version bump

(Portage version: 2.2.0_alpha143/cvs/Linux i686, signed Manifest commit with key C2000586)

3 files changed, 260 insertions, 4 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/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>