Version bump =D

Package-Manager: portage-2.2.7/cvs/Linux x86_64
Manifest-Sign-Key: 0xF82F92E6

3 files changed, 307 insertions, 9 deletions

diff --git a/sci-chemistry/gromacs/ChangeLog b/sci-chemistry/gromacs/ChangeLog
index 7dd53f370e59..1e995663e89b 100644
--- a/sci-chemistry/gromacs/ChangeLog
+++ b/sci-chemistry/gromacs/ChangeLog
@@ -1,6 +1,11 @@
 # ChangeLog for sci-chemistry/gromacs
 # Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2
-# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/gromacs/ChangeLog,v 1.133 2013/11/13 18:17:42 ottxor Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/gromacs/ChangeLog,v 1.134 2013/12/05 18:10:06 alexxy Exp $
+
+*gromacs-4.6.5 (05 Dec 2013)
+
+  05 Dec 2013; Alexey Shvetsov <alexxy@gentoo.org> +gromacs-4.6.5.ebuild:
+  Version bump =D
 
 *gromacs-4.6.4 (13 Nov 2013)
 
diff --git a/sci-chemistry/gromacs/Manifest b/sci-chemistry/gromacs/Manifest
index 91398bc4b38d..356b6af6e1ad 100644
--- a/sci-chemistry/gromacs/Manifest
+++ b/sci-chemistry/gromacs/Manifest
@@ -12,27 +12,37 @@ DIST gromacs-4.5.7.tar.gz 10668518 SHA256 c344579ace3c35fbae87abdb0aceadaf71b060
 DIST gromacs-4.6.2.tar.gz 10986082 SHA256 7bcccd15f02e7163455e1f342fc13e609e9088735b962d96afe0a79aaad92d4c SHA512 fe5991f66a638edd5af42c226302ccac4968b722df92eaeb8f65536fd5c7eb64cf7f0264bbfaa09998c870e396087f23b91e377d3abcc9a2d9456850b622b371 WHIRLPOOL 6d563046e2f7fc6178b4c94c7bb9a73a19df02a51b53e2556a5141809b6f286cac86c7b04afafab9e6038733c06ee67965a7dbe6db67d44e0363c18c036d3051
 DIST gromacs-4.6.3.tar.gz 10985615 SHA256 b748f912b606032471e7da2db349db44f53d717b2490ad9316eb962bd75eccd4 SHA512 dbb884af718406044cfcd0bf5f65c098435f79dafe4dc23b9bfcab9a8be936ed5e5a50c53afafbc15a1eb0970008cee30757999d09eef4a05b2c905d9a251775 WHIRLPOOL f074df431145e77bcae7ba0142b60c8bd70d73ca2f1fbff8cd3b8c4c4b9fcce6fbdfb044269b6256099d3dd12e344e065ba572f35dca20337a55e307163ba2c0
 DIST gromacs-4.6.4.tar.gz 10990996 SHA256 4d4f15e6d10e97aff7a21d3bb5536283cf8ba669589310c456c1bb22bdfe7d8e SHA512 b2d3d9ea7e31cd7831060e633aa4e6c014e00b94fff2814a5924f5bf652cfef5100c089b8f79167f1cb329f115d7ab7ea316f50d4bb107210dc084bac7e0a5cc WHIRLPOOL c3abc973e46a66f071978d618431dae9dd4deb4c3a8321ce170fb7b63ff470d0e44eff13826a8c93cb7bf74c5a61bc0173183320d936405ed8db229f45403aed
+DIST gromacs-4.6.5.tar.gz 10991576 SHA256 a7242f315963a111e87fd28795696b1e818ac97479788356c4f73a04e9cdef09 SHA512 6ebb3ef74cf9ef2a749bdad6ce7c2deca607ef3b04cab3ce0be25ac1e7c69b3716761a66b5214642b82a96571e488d8a7bffda651840e56d95c14ba099cc1e0c WHIRLPOOL e639f0d1256173dafe8ba1231d46596f23a29b5ab97883600673b078e2927492dd473834398cd9fd864eb3d529ef853c2592d0b2c5ebb18ebb25ca171568aa72
 DIST gromacs-manual-4.5.4.pdf 2463242 SHA256 dc14504a7072b61e7aa576c48f04df03356824f3a9d9e744dfaf51529ab46252 SHA512 957995333163f6f28568a18d5423a75dc6c315215692da94d0916f09b6221e2a875c5ff4b05385ad6604bd8ae38f0cb61c740cd734c76b360aa4b598cd2c3380 WHIRLPOOL 07077d81ea89bc02207e45e56c77a668375a7284bf6f4a3cc7fe637f1f53ce4ab687c722f13f208cdd2c056b9d766ebfcbe5ea9579ce7649ec9e088371e7db8d
 DIST gromacs-manual-4.5.6.pdf 2650364 SHA256 5c2a086c9cf1627008e3909b37ea5320eb9eeedf9833147d7b0f4e3688aaf339 SHA512 4035623df74d500abff35c7e08d0dbc8cd80f4fae4f580b6f72939d31a456c02fa00b5b47659767125cdf318db10c0cfac4d3f9584b7b384a48300efbfc590bc WHIRLPOOL 089bb4da2e5f51a0e8dfe4f76195b79daec10f661a48c48e491b9cda711f49e67a7e2d77c5bb884eaf4176ca3b0c20c389fc3a77e719a0870d548c3803929cdc
 DIST gromacs-manual-4.6.2.pdf 6208213 SHA256 b95e4681d474caf0596d179a83f3e499b49e8900eb013900027a783a4c16c3d7 SHA512 e61fef9c2f1d978809c47723b48b35eddcfa5e98e573924d4b53d6aa686e893641b44ce07b217b9b3ecb34221f7eab3e7d0d6a8e1ced7f9db1ff478a32864574 WHIRLPOOL cd313c78472614f242e639d40764d3d797f4202bd52f706b4d0f0385b40dd6dac01a1676ec12374a2fb63e4490dc0a9ef39bbbc319d50fa59eaafcc6213df5f1
 DIST gromacs-manual-4.6.4.pdf 5525415 SHA256 07aae3c22b171a3ae130c3b4287e9f1d2fedb23b6eac5e41798ad557ed6135b2 SHA512 2f9b4959a80b0bf2e8139b826e6cdddbc5b2c1d3295313272a66ecca00ee45e9055c01a4ad932d452fde48c8345a37e5bac0bb11894db04fec533ee05822f151 WHIRLPOOL ee6d596f224d6c470a6966e21bf4c5b7f9db1a0b4579f8289a427cb48bca228032c4ca4bf8172da6ceb513bc056ff65d54ce5aec1c31f62f61600824951d0792
+DIST gromacs-manual-4.6.5.pdf 5525415 SHA256 0ae0a1f38c236a9b03200f32fc87a70e74adc2a446669973db1e6069e45dedfe SHA512 31174cc17bebf637a5c565fa307aae6cd5a434cceddab005b2ca8dd10a2e1252818b7f2d9e8f9571ef3fcdb904f1043280ea40c1ac38c4a3fd02ab1397ab8c92 WHIRLPOOL a2f49c2f3241ca2d50e678d452bbf57a8d50b282045d0b8afaca4f5fa96b7e92fe77894376244b45f7286de54a91eb87abeaa9170f56c81433c4cfa703352dd8
 DIST regressiontests-4.6.2.tar.gz 43576124 SHA256 6f79d545affa86c027f1e023dee282885b481551e522e441f772112bcd6295ff SHA512 fa78221201c6390d9b4649c848e464051993cb3acff6f7fb07e8e0e68f70f5ba2d917ba7ff9b5d5fd7a0c3a7435c98e2dbc02925e44f8a220ed073e054f510a0 WHIRLPOOL 1316fd0fe98b2b89ee95a2bccfbb5c4a7f0661bc30ceb04c5d1654b60513097e094ebca661b3fc4df32fad774bc6c14bb68841227530f0618d39fadf2e56d358
 DIST regressiontests-4.6.4.tar.gz 44029478 SHA256 1c3dacd5575487ba8e8d543b64bddc3a4bd1add1da996abdc99dd758bb654f60 SHA512 e547f04dacbd2baafd001cc896daac0257560956b0045fb12fb224b56a0a68a088c8b28206fc1dbf52afdbb748efdde9590fbf6a6fd7da021a5c151bcdaa012c WHIRLPOOL 06b93ee2ff1d5b50fd3cb461f4d4fe94e60fb52311f78cb00730360a70209b5ea7fdbb5857668c111503a4ae72a2e7adf11f1579f3e38eb1d33aa70e3d367f30
+DIST regressiontests-4.6.5.tar.gz 44026759 SHA256 50b611970c68eef3d1d3d043a6ca419c681540d73c96f26d6e9d2857fda3fb91 SHA512 817743f531a072b9940dc916daf79a83980eae7411e36cb003cbf7790282ca33375bdf0cb0e764500e5fac3ff09903b44588bc14a6c92bf73c020ea1fbaa7b38 WHIRLPOOL 835584596f630cea28ba76bb0fa5d131f8f781f64dc98292e20249ec8c9f063e329c15781fe473b66fc0b97292e3f68dce6a868094a45c9139c822425e669de7
 EBUILD gromacs-4.5.5-r1.ebuild 7808 SHA256 ffedeea7d72e555a7ee13232b252c536d917ea9f428558386e72ccc010779b01 SHA512 1c21a6b55611c7aff88bf67a5519e5926cb9277bba44db36eebdf4e22f9fcc733a157ae2e2643123f1e38f998fd8d1524a5440b20de5c041d832567e12976497 WHIRLPOOL 7a2664e943bbd2eac9e095a37946794a32f843ec90dcc3c05209a77c454a17c61ea19ed5105bd81ccc1014f500ac434f4a2e73802decbbed0041a298f1c7dc54
 EBUILD gromacs-4.5.7.ebuild 7759 SHA256 9e14bea3e2820803197ab478a04af246aa155db5e48a45c883ab5f93bfb98527 SHA512 7d113988e36511008aa5b09e4b5bb6b7011c6b326ac1f3bd6d31565805a836def1aa787d8bd677a383d19719dd97c0da954c2eace4160ad7b088c42d542e58ca WHIRLPOOL d071bfe72e5963b12f8b74c207b50ebc32e43f0f9ecc8c82496345a75033d8485b2b2f9f9a006c5fb3888c367563b9ccdc8e6df18e4a3dfa16402ad5d62d2aeb
 EBUILD gromacs-4.6.2.ebuild 9000 SHA256 508e8217912fa496d26374d0b4f67276f827a2449681a44d76fa883f18dd7b23 SHA512 8326acfa706b7ad0d3b59671ae3e51ebb420809d093e9fc4a5d9a49970c0b4ec8fd2e35162d90c8607826a052295aeeab57cb5ab2480b4488fd8ca6f77f01c93 WHIRLPOOL 388b819a622f1df21371468ec3579b1bc6896165d35d4570fb9c08c823abc80648055a7ba45db4ce1e7d7ac2912390c7c0d176edf95c686d631eca78b7fd1a0c
 EBUILD gromacs-4.6.3.ebuild 9008 SHA256 fd621d6ae8a1a858e96435779502b82131ad8663b3041597d66aa53c04e5ab39 SHA512 747c8d00093133eaf7c2557db5892ba5bef2eb2f108d82a9f9473dfc47bafb28db4b2f7cedf32fed975c70c4691742bb09dcb18c1b32ca55f3620b6fb87f6110 WHIRLPOOL bcc44898f5dfcb76de06c088e60142f51ea42f45a08b12f3ef8766bf22d3e11cf74524f3cdf6a6fa3dcc0dbd2525690716bb66c816cd3bbc3521796078d57083
 EBUILD gromacs-4.6.4.ebuild 9008 SHA256 4e3c71b4a07b82259c17a8d4b472bce42f73622a098d7a52d7c58aab3a437c48 SHA512 3537e5393ff3943829a2b5b0a3a327c791b55ded39104695943d03a63a3013fc4c528aa433ef0e9a78d2ed0b64d6f3f502fd304a23057040809f4a628e46b6ee WHIRLPOOL 4b9303deb6e1712c101f596cb5676946eb32bf285658ba1b00cd78c5ce3bbe0bac2c227f7e963fca6ab472b26735121daef9b558d85efbdc2c99f2d23fba5b7d
-MISC ChangeLog 21714 SHA256 81bc883130192031048f20cf5827bf46dc72d35af4e902431dca7187079df64d SHA512 f0f332dac180b529c306d51e59d9fb32cd971b05c39d1b8fc7ca23a472258b4dd7fb046905399ebf9310c4255f1022f1ee01268088ae509a552ef6577946a0a3 WHIRLPOOL cf07abeb210c071bba7ac153fd7d0b6dbd79ce328f687fab831174d589daf344c732367a8a13b6f179ea4f3cc0d2eb55de94e2f66422593ff113986b9c659e4c
+EBUILD gromacs-4.6.5.ebuild 9008 SHA256 08956c86109fe2c76b7b1d3922125adeac9fc909f3ecdc9a96e646c0bcb7d2aa SHA512 090a313beb3276f9f7cdbcfc518741d590e1791e87037901988d9c96ca28d65aafb268b23733fb96bf8d5213f678f6058997ea8b67353f4a53594c37d4b69221 WHIRLPOOL d2786854b1307e93e53fef0502934bcd38bb18cc49eb90cf99a597cadf7d73217d948f29d397b68ec117d06e37b719444c37fd561f049f1c17aecf444b282ea0
+MISC ChangeLog 21837 SHA256 561392e49ad2d1db367c54c6c3d3df814058474f2ed685fe3887f7335ffd63f9 SHA512 50ff96c9106577f1d0247b43be1342a4955c83915961e176a88d19b8adc171b4a5316a6b64fcaac88f44a45cd9e0ac398415e7087602c296bd044a21e61d1f66 WHIRLPOOL f546060bc13a010e95eb993c8ef47a7d1bce94559dcda9a67c3585ab2e45e12103b827a8511054f0ee6c31e500900e88cf68d8cb3d789e07b486c9b05165e3c8
 MISC metadata.xml 1111 SHA256 9ac7c2d8dc6b9e6523565bb9d2ba681cd784ce508bbc948f108c54ac554b3d15 SHA512 43365c5266138f79136937fe38d00161b0ac808b2fef1af6bf260ef3043b2d9504e35b83f4ae4564f212b7393e65743e73b123b7c15e989b880a5b266005225e WHIRLPOOL ba60f8ae78266b140b89eab018235475401ae8a9dd7b9333b3fee720081be047db6f5f3f81c63b5289e8a50089ae480883dbc18e1f70bdda4751d51df70f01b9
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diff --git a/sci-chemistry/gromacs/gromacs-4.6.5.ebuild b/sci-chemistry/gromacs/gromacs-4.6.5.ebuild
new file mode 100644
index 000000000000..a02b40beda75
--- /dev/null
+++ b/sci-chemistry/gromacs/gromacs-4.6.5.ebuild
@@ -0,0 +1,283 @@
+# 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-4.6.5.ebuild,v 1.1 2013/12/05 18:10:06 alexxy Exp $
+
+EAPI=5
+
+TEST_PV="4.6.5"
+MANUAL_PV="4.6.5"
+
+CMAKE_MAKEFILE_GENERATOR="ninja"
+
+inherit bash-completion-r1 cmake-utils cuda eutils multilib readme.gentoo toolchain-funcs
+
+if [[ $PV = *9999* ]]; then
+	EGIT_REPO_URI="git://git.gromacs.org/gromacs.git
+		https://gerrit.gromacs.org/gromacs.git
+		git://github.com/gromacs/gromacs.git
+		http://repo.or.cz/r/gromacs.git"
+	EGIT_BRANCH="release-4-6"
+	inherit git-2
+	LIVE_DEPEND="doc? (
+		dev-texlive/texlive-latex
+		dev-texlive/texlive-latexextra
+		media-gfx/imagemagick
+		sys-apps/coreutils
+	)"
+else
+	SRC_URI="ftp://ftp.gromacs.org/pub/${PN}/${P}.tar.gz
+		doc? ( ftp://ftp.gromacs.org/pub/manual/manual-${MANUAL_PV}.pdf -> ${PN}-manual-${MANUAL_PV}.pdf )
+		test? ( http://${PN}.googlecode.com/files/regressiontests-${TEST_PV}.tar.gz )"
+	LIVE_DEPEND=""
+fi
+
+ACCE_IUSE="sse2 sse4_1 avx128fma avx256"
+
+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 ~x86-macos"
+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
+	${LIVE_DEPEND}"
+RDEPEND="${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="master" \
+			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 sse2 && acce="SSE2"
+	use sse4_1 && 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)
+	[[ ${CHOST} = *-darwin* ]] && \
+		extra+=" -DCMAKE_BUILD_WITH_INSTALL_RPATH=OFF"
+
+	if use fftw; then
+		fft_opts=( -DGMX_FFT_LIBRARY=fftw3 )
+	elif use mkl && has_version "=sci-libs/mkl-10*"; then
+		fft_opts=( -DGMX_FFT_LIBRARY=mkl
+			-DMKL_INCLUDE_DIR="${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
+}