version bump

(Portage version: 2.2.0_alpha155/cvs/Linux x86_64, signed Manifest commit with key C2000586)

2 files changed, 233 insertions, 2 deletions

diff --git a/sci-chemistry/gromacs/ChangeLog b/sci-chemistry/gromacs/ChangeLog
index a564a3dd430d..74a5da6abba9 100644
--- a/sci-chemistry/gromacs/ChangeLog
+++ b/sci-chemistry/gromacs/ChangeLog
@@ -1,6 +1,11 @@
 # ChangeLog for sci-chemistry/gromacs
-# Copyright 1999-2012 Gentoo Foundation; Distributed under the GPL v2
-# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/gromacs/ChangeLog,v 1.116 2012/12/29 23:00:35 ottxor Exp $
+# Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2
+# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/gromacs/ChangeLog,v 1.117 2013/01/19 21:49:38 ottxor Exp $
+
+*gromacs-4.6 (19 Jan 2013)
+
+  19 Jan 2013; Christoph Junghans <ottxor@gentoo.org> +gromacs-4.6.ebuild:
+  version bump
 
   29 Dec 2012; Christoph Junghans <ottxor@gentoo.org>
   gromacs-4.6_beta3-r1.ebuild:
diff --git a/sci-chemistry/gromacs/gromacs-4.6.ebuild b/sci-chemistry/gromacs/gromacs-4.6.ebuild
new file mode 100644
index 000000000000..6f63b7c02272
--- /dev/null
+++ b/sci-chemistry/gromacs/gromacs-4.6.ebuild
@@ -0,0 +1,226 @@
+# 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 1.1 2013/01/19 21:49:38 ottxor Exp $
+
+EAPI=5
+
+TEST_PV="4.6"
+MANUAL_PV="4.6"
+
+CMAKE_MAKEFILE_GENERATOR="ninja"
+
+inherit bash-completion-r1 cmake-utils eutils multilib toolchain-funcs
+
+if [[ $PV = *9999* ]]; then
+	EGIT_REPO_URI="git://git.gromacs.org/gromacs.git
+		https://gerrit.gromacs.org/gromacs.git
+		git://github.com/gromacs/gromacs.git
+		http://repo.or.cz/r/gromacs.git"
+	EGIT_BRANCH="release-4-6"
+	inherit git-2
+	PDEPEND="doc? ( ~app-doc/${PN}-manual-${PV} )"
+else
+	SRC_URI="ftp://ftp.gromacs.org/pub/${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 )"
+fi
+
+ACCE_IUSE="sse2 sse41 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"
+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 openmp +single-precision test +threads zsh-completion ${ACCE_IUSE}"
+
+CDEPEND="
+	X? (
+		x11-libs/libX11
+		x11-libs/libSM
+		x11-libs/libICE
+		)
+	blas? ( virtual/blas )
+	cuda? ( dev-util/nvidia-cuda-toolkit )
+	fftw? ( sci-libs/fftw:3.0 )
+	gsl? ( sci-libs/gsl )
+	lapack? ( virtual/lapack )
+	mkl? ( sci-libs/mkl )
+	mpi? ( virtual/mpi )"
+DEPEND="${CDEPEND}
+	virtual/pkgconfig"
+RDEPEND="${CDEPEND}"
+
+REQUIRED_USE="
+	|| ( single-precision double-precision )
+	cuda? ( 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"
+
+	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
+		done
+	fi
+}
+
+src_configure() {
+	local mycmakeargs_pre=( ) extra fft_opts=( )
+
+	#go from slowest to fastest acceleration
+	local acce="None"
+	use sse2 && acce="SSE2"
+	use sse41 && 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
+		[[ ${x} = "double" ]] && p="-DGMX_DOUBLE=ON" || p="-DGMX_DOUBLE=OFF"
+		local cuda=$(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) ${cuda} -DGMX_OPENMM=OFF
+			"$(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
+		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
+		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
+		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"
+}