version bump

(Portage version: 2.2.0_alpha165/cvs/Linux x86_64, signed Manifest commit with key C2000586)

4 files changed, 241 insertions, 276 deletions

diff --git a/sci-chemistry/gromacs/ChangeLog b/sci-chemistry/gromacs/ChangeLog
index b12fe733590b..aeaf99af3f11 100644
--- a/sci-chemistry/gromacs/ChangeLog
+++ b/sci-chemistry/gromacs/ChangeLog
@@ -1,6 +1,13 @@
 # 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 1.120 2013/02/12 04:11:10 ottxor Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/gromacs/ChangeLog,v 1.121 2013/03/06 02:02:01 ottxor Exp $
+
+*gromacs-4.6.1 (06 Mar 2013)
+
+  06 Mar 2013; Christoph Junghans <ottxor@gentoo.org>
+  +files/gromacs-4.6.1-openmm.patch, +gromacs-4.6.1.ebuild, -gromacs-4.6.ebuild,
+  -gromacs-4.6_beta3-r1.ebuild:
+  version bump
 
   12 Feb 2013; Christoph Junghans <ottxor@gentoo.org> gromacs-4.6.ebuild,
   gromacs-4.6_beta3-r1.ebuild, metadata.xml:
diff --git a/sci-chemistry/gromacs/files/gromacs-4.6.1-openmm.patch b/sci-chemistry/gromacs/files/gromacs-4.6.1-openmm.patch
new file mode 100644
index 000000000000..dd4214af0513
--- /dev/null
+++ b/sci-chemistry/gromacs/files/gromacs-4.6.1-openmm.patch
@@ -0,0 +1,151 @@
+From e96c29f92e6cd1dd05945ef80e6a78d55747cf2e Mon Sep 17 00:00:00 2001
+From: Christoph Junghans <junghans@votca.org>
+Date: Thu, 17 Jan 2013 20:30:30 -0700
+Subject: [PATCH] fix out of source build for OpenMM
+
+* introduced in e508a07b6e127fa1cf31d263bcbd33e4040066cb
+
+Change-Id: I6ad45fd2d5766d1c4a91ef2e0c442ff030fc1296
+---
+ CMakeLists.txt                     |  2 +-
+ src/contrib/BuildMdrunOpenMM.cmake |  6 +++---
+ src/contrib/CMakeLists.txt         |  3 ---
+ src/contrib/mdrun_openmm.c         | 12 +++++++-----
+ src/contrib/openmm_wrapper.cpp     |  1 +
+ src/kernel/CMakeLists.txt          |  5 ++++-
+ 6 files changed, 16 insertions(+), 13 deletions(-)
+
+diff --git a/CMakeLists.txt b/CMakeLists.txt
+index df12172..4c11a29 100644
+--- a/CMakeLists.txt
++++ b/CMakeLists.txt
+@@ -153,7 +153,7 @@ mark_as_advanced(GMX_FORCE_CXX)
+ option(GMX_COOL_QUOTES "Enable Gromacs cool quotes" ON)
+ mark_as_advanced(GMX_COOL_QUOTES)
+ 
+-if(GMX_GPU OR GMX_FORCE_CXX)
++if(GMX_GPU OR GMX_FORCE_CXX OR GMX_OPENMM)
+     enable_language(CXX)
+ endif()
+ set(CMAKE_PREFIX_PATH "" CACHE STRING "Extra locations to search for external libraries and tools (give directory without lib, bin, or include)")
+diff --git a/src/contrib/BuildMdrunOpenMM.cmake b/src/contrib/BuildMdrunOpenMM.cmake
+index bc954d6..6d04958 100644
+--- a/src/contrib/BuildMdrunOpenMM.cmake
++++ b/src/contrib/BuildMdrunOpenMM.cmake
+@@ -39,14 +39,14 @@ link_directories(${OpenMM_LIBRARY_DIR})
+ # if the same OpenMM installation is used for running and building 
+ add_definitions( -DOPENMM_PLUGIN_DIR="${OpenMM_PLUGIN_DIR}" ) 
+ file(TO_CMAKE_PATH ${OpenMM_PLUGIN_DIR} _path)
+-add_library(openmm_api_wrapper STATIC openmm_wrapper.cpp)
++add_library(openmm_api_wrapper STATIC ${CMAKE_SOURCE_DIR}/src/contrib/openmm_wrapper.cpp)
+ target_link_libraries(openmm_api_wrapper ${OpenMM_LIBRARIES})
+ list(APPEND GMX_EXTRA_LIBRARIES openmm_api_wrapper ${OpenMM_LIBRARIES})   
+ 
+ list(REMOVE_ITEM MDRUN_SOURCES mdrun.c)
+ list(APPEND MDRUN_SOURCES
+-    ${CMAKE_CURRENT_SOURCE_DIR}/src/contrib/md_openmm.c
+-    ${CMAKE_CURRENT_SOURCE_DIR}/src/contrib/mdrun_openmm.c)
++    ${CMAKE_SOURCE_DIR}/src/contrib/md_openmm.c
++    ${CMAKE_SOURCE_DIR}/src/contrib/mdrun_openmm.c)
+ 
+ # this is to circumvent the following MSVC error: 
+ # warning LNK4098: defaultlib 'LIBCMT' conflicts with use of other libs
+diff --git a/src/contrib/CMakeLists.txt b/src/contrib/CMakeLists.txt
+index 7c5bb83..7725210 100644
+--- a/src/contrib/CMakeLists.txt
++++ b/src/contrib/CMakeLists.txt
+@@ -49,7 +49,6 @@ if(GMX_OPENMM)
+         message(FATAL_ERROR "The OpenMM build is not compatible with the native GPU build")
+     endif()
+ 
+-    enable_language(CXX)
+     set (GMX_BINARY_SUFFIX "-openmm")
+     set (GMX_LIBS_SUFFIX "_openmm")
+ 
+@@ -99,8 +98,6 @@ if(GMX_OPENMM)
+     if(CMAKE_BUILD_TYPE STREQUAL "DEBUG")    
+         set(CUDA_VERBOSE_BUILD ON)
+     endif()
+-    list(APPEND CMAKE_MODULE_PATH ${CMAKE_CURRENT_SOURCE_DIR}/src/contrib)
+-    find_package(OpenMM) 
+ 
+     # mark as advanced the unused variables
+     mark_as_advanced(FORCE GMX_CPU_ACCELERATION GMX_MPI GMX_FFT_LIBRARY 
+diff --git a/src/contrib/mdrun_openmm.c b/src/contrib/mdrun_openmm.c
+index 7771dcd..aeedeb4 100644
+--- a/src/contrib/mdrun_openmm.c
++++ b/src/contrib/mdrun_openmm.c
+@@ -153,7 +153,7 @@ int cmain(int argc,char *argv[])
+     { efXVG, "-tpi",    "tpi",      ffOPTWR },
+     { efXVG, "-tpid",   "tpidist",  ffOPTWR },
+     { efEDI, "-ei",     "sam",      ffOPTRD },
+-    { efEDO, "-eo",     "sam",      ffOPTWR },
++    { efXVG, "-eo",     "sam",      ffOPTWR },
+     { efGCT, "-j",      "wham",     ffOPTRD },
+     { efGCT, "-jo",     "bam",      ffOPTWR },
+     { efXVG, "-ffout",  "gct",      ffOPTWR },
+@@ -205,6 +205,8 @@ int cmain(int argc,char *argv[])
+     { NULL, "interleave", "pp_pme", "cartesian", NULL };
+   const char *dddlb_opt[] =
+     { NULL, "auto", "no", "yes", NULL };
++  const char   *thread_aff_opt[threadaffNR+1] =
++    { NULL, "auto", "no", "yes", NULL };
+   const char *nbpu_opt[] =
+     { NULL, "auto", "cpu", "gpu", "gpu_cpu", NULL };
+   real rdd=0.0,rconstr=0.0,dlb_scale=0.8,pforce=-1;
+@@ -236,12 +238,12 @@ int cmain(int argc,char *argv[])
+       "Number of OpenMP threads per MPI process/thread to start (0 is guess)" },
+     { "-ntomp_pme", FALSE, etINT, {&hw_opt.nthreads_omp_pme},
+       "Number of OpenMP threads per MPI process/thread to start (0 is -ntomp)" },
+-    { "-pin",     FALSE, etBOOL, {&hw_opt.bThreadPinning},
++    { "-pin",     FALSE, etBOOL, {thread_aff_opt},
+       "Pin OpenMP threads to cores" },
+-    { "-pinht",   FALSE, etBOOL, {&hw_opt.bPinHyperthreading},
+-      "Always pin threads to Hyper-Threading cores" },
+     { "-pinoffset", FALSE, etINT, {&hw_opt.core_pinning_offset},
+       "Core offset for pinning (for running multiple mdrun processes on a single physical node)" },
++    { "-pinstride", FALSE, etINT, {&hw_opt.core_pinning_stride},
++      "Pinning distance in logical cores for threads, use 0 to minimize the number of threads per physical core" },
+     { "-gpu_id",  FALSE, etSTR, {&hw_opt.gpu_id},
+       "List of GPU id's to use" },
+     { "-ddcheck", FALSE, etBOOL, {&bDDBondCheck},
+@@ -413,7 +415,7 @@ int cmain(int argc,char *argv[])
+ 
+       if (MULTISIM(cr) && MASTER(cr))
+       {
+-          check_multi_int(stdout,cr->ms,sim_part,"simulation part");
++          check_multi_int(stdout,cr->ms,sim_part,"simulation part", TRUE);
+       }
+   } 
+   else
+diff --git a/src/contrib/openmm_wrapper.cpp b/src/contrib/openmm_wrapper.cpp
+index 07f0eca..05c3210 100644
+--- a/src/contrib/openmm_wrapper.cpp
++++ b/src/contrib/openmm_wrapper.cpp
+@@ -63,6 +63,7 @@ using namespace std;
+ #include "mdrun.h"
+ #include "physics.h"
+ #include "string2.h"
++#include "openmm_gpu_utils.h"
+ #include "gpu_utils.h"
+ #include "mtop_util.h"
+ 
+diff --git a/src/kernel/CMakeLists.txt b/src/kernel/CMakeLists.txt
+index 01e290c..3f95d33 100644
+--- a/src/kernel/CMakeLists.txt
++++ b/src/kernel/CMakeLists.txt
+@@ -88,7 +88,10 @@ if(GMX_OPENMM)
+     # Even though the OpenMM build has "moved to contrib", many things
+     # have be be done from within the scope of the CMakeLists.txt that
+     # builds its mdrun, and that is here
+-    include(../contrib/BuildMdrunOpenMM)
++    list(APPEND CMAKE_MODULE_PATH ${CMAKE_SOURCE_DIR}/src/contrib)
++    find_package(OpenMM)
++    include_directories(${CMAKE_CURRENT_SOURCE_DIR})
++    include(${CMAKE_SOURCE_DIR}/src/contrib/BuildMdrunOpenMM.cmake)
+ endif(GMX_OPENMM)
+ 
+ if(GMX_GPU OR GMX_FORCE_CXX)
+-- 
+1.8.1.5
+
diff --git a/sci-chemistry/gromacs/gromacs-4.6.ebuild b/sci-chemistry/gromacs/gromacs-4.6.1.ebuild
index cbf14cd62ed1..226082edf7c4 100644
--- a/sci-chemistry/gromacs/gromacs-4.6.ebuild
+++ b/sci-chemistry/gromacs/gromacs-4.6.1.ebuild
@@ -1,13 +1,15 @@
 # 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.ebuild,v 1.4 2013/02/12 04:11:10 ottxor Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/gromacs/gromacs-4.6.1.ebuild,v 1.1 2013/03/06 02:02:01 ottxor Exp $
 
 EAPI=5
 
-TEST_PV="4.6"
-MANUAL_PV="4.6"
+TEST_PV="4.6.1"
+MANUAL_PV="4.6.1"
 
-inherit bash-completion-r1 cmake-utils eutils multilib readme.gentoo toolchain-funcs
+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
@@ -16,11 +18,17 @@ if [[ $PV = *9999* ]]; then
 		http://repo.or.cz/r/gromacs.git"
 	EGIT_BRANCH="release-4-6"
 	inherit git-2
-	PDEPEND="doc? ( ~app-doc/${PN}-manual-${PV} )"
+	LIVE_DEPEND="doc? (
+		dev-texlive/texlive-latex
+		media-gfx/imagemagick
+		sys-apps/coreutils
+	)"
 else
 	SRC_URI="ftp://ftp.gromacs.org/pub/${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 )"
+	PATCHES=( "${FILESDIR}/${P}-openmm.patch" )
+	LIVE_DEPEND=""
 fi
 
 ACCE_IUSE="sse2 sse4_1 avx128fma avx256"
@@ -32,9 +40,9 @@ HOMEPAGE="http://www.gromacs.org/"
 # 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"
+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 openmp +single-precision test +threads zsh-completion ${ACCE_IUSE}"
+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? (
@@ -43,33 +51,63 @@ CDEPEND="
 		x11-libs/libICE
 		)
 	blas? ( virtual/blas )
-	cuda? ( dev-util/nvidia-cuda-toolkit )
+	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 )"
+	mpi? ( virtual/mpi )
+	openmm? (
+		>=dev-util/nvidia-cuda-toolkit-4.2.9-r1
+		sci-libs/openmm[cuda,opencl]
+	)"
 DEPEND="${CDEPEND}
-	virtual/pkgconfig"
+	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
 
-	#add user patches from /etc/portage/patches/sci-chemistry/gromacs
-	epatch_user
+	cmake-utils_src_prepare
+
+	use cuda && cuda_src_prepare
 
 	GMX_DIRS=""
 	use single-precision && GMX_DIRS+=" float"
@@ -78,7 +116,7 @@ src_prepare() {
 	if use test; then
 		for x in ${GMX_DIRS}; do
 			mkdir -p "${WORKDIR}/${P}_${x}" || die
-			cp -al "${WORKDIR}/regressiontests-${TEST_PV}" "${WORKDIR}/${P}_${x}/tests" || die
+			cp -al "${WORKDIR}/regressiontests"* "${WORKDIR}/${P}_${x}/tests" || die
 		done
 	fi
 
@@ -149,6 +187,15 @@ src_configure() {
 			"$(use test && echo -DREGRESSIONTEST_PATH="${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
@@ -163,6 +210,11 @@ src_compile() {
 		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"\
@@ -181,34 +233,33 @@ 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
+			BUILD_DIR="${WORKDIR}"/manual_build cmake-utils_src_make
+			newdoc "${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
 
-	rm -f "${ED}"/usr/bin/GMXRC*
-
+	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.*
-
-	cd "${S}"
-	dodoc AUTHORS INSTALL* README*
-	if use doc; then
-		dohtml -r "${ED}usr/share/gromacs/html/"
-		if [[ $PV = *9999* ]]; then
-			insinto /usr/share/gromacs
-			doins "admin/programs.txt"
-			ls -1 "${ED}"/usr/bin | sed -e '/_d$/d' > "${T}"/programs.list
-			doins "${T}"/programs.list
-		else
-			dodoc "${DISTDIR}/${PN}-manual-${MANUAL_PV}.pdf"
-		fi
-	fi
-	rm -rf "${ED}usr/share/gromacs/html/"
+	rm -f "${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
 }
diff --git a/sci-chemistry/gromacs/gromacs-4.6_beta3-r1.ebuild b/sci-chemistry/gromacs/gromacs-4.6_beta3-r1.ebuild
deleted file mode 100644
index fe224cb808d4..000000000000
--- a/sci-chemistry/gromacs/gromacs-4.6_beta3-r1.ebuild
+++ /dev/null
@@ -1,244 +0,0 @@
-# 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_beta3-r1.ebuild,v 1.3 2013/02/12 04:11:10 ottxor Exp $
-
-EAPI=5
-
-TEST_PV="4.0.4"
-MANUAL_PV="4.6-beta1"
-
-inherit bash-completion-r1 cmake-utils eutils multilib toolchain-funcs
-
-SRC_URI="test? ( ftp://ftp.gromacs.org/pub/tests/gmxtest-${TEST_PV}.tgz )"
-
-if [[ $PV = *9999* ]]; then
-	EGIT_REPO_URI="git://git.gromacs.org/gromacs.git
-		https://gerrit.gromacs.org/gromacs.git
-		git://github.com/gromacs/gromacs.git
-		http://repo.or.cz/r/gromacs.git"
-	EGIT_BRANCH="release-4-6"
-	inherit git-2
-	PDEPEND="doc? ( ~app-doc/${PN}-manual-${PV} )"
-else
-	S="${WORKDIR}/${P//_/-}"
-	SRC_URI="${SRC_URI} ftp://ftp.gromacs.org/pub/${PN}/${P//_/-}.tar.gz
-		doc? (  ftp://ftp.gromacs.org/pub/manual/${PN}-manual-${MANUAL_PV}.pdf )"
-fi
-
-ACCE_IUSE="sse2 sse4_1 avx128fma avx256"
-
-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 blas cuda doc -double-precision +fftw gsl lapack mkl mpi +offensive openmm openmp +single-precision test +threads zsh-completion ${ACCE_IUSE}"
-
-CDEPEND="
-	X? (
-		x11-libs/libX11
-		x11-libs/libSM
-		x11-libs/libICE
-		)
-	blas? ( virtual/blas )
-	cuda? ( dev-util/nvidia-cuda-toolkit )
-	fftw? ( sci-libs/fftw:3.0 )
-	gsl? ( sci-libs/gsl )
-	lapack? ( virtual/lapack )
-	mkl? ( sci-libs/mkl )
-	mpi? ( virtual/mpi )
-	openmm? (
-		dev-util/nvidia-cuda-toolkit
-		sci-libs/openmm[cuda,opencl]
-	)"
-DEPEND="${CDEPEND}
-	virtual/pkgconfig"
-RDEPEND="${CDEPEND}"
-
-RESTRICT="test"
-
-REQUIRED_USE="
-	|| ( single-precision double-precision )
-	cuda? ( single-precision )
-	openmm? ( single-precision )
-	mkl? ( !blas !fftw !lapack )"
-
-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_prepare() {
-	#notes/todos
-	# -on apple: there is framework support
-
-	#add user patches from /etc/portage/patches/sci-chemistry/gromacs
-	epatch_user
-
-	GMX_DIRS=""
-	use single-precision && GMX_DIRS+=" float"
-	use double-precision && GMX_DIRS+=" double"
-
-	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=( ) 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)
-		$(cmake-utils_use !offensive GMX_NO_QUOTES)
-		-DGMX_DEFAULT_SUFFIX=off
-		-DGMX_ACCELERATION="$acce"
-		-DGMXLIB="$(get_libdir)"
-		-DGMX_VMD_PLUGIN_PATH="${EPREFIX}/usr/$(get_libdir)/vmd/plugins/*/molfile/"
-		${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
-		[[ ${x} = "double" ]] && p="-DGMX_DOUBLE=ON" || p="-DGMX_DOUBLE=OFF"
-		local cuda=$(cmake-utils_use cuda GMX_GPU)
-		[[ ${x} = "double" ]] && use cuda && cuda="-DGMX_GPU=OFF"
-		mycmakeargs=( ${mycmakeargs_pre[@]} ${p} -DGMX_MPI=OFF
-			$(cmake-utils_use threads GMX_THREAD_MPI) ${cuda}
-			-DGMX_BINARY_SUFFIX="${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[@]} ${p} -DGMX_MPI=OFF
-				-DGMX_THREAD_MPI=OFF -DGMX_GPU=OFF -DGMX_OPENMM=ON
-				-DGMX_BINARY_SUFFIX="_openmm" -DGMX_LIBS_SUFFIX="_openmm" )
-			BUILD_DIR="${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 ${cuda}
-			-DGMX_BINARY_SUFFIX="_mpi${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 ${GMX_DIRS}; do
-		local oldpath="${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
-		if [[ ${x} = float ]] && use openmm; then
-			BUILD_DIR="${WORKDIR}/${P}_openmm" \
-				DESTDIR="${D}" cmake-utils_src_make install-mdrun
-		fi
-		use mpi || continue
-		BUILD_DIR="${WORKDIR}/${P}_${x}_mpi" \
-			DESTDIR="${D}" cmake-utils_src_make install-mdrun
-	done
-
-	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.*
-
-	cd "${S}"
-	dodoc AUTHORS INSTALL* README*
-	if use doc; then
-		dohtml -r "${ED}usr/share/gromacs/html/"
-		if [[ $PV = *9999* ]]; then
-			insinto /usr/share/gromacs
-			doins "admin/programs.txt"
-			ls -1 "${ED}"/usr/bin | sed -e '/_d$/d' > "${T}"/programs.list
-			doins "${T}"/programs.list
-		else
-			dodoc "${DISTDIR}/${PN}-manual-${MANUAL_PV}.pdf"
-		fi
-	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"
-	if use offensive; then
-		einfo
-		einfo  $(g_luck)
-		einfo  "For more Gromacs cool quotes (gcq) add g_luck to your .bashrc"
-	fi
-	einfo
-	elog  "Gromacs can use sci-chemistry/vmd to read additional file formats"
-}