version bump

Package-Manager: portage-2.2.8-r1/cvs/Linux x86_64
Manifest-Sign-Key: 0xC2000586

3 files changed, 279 insertions, 9 deletions

diff --git a/sci-chemistry/gromacs/ChangeLog b/sci-chemistry/gromacs/ChangeLog
index 3558c3dfb258..a3adc7bddcf2 100644
--- a/sci-chemistry/gromacs/ChangeLog
+++ b/sci-chemistry/gromacs/ChangeLog
@@ -1,6 +1,11 @@
 # ChangeLog for sci-chemistry/gromacs
 # Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2
-# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/gromacs/ChangeLog,v 1.144 2014/09/04 15:04:24 ottxor Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/gromacs/ChangeLog,v 1.145 2014/09/06 18:44:08 ottxor Exp $
+
+*gromacs-5.0.1 (06 Sep 2014)
+
+  06 Sep 2014; Christoph Junghans <ottxor@gentoo.org> +gromacs-5.0.1.ebuild:
+  version bump
 
   04 Sep 2014; Christoph Junghans <ottxor@gentoo.org> gromacs-5.0.ebuild:
   added ~x64-macos (tested by me)
diff --git a/sci-chemistry/gromacs/Manifest b/sci-chemistry/gromacs/Manifest
index aa219d38bba4..b18671d01c54 100644
--- a/sci-chemistry/gromacs/Manifest
+++ b/sci-chemistry/gromacs/Manifest
@@ -4,6 +4,7 @@ Hash: SHA256
 DIST gromacs-4.6.5.tar.gz 10991576 SHA256 a7242f315963a111e87fd28795696b1e818ac97479788356c4f73a04e9cdef09 SHA512 6ebb3ef74cf9ef2a749bdad6ce7c2deca607ef3b04cab3ce0be25ac1e7c69b3716761a66b5214642b82a96571e488d8a7bffda651840e56d95c14ba099cc1e0c WHIRLPOOL e639f0d1256173dafe8ba1231d46596f23a29b5ab97883600673b078e2927492dd473834398cd9fd864eb3d529ef853c2592d0b2c5ebb18ebb25ca171568aa72
 DIST gromacs-4.6.6.tar.gz 10991950 SHA256 294b6e8eacf7064bd609edd6e9a6ce2ce9122876bc1abd593ddcb018a9b01bb0 SHA512 ff790db256d6759cde0eeb34e71937d63714c4efc9aa390532593c807ebcfa061036a16c8dd4e634c6f90b7ab120a0bf041daeab1e6e2a37f3ac4065213d8a70 WHIRLPOOL aba06e7a688a4bea7b0a9250b15789dc97157c583d08a13b78c76a581d41f2fcf63955a85c482679ab08564bad12ef81c95a712796193cf45f2b3d1051a089bd
 DIST gromacs-4.6.7.tar.gz 11031209 SHA256 6afb1837e363192043de34b188ca3cf83db6bd189601f2001a1fc5b0b2a214d9 SHA512 8472aa06e2050b469dac4c3a0b039014fa45055cdc550226605d90abec6956830ad2a1b634d10529fbf2e55e686a497e689dd165333bef7fe89b193227fa98e5 WHIRLPOOL 221b3d4e5ce6505edb5badc0e14391e6861cb7efad108b8b6eeaed435df6df15bc3580e52f18007c98e987b02a7d003381400d8adca246dc47c680954dcfe25a
+DIST gromacs-5.0.1.tar.gz 26339530 SHA256 5ebe5d5aa176882060f247fe70e9126fcbc12fe40222df75fb7546bb931e86ed SHA512 b9690e3fa5d695c3ab65561f5b713961ca85b207be93911745dbec69fdd58efa20b92b9ea6216383fbdad40b1916e791905d23c07e4d99a898e31fbfc421da3e WHIRLPOOL 216e61c35a1a9e32abfd10ba442d061909f206dd0ddf05a96bf3abaa4b8e6a455e13b623be484e6c2192d22f19041c3d9c2259742f394e5071e99c1069cad3f8
 DIST gromacs-5.0.tar.gz 26862408 SHA256 c2c9b5e75e014785641f39fbbde9829ce200f963344b35fa942f041a0dcfeb20 SHA512 4b3cf7cad06ae7e98d8d794a05561874d8e5061e8c9ee91e5f028e7c7d4b42669b74efa3f52e5d864efa86da78d76637e8917edc99cd1cbf7c8dd9c2681e1270 WHIRLPOOL d9020a1c0e3aaf716a98ac1280e4d67e3f8f611cadc94465119711195c58c6bdc962926dfd579b8e13b1c1092539a1aa9768cb442dd7752c6b310a8116b7aaa3
 DIST gromacs-manual-4.6.5.pdf 5525415 SHA256 0ae0a1f38c236a9b03200f32fc87a70e74adc2a446669973db1e6069e45dedfe SHA512 31174cc17bebf637a5c565fa307aae6cd5a434cceddab005b2ca8dd10a2e1252818b7f2d9e8f9571ef3fcdb904f1043280ea40c1ac38c4a3fd02ab1397ab8c92 WHIRLPOOL a2f49c2f3241ca2d50e678d452bbf57a8d50b282045d0b8afaca4f5fa96b7e92fe77894376244b45f7286de54a91eb87abeaa9170f56c81433c4cfa703352dd8
 DIST gromacs-manual-4.6.6.pdf 5526314 SHA256 e44b601dc2cff6b095927b5d4c718b073ddf04e64f5c1c2fd6e5bd61c2770f05 SHA512 cef295c9eb64766f7fccf89c1fb077d492488319d7c688c37a2f19dc7771c85d4cbefc49269d9c715094075e8b0206832c4f32c80873889855a2037bf06d6c9c WHIRLPOOL fbd789c5787ce9c92b5fb2fae4ff4ccc758265fdd005a27a93295675c9625f9a4bf4eabe3761699bbf7861fb11eee75104e7183097307b52bbc01e5ee3ab665b
@@ -11,21 +12,23 @@ DIST gromacs-manual-4.6.7.pdf 5526315 SHA256 ed4e870619626b776958bb4bcc94fc9a5d0
 DIST regressiontests-4.6.5.tar.gz 44026759 SHA256 50b611970c68eef3d1d3d043a6ca419c681540d73c96f26d6e9d2857fda3fb91 SHA512 817743f531a072b9940dc916daf79a83980eae7411e36cb003cbf7790282ca33375bdf0cb0e764500e5fac3ff09903b44588bc14a6c92bf73c020ea1fbaa7b38 WHIRLPOOL 835584596f630cea28ba76bb0fa5d131f8f781f64dc98292e20249ec8c9f063e329c15781fe473b66fc0b97292e3f68dce6a868094a45c9139c822425e669de7
 DIST regressiontests-4.6.6.tar.gz 44035165 SHA256 498ecc2ed24cf41ca1e5d82e27c76b869d0a9f9bfaaea77774c4d63c33bb62f8 SHA512 675245785bcb49a88e6bff098b0a794e5c3b01f9f963fa234daffca7e6af8b69df3ae6f8b032ebfa8378b6cb7753355bca559f15958a9a72ddd9d5ec8410a74f WHIRLPOOL 07f19377d2260bf22461c7d50971e1a9acb3e56d00ff5b892de4440a549f23aebb3f633c912fc22a416046c8102d27dbb40b4f0b3019070405713d1163037b47
 DIST regressiontests-4.6.7.tar.gz 44036109 SHA256 afe433fb40860392970851d9c317e63b9b7f1527c7d4e37d530c23fed4518457 SHA512 c8253d6127f5cd6829bf765605f7aa1882b22970d1ce34b92403d75339f3d988556f472b54fd8d35e63e7b272e07bd68cde734df338ab3d67232967361ac7739 WHIRLPOOL ee63d85051d22e60f8b976f5dc105c8def4694f164cf9fb3fdfad5e3fb8e3642e949d36c58a2a08b8f91b96615a17d696650d477ba8b060ab19cb99d012d10da
+DIST regressiontests-5.0.1.tar.gz 61643316 SHA256 8ff1efa3552da113bc57a89acc9a135c3af852545bb09486df91ffce258f9c5e SHA512 452c41d8e1089cc7dcd4edef6e825542ba4eaf5f5d0ddebfdc29df117b1bea0dadc83c4b6c1269559a9d7f1018555442977f7fccb768efc30880cfe566a20041 WHIRLPOOL ae841f1c736f82399bbfd8eb659fe2e7ec5fe9b90451c981ba98334d5a597d70b44701e0502b59e1f8c4a11aca72bc56e4e44e460017f2e623f1b63905ea0952
 DIST regressiontests-5.0.tar.gz 60961669 SHA256 d1c83bc855eec9a210e8f55362fa99e12f715c16a8bf3d62fe232ad94027c824 SHA512 6c5a11ec0ec9b67ecd80cfed1ed726f5bf2a3821624ca43097393fd7ec76c83ae4bfa0af2e69e6be0fe499b57504bb02e1007da39479daf82ca7c0a10342a10e WHIRLPOOL fcd20ad5db82d6b5fdba41da55d4c6e7998028d03b02c16e222ec292a8291f5aeac959993461dbc867a2ec55085e6bf71f7be06afee0389e8d3dacf7eee3b623
 EBUILD gromacs-4.6.5.ebuild 9004 SHA256 b6dc5dc03033100defe0ab09e0573a7c83c3042c250a5361ca23d237cb1ebca5 SHA512 4e7b348c4643f8b9d4c7771d53988f5479f389944993b1930714b0a92c59013fd958926b6da85e5f0f61b12301528e58735db028db2f2dc4a5e82324dfb8ccd7 WHIRLPOOL 4f103cfc28bc3cb10f30e4f087fef0edba7eff0d6328299551022bdde481fc8b38dce32387a8e0f6bb64fc2e1dbad19c1dd947a39978c5025aab7f40d68e5c88
 EBUILD gromacs-4.6.6.ebuild 9072 SHA256 0e2f3f1ac07c8db2ac3ac114c1279d988d8e0536e02dc0d6bd0e014a0046cf6f SHA512 37170e342f3f6b6d4927c22fba7453b5e21ee44703d2756cd93ed3eec452b478941c2009351f6683d11063e45a9c195d54e3f5294f278086804e0437f370a84d WHIRLPOOL d7f76dd0c19cf7c0f756bbc08aca24b2d96096575f1cc655adba10c6b655aa90776cef365ba68501f9732727385952cc0fd585cff34f830f1d6e30cf79b671d7
 EBUILD gromacs-4.6.7.ebuild 9072 SHA256 d9d7d1725e104a19e060d327be136874e68e0b3cbf738c92c35f520217b3aa53 SHA512 7df1968b428a6ae098fbcd84ab403dba7adb5803a3eede1d75b8b0293b3da2aa08ed58ec0462fc7eb38a3af2e6b1b5b0a49e41f1e00987dac6228cd51f793bd8 WHIRLPOOL b0bd2c28e57b22a9f810299ae527ba50fbeeae74abe514402e9b2aa0712319d145f5aaa6bd15d104f7c1699ed08c5bc1bf0fe25f3a355ad8e6071d61f23bb851
+EBUILD gromacs-5.0.1.ebuild 7656 SHA256 48da04e5e6589bc82836dea034f93271cc0e6161cfe4774002196d66c56b50dd SHA512 643e3ef402d8a9a33fb3d40186f1562b794e05cfefba4dcacb7bbf90f2e51e1dcd0024f30e93e03069b96998f26d3d8f30e3ca89b8271a7b6f4e0a6798b52b3b WHIRLPOOL 35d53661f53e0127be3d7b1e27e9ec59af25ff34cb61971fc11e78fd287bcba1c4f05357d8d4214e2f132af1ff4d7765bc408acb968288aba1a60e733f592e97
 EBUILD gromacs-5.0.ebuild 7781 SHA256 7ce7eef26b173d60e85cbcc87e721465a05983c41033321568d6e9a8604b8830 SHA512 a15b6a8809522c2fc708bf389fb5862882deb1416f30702fe7ab3ba6128c6d4a127fcebc2b097256ee4dd59a5c4165ee43cc886026035cff9b030ff1e4556e52 WHIRLPOOL 888be2a1e032a164d31b8b7aa9e9419ff5c582525a326a1184c35f3cfa1cf0199e4dbd394946b1d12503eeb1ea1216aabed9c9571fdaae72ddd2b13521fc45e5
-MISC ChangeLog 23170 SHA256 d10b3ebe201d1d2bc9c08b186b1952c1456f46af7f9457fe58ebda66b9cd413b SHA512 b69867014a412ff47526e5ed1d97fd206f75d62c72bec03f562d5ef10f6560cd8b019e698f5748c517f4d55c8e2183926f99dfc82f8fa4bb4df6dd5eb4ca1e9d WHIRLPOOL 41693e3c612f95e1f2432eed81636f435bf6eee332e5aea93ff7c79259d73ec7f7c6bfd6a371ada344df29224ec305494df35300db718b290bc4694a88860246
+MISC ChangeLog 23293 SHA256 b995533f263d4b8cdff69e2db79283be95f8cf95ecbdbfec499514bd4f1ffe66 SHA512 f0419191a3d23141592927bfa4e65b41351e166a4183925e423b6faf5e69632653884adb33d8b2a03dfb001973600ce8d4358f94c4bd30ca93067404a9071225 WHIRLPOOL c180e9ded38c3b0ffb95c0d141b15ef9c1145cf3730bbf5b561c94a9d7aad8ba38ffd62c085278d364a781883da23c17b70d7f043f63cdd8171d1c210d2eb43b
 MISC metadata.xml 1444 SHA256 e58e4769cc016220f8423b30f758dee28183f51c61d7ae7ed5611be07ad372e6 SHA512 f44febb5c06bca01bd788766ddf4cba6c44f21e79eb7d9f2e6cc5ba65be2cac4df5f8b4e4ccfc08fc66df181c8ecd2ae858c67e713e33b5ae8bdaecde3dcf974 WHIRLPOOL df5bc1089c4118f86b289e655a6bd69e66ef5232c854e8e79d6edc69feb506ecea064ff7ba088dac2dd656ddf896c3b84626856ce7da6779722b01acb9672052
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diff --git a/sci-chemistry/gromacs/gromacs-5.0.1.ebuild b/sci-chemistry/gromacs/gromacs-5.0.1.ebuild
new file mode 100644
index 000000000000..8a426db5672b
--- /dev/null
+++ b/sci-chemistry/gromacs/gromacs-5.0.1.ebuild
@@ -0,0 +1,262 @@
+# Copyright 1999-2014 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 1.1 2014/09/06 18:44:08 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-${PV}.tar.gz )"
+	KEYWORDS="~alpha ~amd64 ~arm ~ppc64 ~sparc ~x86 ~amd64-linux ~x86-linux ~x64-macos ~x86-macos"
+fi
+
+ACCE_IUSE="sse2 sse4_1 avx_128_fma avx_256 avx2_256"
+
+DESCRIPTION="The ultimate molecular dynamics simulation package"
+HOMEPAGE="http://www.gromacs.org/"
+
+# see COPYING for details
+# http://repo.or.cz/w/gromacs.git/blob/HEAD:/COPYING
+#        base,    vmd plugins, fftpack from numpy,  blas/lapck from netlib,        memtestG80 library,  mpi_thread lib
+LICENSE="LGPL-2.1 UoI-NCSA !mkl? ( !fftw? ( BSD ) !blas? ( BSD ) !lapack? ( BSD ) ) cuda? ( LGPL-3 ) threads? ( BSD )"
+SLOT="0/${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 sse2 && acce="SSE2"
+	use sse4_1 && acce="SSE4.1"
+	use avx_128_fma && acce="AVX_128_FMA"
+	use avx_256 && acce="AVX_256"
+	use avx2_256 && acee="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
+}