double-mpi
+	fi
+}
+
+src_compile() {
+	# static should work but something's broken.
+	# gcc spec file may be screwed up.
+	# Static linking should try -lgcc instead of -lgcc_s.
+	# For more info:
+	# http://lists.debian.org/debian-gcc/2002/debian-gcc-200201/msg00150.html
+
+# We will compile single precision by default, and suffix double-precision with _d.
+# Sparc is the only arch I can test on that needs to use fortran.
+local myconf ;
+
+case "${ARCH}" in
+
+	x86)
+			myconf="$myconf $(use_enable sse ia32-sse)"
+			myconf="$myconf $(use_enable sse2 ia32-sse)"
+			myconf="$myconf $(use_enable 3dnow ia32-3dnow)"
+
+# If you don't enable at least one of the above, you must use g77, not gfortran.
+			if ! use sse && ! use sse2 && ! use 3dnow ; then
+
+				if ! has_version "=sys-devel/gcc-3*" ; then
+					die "If you must run gromacs without sse (not recommended) gfortran will not work."
+				else myconf="$myconf --enable-fortran" && fortran_pkg_setup
+
+				fi
+			fi
+		;;
+
+	amd64)
+			myconf="$myconf --enable-x86-64-sse"
+		;;
+
+	ppc)
+			if use altivec ; then
+				myconf="$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."
+				fi
+				myconf="$myconf --enable-fortran" && fortran_pkg_setup
+			fi
+		;;
+
+	ppc64)
+			if use altivec ; then
+				myconf="$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."
+				fi
+				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
+		;;
+
+	ia64)
+			myconf="$myconf --enable-ia64-asm"
+		;;
+
+	alpha)
+			myconf="$myconf --enable-axp-asm"
+		;;
+
+esac
+
+myconf="--enable-shared \
+		--datadir=/usr/share \
+		--bindir=/usr/bin \
+		--libdir=/usr/$(get_libdir) \
+		--with-fft=fftw3 \
+		$(use_with X x) \
+		${myconf}"
+
+#		$(use_with mopac7 qmmm-mopac) \
+
+cd "${WORKDIR}"/${P}-single
+	econf ${myconf} --enable-float || die "configure single-precision failed"
+
+	emake || die "emake single failed"
+
+	if use mpi ; then
+		cd "${WORKDIR}"/${P}-single-mpi
+		econf ${myconf} --enable-float --enable-mpi --program-suffix=_mpi \
+			|| die "failed to configure single-mpi mdrun"
+		emake mdrun || die "failed to make single-precision mpi mdrun" ;
+	fi
+
+	if use double-precision ; then
+		cd "${WORKDIR}"/${P}-double
+
+		econf ${myconf} --enable-double --program-suffix=_d \
+			|| die "configure double-precision failed"
+
+		emake || die "emake double failed"
+
+		if use mpi ; then
+			cd "${WORKDIR}"/${P}-double-mpi
+			econf ${myconf} --enable-double --enable-mpi --program-suffix=_mpi_d \
+				|| die "failed to configure double-mpi mdrun" ;
+
+			emake mdrun \
+				|| die "failed to make double-precision mpi mdrun" ;
+		fi
+	fi
+
+}
+
+src_install () {
+	cd ${WORKDIR}/${P}-single ;
+	emake DESTDIR=${D} install || die "installing single failed"
+
+	if use mpi ; then
+		cd "${WORKDIR}"/${P}-single-mpi
+		emake DESTDIR=${D} install-mdrun \
+		|| die "installing mdrun_mpi failed"
+	fi
+
+	if use double-precision ; then
+		cd ${WORKDIR}/${P}-double && emake DESTDIR=${D} install \
+		|| die "installing double failed"
+
+		if use mpi ; then
+			cd "${WORKDIR}"/${P}-double-mpi
+			emake DESTDIR=${D} install-mdrun \
+		|| die "installing mdrun_mpi_d failed"
+		fi
+
+	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}"/
+}