[sci-chemistry/gromacs] Fix QA execstack bug #361687

Package-Manager: portage-2.2.0_alpha29/cvs/Linux x86_64

3 files changed, 281 insertions, 10 deletions

diff --git a/sci-chemistry/gromacs/ChangeLog b/sci-chemistry/gromacs/ChangeLog
index 938e46814f6b..f65568820a73 100644
--- a/sci-chemistry/gromacs/ChangeLog
+++ b/sci-chemistry/gromacs/ChangeLog
@@ -1,6 +1,11 @@
 # ChangeLog for sci-chemistry/gromacs
 # Copyright 1999-2011 Gentoo Foundation; Distributed under the GPL v2
-# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/gromacs/ChangeLog,v 1.79 2011/04/04 18:56:42 ottxor Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/gromacs/ChangeLog,v 1.80 2011/04/04 21:26:20 alexxy Exp $
+
+*gromacs-4.5.4-r1 (04 Apr 2011)
+
+  04 Apr 2011; Alexey Shvetsov <alexxy@gentoo.org> +gromacs-4.5.4-r1.ebuild:
+  Fix QA execstack bug #361687
 
   04 Apr 2011; Christoph Junghans <ottxor@gentoo.org> -gromacs-4.0.7-r5.ebuild,
   -gromacs-4.5.3.ebuild, -gromacs-4.5.3-r3.ebuild:
diff --git a/sci-chemistry/gromacs/Manifest b/sci-chemistry/gromacs/Manifest
index ce686ff5e8cb..31c4c00887aa 100644
--- a/sci-chemistry/gromacs/Manifest
+++ b/sci-chemistry/gromacs/Manifest
@@ -1,7 +1,9 @@
 -----BEGIN PGP SIGNED MESSAGE-----
-Hash: SHA1
+Hash: SHA256
 
 AUX gromacs-4.0.9999-docdir.patch 1352 RMD160 336ab23b4b65430caf3205650a8787e8e33d2137 SHA1 77e0cc966c4d755f603b2d0ab9a075c0ee6b7361 SHA256 8ead457b06f7f943455a95494be4648e539934699d29e955d2e05ac02f1ca4ef
+DIST 0001-Make-stack-non-executable-for-GAS-assembly.patch.gz 3569527 RMD160 862efb96bee960f4bab4ce726d2524529bddde81 SHA1 a1d01348b421a1209d25d558ba6e0d8762c595f0 SHA256 17a948d221b67faeaf635a0b5ee9564067bc261e9279294c0c7c58ae9580ae5f
+DIST 0002-Make-stack-non-executable-for-ATT-assembly.patch.gz 3868244 RMD160 1b98ad7a1216b78aaa04f6f83a04d8be94cf234c SHA1 bc2a2ab012e42189710d6a38798add01e7813003 SHA256 af12b3632aaf4e3d0c49ce99e0a4ed5de61c40d293bc592b70f89e08738f2581
 DIST ffamber_v4.0-doc.tar.gz 7915520 RMD160 aeadb18bd88bcd9e6fc45af22af15c51e32c66a3 SHA1 8d4969fa7eec660b41f769874be9698980b49ed0 SHA256 0b3395570dfe9bf808a297fcb120e1f525f38a91791fbafe6e444d542d7754aa
 DIST gmxtest-4.0.4.tgz 14845017 RMD160 c7c583415438bdef4c9996da9064254e9460cf16 SHA1 998179aa2bfbc4f80514f10ed774762f85c854c3 SHA256 6a7f787f4bb7cbecb688115ff0854a5ffd2ef33487d7bce4b031e63848b6f361
 DIST gromacs-4.0.7.tar.gz 8404518 RMD160 4fa8e5c90f549ef627a98a907a166676692a4c4b SHA1 8519bef2fa989fb487d54612b0a2d0228f228b30 SHA256 048f8ece2829f01d99f7e04e1d6e8f88d3a32273192274f2e9fcf71f41f212c1
@@ -14,17 +16,24 @@ DIST gromacs-manual-4.5.3.pdf 2438528 RMD160 07f5ec0db1a773e77806c79554e5bb4fa85
 DIST gromacs-manual-4.5.4.pdf 2463242 RMD160 309a1d9bc5f4821076d53f668c36f1c6bfc1714f SHA1 58c0261308212af29fa0c4f4a6d1b81da6d84766 SHA256 dc14504a7072b61e7aa576c48f04df03356824f3a9d9e744dfaf51529ab46252
 EBUILD gromacs-4.0.7-r4.ebuild 9967 RMD160 168b3d2e5273634e710d45e293845ef6e97dd518 SHA1 4fb7f526ed22f2069e955317d8076f0446c3ca53 SHA256 b827418a2513499f9faaddac78450e1fc3245a9b392fd30692db179a1e130748
 EBUILD gromacs-4.5.3-r4.ebuild 8119 RMD160 416df204a948bd7ed224d16827565f6da1446b67 SHA1 18c3836131f570e6378abb61607f5ceb293abb5c SHA256 7b1ba5a26a7f8d7636dfc240c21c4238c0534f78551ebd0b04b376253a7ff46d
+EBUILD gromacs-4.5.4-r1.ebuild 8076 RMD160 d759804c20a20601e0da44bf2b3cde770b8e0926 SHA1 f9fda6f4f04e3197602f851357cfe1d82709bb19 SHA256 4d784681ee4e2bc620fa8b256411306defabf42c2ea3b4b6b304fe1472dcb002
 EBUILD gromacs-4.5.4.ebuild 7988 RMD160 3b6fa3eaf3a3bb93b52c7f6be7590f62c6d1b697 SHA1 2d65cb9fe402d68da1d4e9a4fdeff47a09d8c26c SHA256 350a167152abdbd250a1afe6d14d2e4c0bb58c25c8839c6e8ff9885dbf1d2015
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diff --git a/sci-chemistry/gromacs/gromacs-4.5.4-r1.ebuild b/sci-chemistry/gromacs/gromacs-4.5.4-r1.ebuild
new file mode 100644
index 000000000000..84b4877810ba
--- /dev/null
+++ b/sci-chemistry/gromacs/gromacs-4.5.4-r1.ebuild
@@ -0,0 +1,257 @@
+# Copyright 1999-2011 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/gromacs/gromacs-4.5.4-r1.ebuild,v 1.1 2011/04/04 21:26:20 alexxy Exp $
+
+EAPI="4"
+
+LIBTOOLIZE="true"
+TEST_PV="4.0.4"
+MANUAL_PV="4.5.4"
+
+inherit autotools-utils bash-completion flag-o-matic multilib toolchain-funcs
+
+SRC_URI="test? ( ftp://ftp.gromacs.org/pub/tests/gmxtest-${TEST_PV}.tgz )
+		doc? ( ftp://ftp.gromacs.org/pub/manual/manual-${MANUAL_PV}.pdf -> gromacs-manual-${MANUAL_PV}.pdf )"
+
+if [ "${PV%9999}" != "${PV}" ]; then
+	EGIT_REPO_URI="git://git.gromacs.org/gromacs"
+	EGIT_BRANCH="release-4-5-patches"
+	inherit git
+else
+	SRC_URI="${SRC_URI} ftp://ftp.gromacs.org/pub/${PN}/${P}.tar.gz"
+fi
+
+SRC_URI="${SRC_URI}
+		http://dev.gentoo.org/~alexxy/gromacs/0001-Make-stack-non-executable-for-GAS-assembly.patch.gz
+		http://dev.gentoo.org/~alexxy/gromacs/0002-Make-stack-non-executable-for-ATT-assembly.patch.gz
+		"
+
+DESCRIPTION="The ultimate molecular dynamics simulation package"
+HOMEPAGE="http://www.gromacs.org/"
+
+LICENSE="GPL-2"
+SLOT="0"
+KEYWORDS="~alpha ~amd64 ~ppc64 ~sparc ~x86 ~amd64-linux ~x86-linux"
+IUSE="X altivec blas dmalloc doc -double-precision +fftw fkernels +gsl lapack
+mpi +single-precision sse2 static-libs test +threads +xml zsh-completion"
+REQUIRED_USE="fkernels? ( !threads )"
+
+CDEPEND="
+	X? ( x11-libs/libX11
+		x11-libs/libSM
+		x11-libs/libICE )
+	dmalloc? ( dev-libs/dmalloc )
+	blas? ( virtual/blas )
+	fftw? ( sci-libs/fftw:3.0 )
+	gsl? ( sci-libs/gsl )
+	lapack? ( virtual/lapack )
+	mpi? ( virtual/mpi )
+	xml? ( dev-libs/libxml2:2 )"
+DEPEND="${CDEPEND}
+	dev-util/pkgconfig"
+RDEPEND="${CDEPEND}
+	app-shells/tcsh"
+
+RESTRICT="test"
+
+src_prepare() {
+	if use mpi && use threads; then
+		elog "mdrun uses only threads OR mpi, and gromacs favours the"
+		elog "use of mpi over threads, so a mpi-version of mdrun will"
+		elog "be compiled. If you want to run mdrun on shared memory"
+		elog "machines only, you can safely disable mpi"
+	fi
+
+	# Add patches for non-exec stack
+	epatch "${WORKDIR}/0001-Make-stack-non-executable-for-GAS-assembly.patch"
+	epatch "${WORKDIR}/0002-Make-stack-non-executable-for-ATT-assembly.patch"
+
+	autotools-utils_src_prepare || die
+
+	eautoreconf || die
+
+	GMX_DIRS=""
+	use single-precision && GMX_DIRS+=" float"
+	use double-precision && GMX_DIRS+=" double"
+	#if neither single-precision nor double-precision is enabled
+	#build at least default (single)
+	[ -z "$GMX_DIRS" ] && GMX_DIRS+=" float"
+
+	for x in ${GMX_DIRS}; do
+		mkdir -p "${WORKDIR}/${P}_${x}" || die
+		use test && cp -r "${WORKDIR}"/gmxtest "${WORKDIR}/${P}_${x}"
+	done
+}
+
+src_configure() {
+	#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
+		eerror "gcc 4.1 is not supported by gromacs"
+		eerror "please run test suite"
+		die
+	fi
+
+	#note for gentoo-PREFIX on apple: use --enable-apple-64bit
+
+	#fortran will gone in gromacs 5.0 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..."
+	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
+	fi
+
+	if use mpi ; then
+		elog "You have enabled mpi, only mdrun will make use of mpi, that is why"
+		elog "we configure/compile gromacs twice (with and without mpi) and only"
+		elog "install mdrun with mpi support. In addtion you will get libgmx and"
+		elog "libmd with and without mpi support."
+	fi
+
+	# if we need external blas or lapack
+	use blas && export LIBS+=" $(pkg-config blas --libs)"
+	use lapack && export LIBS+=" $(pkg-config lapack --libs)"
+	local sseflag="x86-64-sse"
+	use x86 && sseflag="ia32-sse"
+
+	#missing flag in autotools (bug #339837)
+	use sse2 && append-flags -msse2
+
+	for x in ${GMX_DIRS}; do
+		#if we build single and double - double is suffixed
+		use double-precision && use single-precision && \
+			[ "${x}" = "double" ] && suffix="_d"
+		myeconfargs=(
+			--bindir="${EPREFIX}"/usr/bin
+			--docdir="${EPREFIX}"/usr/share/doc/"${PF}"
+			--enable-"${x}"
+			$(use_with dmalloc)
+			$(use_with fftw fft fftw3)
+			$(use_with gsl)
+			$(use_with X x)
+			$(use_with xml)
+			$(use_enable threads)
+			$(use_enable altivec ppc-altivec)
+			$(use_enable ia64 ia64-asm)
+			$(use_with lapack external-lapack)
+			$(use_with blas external-blas)
+			$(use_enable fkernels fortran)
+			--disable-bluegene
+			--disable-la-files
+			--disable-power6
+			--disable-ia32-sse
+			--disable-x86-64-sse
+			$(use_enable sse2 $sseflag)
+		)
+		#disable ia32-sse and x86-64-sse and enable what we really need in last line
+
+		einfo "Configuring for ${x} precision"
+		AUTOTOOLS_BUILD_DIR="${WORKDIR}/${P}_${x}"\
+			autotools-utils_src_configure --disable-mpi	--program-suffix="${suffix}" \
+			CC="$(tc-getCC)" F77="$(tc-getFC)"
+		use mpi || continue
+		einfo "Configuring for ${x} precision with mpi"
+		AUTOTOOLS_BUILD_DIR="${WORKDIR}/${P}_${x}_mpi"\
+			autotools-utils_src_configure --enable-mpi --program-suffix="_mpi${suffix}" \
+			CC="$(tc-getCC)" F77="$(tc-getFC)"
+	done
+}
+
+src_compile() {
+	for x in ${GMX_DIRS}; do
+		einfo "Compiling for ${x} precision"
+		AUTOTOOLS_BUILD_DIR="${WORKDIR}/${P}_${x}"\
+			autotools-utils_src_compile
+		use mpi || continue
+		einfo "Compiling for ${x} precision with mpi"
+		AUTOTOOLS_BUILD_DIR="${WORKDIR}/${P}_${x}_mpi"\
+			autotools-utils_src_compile mdrun
+	done
+}
+
+src_test() {
+	for x in ${GMX_DIRS}; do
+		local oldpath="${PATH}"
+		export PATH="${WORKDIR}/${P}_${x}/src/kernel:${S}-{x}/src/tools:${PATH}"
+		cd "${WORKDIR}/${P}_${x}"
+		emake -j1 tests || die "${x} Precision test failed"
+		export PATH="${oldpath}"
+	done
+}
+
+src_install() {
+	for x in ${GMX_DIRS}; do
+		AUTOTOOLS_BUILD_DIR="${WORKDIR}/${P}_${x}" \
+			autotools-utils_src_install
+		use mpi || continue
+		#autotools-utils_src_install does not support args
+		#using autotools-utils_src_compile instead
+		AUTOTOOLS_BUILD_DIR="${WORKDIR}/${P}_${x}_mpi" \
+			autotools-utils_src_compile install-mdrun DESTDIR="${D}"
+
+		#stolen from autotools-utils_src_install see comment above
+		local args
+		has static-libs ${IUSE//+} && ! use	static-libs || args='none'
+		remove_libtool_files ${args}
+	done
+
+	sed -n -e '/^GMXBIN/,/^GMXDATA/p' "${ED}"/usr/bin/GMXRC.bash > "${T}/80gromacs"
+	echo "VMD_PLUGIN_PATH=${EPREFIX}/usr/$(get_libdir)/vmd/plugins/*/molfile/" >> "${T}/80gromacs"
+
+	doenvd "${T}/80gromacs"
+	rm -f "${ED}"/usr/bin/GMXRC*
+
+	dobashcompletion "${ED}"/usr/bin/completion.bash ${PN}
+	if use zsh-completion ; then
+		insinto /usr/share/zsh/site-functions
+		newins "${ED}"/usr/bin/completion.zsh _${PN}
+	fi
+	rm -f "${ED}"/usr/bin/completion.*
+
+	# Fix typos in a couple of files.
+	sed -e "s:+0f:-f:" -i "${ED}"usr/share/gromacs/tutor/gmxdemo/demo \
+		|| die "Failed to fixup demo script."
+
+	cd "${S}"
+	dodoc AUTHORS INSTALL* README*
+	if use doc; then
+		newdoc "${DISTDIR}/gromacs-manual-${MANUAL_PV}.pdf" "manual-${MANUAL_PV}.pdf"
+		dohtml -r "${ED}usr/share/gromacs/html/"
+	fi
+	rm -rf "${ED}usr/share/gromacs/html/"
+}
+
+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 $(g_luck)
+	elog "For more Gromacs cool quotes (gcq) add luck to your .bashrc"
+	elog
+	elog "Gromacs can use sci-chemistry/vmd to read additional file formats"
+	elog
+}