remove old

(Portage version: 2.2.14/cvs/Linux x86_64, signed Manifest commit with key C2000586)

6 files changed, 6 insertions, 1352 deletions

diff --git a/sci-chemistry/gromacs/ChangeLog b/sci-chemistry/gromacs/ChangeLog
index 4f0f80a01b80..6ec6f1ec4e46 100644
--- a/sci-chemistry/gromacs/ChangeLog
+++ b/sci-chemistry/gromacs/ChangeLog
@@ -1,6 +1,11 @@
 # ChangeLog for sci-chemistry/gromacs
 # Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2
-# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/gromacs/ChangeLog,v 1.150 2015/01/31 20:23:56 ottxor Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/gromacs/ChangeLog,v 1.151 2015/01/31 20:31:16 ottxor Exp $
+
+  31 Jan 2015; Christoph Junghans <ottxor@gentoo.org> -gromacs-4.6.6.ebuild,
+  -gromacs-5.0.1.ebuild, -gromacs-5.0.2-r1.ebuild, -gromacs-5.0.2.ebuild,
+  -gromacs-5.0.ebuild:
+  remove old
 
   31 Jan 2015; Christoph Junghans <ottxor@gentoo.org> gromacs-4.6.5.ebuild,
   gromacs-4.6.6.ebuild, gromacs-4.6.7.ebuild, gromacs-5.0.1.ebuild,
diff --git a/sci-chemistry/gromacs/gromacs-4.6.6.ebuild b/sci-chemistry/gromacs/gromacs-4.6.6.ebuild
deleted file mode 100644
index 65e796123a07..000000000000
--- a/sci-chemistry/gromacs/gromacs-4.6.6.ebuild
+++ /dev/null
@@ -1,286 +0,0 @@
-# Copyright 1999-2015 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/gromacs/gromacs-4.6.6.ebuild,v 1.2 2015/01/31 20:23:56 ottxor Exp $
-
-EAPI=5
-
-TEST_PV="4.6.6"
-MANUAL_PV="4.6.6"
-
-CMAKE_MAKEFILE_GENERATOR="ninja"
-
-inherit bash-completion-r1 cmake-utils cuda eutils multilib readme.gentoo toolchain-funcs
-
-if [[ $PV = *9999* ]]; then
-	EGIT_REPO_URI="git://git.gromacs.org/gromacs.git
-		https://gerrit.gromacs.org/gromacs.git
-		git://github.com/gromacs/gromacs.git
-		http://repo.or.cz/r/gromacs.git"
-	EGIT_BRANCH="release-4-6"
-	inherit git-2
-	LIVE_DEPEND="doc? (
-		app-doc/doxygen
-		dev-texlive/texlive-latex
-		dev-texlive/texlive-latexextra
-		media-gfx/imagemagick
-		sys-apps/coreutils
-	)"
-	KEYWORDS=""
-else
-	SRC_URI="ftp://ftp.gromacs.org/pub/${PN}/${P}.tar.gz
-		doc? ( ftp://ftp.gromacs.org/pub/manual/manual-${MANUAL_PV}.pdf -> ${PN}-manual-${MANUAL_PV}.pdf )
-		test? ( http://gerrit.gromacs.org/download/regressiontests-${TEST_PV}.tar.gz )"
-	LIVE_DEPEND=""
-	KEYWORDS="~alpha ~amd64 ~arm ~ppc64 ~sparc ~x86 ~amd64-linux ~x86-linux ~x86-macos"
-fi
-
-ACCE_IUSE="cpu_flags_x86_sse2 cpu_flags_x86_sse4_1 cpu_flags_x86_fma4 cpu_flags_x86_avx"
-
-DESCRIPTION="The ultimate molecular dynamics simulation package"
-HOMEPAGE="http://www.gromacs.org/"
-
-# see COPYING for details
-# http://repo.or.cz/w/gromacs.git/blob/HEAD:/COPYING
-#        base,    vmd plugins, fftpack from numpy,  blas/lapck from netlib,        memtestG80 library,  mpi_thread lib
-LICENSE="LGPL-2.1 UoI-NCSA !mkl? ( !fftw? ( BSD ) !blas? ( BSD ) !lapack? ( BSD ) ) cuda? ( LGPL-3 ) threads? ( BSD )"
-SLOT="0/${PV}"
-IUSE="X blas cuda doc -double-precision +fftw gsl lapack mkl mpi +offensive openmm openmp +single-precision test +threads zsh-completion ${ACCE_IUSE}"
-
-CDEPEND="
-	X? (
-		x11-libs/libX11
-		x11-libs/libSM
-		x11-libs/libICE
-		)
-	blas? ( virtual/blas )
-	cuda? ( >=dev-util/nvidia-cuda-toolkit-4.2.9-r1 )
-	fftw? ( sci-libs/fftw:3.0 )
-	gsl? ( sci-libs/gsl )
-	lapack? ( virtual/lapack )
-	mkl? ( sci-libs/mkl )
-	mpi? ( virtual/mpi )
-	openmm? (
-		>=dev-util/nvidia-cuda-toolkit-4.2.9-r1
-		sci-libs/openmm[cuda,opencl]
-	)"
-DEPEND="${CDEPEND}
-	virtual/pkgconfig
-	${LIVE_DEPEND}
-	doc? ( app-doc/doxygen )"
-RDEPEND="${CDEPEND}"
-
-REQUIRED_USE="
-	|| ( single-precision double-precision )
-	cuda? ( single-precision )
-	openmm? ( single-precision )
-	mkl? ( !blas !fftw !lapack )"
-
-DOCS=( AUTHORS README )
-HTML_DOCS=( "${ED}"/usr/share/gromacs/html/ )
-
-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"
-}
-
-src_unpack() {
-	if [[ ${PV} != *9999 ]]; then
-		default
-	else
-		git-2_src_unpack
-		if use doc; then
-			EGIT_REPO_URI="git://git.gromacs.org/manual.git" \
-			EGIT_BRANCH="release-4-6" EGIT_NOUNPACK="yes" EGIT_COMMIT="release-4-6" \
-			EGIT_SOURCEDIR="${WORKDIR}/manual"\
-				git-2_src_unpack
-		fi
-		if use test; then
-			EGIT_REPO_URI="git://git.gromacs.org/regressiontests.git" \
-			EGIT_BRANCH="master" EGIT_NOUNPACK="yes" EGIT_COMMIT="release-4-6" \
-			EGIT_SOURCEDIR="${WORKDIR}/regressiontests"\
-				git-2_src_unpack
-		fi
-	fi
-}
-
-src_prepare() {
-	#notes/todos
-	# -on apple: there is framework support
-
-	cmake-utils_src_prepare
-
-	use cuda && cuda_src_prepare
-
-	GMX_DIRS=""
-	use single-precision && GMX_DIRS+=" float"
-	use double-precision && GMX_DIRS+=" double"
-
-	if use test; then
-		for x in ${GMX_DIRS}; do
-			mkdir -p "${WORKDIR}/${P}_${x}" || die
-			cp -al "${WORKDIR}/regressiontests"* "${WORKDIR}/${P}_${x}/tests" || die
-		done
-	fi
-
-	DOC_CONTENTS="Gromacs can use sci-chemistry/vmd to read additional file formats"
-}
-
-src_configure() {
-	local mycmakeargs_pre=( ) extra fft_opts=( )
-
-	#go from slowest to fastest acceleration
-	local acce="None"
-	use cpu_flags_x86_sse2 && acce="SSE2"
-	use cpu_flags_x86_sse4_1 && acce="SSE4.1"
-	use cpu_flags_x86_fma4 && acce="AVX_128_FMA"
-	use cpu_flags_x86_avx && acce="AVX_256"
-
-	#to create man pages, build tree binaries are executed (bug #398437)
-	[[ ${CHOST} = *-darwin* ]] && \
-		extra+=" -DCMAKE_BUILD_WITH_INSTALL_RPATH=OFF"
-
-	if use fftw; then
-		fft_opts=( -DGMX_FFT_LIBRARY=fftw3 )
-	elif use mkl && has_version "=sci-libs/mkl-10*"; then
-		fft_opts=( -DGMX_FFT_LIBRARY=mkl
-			-DMKL_INCLUDE_DIR="${MKLROOT}/include"
-			-DMKL_LIBRARIES="$(echo /opt/intel/mkl/10.0.5.025/lib/*/libmkl.so);$(echo /opt/intel/mkl/10.0.5.025/lib/*/libiomp*.so)"
-		)
-	elif use mkl; then
-		local bits=$(get_libdir)
-		fft_opts=( -DGMX_FFT_LIBRARY=mkl
-			-DMKL_INCLUDE_DIR="$(echo /opt/intel/*/mkl/include)"
-			-DMKL_LIBRARIES="$(echo /opt/intel/*/mkl/lib/*${bits/lib}/libmkl_rt.so)"
-		)
-	else
-		fft_opts=( -DGMX_FFT_LIBRARY=fftpack )
-	fi
-
-	mycmakeargs_pre+=(
-		"${fft_opts[@]}"
-		$(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)
-		$(cmake-utils_use offensive GMX_COOL_QUOTES)
-		-DGMX_DEFAULT_SUFFIX=off
-		-DGMX_ACCELERATION="$acce"
-		-DGMXLIB="$(get_libdir)"
-		-DGMX_VMD_PLUGIN_PATH="${EPREFIX}/usr/$(get_libdir)/vmd/plugins/*/molfile/"
-		-DGMX_PREFIX_LIBMD=ON
-		-DGMX_X86_AVX_GCC_MASKLOAD_BUG=OFF
-		-DGMX_USE_GCC44_BUG_WORKAROUND=OFF
-		${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=( "-DGMX_GPU=OFF" )
-		[[ ${x} = "float" ]] && use cuda && \
-			cuda=( -DGMX_GPU=ON )
-		mycmakeargs=( ${mycmakeargs_pre[@]} ${p} -DGMX_MPI=OFF
-			$(cmake-utils_use threads GMX_THREAD_MPI) "${cuda[@]}" -DGMX_OPENMM=OFF
-			"$(use test && echo -DREGRESSIONTEST_PATH="${WORKDIR}/${P}_${x}/tests")"
-			-DGMX_BINARY_SUFFIX="${suffix}" -DGMX_LIBS_SUFFIX="${suffix}" )
-		BUILD_DIR="${WORKDIR}/${P}_${x}" cmake-utils_src_configure
-		if [[ ${x} = float ]] && use openmm; then
-			einfo "Configuring for openmm build"
-			mycmakeargs=( ${mycmakeargs_pre[@]} ${p} -DGMX_MPI=OFF
-				-DGMX_THREAD_MPI=OFF -DGMX_GPU=OFF -DGMX_OPENMM=ON
-				-DOpenMM_PLUGIN_DIR="${EPREFIX}/usr/$(get_libdir)/plugins"
-				-DGMX_BINARY_SUFFIX="_openmm" -DGMX_LIBS_SUFFIX="_openmm" )
-			BUILD_DIR="${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 ${cuda} -DGMX_OPENMM=OFF
-			-DGMX_BINARY_SUFFIX="_mpi${suffix}" -DGMX_LIBS_SUFFIX="_mpi${suffix}" )
-		BUILD_DIR="${WORKDIR}/${P}_${x}_mpi" CC="mpicc" cmake-utils_src_configure
-	done
-}
-
-src_compile() {
-	for x in ${GMX_DIRS}; do
-		einfo "Compiling for ${x} precision"
-		BUILD_DIR="${WORKDIR}/${P}_${x}"\
-			cmake-utils_src_compile
-		if [[ ${x} = float ]] && use openmm; then
-			einfo "Compiling for openmm build"
-			BUILD_DIR="${WORKDIR}/${P}_openmm"\
-				cmake-utils_src_compile mdrun
-		fi
-		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 ${GMX_DIRS}; do
-		BUILD_DIR="${WORKDIR}/${P}_${x}"\
-			cmake-utils_src_make check
-	done
-}
-
-src_install() {
-	for x in ${GMX_DIRS}; do
-		BUILD_DIR="${WORKDIR}/${P}_${x}" \
-			cmake-utils_src_install
-		if [[ ${x} = float ]] && use openmm; then
-			BUILD_DIR="${WORKDIR}/${P}_openmm" \
-				DESTDIR="${D}" cmake-utils_src_make install-mdrun
-		fi
-		#manual can only be build after gromacs was installed once in image
-		if use doc && [[ $PV = *9999*  && ! -d ${WORKDIR}/manual_build ]]; then
-			mycmakeargs=( -DGMXBIN="${ED}"/usr/bin -DGMXSRC="${WORKDIR}/${P}" )
-			BUILD_DIR="${WORKDIR}"/manual_build \
-				CMAKE_USE_DIR="${WORKDIR}/manual" cmake-utils_src_configure
-			[[ ${CHOST} = *-darwin* ]] && \
-				export DYLD_LIBRARY_PATH="${DYLD_LIBRARY_PATH}${DYLD_LIBRARY_PATH:+:}${ED}/usr/$(get_libdir)"
-			BUILD_DIR="${WORKDIR}"/manual_build cmake-utils_src_make
-			[[ ${CHOST} = *-darwin* ]] && DYLD_LIBRARY_PATH="${ED}/usr/$(get_libdir)"
-			newdoc "${WORKDIR}"/manual_build/gromacs.pdf "${PN}-manual-${PV}.pdf"
-		fi
-		use mpi || continue
-		BUILD_DIR="${WORKDIR}/${P}_${x}_mpi" \
-			DESTDIR="${D}" cmake-utils_src_make install-mdrun
-	done
-
-	use doc && [[ $PV != *9999* ]] && dodoc "${DISTDIR}/${PN}-manual-${MANUAL_PV}.pdf"
-	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.*
-	rm -rf "${ED}"usr/share/gromacs/html
-	rm -f "${ED}"usr/bin/g_options*
-	rm -f "${ED}"usr/bin/GMXRC*
-
-	readme.gentoo_create_doc
-}
-
-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"
-	if use offensive; then
-		einfo
-		einfo  $(g_luck)
-		einfo  "For more Gromacs cool quotes (gcq) add g_luck to your .bashrc"
-	fi
-	einfo
-	readme.gentoo_print_elog
-}
diff --git a/sci-chemistry/gromacs/gromacs-5.0.1.ebuild b/sci-chemistry/gromacs/gromacs-5.0.1.ebuild
deleted file mode 100644
index c2b748bd257b..000000000000
--- a/sci-chemistry/gromacs/gromacs-5.0.1.ebuild
+++ /dev/null
@@ -1,262 +0,0 @@
-# Copyright 1999-2015 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/gromacs/gromacs-5.0.1.ebuild,v 1.3 2015/01/31 20:23:56 ottxor Exp $
-
-EAPI=5
-
-CMAKE_MAKEFILE_GENERATOR="ninja"
-
-inherit bash-completion-r1 cmake-utils cuda eutils multilib readme.gentoo toolchain-funcs
-
-if [[ $PV = *9999* ]]; then
-	EGIT_REPO_URI="git://git.gromacs.org/gromacs.git
-		https://gerrit.gromacs.org/gromacs.git
-		git://github.com/gromacs/gromacs.git
-		http://repo.or.cz/r/gromacs.git"
-	EGIT_BRANCH="release-5-0"
-	inherit git-r3
-	KEYWORDS=""
-else
-	SRC_URI="ftp://ftp.gromacs.org/pub/${PN}/${PN}-${PV/_/-}.tar.gz
-		test? ( http://gerrit.gromacs.org/download/regressiontests-${PV}.tar.gz )"
-	KEYWORDS="~alpha ~amd64 ~arm ~ppc64 ~sparc ~x86 ~amd64-linux ~x86-linux ~x64-macos ~x86-macos"
-fi
-
-ACCE_IUSE="cpu_flags_x86_sse2 cpu_flags_x86_sse4_1 cpu_flags_x86_fma4 cpu_flags_x86_avx cpu_flags_x86_avx2"
-
-DESCRIPTION="The ultimate molecular dynamics simulation package"
-HOMEPAGE="http://www.gromacs.org/"
-
-# see COPYING for details
-# http://repo.or.cz/w/gromacs.git/blob/HEAD:/COPYING
-#        base,    vmd plugins, fftpack from numpy,  blas/lapck from netlib,        memtestG80 library,  mpi_thread lib
-LICENSE="LGPL-2.1 UoI-NCSA !mkl? ( !fftw? ( BSD ) !blas? ( BSD ) !lapack? ( BSD ) ) cuda? ( LGPL-3 ) threads? ( BSD )"
-SLOT="0/${PV}"
-IUSE="X blas boost cuda +doc -double-precision +fftw lapack +make-symlinks mkl mpi +offensive openmp +single-precision test +threads +tng ${ACCE_IUSE}"
-
-CDEPEND="
-	X? (
-		x11-libs/libX11
-		x11-libs/libSM
-		x11-libs/libICE
-		)
-	blas? ( virtual/blas )
-	boost? ( >=dev-libs/boost-1.55 )
-	cuda? ( >=dev-util/nvidia-cuda-toolkit-4.2.9-r1 )
-	fftw? ( sci-libs/fftw:3.0 )
-	lapack? ( virtual/lapack )
-	mkl? ( sci-libs/mkl )
-	mpi? ( virtual/mpi )
-	"
-DEPEND="${CDEPEND}
-	virtual/pkgconfig
-	doc? (
-		app-doc/doxygen
-		dev-texlive/texlive-latex
-		dev-texlive/texlive-latexextra
-		media-gfx/imagemagick
-	)"
-RDEPEND="${CDEPEND}"
-
-REQUIRED_USE="
-	|| ( single-precision double-precision )
-	cuda? ( single-precision )
-	mkl? ( !blas !fftw !lapack )"
-
-DOCS=( AUTHORS README )
-
-if [[ ${PV} != *9999 ]]; then
-	S="${WORKDIR}/${PN}-${PV/_/-}"
-fi
-
-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"
-}
-
-src_unpack() {
-	if [[ ${PV} != *9999 ]]; then
-		default
-	else
-		git-r3_src_unpack
-		if use test; then
-			EGIT_REPO_URI="git://git.gromacs.org/regressiontests.git" \
-			EGIT_BRANCH="master" EGIT_COMMIT="master" \
-			EGIT_CHECKOUT_DIR="${WORKDIR}/regressiontests"\
-				git-r3_src_unpack
-		fi
-	fi
-}
-
-src_prepare() {
-	#notes/todos
-	# -on apple: there is framework support
-
-	cmake-utils_src_prepare
-
-	use cuda && cuda_src_prepare
-
-	GMX_DIRS=""
-	use single-precision && GMX_DIRS+=" float"
-	use double-precision && GMX_DIRS+=" double"
-
-	if use test; then
-		for x in ${GMX_DIRS}; do
-			mkdir -p "${WORKDIR}/${P}_${x}" || die
-			cp -al "${WORKDIR}/regressiontests"* "${WORKDIR}/${P}_${x}/tests" || die
-		done
-	fi
-
-	DOC_CONTENTS="Gromacs can use sci-chemistry/vmd to read additional file formats"
-}
-
-src_configure() {
-	local mycmakeargs_pre=( ) extra fft_opts=( )
-
-	#go from slowest to fastest acceleration
-	local acce="None"
-	use cpu_flags_x86_sse2 && acce="SSE2"
-	use cpu_flags_x86_sse4_1 && acce="SSE4.1"
-	use cpu_flags_x86_fma4 && acce="AVX_128_FMA"
-	use cpu_flags_x86_avx && acce="AVX_256"
-	use cpu_flags_x86_avx2 && acce="AVX2_256"
-
-	#to create man pages, build tree binaries are executed (bug #398437)
-	[[ ${CHOST} = *-darwin* ]] && \
-		extra+=" -DCMAKE_BUILD_WITH_INSTALL_RPATH=OFF"
-
-	if use fftw; then
-		fft_opts=( -DGMX_FFT_LIBRARY=fftw3 )
-	elif use mkl && has_version "=sci-libs/mkl-10*"; then
-		fft_opts=( -DGMX_FFT_LIBRARY=mkl
-			-DMKL_INCLUDE_DIR="${MKLROOT}/include"
-			-DMKL_LIBRARIES="$(echo /opt/intel/mkl/10.0.5.025/lib/*/libmkl.so);$(echo /opt/intel/mkl/10.0.5.025/lib/*/libiomp*.so)"
-		)
-	elif use mkl; then
-		local bits=$(get_libdir)
-		fft_opts=( -DGMX_FFT_LIBRARY=mkl
-			-DMKL_INCLUDE_DIR="$(echo /opt/intel/*/mkl/include)"
-			-DMKL_LIBRARIES="$(echo /opt/intel/*/mkl/lib/*${bits/lib}/libmkl_rt.so)"
-		)
-	else
-		fft_opts=( -DGMX_FFT_LIBRARY=fftpack )
-	fi
-
-	mycmakeargs_pre+=(
-		"${fft_opts[@]}"
-		$(cmake-utils_use X GMX_X11)
-		$(cmake-utils_use blas GMX_EXTERNAL_BLAS)
-		$(cmake-utils_use lapack GMX_EXTERNAL_LAPACK)
-		$(cmake-utils_use openmp GMX_OPENMP)
-		$(cmake-utils_use offensive GMX_COOL_QUOTES)
-		$(cmake-utils_use boost GMX_EXTERNAL_BOOST)
-		$(cmake-utils_use tng GMX_USE_TNG)
-		$(cmake-utils_use doc GMX_BUILD_MANUAL)
-		$(cmake-utils_use make-symlinks GMX_SYMLINK_OLD_BINARY_NAMES)
-		-DGMX_DEFAULT_SUFFIX=off
-		-DGMX_SIMD="$acce"
-		-DGMX_LIB_INSTALL_DIR="$(get_libdir)"
-		-DGMX_VMD_PLUGIN_PATH="${EPREFIX}/usr/$(get_libdir)/vmd/plugins/*/molfile/"
-		-DGMX_X86_AVX_GCC_MASKLOAD_BUG=OFF
-		-DGMX_USE_GCC44_BUG_WORKAROUND=OFF
-		-DBUILD_TESTING=OFF
-		-DGMX_BUILD_UNITTESTS=OFF
-		${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=( "-DGMX_GPU=OFF" )
-		[[ ${x} = "float" ]] && use cuda && \
-			cuda=( -DGMX_GPU=ON )
-		mycmakeargs=(
-			${mycmakeargs_pre[@]} ${p}
-			-DGMX_MPI=OFF
-			$(cmake-utils_use threads GMX_THREAD_MPI)
-			"${cuda[@]}"
-			-DGMX_OPENMM=OFF
-			"$(use test && echo -DREGRESSIONTEST_PATH="${WORKDIR}/${P}_${x}/tests")"
-			-DGMX_BINARY_SUFFIX="${suffix}"
-			-DGMX_LIBS_SUFFIX="${suffix}"
-			)
-		BUILD_DIR="${WORKDIR}/${P}_${x}" cmake-utils_src_configure
-		[[ ${CHOST} != *-darwin* ]] || \
-		  sed -i '/SET(CMAKE_INSTALL_NAME_DIR/s/^/#/' "${WORKDIR}/${P}_${x}/gentoo_rules.cmake" || die
-		use mpi || continue
-		einfo "Configuring for ${x} precision with mpi"
-		mycmakeargs=(
-			${mycmakeargs_pre[@]} ${p}
-			-DGMX_THREAD_MPI=OFF
-			-DGMX_MPI=ON ${cuda}
-			-DGMX_OPENMM=OFF
-			-DGMX_BUILD_MDRUN_ONLY=ON
-			-DBUILD_SHARED_LIBS=OFF
-			-DGMX_BUILD_MANUAL=OFF
-			-DGMX_BINARY_SUFFIX="_mpi${suffix}"
-			-DGMX_LIBS_SUFFIX="_mpi${suffix}"
-			)
-		BUILD_DIR="${WORKDIR}/${P}_${x}_mpi" CC="mpicc" cmake-utils_src_configure
-		[[ ${CHOST} != *-darwin* ]] || \
-		  sed -i '/SET(CMAKE_INSTALL_NAME_DIR/s/^/#/' "${WORKDIR}/${P}_${x}_mpi/gentoo_rules.cmake" || die
-	done
-}
-
-src_compile() {
-	for x in ${GMX_DIRS}; do
-		einfo "Compiling for ${x} precision"
-		BUILD_DIR="${WORKDIR}/${P}_${x}"\
-			cmake-utils_src_compile
-		# generate bash completion
-		BUILD_DIR="${WORKDIR}/${P}_${x}"\
-			cmake-utils_src_compile completion
-		if use doc; then
-			BUILD_DIR="${WORKDIR}/${P}_${x}"\
-				cmake-utils_src_compile manual
-		fi
-		use mpi || continue
-		einfo "Compiling for ${x} precision with mpi"
-		BUILD_DIR="${WORKDIR}/${P}_${x}_mpi"\
-			cmake-utils_src_compile
-	done
-}
-
-src_test() {
-	for x in ${GMX_DIRS}; do
-		BUILD_DIR="${WORKDIR}/${P}_${x}"\
-			cmake-utils_src_make check
-	done
-}
-
-src_install() {
-	for x in ${GMX_DIRS}; do
-		BUILD_DIR="${WORKDIR}/${P}_${x}" \
-			cmake-utils_src_install
-		if use doc; then
-			newdoc "${WORKDIR}/${P}_${x}"/docs/manual/gromacs.pdf "${PN}-manual-${PV}.pdf"
-		fi
-		newbashcomp "${WORKDIR}/${P}_${x}"/src/programs/completion/gmx-completion.bash gromacs
-		use mpi || continue
-		BUILD_DIR="${WORKDIR}/${P}_${x}_mpi" \
-			cmake-utils_src_install
-	done
-	# drop unneeded stuff
-	rm "${ED}"usr/bin/GMXRC* || die
-
-	readme.gentoo_create_doc
-}
-
-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
-	readme.gentoo_print_elog
-}
diff --git a/sci-chemistry/gromacs/gromacs-5.0.2-r1.ebuild b/sci-chemistry/gromacs/gromacs-5.0.2-r1.ebuild
deleted file mode 100644
index 9bc9dcee939a..000000000000
--- a/sci-chemistry/gromacs/gromacs-5.0.2-r1.ebuild
+++ /dev/null
@@ -1,275 +0,0 @@
-# Copyright 1999-2015 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/gromacs/gromacs-5.0.2-r1.ebuild,v 1.3 2015/01/31 20:23:56 ottxor Exp $
-
-EAPI=5
-
-CMAKE_MAKEFILE_GENERATOR="ninja"
-
-inherit bash-completion-r1 cmake-utils cuda eutils multilib readme.gentoo toolchain-funcs
-
-if [[ $PV = *9999* ]]; then
-	EGIT_REPO_URI="git://git.gromacs.org/gromacs.git
-		https://gerrit.gromacs.org/gromacs.git
-		git://github.com/gromacs/gromacs.git
-		http://repo.or.cz/r/gromacs.git"
-	EGIT_BRANCH="release-5-0"
-	inherit git-r3
-	KEYWORDS=""
-else
-	SRC_URI="ftp://ftp.gromacs.org/pub/${PN}/${PN}-${PV/_/-}.tar.gz
-		test? ( http://gerrit.gromacs.org/download/regressiontests-${PV}.tar.gz )"
-	KEYWORDS="~alpha ~amd64 ~arm ~ppc64 ~sparc ~x86 ~amd64-linux ~x86-linux ~x64-macos ~x86-macos"
-fi
-
-ACCE_IUSE="cpu_flags_x86_sse2 cpu_flags_x86_sse4_1 cpu_flags_x86_fma4 cpu_flags_x86_avx cpu_flags_x86_avx2"
-
-DESCRIPTION="The ultimate molecular dynamics simulation package"
-HOMEPAGE="http://www.gromacs.org/"
-
-# see COPYING for details
-# http://repo.or.cz/w/gromacs.git/blob/HEAD:/COPYING
-#        base,    vmd plugins, fftpack from numpy,  blas/lapck from netlib,        memtestG80 library,  mpi_thread lib
-LICENSE="LGPL-2.1 UoI-NCSA !mkl? ( !fftw? ( BSD ) !blas? ( BSD ) !lapack? ( BSD ) ) cuda? ( LGPL-3 ) threads? ( BSD )"
-SLOT="0/${PV}"
-IUSE="X blas boost cuda +doc -double-precision +fftw lapack +make-symlinks mkl mpi +offensive openmp +single-precision test +threads +tng ${ACCE_IUSE}"
-
-CDEPEND="
-	X? (
-		x11-libs/libX11
-		x11-libs/libSM
-		x11-libs/libICE
-		)
-	blas? ( virtual/blas )
-	boost? ( >=dev-libs/boost-1.55 )
-	cuda? ( >=dev-util/nvidia-cuda-toolkit-4.2.9-r1 )
-	fftw? ( sci-libs/fftw:3.0 )
-	lapack? ( virtual/lapack )
-	mkl? ( sci-libs/mkl )
-	mpi? ( virtual/mpi )
-	"
-DEPEND="${CDEPEND}
-	virtual/pkgconfig
-	doc? (
-		app-doc/doxygen
-		dev-texlive/texlive-latex
-		dev-texlive/texlive-latexextra
-		media-gfx/imagemagick
-	)"
-RDEPEND="${CDEPEND}"
-
-REQUIRED_USE="
-	|| ( single-precision double-precision )
-	cuda? ( single-precision )
-	mkl? ( !blas !fftw !lapack )"
-
-DOCS=( AUTHORS README )
-
-if [[ ${PV} != *9999 ]]; then
-	S="${WORKDIR}/${PN}-${PV/_/-}"
-fi
-
-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"
-}
-
-src_unpack() {
-	if [[ ${PV} != *9999 ]]; then
-		default
-	else
-		git-r3_src_unpack
-		if use test; then
-			EGIT_REPO_URI="git://git.gromacs.org/regressiontests.git" \
-			EGIT_BRANCH="master" EGIT_COMMIT="master" \
-			EGIT_CHECKOUT_DIR="${WORKDIR}/regressiontests"\
-				git-r3_src_unpack
-		fi
-	fi
-}
-
-src_prepare() {
-	#notes/todos
-	# -on apple: there is framework support
-
-	cmake-utils_src_prepare
-
-	use cuda && cuda_src_prepare
-
-	GMX_DIRS=""
-	use single-precision && GMX_DIRS+=" float"
-	use double-precision && GMX_DIRS+=" double"
-
-	if use test; then
-		for x in ${GMX_DIRS}; do
-			mkdir -p "${WORKDIR}/${P}_${x}" || die
-			cp -al "${WORKDIR}/regressiontests"* "${WORKDIR}/${P}_${x}/tests" || die
-		done
-	fi
-
-	DOC_CONTENTS="Gromacs can use sci-chemistry/vmd to read additional file formats"
-}
-
-src_configure() {
-	local mycmakeargs_pre=( ) extra fft_opts=( )
-
-	#go from slowest to fastest acceleration
-	local acce="None"
-	use cpu_flags_x86_sse2 && acce="SSE2"
-	use cpu_flags_x86_sse4_1 && acce="SSE4.1"
-	use cpu_flags_x86_fma4 && acce="AVX_128_FMA"
-	use cpu_flags_x86_avx && acce="AVX_256"
-	use cpu_flags_x86_avx2 && acce="AVX2_256"
-
-	#to create man pages, build tree binaries are executed (bug #398437)
-	[[ ${CHOST} = *-darwin* ]] && \
-		extra+=" -DCMAKE_BUILD_WITH_INSTALL_RPATH=OFF"
-
-	if use fftw; then
-		fft_opts=( -DGMX_FFT_LIBRARY=fftw3 )
-	elif use mkl && has_version "=sci-libs/mkl-10*"; then
-		fft_opts=( -DGMX_FFT_LIBRARY=mkl
-			-DMKL_INCLUDE_DIR="${MKLROOT}/include"
-			-DMKL_LIBRARIES="$(echo /opt/intel/mkl/10.0.5.025/lib/*/libmkl.so);$(echo /opt/intel/mkl/10.0.5.025/lib/*/libiomp*.so)"
-		)
-	elif use mkl; then
-		local bits=$(get_libdir)
-		fft_opts=( -DGMX_FFT_LIBRARY=mkl
-			-DMKL_INCLUDE_DIR="$(echo /opt/intel/*/mkl/include)"
-			-DMKL_LIBRARIES="$(echo /opt/intel/*/mkl/lib/*${bits/lib}/libmkl_rt.so)"
-		)
-	else
-		fft_opts=( -DGMX_FFT_LIBRARY=fftpack )
-	fi
-
-	mycmakeargs_pre+=(
-		"${fft_opts[@]}"
-		$(cmake-utils_use X GMX_X11)
-		$(cmake-utils_use blas GMX_EXTERNAL_BLAS)
-		$(cmake-utils_use lapack GMX_EXTERNAL_LAPACK)
-		$(cmake-utils_use openmp GMX_OPENMP)
-		$(cmake-utils_use offensive GMX_COOL_QUOTES)
-		$(cmake-utils_use boost GMX_EXTERNAL_BOOST)
-		$(cmake-utils_use tng GMX_USE_TNG)
-		$(cmake-utils_use doc GMX_BUILD_MANUAL)
-		$(cmake-utils_use make-symlinks GMX_SYMLINK_OLD_BINARY_NAMES)
-		-DGMX_DEFAULT_SUFFIX=off
-		-DGMX_SIMD="$acce"
-		-DGMX_LIB_INSTALL_DIR="$(get_libdir)"
-		-DGMX_VMD_PLUGIN_PATH="${EPREFIX}/usr/$(get_libdir)/vmd/plugins/*/molfile/"
-		-DGMX_X86_AVX_GCC_MASKLOAD_BUG=OFF
-		-DGMX_USE_GCC44_BUG_WORKAROUND=OFF
-		-DBUILD_TESTING=OFF
-		-DGMX_BUILD_UNITTESTS=OFF
-		${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=( "-DGMX_GPU=OFF" )
-		[[ ${x} = "float" ]] && use cuda && \
-			cuda=( -DGMX_GPU=ON )
-		mycmakeargs=(
-			${mycmakeargs_pre[@]} ${p}
-			-DGMX_MPI=OFF
-			$(cmake-utils_use threads GMX_THREAD_MPI)
-			"${cuda[@]}"
-			-DGMX_OPENMM=OFF
-			"$(use test && echo -DREGRESSIONTEST_PATH="${WORKDIR}/${P}_${x}/tests")"
-			-DGMX_BINARY_SUFFIX="${suffix}"
-			-DGMX_LIBS_SUFFIX="${suffix}"
-			)
-		BUILD_DIR="${WORKDIR}/${P}_${x}" cmake-utils_src_configure
-		[[ ${CHOST} != *-darwin* ]] || \
-		  sed -i '/SET(CMAKE_INSTALL_NAME_DIR/s/^/#/' "${WORKDIR}/${P}_${x}/gentoo_rules.cmake" || die
-		use mpi || continue
-		einfo "Configuring for ${x} precision with mpi"
-		mycmakeargs=(
-			${mycmakeargs_pre[@]} ${p}
-			-DGMX_THREAD_MPI=OFF
-			-DGMX_MPI=ON ${cuda}
-			-DGMX_OPENMM=OFF
-			-DGMX_BUILD_MDRUN_ONLY=ON
-			-DBUILD_SHARED_LIBS=OFF
-			-DGMX_BUILD_MANUAL=OFF
-			-DGMX_BINARY_SUFFIX="_mpi${suffix}"
-			-DGMX_LIBS_SUFFIX="_mpi${suffix}"
-			)
-		BUILD_DIR="${WORKDIR}/${P}_${x}_mpi" CC="mpicc" cmake-utils_src_configure
-		[[ ${CHOST} != *-darwin* ]] || \
-		  sed -i '/SET(CMAKE_INSTALL_NAME_DIR/s/^/#/' "${WORKDIR}/${P}_${x}_mpi/gentoo_rules.cmake" || die
-	done
-}
-
-src_compile() {
-	for x in ${GMX_DIRS}; do
-		einfo "Compiling for ${x} precision"
-		BUILD_DIR="${WORKDIR}/${P}_${x}"\
-			cmake-utils_src_compile
-		# generate bash completion, not 100% necessary for
-		# rel ebuilds as bundled
-		BUILD_DIR="${WORKDIR}/${P}_${x}"\
-			cmake-utils_src_compile completion
-		# not 100% necessary for rel ebuilds as available from website
-		if use doc; then
-			BUILD_DIR="${WORKDIR}/${P}_${x}"\
-				cmake-utils_src_compile manual
-		fi
-		use mpi || continue
-		einfo "Compiling for ${x} precision with mpi"
-		BUILD_DIR="${WORKDIR}/${P}_${x}_mpi"\
-			cmake-utils_src_compile
-	done
-}
-
-src_test() {
-	for x in ${GMX_DIRS}; do
-		BUILD_DIR="${WORKDIR}/${P}_${x}"\
-			cmake-utils_src_make check
-	done
-}
-
-src_install() {
-	for x in ${GMX_DIRS}; do
-		BUILD_DIR="${WORKDIR}/${P}_${x}" \
-			cmake-utils_src_install
-		if use doc; then
-			newdoc "${WORKDIR}/${P}_${x}"/docs/manual/gromacs.pdf "${PN}-manual-${PV}.pdf"
-		fi
-		#release ebuild does this automatically
-		if [[ $PV = *9999* ]]; then
-			cp "${WORKDIR}/${P}_${x}"/src/programs/completion/gmx-completion.bash "${ED}/usr/bin" || die
-			echo "complete -o nospace -F _gmx_compl gmx" > "${ED}/usr/bin/gmx-completion-gmx.bash" || die
-		fi
-		use mpi || continue
-		BUILD_DIR="${WORKDIR}/${P}_${x}_mpi" \
-			cmake-utils_src_install
-	done
-	# drop unneeded stuff
-	rm "${ED}"usr/bin/GMXRC* || die
-	#concatenate all gmx-completion*, starting with gmx-completion.bash (fct defs)
-	#little hacckery as some gmx-completion* newlines ,so cat won't work
-	for x in "${ED}"usr/bin/gmx-completion{,?*}.bash ; do
-		echo $(<${x})
-	done > "${T}"/gmx-bashcomp || die
-	newbashcomp "${T}"/gmx-bashcomp gromacs
-	rm "${ED}"usr/bin/gmx-completion{,?*}.bash || die
-
-	readme.gentoo_create_doc
-}
-
-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
-	readme.gentoo_print_elog
-}
diff --git a/sci-chemistry/gromacs/gromacs-5.0.2.ebuild b/sci-chemistry/gromacs/gromacs-5.0.2.ebuild
deleted file mode 100644
index d63bd4903e4e..000000000000
--- a/sci-chemistry/gromacs/gromacs-5.0.2.ebuild
+++ /dev/null
@@ -1,262 +0,0 @@
-# Copyright 1999-2015 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/gromacs/gromacs-5.0.2.ebuild,v 1.3 2015/01/31 20:23:56 ottxor Exp $
-
-EAPI=5
-
-CMAKE_MAKEFILE_GENERATOR="ninja"
-
-inherit bash-completion-r1 cmake-utils cuda eutils multilib readme.gentoo toolchain-funcs
-
-if [[ $PV = *9999* ]]; then
-	EGIT_REPO_URI="git://git.gromacs.org/gromacs.git
-		https://gerrit.gromacs.org/gromacs.git
-		git://github.com/gromacs/gromacs.git
-		http://repo.or.cz/r/gromacs.git"
-	EGIT_BRANCH="release-5-0"
-	inherit git-r3
-	KEYWORDS=""
-else
-	SRC_URI="ftp://ftp.gromacs.org/pub/${PN}/${PN}-${PV/_/-}.tar.gz
-		test? ( http://gerrit.gromacs.org/download/regressiontests-${PV}.tar.gz )"
-	KEYWORDS="~alpha ~amd64 ~arm ~ppc64 ~sparc ~x86 ~amd64-linux ~x86-linux ~x64-macos ~x86-macos"
-fi
-
-ACCE_IUSE="cpu_flags_x86_sse2 cpu_flags_x86_sse4_1 cpu_flags_x86_fma4 cpu_flags_x86_avx cpu_flags_x86_avx2"
-
-DESCRIPTION="The ultimate molecular dynamics simulation package"
-HOMEPAGE="http://www.gromacs.org/"
-
-# see COPYING for details
-# http://repo.or.cz/w/gromacs.git/blob/HEAD:/COPYING
-#        base,    vmd plugins, fftpack from numpy,  blas/lapck from netlib,        memtestG80 library,  mpi_thread lib
-LICENSE="LGPL-2.1 UoI-NCSA !mkl? ( !fftw? ( BSD ) !blas? ( BSD ) !lapack? ( BSD ) ) cuda? ( LGPL-3 ) threads? ( BSD )"
-SLOT="0/${PV}"
-IUSE="X blas boost cuda +doc -double-precision +fftw lapack +make-symlinks mkl mpi +offensive openmp +single-precision test +threads +tng ${ACCE_IUSE}"
-
-CDEPEND="
-	X? (
-		x11-libs/libX11
-		x11-libs/libSM
-		x11-libs/libICE
-		)
-	blas? ( virtual/blas )
-	boost? ( >=dev-libs/boost-1.55 )
-	cuda? ( >=dev-util/nvidia-cuda-toolkit-4.2.9-r1 )
-	fftw? ( sci-libs/fftw:3.0 )
-	lapack? ( virtual/lapack )
-	mkl? ( sci-libs/mkl )
-	mpi? ( virtual/mpi )
-	"
-DEPEND="${CDEPEND}
-	virtual/pkgconfig
-	doc? (
-		app-doc/doxygen
-		dev-texlive/texlive-latex
-		dev-texlive/texlive-latexextra
-		media-gfx/imagemagick
-	)"
-RDEPEND="${CDEPEND}"
-
-REQUIRED_USE="
-	|| ( single-precision double-precision )
-	cuda? ( single-precision )
-	mkl? ( !blas !fftw !lapack )"
-
-DOCS=( AUTHORS README )
-
-if [[ ${PV} != *9999 ]]; then
-	S="${WORKDIR}/${PN}-${PV/_/-}"
-fi
-
-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"
-}
-
-src_unpack() {
-	if [[ ${PV} != *9999 ]]; then
-		default
-	else
-		git-r3_src_unpack
-		if use test; then
-			EGIT_REPO_URI="git://git.gromacs.org/regressiontests.git" \
-			EGIT_BRANCH="master" EGIT_COMMIT="master" \
-			EGIT_CHECKOUT_DIR="${WORKDIR}/regressiontests"\
-				git-r3_src_unpack
-		fi
-	fi
-}
-
-src_prepare() {
-	#notes/todos
-	# -on apple: there is framework support
-
-	cmake-utils_src_prepare
-
-	use cuda && cuda_src_prepare
-
-	GMX_DIRS=""
-	use single-precision && GMX_DIRS+=" float"
-	use double-precision && GMX_DIRS+=" double"
-
-	if use test; then
-		for x in ${GMX_DIRS}; do
-			mkdir -p "${WORKDIR}/${P}_${x}" || die
-			cp -al "${WORKDIR}/regressiontests"* "${WORKDIR}/${P}_${x}/tests" || die
-		done
-	fi
-
-	DOC_CONTENTS="Gromacs can use sci-chemistry/vmd to read additional file formats"
-}
-
-src_configure() {
-	local mycmakeargs_pre=( ) extra fft_opts=( )
-
-	#go from slowest to fastest acceleration
-	local acce="None"
-	use cpu_flags_x86_sse2 && acce="SSE2"
-	use cpu_flags_x86_sse4_1 && acce="SSE4.1"
-	use cpu_flags_x86_fma4 && acce="AVX_128_FMA"
-	use cpu_flags_x86_avx && acce="AVX_256"
-	use cpu_flags_x86_avx2 && acce="AVX2_256"
-
-	#to create man pages, build tree binaries are executed (bug #398437)
-	[[ ${CHOST} = *-darwin* ]] && \
-		extra+=" -DCMAKE_BUILD_WITH_INSTALL_RPATH=OFF"
-
-	if use fftw; then
-		fft_opts=( -DGMX_FFT_LIBRARY=fftw3 )
-	elif use mkl && has_version "=sci-libs/mkl-10*"; then
-		fft_opts=( -DGMX_FFT_LIBRARY=mkl
-			-DMKL_INCLUDE_DIR="${MKLROOT}/include"
-			-DMKL_LIBRARIES="$(echo /opt/intel/mkl/10.0.5.025/lib/*/libmkl.so);$(echo /opt/intel/mkl/10.0.5.025/lib/*/libiomp*.so)"
-		)
-	elif use mkl; then
-		local bits=$(get_libdir)
-		fft_opts=( -DGMX_FFT_LIBRARY=mkl
-			-DMKL_INCLUDE_DIR="$(echo /opt/intel/*/mkl/include)"
-			-DMKL_LIBRARIES="$(echo /opt/intel/*/mkl/lib/*${bits/lib}/libmkl_rt.so)"
-		)
-	else
-		fft_opts=( -DGMX_FFT_LIBRARY=fftpack )
-	fi
-
-	mycmakeargs_pre+=(
-		"${fft_opts[@]}"
-		$(cmake-utils_use X GMX_X11)
-		$(cmake-utils_use blas GMX_EXTERNAL_BLAS)
-		$(cmake-utils_use lapack GMX_EXTERNAL_LAPACK)
-		$(cmake-utils_use openmp GMX_OPENMP)
-		$(cmake-utils_use offensive GMX_COOL_QUOTES)
-		$(cmake-utils_use boost GMX_EXTERNAL_BOOST)
-		$(cmake-utils_use tng GMX_USE_TNG)
-		$(cmake-utils_use doc GMX_BUILD_MANUAL)
-		$(cmake-utils_use make-symlinks GMX_SYMLINK_OLD_BINARY_NAMES)
-		-DGMX_DEFAULT_SUFFIX=off
-		-DGMX_SIMD="$acce"
-		-DGMX_LIB_INSTALL_DIR="$(get_libdir)"
-		-DGMX_VMD_PLUGIN_PATH="${EPREFIX}/usr/$(get_libdir)/vmd/plugins/*/molfile/"
-		-DGMX_X86_AVX_GCC_MASKLOAD_BUG=OFF
-		-DGMX_USE_GCC44_BUG_WORKAROUND=OFF
-		-DBUILD_TESTING=OFF
-		-DGMX_BUILD_UNITTESTS=OFF
-		${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=( "-DGMX_GPU=OFF" )
-		[[ ${x} = "float" ]] && use cuda && \
-			cuda=( -DGMX_GPU=ON )
-		mycmakeargs=(
-			${mycmakeargs_pre[@]} ${p}
-			-DGMX_MPI=OFF
-			$(cmake-utils_use threads GMX_THREAD_MPI)
-			"${cuda[@]}"
-			-DGMX_OPENMM=OFF
-			"$(use test && echo -DREGRESSIONTEST_PATH="${WORKDIR}/${P}_${x}/tests")"
-			-DGMX_BINARY_SUFFIX="${suffix}"
-			-DGMX_LIBS_SUFFIX="${suffix}"
-			)
-		BUILD_DIR="${WORKDIR}/${P}_${x}" cmake-utils_src_configure
-		[[ ${CHOST} != *-darwin* ]] || \
-		  sed -i '/SET(CMAKE_INSTALL_NAME_DIR/s/^/#/' "${WORKDIR}/${P}_${x}/gentoo_rules.cmake" || die
-		use mpi || continue
-		einfo "Configuring for ${x} precision with mpi"
-		mycmakeargs=(
-			${mycmakeargs_pre[@]} ${p}
-			-DGMX_THREAD_MPI=OFF
-			-DGMX_MPI=ON ${cuda}
-			-DGMX_OPENMM=OFF
-			-DGMX_BUILD_MDRUN_ONLY=ON
-			-DBUILD_SHARED_LIBS=OFF
-			-DGMX_BUILD_MANUAL=OFF
-			-DGMX_BINARY_SUFFIX="_mpi${suffix}"
-			-DGMX_LIBS_SUFFIX="_mpi${suffix}"
-			)
-		BUILD_DIR="${WORKDIR}/${P}_${x}_mpi" CC="mpicc" cmake-utils_src_configure
-		[[ ${CHOST} != *-darwin* ]] || \
-		  sed -i '/SET(CMAKE_INSTALL_NAME_DIR/s/^/#/' "${WORKDIR}/${P}_${x}_mpi/gentoo_rules.cmake" || die
-	done
-}
-
-src_compile() {
-	for x in ${GMX_DIRS}; do
-		einfo "Compiling for ${x} precision"
-		BUILD_DIR="${WORKDIR}/${P}_${x}"\
-			cmake-utils_src_compile
-		# generate bash completion
-		BUILD_DIR="${WORKDIR}/${P}_${x}"\
-			cmake-utils_src_compile completion
-		if use doc; then
-			BUILD_DIR="${WORKDIR}/${P}_${x}"\
-				cmake-utils_src_compile manual
-		fi
-		use mpi || continue
-		einfo "Compiling for ${x} precision with mpi"
-		BUILD_DIR="${WORKDIR}/${P}_${x}_mpi"\
-			cmake-utils_src_compile
-	done
-}
-
-src_test() {
-	for x in ${GMX_DIRS}; do
-		BUILD_DIR="${WORKDIR}/${P}_${x}"\
-			cmake-utils_src_make check
-	done
-}
-
-src_install() {
-	for x in ${GMX_DIRS}; do
-		BUILD_DIR="${WORKDIR}/${P}_${x}" \
-			cmake-utils_src_install
-		if use doc; then
-			newdoc "${WORKDIR}/${P}_${x}"/docs/manual/gromacs.pdf "${PN}-manual-${PV}.pdf"
-		fi
-		newbashcomp "${WORKDIR}/${P}_${x}"/src/programs/completion/gmx-completion.bash gromacs
-		use mpi || continue
-		BUILD_DIR="${WORKDIR}/${P}_${x}_mpi" \
-			cmake-utils_src_install
-	done
-	# drop unneeded stuff
-	rm "${ED}"usr/bin/GMXRC* || die
-
-	readme.gentoo_create_doc
-}
-
-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
-	readme.gentoo_print_elog
-}
diff --git a/sci-chemistry/gromacs/gromacs-5.0.ebuild b/sci-chemistry/gromacs/gromacs-5.0.ebuild
deleted file mode 100644
index 8f5dfac11044..000000000000
--- a/sci-chemistry/gromacs/gromacs-5.0.ebuild
+++ /dev/null
@@ -1,266 +0,0 @@
-# Copyright 1999-2015 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/gromacs/gromacs-5.0.ebuild,v 1.4 2015/01/31 20:23:56 ottxor Exp $
-
-EAPI=5
-
-TEST_PV="5.0"
-
-CMAKE_MAKEFILE_GENERATOR="ninja"
-
-inherit bash-completion-r1 cmake-utils cuda eutils multilib readme.gentoo toolchain-funcs
-
-if [[ $PV = *9999* ]]; then
-	EGIT_REPO_URI="git://git.gromacs.org/gromacs.git
-		https://gerrit.gromacs.org/gromacs.git
-		git://github.com/gromacs/gromacs.git
-		http://repo.or.cz/r/gromacs.git"
-	EGIT_BRANCH="release-5-0"
-	inherit git-r3
-else
-	SRC_URI="ftp://ftp.gromacs.org/pub/${PN}/${PN}-${PV/_/-}.tar.gz
-		test? ( http://gerrit.gromacs.org/download/regressiontests-${TEST_PV}.tar.gz )"
-fi
-
-ACCE_IUSE="cpu_flags_x86_sse2 cpu_flags_x86_sse4_1 cpu_flags_x86_fma4 cpu_flags_x86_avx cpu_flags_x86_avx2"
-
-DESCRIPTION="The ultimate molecular dynamics simulation package"
-HOMEPAGE="http://www.gromacs.org/"
-
-# see COPYING for details
-# http://repo.or.cz/w/gromacs.git/blob/HEAD:/COPYING
-#        base,    vmd plugins, fftpack from numpy,  blas/lapck from netlib,        memtestG80 library,  mpi_thread lib
-LICENSE="LGPL-2.1 UoI-NCSA !mkl? ( !fftw? ( BSD ) !blas? ( BSD ) !lapack? ( BSD ) ) cuda? ( LGPL-3 ) threads? ( BSD )"
-SLOT="0/${PV}"
-KEYWORDS="~alpha ~amd64 ~arm ~ppc64 ~sparc ~x86 ~amd64-linux ~x86-linux ~x64-macos ~x86-macos"
-IUSE="X blas boost cuda +doc -double-precision +fftw lapack +make-symlinks mkl mpi +offensive openmp +single-precision test +threads +tng ${ACCE_IUSE}"
-
-CDEPEND="
-	X? (
-		x11-libs/libX11
-		x11-libs/libSM
-		x11-libs/libICE
-		)
-	blas? ( virtual/blas )
-	boost? ( >=dev-libs/boost-1.55 )
-	cuda? ( >=dev-util/nvidia-cuda-toolkit-4.2.9-r1 )
-	fftw? ( sci-libs/fftw:3.0 )
-	lapack? ( virtual/lapack )
-	mkl? ( sci-libs/mkl )
-	mpi? ( virtual/mpi )
-	"
-DEPEND="${CDEPEND}
-	virtual/pkgconfig
-	doc? (
-		app-doc/doxygen
-		dev-texlive/texlive-latex
-		dev-texlive/texlive-latexextra
-		media-gfx/imagemagick
-	)"
-RDEPEND="${CDEPEND}"
-
-REQUIRED_USE="
-	|| ( single-precision double-precision )
-	cuda? ( single-precision )
-	mkl? ( !blas !fftw !lapack )"
-
-DOCS=( AUTHORS README )
-
-if [[ ${PV} != *9999 ]]; then
-	S="${WORKDIR}/${PN}-${PV/_/-}"
-fi
-
-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"
-}
-
-src_unpack() {
-	if [[ ${PV} != *9999 ]]; then
-		default
-	else
-		git-r3_src_unpack
-		if use test; then
-			EGIT_REPO_URI="git://git.gromacs.org/regressiontests.git" \
-			EGIT_BRANCH="master" EGIT_NOUNPACK="yes" EGIT_COMMIT="master" \
-			EGIT_SOURCEDIR="${WORKDIR}/regressiontests"\
-				git-r3_src_unpack
-		fi
-	fi
-}
-
-src_prepare() {
-	#notes/todos
-	# -on apple: there is framework support
-
-	cmake-utils_src_prepare
-
-	use cuda && cuda_src_prepare
-
-	GMX_DIRS=""
-	use single-precision && GMX_DIRS+=" float"
-	use double-precision && GMX_DIRS+=" double"
-
-	if use test; then
-		for x in ${GMX_DIRS}; do
-			mkdir -p "${WORKDIR}/${P}_${x}" || die
-			cp -al "${WORKDIR}/regressiontests"* "${WORKDIR}/${P}_${x}/tests" || die
-		done
-	fi
-
-	DOC_CONTENTS="Gromacs can use sci-chemistry/vmd to read additional file formats"
-}
-
-src_configure() {
-	local mycmakeargs_pre=( ) extra fft_opts=( )
-
-	#go from slowest to fastest acceleration
-	local acce="None"
-	use cpu_flags_x86_sse2 && acce="SSE2"
-	use cpu_flags_x86_sse4_1 && acce="SSE4.1"
-	use cpu_flags_x86_fma4 && acce="AVX_128_FMA"
-	use cpu_flags_x86_avx && acce="AVX_256"
-	use cpu_flags_x86_avx2 && acce="AVX2_256"
-
-	#to create man pages, build tree binaries are executed (bug #398437)
-	[[ ${CHOST} = *-darwin* ]] && \
-		extra+=" -DCMAKE_BUILD_WITH_INSTALL_RPATH=OFF"
-
-	if use fftw; then
-		fft_opts=( -DGMX_FFT_LIBRARY=fftw3 )
-	elif use mkl && has_version "=sci-libs/mkl-10*"; then
-		fft_opts=( -DGMX_FFT_LIBRARY=mkl
-			-DMKL_INCLUDE_DIR="${MKLROOT}/include"
-			-DMKL_LIBRARIES="$(echo /opt/intel/mkl/10.0.5.025/lib/*/libmkl.so);$(echo /opt/intel/mkl/10.0.5.025/lib/*/libiomp*.so)"
-		)
-	elif use mkl; then
-		local bits=$(get_libdir)
-		fft_opts=( -DGMX_FFT_LIBRARY=mkl
-			-DMKL_INCLUDE_DIR="$(echo /opt/intel/*/mkl/include)"
-			-DMKL_LIBRARIES="$(echo /opt/intel/*/mkl/lib/*${bits/lib}/libmkl_rt.so)"
-		)
-	else
-		fft_opts=( -DGMX_FFT_LIBRARY=fftpack )
-	fi
-
-	mycmakeargs_pre+=(
-		"${fft_opts[@]}"
-		$(cmake-utils_use X GMX_X11)
-		$(cmake-utils_use blas GMX_EXTERNAL_BLAS)
-		$(cmake-utils_use lapack GMX_EXTERNAL_LAPACK)
-		$(cmake-utils_use openmp GMX_OPENMP)
-		$(cmake-utils_use offensive GMX_COOL_QUOTES)
-		$(cmake-utils_use boost GMX_EXTERNAL_BOOST)
-		$(cmake-utils_use tng GMX_USE_TNG)
-		$(cmake-utils_use doc GMX_BUILD_MANUAL)
-		$(cmake-utils_use make-symlinks GMX_SYMLINK_OLD_BINARY_NAMES)
-		-DGMX_DEFAULT_SUFFIX=off
-		-DGMX_SIMD="$acce"
-		-DGMX_LIB_INSTALL_DIR="$(get_libdir)"
-		-DGMX_VMD_PLUGIN_PATH="${EPREFIX}/usr/$(get_libdir)/vmd/plugins/*/molfile/"
-		-DGMX_X86_AVX_GCC_MASKLOAD_BUG=OFF
-		-DGMX_USE_GCC44_BUG_WORKAROUND=OFF
-		-DBUILD_TESTING=OFF
-		-DGMX_BUILD_UNITTESTS=OFF
-		${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=( "-DGMX_GPU=OFF" )
-		[[ ${x} = "float" ]] && use cuda && \
-			cuda=( -DGMX_GPU=ON )
-		mycmakeargs=(
-			${mycmakeargs_pre[@]} ${p}
-			-DGMX_MPI=OFF
-			$(cmake-utils_use threads GMX_THREAD_MPI)
-			"${cuda[@]}"
-			-DGMX_OPENMM=OFF
-			"$(use test && echo -DREGRESSIONTEST_PATH="${WORKDIR}/${P}_${x}/tests")"
-			-DGMX_BINARY_SUFFIX="${suffix}"
-			-DGMX_LIBS_SUFFIX="${suffix}"
-			)
-		BUILD_DIR="${WORKDIR}/${P}_${x}" cmake-utils_src_configure
-		[[ ${CHOST} != *-darwin* ]] || \
-		  sed -i '/SET(CMAKE_INSTALL_NAME_DIR/s/^/#/' "${WORKDIR}/${P}_${x}/gentoo_rules.cmake" || die
-		use mpi || continue
-		einfo "Configuring for ${x} precision with mpi"
-		mycmakeargs=(
-			${mycmakeargs_pre[@]} ${p}
-			-DGMX_THREAD_MPI=OFF
-			-DGMX_MPI=ON ${cuda}
-			-DGMX_OPENMM=OFF
-			-DGMX_BUILD_MDRUN_ONLY=ON
-			-DBUILD_SHARED_LIBS=OFF
-			-DGMX_BUILD_MANUAL=OFF
-			-DGMX_BINARY_SUFFIX="_mpi${suffix}"
-			-DGMX_LIBS_SUFFIX="_mpi${suffix}"
-			)
-		BUILD_DIR="${WORKDIR}/${P}_${x}_mpi" CC="mpicc" cmake-utils_src_configure
-		[[ ${CHOST} != *-darwin* ]] || \
-		  sed -i '/SET(CMAKE_INSTALL_NAME_DIR/s/^/#/' "${WORKDIR}/${P}_${x}_mpi/gentoo_rules.cmake" || die
-	done
-}
-
-src_compile() {
-	for x in ${GMX_DIRS}; do
-		einfo "Compiling for ${x} precision"
-		BUILD_DIR="${WORKDIR}/${P}_${x}"\
-			cmake-utils_src_compile
-		# generate bash completion
-		BUILD_DIR="${WORKDIR}/${P}_${x}"\
-			cmake-utils_src_compile completion
-		if use doc; then
-			BUILD_DIR="${WORKDIR}/${P}_${x}"\
-				cmake-utils_src_compile manual
-		fi
-		use mpi || continue
-		einfo "Compiling for ${x} precision with mpi"
-		BUILD_DIR="${WORKDIR}/${P}_${x}_mpi"\
-			cmake-utils_src_compile
-	done
-}
-
-src_test() {
-	for x in ${GMX_DIRS}; do
-		BUILD_DIR="${WORKDIR}/${P}_${x}"\
-			cmake-utils_src_make check
-	done
-}
-
-src_install() {
-	for x in ${GMX_DIRS}; do
-		BUILD_DIR="${WORKDIR}/${P}_${x}" \
-			cmake-utils_src_install
-		if use doc; then
-			newdoc "${WORKDIR}/${P}_${x}"/manual/gromacs.pdf "${PN}-manual-${PV}.pdf"
-		fi
-		newbashcomp "${WORKDIR}/${P}_${x}"/src/programs/completion/gmx-completion.bash gromacs
-		use mpi || continue
-		BUILD_DIR="${WORKDIR}/${P}_${x}_mpi" \
-			cmake-utils_src_install
-	done
-	# drop unneeded stuff
-	rm -f "${ED}"usr/bin/gmx-completion*
-	rm -f "${ED}"usr/bin/g_options*
-	rm -f "${ED}"usr/bin/GMXRC*
-	rm -f "${ED}"usr/$(get_libdir)/libtng*.a
-
-	readme.gentoo_create_doc
-}
-
-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
-	readme.gentoo_print_elog
-}