version bump

Package-Manager: portage-2.2.0_alpha143/cvs/Linux i686
Manifest-Sign-Key: 0xC2000586

4 files changed, 274 insertions, 12 deletions

diff --git a/sci-chemistry/gromacs/ChangeLog b/sci-chemistry/gromacs/ChangeLog
index 1376bb7a015a..3ab43a66d5a3 100644
--- a/sci-chemistry/gromacs/ChangeLog
+++ b/sci-chemistry/gromacs/ChangeLog
@@ -1,6 +1,12 @@
 # ChangeLog for sci-chemistry/gromacs
 # Copyright 1999-2012 Gentoo Foundation; Distributed under the GPL v2
-# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/gromacs/ChangeLog,v 1.110 2012/10/19 09:50:26 jlec Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/gromacs/ChangeLog,v 1.111 2012/11/30 21:08:14 ottxor Exp $
+
+*gromacs-4.6_beta1 (30 Nov 2012)
+
+  30 Nov 2012; Christoph Junghans <ottxor@gentoo.org> +gromacs-4.6_beta1.ebuild,
+  metadata.xml:
+  version bump
 
   19 Oct 2012; Justin Lecher <jlec@gentoo.org> gromacs-4.5.5-r1.ebuild:
   Remove virtual/fortran and always call fortran-2_pkg_setup as intend by the
diff --git a/sci-chemistry/gromacs/Manifest b/sci-chemistry/gromacs/Manifest
index 8d60c42d3217..1f9362e80afd 100644
--- a/sci-chemistry/gromacs/Manifest
+++ b/sci-chemistry/gromacs/Manifest
@@ -5,17 +5,23 @@ AUX gromacs-4.5.5-cmake-cpp-asm.patch 2051 SHA256 b83f9252187caa3647a44166004191
 AUX gromacs-4.5.5-enable-see.patch 1916 SHA256 bd4cbe8b46de33c0a62cd7234265b3e27c6363959f4b97aad447ef18c4e16bb3 SHA512 ff5e29f842eaf8808ed7e00985770c94adfceaf5f0a63bda80d61d09b6ee53a2bfa02cf13b7d0e7a06cc6aa4957bcd24e6e93679673d97116a96726500bbfe86 WHIRLPOOL af6c3b767341762851e1fd356d83f72d936d0f2a2257127053736a552ccbc1e7a06af91ead31ba24b0d03e2a12b5918ac86315478cf2cdbb5fdb5bd7c6f13df1
 DIST 0001-Make-stack-non-executable-for-GAS-assembly.patch.gz 3569527 SHA256 17a948d221b67faeaf635a0b5ee9564067bc261e9279294c0c7c58ae9580ae5f SHA512 c46c1891513968f814efa299f85a4bc86a70a186d54779d64f2c94f21cdce3d056f94ec0ff7e80dfa22ba54bff865d6f22f09172742b22eef023de7c49d056a6 WHIRLPOOL c367eb38644a9afc46c4130596d7604489b06525d230b92b6e881a1b9bf67facaab1da2ae7f9fa63b207897ff470231abd67c30a49c862e8c6cea26018de4169
 DIST 0002-Make-stack-non-executable-for-ATT-assembly.patch.gz 3868244 SHA256 af12b3632aaf4e3d0c49ce99e0a4ed5de61c40d293bc592b70f89e08738f2581 SHA512 321d70aaf2c0bc7f9b22155029b0ac8a65c585a92f3473ce3eed3e39d9609f67d3dd28029f04a7d007dc03be9820c1e694ee76630557a6eb0bc875c4302edb8a WHIRLPOOL 47519f2e0a8aa3658841c32b18e8696f32b691236d9378c8ee57668c1762e21b781d24bcdcd903bb1ece66b3667215843610354f88e8647952bb81afb33951d4
-DIST gmxtest-4.0.4.tgz 14845017 SHA256 6a7f787f4bb7cbecb688115ff0854a5ffd2ef33487d7bce4b031e63848b6f361
+DIST gmxtest-4.0.4.tgz 14845017 SHA256 6a7f787f4bb7cbecb688115ff0854a5ffd2ef33487d7bce4b031e63848b6f361 SHA512 f8165ef1d7e2ed69db0a069a1c85fc5fa440d66e96aa54b474392a6331d2327b60f76b8dceb02f9233ce06eb6b7a4e7c448fc71f666e244efa571cf94f1e86ec WHIRLPOOL dbb122736a588deb7931204b29142dd3d9b074691e94341b04dcad2cdf428eb0aae739aa37ef6f61d1dcd6fb96ddcc1292e76f267694f3c18ee67d17352bfd9b
 DIST gromacs-4.5.5.tar.gz 10398178 SHA256 e0605e4810b0d552a8761fef5540c545beeaf85893f4a6e21df9905a33f871ba SHA512 8af0b81261a6b08c461275bccc4e72d23efd664ed5af12e3579956b5822ab6c6eea2ccbfbfe6ea1f4b30403a3c1367f52638e281cd1d7bc49e9220332c3e2b8c WHIRLPOOL 021a07171c3301184c48d31e2ad2068ce54b7746b9b0f9086d34796ddcfe750006e6f23bc0d8c52942fb491bd047411d7f5f21aaa9d7eb8ab9b7485fcb587f8c
-DIST gromacs-manual-4.5.4.pdf 2463242 SHA256 dc14504a7072b61e7aa576c48f04df03356824f3a9d9e744dfaf51529ab46252
+DIST gromacs-4.6-beta1.tar.gz 10352659 SHA256 cc3179e9a73e768331356651cbccda78228121ad43347dba0554343743810672 SHA512 0f9074743ef272178ef3226d40b249f80247392b6f1304180eb6655b390fafc3157404e85f359e3ab029f1917ea2147a95e021590dbc2c5ebdf3218f71fac82e WHIRLPOOL abe6de58e22731a1594e53b07d76d73ad0996856471160009ef821757b7197c73fefdf9640b8ab920cd24991a707e561f2fa98cf90716f93cb05bfc0dd45d926
+DIST gromacs-manual-4.5.4.pdf 2463242 SHA256 dc14504a7072b61e7aa576c48f04df03356824f3a9d9e744dfaf51529ab46252 SHA512 957995333163f6f28568a18d5423a75dc6c315215692da94d0916f09b6221e2a875c5ff4b05385ad6604bd8ae38f0cb61c740cd734c76b360aa4b598cd2c3380 WHIRLPOOL 07077d81ea89bc02207e45e56c77a668375a7284bf6f4a3cc7fe637f1f53ce4ab687c722f13f208cdd2c056b9d766ebfcbe5ea9579ce7649ec9e088371e7db8d
+DIST gromacs-manual-4.6-beta1.pdf 5527287 SHA256 788a424720b149d905d236d3c792d72c3f5af1c054f6ef19192bd12f44fe1fb9 SHA512 5a76aa847a865bfa8ca77bbad67eec18e8328c3db8af411a609a7039f48bcc1973ac6af0201c78f1428ed05040102cbe96638399413520bb1f1c1013031662c6 WHIRLPOOL 1c189bc1cc1da42bcb7332c45c13789ca822e57dbbff6452be7328163a95ed29b678a201250018a214a95e23fb43258d7cc6a58bdde88afcdf718db0c80cf45a
 EBUILD gromacs-4.5.5-r1.ebuild 7842 SHA256 1ba4a48edc07438bac8d3e33d2e760c02aee71ed831ecc48c0112b26b0ab4676 SHA512 41f08d9279667e9f6bbad390d2d9bef5ed07a1c51510d5c0e52466780ad56a38ed47a1514de7469c2d9e23eaaf17483cbe51fc1af1898cfa84f5cc234fb5b336 WHIRLPOOL 92a420817efd8540b8009699042f8907821a6b87df42b2517864fcea4d17f22b6fb866d4b957232b95278805c7d45cf1b4042ce9835e03fbb4856c996fcbc4bc
-MISC ChangeLog 18571 SHA256 4527d54d1b1f9699f0598404b73c6078a117c2b6c919fb8505ef618dd2fee0fc SHA512 d3378ec426016d14a90223e033e0208047babe89817945a3156a137a1e290dd0e27b47d0d0dc74e29e1fe2b792968cf8f4f3efb6d0ec8c22887bf1c48537eea5 WHIRLPOOL c4b86f68d8578ed1d922688ad25489832799bb11d6b255a3cd9f3d482020189a0b681486955e16a454c83d87189406874f08850a533f669ccadd1b06ba36d908
-MISC metadata.xml 459 SHA256 c7a204771a5e8997239e8b4676cc32a2cfa8d923366a07b463c79d0a0ea36153 SHA512 4914f5606d8bf8c75a67545d4ac01c071aadd32fa3b74c52706d9c421fafd99edb6a247323e3f127c864248f234ee1eeea809fbc89ca4618cffb43e9c9c2e50a WHIRLPOOL 33afe4ee83ced7f9f82b7b726d02b97ead15abdf15142c386e0d7f7766ee032993a2c8b8ec0d9db7da8cbc2cdcfbee81941d1c02d02f6ac1bbef44638fe63b1e
+EBUILD gromacs-4.6_beta1.ebuild 7226 SHA256 4b7a9a58198d146172ed0c08ea1d4a5194dcfcea1a02d0ce38c98bdbba0f5b79 SHA512 13dbf8c74da45b1a86dec18913ea46ec613cf9c9ca0c33d712b3c1fc0484e83a91429733e72dc4e77bc6d847b3f86d0f64d1156981b8fac0b81166f5e572b047 WHIRLPOOL 29d9d2aa3d701fe86499c801b17abc6635948d7e18e295b5ea190a5d134080b460672b5cd5a6d031584c674fdf2939a75ff10f28f7dbe6bfd094fc4a432c048d
+MISC ChangeLog 18720 SHA256 544537db18ddec44deb9fbed8aa8087cfff2547b78296c1369cd9c3ee0aa1e9c SHA512 b15b9314a37b2a1a044e2472492edcafdbdaf91dd893c377c09b3ccf445ea22dee40372303d684470aab51e0c030df5730a0e2a7fdf847c9a493040a783f3987 WHIRLPOOL dd8f5f6b854970caa23052ff01b3c4ddb1eb661ee455fe89e9fa4e9e6ba3c5ed397dbf4638768189026ffdc83fb20c968fdbfe69d9ef2416213f25cc9c8c05c6
+MISC metadata.xml 1011 SHA256 86b258212de20c0346564d9e1705da78bf98c38b3a167417754f980734f12c20 SHA512 b824647ab78588b7312fb8b1cff5931e65940b0027b9f1edc7a258dfb981b8dd2cd88757d2b479d99cb150dd51dc3c93cc888b85aaa238403519dd28fed586e3 WHIRLPOOL 8cd1dc1682ad266ff47d5bf0770cf60649e30ce40e8fd2a072cf040efc6db99374242a5d0d1ea5eb24c5f68a4f04d1d946883d8d88741036256e0ba10d80da12
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diff --git a/sci-chemistry/gromacs/gromacs-4.6_beta1.ebuild b/sci-chemistry/gromacs/gromacs-4.6_beta1.ebuild
new file mode 100644
index 000000000000..5cf24339f8a0
--- /dev/null
+++ b/sci-chemistry/gromacs/gromacs-4.6_beta1.ebuild
@@ -0,0 +1,240 @@
+# Copyright 1999-2012 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/gromacs/gromacs-4.6_beta1.ebuild,v 1.1 2012/11/30 21:08:14 ottxor Exp $
+
+EAPI=5
+
+TEST_PV="4.0.4"
+MANUAL_PV="4.6-beta1"
+
+#to find external blas/lapack
+CMAKE_MIN_VERSION="2.8.5-r2"
+
+CMAKE_MAKEFILE_GENERATOR="ninja"
+
+inherit bash-completion-r1 cmake-utils eutils fortran-2 multilib toolchain-funcs
+
+SRC_URI="test? ( ftp://ftp.gromacs.org/pub/tests/gmxtest-${TEST_PV}.tgz )"
+
+if [[ $PV = *9999* ]]; then
+	EGIT_REPO_URI="git://git.gromacs.org/gromacs.git
+		https://gerrit.gromacs.org/gromacs.git
+		git://github.com/gromacs/gromacs.git
+		http://repo.or.cz/r/gromacs.git"
+	EGIT_BRANCH="release-4-6"
+	inherit git-2
+	PDEPEND="doc? ( ~app-doc/gromacs-manual-${PV} )"
+else
+	S="${WORKDIR}/${P//_/-}"
+	SRC_URI="${SRC_URI} ftp://ftp.gromacs.org/pub/${PN}/${P//_/-}.tar.gz
+		doc? (  ftp://ftp.gromacs.org/pub/manual/gromacs-manual-${MANUAL_PV}.pdf )"
+fi
+
+ACCE_IUSE="fkernels power6 sse2 sse41 avx128fma avx256"
+
+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 ~x86-macos"
+IUSE="X blas cuda doc -double-precision +fftw gsl lapack
+mpi openmm openmp +single-precision test +threads zsh-completion ${ACCE_IUSE}"
+
+CDEPEND="
+	X? (
+		x11-libs/libX11
+		x11-libs/libSM
+		x11-libs/libICE
+		)
+	blas? ( virtual/blas )
+	cuda? ( dev-util/nvidia-cuda-toolkit )
+	fftw? ( sci-libs/fftw:3.0 )
+	fkernels? ( !threads? ( !sse2? ( virtual/fortran ) ) )
+	gsl? ( sci-libs/gsl )
+	lapack? ( virtual/lapack )
+	mpi? ( virtual/mpi )
+	openmm? ( sci-libs/openmm[cuda,opencl] )"
+DEPEND="${CDEPEND}
+	virtual/pkgconfig"
+RDEPEND="${CDEPEND}"
+
+RESTRICT="test"
+
+REQUIRED_USE="cuda? ( single-precision ) openmm? ( single-precision cuda )"
+
+pkg_pretend() {
+	[[ $(gcc-version) == "4.1" ]] && die "gcc 4.1 is not supported by gromacs"
+	use openmp && ! tc-has-openmp && \
+		die "Please switch to an openmp compatible compiler"
+}
+
+pkg_setup() {
+	#notes/todos
+	# -on apple: there is framework support
+	# -mkl support
+	# -there are power6 kernels
+	if use fkernels; then
+		if use threads; then
+			ewarn "Fortran kernels and threads do not work together, disabling"
+			ewarn "fortran kernels"
+		else
+			fortran-2_pkg_setup
+		fi
+	fi
+}
+
+src_prepare() {
+	#add user patches from /etc/portage/patches/sci-chemistry/gromacs
+	epatch_user
+
+	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() {
+	local mycmakeargs_pre=( ) extra
+
+	#go from slowest to fastest acceleration
+	local acce="None"
+	use fkernels && use !threads && acce="Fortran"
+	use power6 && acce="Power6"
+	use sse2 && acce="SSE2"
+	use sse41 && acce="SSE4.1"
+	use avx128fma && acce="AVX_128_FMA"
+	use avx256 && acce="AVX_256"
+
+	#to create man pages, build tree binaries are executed (bug #398437)
+	[[ ${CHOST} = *-darwin* ]] && \
+		extra+=" -DCMAKE_BUILD_WITH_INSTALL_RPATH=OFF"
+
+	mycmakeargs_pre+=(
+		-DGMX_FFT_LIBRARY=$(usex fftw fftw3 fftwpack)
+		$(cmake-utils_use X GMX_X11)
+		$(cmake-utils_use blas GMX_EXTERNAL_BLAS)
+		$(cmake-utils_use gsl GMX_GSL)
+		$(cmake-utils_use lapack GMX_EXTERNAL_LAPACK)
+		$(cmake-utils_use openmp GMX_OPENMP)
+		-DGMX_DEFAULT_SUFFIX=off
+		-DGMX_ACCELERATION="$acce"
+		-DGMXLIB="$(get_libdir)"
+	    -DGMX_VMD_PLUGIN_PATH="${EPREFIX}/usr/$(get_libdir)/vmd/plugins/*/molfile/"
+		${extra}
+	)
+
+	for x in ${GMX_DIRS}; do
+		einfo "Configuring for ${x} precision"
+		local suffix=""
+		#if we build single and double - double is suffixed
+		use double-precision && use single-precision && \
+			[[ ${x} = "double" ]] && suffix="_d"
+		local p
+		[[ ${x} = "double" ]] && p="-DGMX_DOUBLE=ON" || p="-DGMX_DOUBLE=OFF"
+		local cuda=$(cmake-utils_use cuda GMX_GPU)
+		[[ ${x} = "double" ]] && use cuda && cuda="-DGMX_GPU=OFF"
+		mycmakeargs=( ${mycmakeargs_pre[@]} ${p} -DGMX_MPI=OFF
+			$(cmake-utils_use threads GMX_THREAD_MPI) ${cuda}
+			-DGMX_BINARY_SUFFIX="${suffix}" -DGMX_LIBS_SUFFIX="${suffix}" )
+		CMAKE_BUILD_DIR="${WORKDIR}/${P}_${x}" cmake-utils_src_configure
+		if [[ ${x} = float ]] && use openmm; then
+			einfo "Configuring for openmm build"
+			mycmakeargs=( ${mycmakeargs_pre[@]} ${p} -DGMX_MPI=OFF
+				-DGMX_THREAD_MPI=OFF -DGMX_GPU=OFF -DGMX_OPENMM=ON
+				-DGMX_BINARY_SUFFIX="openmm" -DGMX_LIBS_SUFFIX="openmm" )
+			CMAKE_BUILD_DIR="${WORKDIR}/${P}_openmm" \
+				OPENMM_ROOT_DIR="${EPREFIX}/usr" cmake-utils_src_configure
+		fi
+		use mpi || continue
+		einfo "Configuring for ${x} precision with mpi"
+		mycmakeargs=( ${mycmakeargs_pre[@]} ${p} -DGMX_THREAD_MPI=OFF
+			-DGMX_MPI=ON ${cuda}
+			-DGMX_BINARY_SUFFIX="_mpi${suffix}" -DGMX_LIBS_SUFFIX="_mpi${suffix}" )
+		CMAKE_BUILD_DIR="${WORKDIR}/${P}_${x}_mpi" CC="mpicc" cmake-utils_src_configure
+	done
+}
+
+src_compile() {
+	for x in ${GMX_DIRS}; do
+		einfo "Compiling for ${x} precision"
+		CMAKE_BUILD_DIR="${WORKDIR}/${P}_${x}"\
+			cmake-utils_src_compile
+		if [[ ${x} = float ]] && use openmm; then
+			einfo "Compiling for openmm build"
+			CMAKE_BUILD_DIR="${WORKDIR}/${P}_openmm"\
+				cmake-utils_src_compile mdrun
+		fi
+		use mpi || continue
+		einfo "Compiling for ${x} precision with mpi"
+		CMAKE_BUILD_DIR="${WORKDIR}/${P}_${x}_mpi"\
+			cmake-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 ${GMX_DIRS}; do
+		CMAKE_BUILD_DIR="${WORKDIR}/${P}_${x}" \
+			cmake-utils_src_install
+		if [[ ${x} = float ]] && use openmm; then
+			CMAKE_BUILD_DIR="${WORKDIR}/${P}_openmm" \
+				DESTDIR="${D}" cmake-utils_src_make install-mdrun
+		fi
+		use mpi || continue
+		CMAKE_BUILD_DIR="${WORKDIR}/${P}_${x}_mpi" \
+			DESTDIR="${D}" cmake-utils_src_make install-mdrun
+	done
+
+	rm -f "${ED}"/usr/bin/GMXRC*
+
+	newbashcomp "${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.*
+
+	cd "${S}"
+	dodoc AUTHORS INSTALL* README*
+	if use doc; then
+		dohtml -r "${ED}usr/share/gromacs/html/"
+		if [[ $PV = *9999* ]]; then
+			insinto /usr/share/gromacs
+			doins "admin/programs.txt"
+			ls -1 "${ED}"/usr/bin | sed -e '/_d$/d' > "${T}"/programs.list
+			doins "${T}"/programs.list
+		else
+			dodoc "${DISTDIR}/gromacs-manual-${MANUAL_PV}.pdf"
+		fi
+	fi
+	rm -rf "${ED}usr/share/gromacs/html/"
+}
+
+pkg_postinst() {
+	einfo
+	einfo  "Please read and cite:"
+	einfo  "Gromacs 4, J. Chem. Theory Comput. 4, 435 (2008). "
+	einfo  "http://dx.doi.org/10.1021/ct700301q"
+	einfo
+	einfo  $(g_luck)
+	einfo  "For more Gromacs cool quotes (gcq) add g_luck to your .bashrc"
+	einfo
+	elog  "Gromacs can use sci-chemistry/vmd to read additional file formats"
+}
diff --git a/sci-chemistry/gromacs/metadata.xml b/sci-chemistry/gromacs/metadata.xml
index 44b30a77c485..41931c0c7a95 100644
--- a/sci-chemistry/gromacs/metadata.xml
+++ b/sci-chemistry/gromacs/metadata.xml
@@ -2,10 +2,20 @@
 <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
 <pkgmetadata>
 	<herd>sci-chemistry</herd>
+	<maintainer>
+		<email>ottxor@gentoo.org</email>
+		<name>Christoph Junghans</name>
+	</maintainer>
 	<use>
+		<flag name="cuda">Enable cuda non-bonded kernels</flag>
 		<flag name="double-precision">More precise calculations at the expense of speed</flag>
-		<flag name="fkernels">Enable building of Fortran Kernels for platforms
-	  that dont have assembly loops</flag>
-		<flag name="single-precision">Single precision version of gromacs</flag>
+		<flag name="single-precision">Single precision version of gromacs (default)</flag>
+		<!-- acceleration optimization flags -->
+		<flag name="fkernels">Enable building of Fortran Kernels for platforms that dont have assembly loops</flag>
+		<flag name="sse41">Enable sse4.1 acceleration</flag>
+		<flag name="avx128fma">Enable 128bit avx with fma (e.g. AMD BullDozer)</flag>
+		<flag name="avx256">Enable 256bit avx (e.g. Intel Sandy Bridge)</flag>
+		<flag name="openmm">Add acceleration through <pkg>sci-libs/openmm</pkg></flag>
+		<flag name="power6">Enable Power6 optimizations</flag>
 	</use>
 </pkgmetadata>