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

5 files changed, 298 insertions, 0 deletions

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>