Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci

* 'master' of git+ssh://git.overlays.gentoo.org/proj/sci:
  sync with gx86
  media-gfx/brlcad: version bumped to 7.22.0, bug#467456
  added recent 4.5.x version from gx86 (bug #468454)
  sci-libs/mkl: Version Bump
  selectively call cuda.eclass, depending on use flag
  reverting inheritance
  refactoring CUDA interaction
  conditional inheritance to fix compilation sans CUDA

13 files changed, 562 insertions, 8 deletions

diff --git a/dev-util/VampirTrace/VampirTrace-5.14.3.ebuild b/dev-util/VampirTrace/VampirTrace-5.14.3.ebuild
index 8aa218119..02a8faa88 100644
--- a/dev-util/VampirTrace/VampirTrace-5.14.3.ebuild
+++ b/dev-util/VampirTrace/VampirTrace-5.14.3.ebuild
@@ -4,7 +4,7 @@
 
 EAPI=5
 
-inherit cuda eutils
+inherit eutils cuda
 
 DESCRIPTION="An open source library that allows detailed logging of program execution for parallel applications"
 HOMEPAGE="http://www.tu-dresden.de/die_tu_dresden/zentrale_einrichtungen/zih/forschung/software_werkzeuge_zur_unterstuetzung_von_programmierung_und_optimierung/vampirtrace"
@@ -19,6 +19,10 @@ DEPEND="
 	virtual/mpi
 	cuda? ( >=dev-util/nvidia-cuda-toolkit-4.0.0 )"
 
+src_prepare() {
+	use cuda && cuda_src_prepare
+}
+
 src_configure() {
 	econf $(use_with cuda cuda-dir "${EPREFIX}"/opt/cuda)
 }
diff --git a/media-gfx/brlcad/ChangeLog b/media-gfx/brlcad/ChangeLog
index a22b70a8c..aade60ce9 100644
--- a/media-gfx/brlcad/ChangeLog
+++ b/media-gfx/brlcad/ChangeLog
@@ -2,7 +2,10 @@
 # Copyright 1999-2011 Gentoo Foundation; Distributed under the GPL v2
 # $Header: /var/cvsroot/gentoo-x86/media-gfx/brlcad/ChangeLog,v 1.3 2011/04/18 22:47:37 dilfridge Exp $
 
-*brlcad-7.20.4 (27 Mar 2012)
+*brlcad-7.22.0 (6 May 2013)
+
+  5 May 2013; Dongxu Li <dongxuli2011@gmail.com> brlcad-9999.ebuild +brlcad-7.22.0.ebuild:
+  version bumped to 7.22.0
 
   27 Mar 2012; Dongxu Li <dongxuli2011@gmail.com> brlcad-9999.ebuild +files/brlcad-7.20.4-cmake.patch:
   added missing patch for 7.20.4
diff --git a/media-gfx/brlcad/Manifest b/media-gfx/brlcad/Manifest
index 85d73fe59..cd637e6b3 100644
--- a/media-gfx/brlcad/Manifest
+++ b/media-gfx/brlcad/Manifest
@@ -1 +1,2 @@
 DIST brlcad-7.20.4.tar.gz 70674938 SHA256 ee6210890f9f2115613b40dc25af95091dc700b5cc1ae390758a62b64854b65e SHA512 ac75675af04bfad444f66c0597aae6738883f49a92b775e1324d981968671adb8ac2a9aec921135498be84d4f6724741a2eeab7c3b3da64add2b20681f87dfdd WHIRLPOOL 8ba8093428c8aeb281538dd0a17c871dd8500affc118e524b0b12356d5dec082db3b136af7f80b524ad25fab6e49b3590dd9ef1f8e1310936ef106d53ee33a29
+DIST brlcad-7.22.0.tar.gz 80633583 SHA256 4cc10161efbf9713c9b5810d259a039431096a37c95eb87b52f4ac669e16bcb1 SHA512 515df65cf0e6a7a2109309c05a31abfad80889a40236f79bf09fe92528cd35742be76a3074d3aa12320c8e85a32d35661af8c7e2acef0b2a2a588de885a0e30d WHIRLPOOL bb5f30edbaf9455330df69406b07ab955b0dfc5d1dffd44c9a94ab0cb0438c5d938d67caeeb2be75e38c88761f1036425881eb3a8cb872b514b1eb480c371bf7
diff --git a/media-gfx/brlcad/brlcad-7.22.0.ebuild b/media-gfx/brlcad/brlcad-7.22.0.ebuild
new file mode 100644
index 000000000..bfd9356dd
--- /dev/null
+++ b/media-gfx/brlcad/brlcad-7.22.0.ebuild
@@ -0,0 +1,112 @@
+# Copyright 1999-2013 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: /var/cvsroot/gentoo-x86/media-gfx/brlcad/brlcad-7.18.4.ebuild,v 1.1 2011/04/18 22:47:37 dilfridge Exp $
+
+EAPI=4
+inherit cmake-utils eutils java-pkg-2 flag-o-matic
+
+DESCRIPTION="Constructive solid geometry modeling system"
+HOMEPAGE="http://brlcad.org/"
+SRC_URI="mirror://sourceforge/${PN}/${P}.tar.gz"
+
+LICENSE="LGPL-2 BSD"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+IUSE="benchmarks debug doc examples java opengl smp"
+
+RDEPEND="media-libs/libpng
+	sys-libs/zlib
+	>=sci-libs/tnt-3
+	sci-libs/jama
+	<dev-lang/tcl-8.6
+	<dev-lang/tk-8.6
+	<dev-tcltk/itcl-4.0
+	<dev-tcltk/itk-4.0
+	dev-tcltk/iwidgets
+	dev-tcltk/tkimg
+	dev-tcltk/tkpng
+	sys-libs/libtermcap-compat
+	media-libs/urt
+	x11-libs/libXt
+	x11-libs/libXi
+	java? ( >=virtual/jre-1.5 )
+	"
+
+DEPEND="${RDEPEND}
+	sys-devel/bison
+	sys-devel/flex
+	dev-tcltk/tktable
+	>=virtual/jre-1.5
+	doc? (
+		dev-libs/libxslt
+		app-doc/doxygen
+	)"
+
+BRLCAD_DIR="${EPREFIX}/usr/${PN}"
+
+#src_prepare() {
+#	epatch "${FILESDIR}/${P}-cmake.patch"
+#}
+
+src_configure() {
+filter-flags -std=c++0x
+append-ldflags $(no-as-needed)
+	if use Debug; then
+		CMAKE_BUILD_TYPE=Debug
+		else
+		CMAKE_BUILD_TYPE=Release
+		fi
+	local mycmakeargs=(
+		-DCMAKE_INSTALL_PREFIX="${BRLCAD_DIR}"
+		-DBRLCAD_ENABLE_STRICT=OFF
+		-DBRLCAD-ENABLE_STRICT=OFF
+		-DBRLCAD-ENABLE_COMPILER_WARNINGS=OFF
+		-DBRLCAD_FLAGS_OPTIMIZATION=ON
+		-DBRLCAD_ENABLE_X11=ON
+		-DBRLCAD_BUNDLED_LIBS=AUTO
+		)
+
+			# use flag triggered options
+	if use debug; then
+		mycmakeargs += "-DCMAKE_BUILD_TYPE=Debug"
+	else
+		mycmakeargs += "-DCMAKE_BUILD_TYPE=Release"
+	fi
+	mycmakeargs+=(
+		$(cmake-utils_use opengl BRLCAD_ENABLE_OPENGL)
+#experimental RTGL support
+	#	$(cmake-utils_use opengl BRLCAD_ENABLE_RTGL)
+		$(cmake-utils_use amd64 BRLCAD_ENABLE_64BIT)
+		$(cmake-utils_use smp BRLCAD_ENABLE_SMP)
+	#	$(cmake-utils_use java BRLCAD_ENABLE_RTSERVER)
+		$(cmake-utils_use examples BRLCAD_INSTALL_EXAMPLE_GEOMETRY)
+		$(cmake-utils_use doc BRLCAD_EXTRADOCS)
+		$(cmake-utils_use doc BRLCAD_EXTRADOCS_PDF)
+		$(cmake-utils_use doc BRLCAD_EXTRADOCS_MAN)
+		$(cmake-utils_use debug BRLCAD_ENABLE_VERBOSE_PROGRESS)
+			)
+	cmake-utils_src_configure
+}
+
+src_compile() {
+	cmake-utils_src_compile
+}
+
+src_test() {
+	cmake-utils_src_test
+	#emake check || die "emake check failed"
+	if use benchmarks; then
+		emake benchmark || die "emake benchmark failed"
+	fi
+}
+
+src_install() {
+	cmake-utils_src_install
+	rm -f "${D}"usr/share/brlcad/{README,NEWS,AUTHORS,HACKING,INSTALL,COPYING}
+	dodoc AUTHORS NEWS README HACKING TODO BUGS ChangeLog
+	echo "PATH=\"${BRLCAD_DIR}/bin\"" >  99brlcad
+	echo "MANPATH=\"${BRLCAD_DIR}/man\"" >> 99brlcad
+	doenvd 99brlcad || die
+	newicon misc/macosx/Resources/ReadMe.rtfd/brlcad_logo_tiny.png brlcad.png
+	make_desktop_entry mged "BRL-CAD" brlcad "Graphics;Engineering"
+}
diff --git a/media-gfx/brlcad/brlcad-9999.ebuild b/media-gfx/brlcad/brlcad-9999.ebuild
index e7cfb1c0f..ffc2b938a 100644
--- a/media-gfx/brlcad/brlcad-9999.ebuild
+++ b/media-gfx/brlcad/brlcad-9999.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2011 Gentoo Foundation
+# Copyright 1999-2013 Gentoo Foundation
 # Distributed under the terms of the GNU General Public License v2
 # $Header: /var/cvsroot/gentoo-x86/media-gfx/brlcad/brlcad-7.18.4.ebuild,v 1.1 2011/04/18 22:47:37 dilfridge Exp $
 
@@ -18,10 +18,6 @@ RDEPEND="media-libs/libpng
 	sys-libs/zlib
 	>=sci-libs/tnt-3
 	sci-libs/jama
-	>=dev-lang/tcl-8.5
-	>=dev-lang/tk-8.5
-	=dev-tcltk/itcl-3.4*
-	=dev-tcltk/itk-3.4*
 	dev-tcltk/iwidgets
 	dev-tcltk/tkimg
 	dev-tcltk/tkpng
@@ -58,7 +54,7 @@ filter-flags -std=c++0x
 		-DBRLCAD_ENABLE_COMPILER_WARNINGS=OFF
 		-DBRLCAD_FLAGS_OPTIMIZATION=ON
 		-DBRLCAD_ENABLE_X11=ON
-		-DBRLCAD_BUNDLED_LIBS=System
+		-DBRLCAD_BUNDLED_LIBS=ON
 		)
 
 			# use flag triggered options
diff --git a/sci-chemistry/gromacs/ChangeLog b/sci-chemistry/gromacs/ChangeLog
index 1cba1c5d4..e91c85aee 100644
--- a/sci-chemistry/gromacs/ChangeLog
+++ b/sci-chemistry/gromacs/ChangeLog
@@ -2,6 +2,16 @@
 # Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2
 # $Header: $
 
+  05 May 2013; Christoph Junghans <ottxor@gentoo.org> gromacs-4.5.9999.ebuild:
+  sync with gx86
+
+*gromacs-4.5.9999 (03 May 2013)
+
+  03 May 2013; Christoph Junghans <ottxor@gentoo.org>
+  +files/gromacs-4.5.7-cmake-cpp-asm.patch, +gromacs-4.5.9999.ebuild,
+  metadata.xml:
+  added recent 4.5.x version from gx86 (bug #468454)
+
   15 Mar 2013; Alexey Shvetsov <alexxy@gentoo.org> gromacs-4.6.9999.ebuild:
   nvcc flags dont needed anymore here
 
diff --git a/sci-chemistry/gromacs/Manifest b/sci-chemistry/gromacs/Manifest
new file mode 100644
index 000000000..18bfd78e0
--- /dev/null
+++ b/sci-chemistry/gromacs/Manifest
@@ -0,0 +1,2 @@
+DIST gmxtest-4.0.4.tgz 14845017 SHA256 6a7f787f4bb7cbecb688115ff0854a5ffd2ef33487d7bce4b031e63848b6f361 SHA512 f8165ef1d7e2ed69db0a069a1c85fc5fa440d66e96aa54b474392a6331d2327b60f76b8dceb02f9233ce06eb6b7a4e7c448fc71f666e244efa571cf94f1e86ec WHIRLPOOL dbb122736a588deb7931204b29142dd3d9b074691e94341b04dcad2cdf428eb0aae739aa37ef6f61d1dcd6fb96ddcc1292e76f267694f3c18ee67d17352bfd9b
+DIST gromacs-manual-4.5.6.pdf 2650364 SHA256 5c2a086c9cf1627008e3909b37ea5320eb9eeedf9833147d7b0f4e3688aaf339 SHA512 4035623df74d500abff35c7e08d0dbc8cd80f4fae4f580b6f72939d31a456c02fa00b5b47659767125cdf318db10c0cfac4d3f9584b7b384a48300efbfc590bc WHIRLPOOL 089bb4da2e5f51a0e8dfe4f76195b79daec10f661a48c48e491b9cda711f49e67a7e2d77c5bb884eaf4176ca3b0c20c389fc3a77e719a0870d548c3803929cdc
diff --git a/sci-chemistry/gromacs/files/gromacs-4.5.7-cmake-cpp-asm.patch b/sci-chemistry/gromacs/files/gromacs-4.5.7-cmake-cpp-asm.patch
new file mode 100644
index 000000000..f39921f69
--- /dev/null
+++ b/sci-chemistry/gromacs/files/gromacs-4.5.7-cmake-cpp-asm.patch
@@ -0,0 +1,43 @@
+diff -Naur gromacs-4.5.7.orig/cmake/CMakeASM-ATTInformation.cmake gromacs-4.5.7/cmake/CMakeASM-ATTInformation.cmake
+--- gromacs-4.5.7.orig/cmake/CMakeASM-ATTInformation.cmake	1969-12-31 17:00:00.000000000 -0700
++++ gromacs-4.5.7/cmake/CMakeASM-ATTInformation.cmake	2013-05-03 10:47:52.779868731 -0600
+@@ -0,0 +1,13 @@
++
++# This a modified version of CMakeASMInformation.cmake coming with cmake 2.8.6, which
++# supports .S files
++
++# support for AT&T syntax assemblers, e.g. GNU as
++
++SET(ASM_DIALECT "-ATT")
++SET(CMAKE_ASM${ASM_DIALECT}_SOURCE_FILE_EXTENSIONS S;s;asm)
++
++SET(CMAKE_ASM${ASM_DIALECT}_COMPILE_OBJECT "<CMAKE_ASM${ASM_DIALECT}_COMPILER> <FLAGS> -o <OBJECT> <SOURCE>")
++
++INCLUDE(CMakeASMInformation)
++SET(ASM_DIALECT)
+diff -Naur gromacs-4.5.7.orig/src/gmxlib/CMakeLists.txt gromacs-4.5.7/src/gmxlib/CMakeLists.txt
+--- gromacs-4.5.7.orig/src/gmxlib/CMakeLists.txt	2013-05-03 10:46:29.029305075 -0600
++++ gromacs-4.5.7/src/gmxlib/CMakeLists.txt	2013-05-03 10:50:34.630582295 -0600
+@@ -47,18 +47,18 @@
+ if(GMX_IA32_ASM)
+   file(GLOB GMX_SSEKERNEL_C_SRC   nonbonded/nb_kernel_ia32_${SSETYPE}/*.c)
+   if(GMX_ASM_USEASM_NASM)
+-    file(GLOB GMX_SSEKERNEL_ASM_SRC nonbonded/nb_kernel_ia32_${SSETYPE}/*intel_syntax*.s)    
++    file(GLOB GMX_SSEKERNEL_ASM_SRC nonbonded/nb_kernel_ia32_${SSETYPE}/*intel_syntax*.S)    
+   else()
+-    file(GLOB GMX_SSEKERNEL_ASM_SRC nonbonded/nb_kernel_ia32_${SSETYPE}/*${SSETYPE}.s nonbonded/nb_kernel_ia32_${SSETYPE}/*asm.s)
++    file(GLOB GMX_SSEKERNEL_ASM_SRC nonbonded/nb_kernel_ia32_${SSETYPE}/*${SSETYPE}.S nonbonded/nb_kernel_ia32_${SSETYPE}/*asm.S)
+   endif()
+ endif(GMX_IA32_ASM)
+ 
+ if(GMX_X86_64_ASM)
+   file(GLOB GMX_SSEKERNEL_C_SRC   nonbonded/nb_kernel_x86_64_${SSETYPE}/*.c)
+   if(GMX_ASM_USEASM_NASM)
+-    file(GLOB GMX_SSEKERNEL_ASM_SRC nonbonded/nb_kernel_x86_64_${SSETYPE}/*intel_syntax*.s)
++    file(GLOB GMX_SSEKERNEL_ASM_SRC nonbonded/nb_kernel_x86_64_${SSETYPE}/*intel_syntax*.S)
+   else()
+-    file(GLOB GMX_SSEKERNEL_ASM_SRC nonbonded/nb_kernel_x86_64_${SSETYPE}/*${SSETYPE}.s nonbonded/nb_kernel_x86_64_${SSETYPE}/*asm.s)
++    file(GLOB GMX_SSEKERNEL_ASM_SRC nonbonded/nb_kernel_x86_64_${SSETYPE}/*${SSETYPE}.S nonbonded/nb_kernel_x86_64_${SSETYPE}/*asm.S)
+   endif()
+ endif(GMX_X86_64_ASM)
+ 
diff --git a/sci-chemistry/gromacs/gromacs-4.5.9999.ebuild b/sci-chemistry/gromacs/gromacs-4.5.9999.ebuild
new file mode 100644
index 000000000..b5ed08545
--- /dev/null
+++ b/sci-chemistry/gromacs/gromacs-4.5.9999.ebuild
@@ -0,0 +1,242 @@
+# Copyright 1999-2013 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/gromacs/gromacs-4.5.7.ebuild,v 1.2 2013/05/05 17:31:09 ottxor Exp $
+
+EAPI="4"
+
+TEST_PV="4.0.4"
+MANUAL_PV="4.5.6"
+
+FORTRAN_NEEDED=fkernels
+
+inherit bash-completion-r1 cmake-utils eutils fortran-2 multilib toolchain-funcs
+
+SRC_URI="test? ( ftp://ftp.gromacs.org/pub/tests/gmxtest-${TEST_PV}.tgz )
+		doc? ( ftp://ftp.gromacs.org/pub/manual/manual-${MANUAL_PV}.pdf -> gromacs-manual-${MANUAL_PV}.pdf )"
+
+if [ "${PV%9999}" != "${PV}" ]; then
+	EGIT_REPO_URI="git://git.gromacs.org/gromacs http://repo.or.cz/r/gromacs.git"
+	EGIT_BRANCH="release-4-5-patches"
+	inherit git-2
+else
+	SRC_URI="${SRC_URI} ftp://ftp.gromacs.org/pub/${PN}/${P}.tar.gz
+		sse2? ( http://dev.gentoo.org/~alexxy/gromacs/0001-Make-stack-non-executable-for-GAS-assembly.patch.gz )
+		sse2? ( http://dev.gentoo.org/~alexxy/gromacs/0002-Make-stack-non-executable-for-ATT-assembly.patch.gz )"
+fi
+
+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 altivec blas doc -double-precision +fftw fkernels gsl lapack
+mpi +single-precision sse2 test +threads xml zsh-completion"
+REQUIRED_USE="fkernels? ( !threads )"
+
+CDEPEND="
+	X? (
+		x11-libs/libX11
+		x11-libs/libSM
+		x11-libs/libICE
+		)
+	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="${CDEPEND}
+	virtual/pkgconfig"
+RDEPEND="${CDEPEND}
+	app-shells/tcsh"
+
+RESTRICT="test"
+
+src_prepare() {
+	#add user patches from /etc/portage/patches/sci-chemistry/gromacs
+	epatch_user
+
+	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
+
+	if [[ ${PV} != *9999 ]] && use sse2; then
+		# Add patches for non-exec stack - qa issue
+		epatch "${WORKDIR}/0001-Make-stack-non-executable-for-GAS-assembly.patch"
+		epatch "${WORKDIR}/0002-Make-stack-non-executable-for-ATT-assembly.patch"
+		#alexxy patches, renamve kernel from .s to .S
+		epatch "${FILESDIR}/${P}-cmake-cpp-asm.patch"
+	fi
+
+	GMX_DIRS=""
+	use single-precision && GMX_DIRS+=" float"
+	use double-precision && GMX_DIRS+=" double"
+	#if neither single-precision nor double-precision is enabled
+	#build at least default (single)
+	[ -z "$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=( )
+	#from gromacs configure
+	if use fftw; then
+		mycmakeargs_pre+=("-DGMX_FFT_LIBRARY=fftw3")
+	else
+		mycmakeargs_pre+=("-DGMX_FFT_LIBRARY=fftpack")
+		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
+
+	#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
+
+	#go from slowest to fasterest acceleration
+	local acce="none"
+	use fkernels && acce="fortran"
+	use altivec && acce="altivec"
+	use ia64 && acce="ia64"
+	use sse2 && acce="sse"
+
+	mycmakeargs_pre+=(
+		$(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 threads GMX_THREADS)
+		$(cmake-utils_use xml GMX_XML)
+		-DGMX_DEFAULT_SUFFIX=off
+		-DGMX_ACCELERATION="$acce"
+		-DGMXLIB="$(get_libdir)"
+	)
+
+	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"
+		mycmakeargs=( ${mycmakeargs_pre[@]} ${p} -DGMX_MPI=OFF
+			-DGMX_BINARY_SUFFIX="${suffix}" -DGMX_LIBS_SUFFIX="${suffix}" )
+		BUILD_DIR="${WORKDIR}/${P}_${x}" cmake-utils_src_configure
+		use mpi || continue
+		einfo "Configuring for ${x} precision with mpi"
+		mycmakeargs=( ${mycmakeargs_pre[@]} ${p} -DGMX_MPI=ON
+			-DGMX_BINARY_SUFFIX="_mpi${suffix}" -DGMX_LIBS_SUFFIX="_mpi${suffix}" )
+		BUILD_DIR="${WORKDIR}/${P}_${x}_mpi" cmake-utils_src_configure
+	done
+}
+
+src_compile() {
+	for x in ${GMX_DIRS}; do
+		einfo "Compiling for ${x} precision"
+		BUILD_DIR="${WORKDIR}/${P}_${x}"\
+			cmake-utils_src_compile
+		use mpi || continue
+		einfo "Compiling for ${x} precision with mpi"
+		BUILD_DIR="${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 ${GMX_DIRS}; do
+		BUILD_DIR="${WORKDIR}/${P}_${x}" \
+			cmake-utils_src_install
+		use mpi || continue
+		#cmake-utils_src_install does not support args
+		#using cmake-utils_src_compile instead
+		BUILD_DIR="${WORKDIR}/${P}_${x}_mpi" \
+			cmake-utils_src_make install-mdrun DESTDIR="${D}"
+	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 "${ED}"/usr/bin/GMXRC*
+
+	newbashcomp "${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.*
+
+	# 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() {
+	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 880233ecb..8a88d53da 100644
--- a/sci-chemistry/gromacs/metadata.xml
+++ b/sci-chemistry/gromacs/metadata.xml
@@ -11,6 +11,7 @@
 		<flag name="double-precision">More precise calculations at the expense of speed</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="sse4_1">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>
diff --git a/sci-libs/mkl/ChangeLog b/sci-libs/mkl/ChangeLog
index 83c216d21..72df03b52 100644
--- a/sci-libs/mkl/ChangeLog
+++ b/sci-libs/mkl/ChangeLog
@@ -2,6 +2,11 @@
 # Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2
 # $Header: $
 
+*mkl-11.0.3.163 (02 May 2013)
+
+  02 May 2013; Justin Lecher <jlec@gentoo.org> +mkl-11.0.3.163.ebuild:
+  Version Bump
+
 *mkl-11.0.2.146 (14 Feb 2013)
 
   14 Feb 2013; Justin Lecher <jlec@gentoo.org> -mkl-11.0.1.117.ebuild,
diff --git a/sci-libs/mkl/Manifest b/sci-libs/mkl/Manifest
index 4e6ed6ce4..b540fb868 100644
--- a/sci-libs/mkl/Manifest
+++ b/sci-libs/mkl/Manifest
@@ -4,3 +4,7 @@ DIST parallel_studio_xe_2013_intel64.tgz 1448188683 SHA256 6d3f5a635e86bc6d71d97
 DIST parallel_studio_xe_2013_update2.tgz 2152945149 SHA256 e8ddf6141f7d84c1f242891fabe0882c40269c358c0b946fee22ee6caa37121c SHA512 633370f58bd9fc14140912d5b3dd251ca4819a926b004a8053f92c83de6f9fdfdad192b425c5224d8b5aee47042a1a99d49628e6e2bb53e623ae429eefcfaac4 WHIRLPOOL 5b4a7c0c9cab758885ccffab25f1aaf64a6f5576d02df81a4797a2b9ae2151efb5e564e43397a2b61040d4af66024107a5a9c537982d3e17723655414dcba166
 DIST parallel_studio_xe_2013_update2_ia32.tgz 1190613262 SHA256 13063ea9c47c781ea8f368566d328434351002e7321b2021b5f04ff741a5d55f SHA512 1488a1b8c9b84881041ccf42d9f856d44aa0654ce3171b0f92114a3408d8cb1f1a18a6d488db6bbfd7322d5a230748612b53378b6ac01b8b7b3e66b3b8f94333 WHIRLPOOL f7d2b307d2f4e226004ddfcf073db087fff6d68e94f849e85350dc18894db884b62362bb3929076fdd531e29f5c49e2cd94eba8685b13fc52e293226516d909d
 DIST parallel_studio_xe_2013_update2_intel64.tgz 1488277925 SHA256 6136774de466de19f4024eeb5a8176ffbf559143b048fecc83848c27008361d6 SHA512 8260ab223d9a959089ae66c8948d90ce119cceeb719ef18c1a9d258ccd77e9b6a67af1a3e203d96a1c3c774def9a6fc302c126001072b7c5aa2bb3cdc68bc4dd WHIRLPOOL 006dc0e925c8265abf174682cd54f2c2fc4c4f1e059e045407d523b3e3b659cadc47da005126236a8b01b882fd0b4dfa7dadce0c52f640d5c0ada8122a9d6d08
+DIST parallel_studio_xe_2013_update3.tgz 2173061577 SHA256 98b3bfe9feefa8caaa1bea533362f31bcfe96aa8f9e59fc89f6a453d50df7508 SHA512 c6115f01b045c840b61e3c2a17fd39142c814d4e387fa5bc935c5cc6ca365c3fedddb6d8c045b5c239b948b42c02254d8b73c42cfe16d046dcf14d3a4597bbde WHIRLPOOL e857fbf0fc73406f7d787400f8ed6e45e93825616fe3d2d10dcd26fa03d56cd956a0b598270724be4ab3886d77502e0f456077ed3008cffc6bdb4abe60acedce
+DIST parallel_studio_xe_2013_update3_ia32.tgz 1207596909 SHA256 57017db1b00345d46ef9dff67dd4e5754ed0fe67fae7335489447f948dbfe7a8 SHA512 f3656fcbda74f253c8cc0ca56e16a84d77854ef51ecc7f24db02c820270bef3954d0d97d1be2aa5cf2ea7703a6e442c3be15df28de570aac7062e5c5958581a4 WHIRLPOOL 0407b59697da8a69c8ac512dec4187bf27eeb2e80516cd6a99968ef3b30a31e55eeaa31ec4bcbd34fe23678e68c4f00cc5dfce579edfb0268b789e1e65285945
+DIST parallel_studio_xe_2013_update3_intel64.tgz 1508395753 SHA256 081bc3d617f04243d459d92d05398df1a3634faf3de554346f732ed83ed4ef06 SHA512 344678ba9c6029ab095cc656c2153b20f0f996dab45115296fb624eca3863763e4010b519595892ffeecfc1a0880901ef5ae53924e41e470aec46efd0abcd822 WHIRLPOOL 1295f579ecc50014b285d47ecf6b92d1b9d0c2cbadd1a5972a832178263a9b3d4cf4208153df40e270c259c1307ed21277239e70371b39eaf4e12171c25a3c1f
+
diff --git a/sci-libs/mkl/mkl-11.0.3.163.ebuild b/sci-libs/mkl/mkl-11.0.3.163.ebuild
new file mode 100644
index 000000000..fee4df062
--- /dev/null
+++ b/sci-libs/mkl/mkl-11.0.3.163.ebuild
@@ -0,0 +1,131 @@
+# Copyright 1999-2013 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: $
+
+EAPI=5
+
+INTEL_DPN=parallel_studio_xe
+INTEL_DID=3078
+INTEL_DPV=2013_update3
+INTEL_SUBDIR=composerxe
+
+inherit intel-sdp multilib alternatives-2
+
+DESCRIPTION="Intel Math Kernel Library: linear algebra, fft, math functions"
+HOMEPAGE="http://software.intel.com/en-us/articles/intel-mkl/"
+
+IUSE=""
+KEYWORDS="-* ~amd64 ~x86 ~amd64-linux ~x86-linux"
+
+DEPEND=""
+RDEPEND=">=dev-libs/intel-common-13"
+
+CHECKREQS_DISK_BUILD=2500M
+
+INTEL_BIN_RPMS="mkl mkl-devel"
+INTEL_DAT_RPMS="mkl-common"
+
+src_prepare() {
+	chmod u+w -R opt
+}
+
+mkl_add_prof() {
+	local pcname=${1} libs cflags x
+	shift
+	[[ ${pcname} = *int64* ]] && cflags=-DMKL_ILP64
+	cat <<-EOF > ${pcname}.pc
+		prefix=${INTEL_SDP_EDIR}/mkl
+		libdir=\${prefix}/lib/${IARCH}
+		includedir=\${prefix}/include
+		Name: ${pcname}
+		Description: ${DESCRIPTION}
+		Version: ${PV}
+		URL: ${HOMEPAGE}
+		Libs: -L\${libdir} ${libs}
+		Cflags: -I\${includedir} ${cflags}
+	EOF
+	insinto /usr/$(get_libdir)/pkgconfig
+	doins ${pcname}.pc
+	for x in $*; do
+		alternatives_for ${x} ${pcname/-${x}} 0 \
+			/usr/$(get_libdir)/pkgconfig/${x}.pc ${pcname}.pc
+	done
+}
+
+# mkl_prof [_ilp64 or _lp64]
+# help: http://software.intel.com/en-us/articles/intel-mkl-link-line-advisor/
+mkl_prof() {
+	local bits=""
+	if [[ ${IARCH} == intel64 ]]; then
+		bits=_lp64
+		[[ ${1} == int64 ]] && bits=_ilp64
+	fi
+	local gf="-Wl,--start-group -lmkl_gf${bits}"
+	local intel="-Wl,--start-group -lmkl_intel${bits}"
+	local core="-lmkl_core -Wl,--end-group"
+	local prof=mkl${IARCH:((${#IARCH} - 2)):2}
+	[[ ${1} == int64 ]] && prof=${prof}-int64
+	local libs
+
+	libs="${gf} -lmkl_sequential ${core} -lpthread" \
+		mkl_add_prof ${prof}-gfortran blas lapack
+	libs="${intel} -lmkl_sequential ${core} -lpthread" \
+		mkl_add_prof ${prof}-intel blas lapack cblas lapacke
+	libs="${gf} -lmkl_gnu_thread ${core} -fopenmp -lpthread" \
+		mkl_add_prof ${prof}-gfortran-openmp blas lapack
+	libs="${intel} -lmkl_gnu_thread ${core} -fopenmp -lpthread" \
+		mkl_add_prof ${prof}-gcc-openmp cblas lapacke
+	libs="${intel} -lmkl_intel_thread ${core} -openmp -lpthread" \
+		mkl_add_prof ${prof}-intel-openmp blas lapack cblas lapacke
+	libs="-lmkl_rt -lpthread" \
+		mkl_add_prof ${prof}-dynamic blas lapack cblas lapacke
+	libs="-lmkl_rt -liomp5 -lpthread" \
+		mkl_add_prof ${prof}-dynamic-openmp blas lapack cblas lapacke
+
+	# blacs and scalapack
+	local scal="-lmkl_scalapack${bits:-_core}"
+	local blacs="-lmkl_blacs_intelmpi${bits}"
+	core="-lmkl_core ${blacs} -Wl,--end-group"
+
+	libs="${gf} -lmkl_sequential ${core} -lpthread" \
+		mkl_add_prof ${prof}-gfortran-blacs blacs
+	libs="${scal} ${gf} -lmkl_sequential ${core} -lpthread" \
+		mkl_add_prof ${prof}-gfortran-scalapack scalapack
+	libs="${intel} -lmkl_sequential ${core} -lpthread" \
+		mkl_add_prof ${prof}-intel-blacs blacs
+	libs="${scal} ${intel} -lmkl_sequential ${core} -lpthread" \
+		mkl_add_prof ${prof}-intel-scalapack scalapack
+	libs="${gf} -lmkl_gnu_thread ${core} -fopenmp -lpthread" \
+		mkl_add_prof ${prof}-gfortran-openmp-blacs blacs
+	libs="${scal} ${gf} -lmkl_gnu_thread ${core} -fopenmp -lpthread" \
+		mkl_add_prof ${prof}-gfortran-openmp-scalapack scalapack
+	libs="${intel} -lmkl_gnu_thread ${core} -fopenmp -lpthread" \
+		mkl_add_prof ${prof}-gcc-openmp-blacs blacs
+	libs="${scal} ${intel} -lmkl_gnu_thread ${core} -fopenmp -lpthread" \
+		mkl_add_prof ${prof}-gcc-openmp-scalapack scalapack
+	libs="${intel} -lmkl_intel_thread ${core} -liomp5 -lpthread" \
+		mkl_add_prof ${prof}-intel-openmp-blacs blacs
+	libs="${scal} ${intel} -lmkl_intel_thread ${core} -liomp5 -lpthread" \
+		mkl_add_prof ${prof}-intel-openmp-scalapack scalapack
+	libs="-lmkl_rt ${blacs} -lpthread" \
+		mkl_add_prof ${prof}-dynamic-blacs blacs
+	libs="${scal} -lmkl_rt ${blacs} -lpthread" \
+		mkl_add_prof ${prof}-dynamic-scalapack scalapack
+	libs="-lmkl_rt ${blacs} -liomp5 -lpthread" \
+		mkl_add_prof ${prof}-dynamic-openmp-blacs blacs
+	libs="${scal} -lmkl_rt ${blacs} -liomp5 -lpthread" \
+		mkl_add_prof ${prof}-dynamic-openmp-scalapack scalapack
+}
+
+src_install() {
+	intel-sdp_src_install
+	echo -n > 35mkl "LDPATH="
+	for IARCH in ${INTEL_ARCH}; do
+		mkl_prof
+		sed -i -e '/mkl/s/$/:/' 35mkl
+		echo -n >> 35mkl "${INTEL_SDP_EDIR}/mkl/lib/${IARCH}"
+		[[ ${IARCH} == intel64 ]] && mkl_prof int64
+	done
+	echo >> 35mkl
+	doenvd 35mkl
+}