[gentoo-commits] proj/sci:master commit in: sci-chemistry/gromacs/

[Christoph Junghans]

commit:     d641b77cf7e5b677eea55c8b689c6945961ed8e8
Author:     Christoph Junghans <ottxor <AT> gentoo <DOT> org>
AuthorDate: Wed Mar  6 02:03:56 2013 +0000
Commit:     Christoph Junghans <ottxor <AT> gentoo <DOT> org>
CommitDate: Wed Mar  6 02:03:56 2013 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=d641b77c

sync with gx86 + clean up

Package-Manager: portage-2.2.0_alpha165

---
 sci-chemistry/gromacs/ChangeLog               |    5 +
 sci-chemistry/gromacs/gromacs-4.5.9999.ebuild |  238 -------------------------
 sci-chemistry/gromacs/gromacs-4.6.9999.ebuild |   36 ++--
 sci-chemistry/gromacs/gromacs-9999.ebuild     |    1 -
 sci-chemistry/gromacs/metadata.xml            |    1 -
 5 files changed, 25 insertions(+), 256 deletions(-)

diff --git a/sci-chemistry/gromacs/ChangeLog b/sci-chemistry/gromacs/ChangeLog
index 7672a1e..45159e4 100644
--- a/sci-chemistry/gromacs/ChangeLog
+++ b/sci-chemistry/gromacs/ChangeLog
@@ -2,6 +2,11 @@
 # Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2
 # $Header: $
 
+  06 Mar 2013; Christoph Junghans <ottxor@g.o> -Manifest,
+  -gromacs-4.5.9999.ebuild, gromacs-4.6.9999.ebuild, gromacs-9999.ebuild,
+  metadata.xml:
+  sync with gx86 + clean up
+
   12 Feb 2013; Christoph Junghans <ottxor@g.o> gromacs-4.6.9999.ebuild,
   gromacs-9999.ebuild, metadata.xml:
   sse41 -> sse4_1 (bug #456886) + ninja has missing keywords

diff --git a/sci-chemistry/gromacs/gromacs-4.5.9999.ebuild b/sci-chemistry/gromacs/gromacs-4.5.9999.ebuild
deleted file mode 100644
index c1a0dd6..0000000
--- a/sci-chemistry/gromacs/gromacs-4.5.9999.ebuild
+++ /dev/null
@@ -1,238 +0,0 @@
-# Copyright 1999-2012 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Header: $
-
-EAPI="4"
-
-TEST_PV="4.0.4"
-MANUAL_PV="4.5.4"
-
-#to find external blas/lapack
-CMAKE_MIN_VERSION="2.8.5-r2"
-
-inherit bash-completion-r1 cmake-utils eutils fortran-2 multilib toolchain-funcs
-
-SRC_URI="test? ( ftp://ftp.gromacs.org/pub/tests/gmxtest-${TEST_PV}.tgz )
-		doc? ( ftp://ftp.gromacs.org/pub/manual/manual-${MANUAL_PV}.pdf -> gromacs-manual-${MANUAL_PV}.pdf )"
-
-if [ "${PV%9999}" != "${PV}" ]; then
-	EGIT_REPO_URI="git://git.gromacs.org/gromacs http://repo.or.cz/r/gromacs.git"
-	EGIT_BRANCH="release-4-5-patches"
-	inherit git-2
-else
-	SRC_URI="${SRC_URI} ftp://ftp.gromacs.org/pub/${PN}/${P}.tar.gz"
-fi
-
-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"
-IUSE="X altivec blas doc -double-precision +fftw fkernels gsl lapack
-mpi +single-precision sse2 test +threads xml zsh-completion"
-REQUIRED_USE="fkernels? ( !threads )"
-
-CDEPEND="
-	X? (
-		x11-libs/libX11
-		x11-libs/libSM
-		x11-libs/libICE
-		)
-	blas? ( virtual/blas )
-	fftw? ( sci-libs/fftw:3.0 )
-	fkernels? ( virtual/fortran )
-	gsl? ( sci-libs/gsl )
-	lapack? ( virtual/lapack )
-	mpi? ( virtual/mpi )
-	xml? ( dev-libs/libxml2:2 )"
-DEPEND="${CDEPEND}
-	virtual/pkgconfig"
-RDEPEND="${CDEPEND}
-	app-shells/tcsh"
-
-RESTRICT="test"
-
-pkg_setup() {
-	use fkernels && fortran-2_pkg_setup
-}
-
-src_prepare() {
-	#add user patches from /etc/portage/patches/sci-chemistry/gromacs
-	epatch_user
-
-	if use mpi && use threads; then
-		elog "mdrun uses only threads OR mpi, and gromacs favours the"
-		elog "use of mpi over threads, so a mpi-version of mdrun will"
-		elog "be compiled. If you want to run mdrun on shared memory"
-		elog "machines only, you can safely disable mpi"
-	fi
-
-	GMX_DIRS=""
-	use single-precision && GMX_DIRS+=" float"
-	use double-precision && GMX_DIRS+=" double"
-	#if neither single-precision nor double-precision is enabled
-	#build at least default (single)
-	[ -z "$GMX_DIRS" ] && GMX_DIRS+=" float"
-
-	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=( )
-	#from gromacs configure
-	if use fftw; then
-		mycmakeargs_pre+=("-DGMX_FFT_LIBRARY=fftw3")
-	else
-		mycmakeargs_pre+=("-DGMX_FFT_LIBRARY=fftpack")
-		ewarn "WARNING: The built-in FFTPACK routines are slow."
-		ewarn "Are you sure you don\'t want to use FFTW?"
-		ewarn "It is free and much faster..."
-	fi
-
-	if [[ $(gcc-version) == "4.1" ]]; then
-		eerror "gcc 4.1 is not supported by gromacs"
-		eerror "please run test suite"
-		die
-	fi
-
-	#note for gentoo-PREFIX on apple: use --enable-apple-64bit
-
-	#note for gentoo-PREFIX on aix, fortran (xlf) is still much faster
-	if use fkernels; then
-		ewarn "Fortran kernels are usually not faster than C kernels and assembly"
-		ewarn "I hope, you know what are you doing..."
-	fi
-
-	if use double-precision ; then
-		#from gromacs manual
-		elog
-		elog "For most simulations single precision is accurate enough. In some"
-		elog "cases double precision is required to get reasonable results:"
-		elog
-		elog "-normal mode analysis, for the conjugate gradient or l-bfgs minimization"
-		elog " and the calculation and diagonalization of the Hessian "
-		elog "-calculation of the constraint force between two large groups of	atoms"
-		elog "-energy conservation: this can only be done without temperature coupling and"
-		elog " without cutoffs"
-		elog
-	fi
-
-	if use mpi ; then
-		elog "You have enabled mpi, only mdrun will make use of mpi, that is why"
-		elog "we configure/compile gromacs twice (with and without mpi) and only"
-		elog "install mdrun with mpi support. In addtion you will get libgmx and"
-		elog "libmd with and without mpi support."
-	fi
-
-	#go from slowest to fasterest acceleration
-	local acce="none"
-	use fkernels && acce="fortran"
-	use altivec && acce="altivec"
-	use ia64 && acce="ia64"
-	use sse2 && acce="sse"
-
-	mycmakeargs_pre+=(
-		$(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 threads GMX_THREADS)
-		$(cmake-utils_use xml GMX_XML)
-		-DGMX_DEFAULT_SUFFIX=off
-		-DGMX_ACCELERATION="$acce"
-		-DGMXLIB="$(get_libdir)"
-	)
-
-	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"
-		mycmakeargs=( ${mycmakeargs_pre[@]} ${p} -DGMX_MPI=OFF
-			-DGMX_BINARY_SUFFIX="${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[@]} ${p} -DGMX_MPI=ON
-			-DGMX_BINARY_SUFFIX="_mpi${suffix}" -DGMX_LIBS_SUFFIX="_mpi${suffix}" )
-		BUILD_DIR="${WORKDIR}/${P}_${x}_mpi" 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 ${GMX_DIRS}; do
-		local oldpath="${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
-		use mpi || continue
-		#cmake-utils_src_install does not support args
-		#using cmake-utils_src_compile instead
-		BUILD_DIR="${WORKDIR}/${P}_${x}_mpi" \
-			cmake-utils_src_make install-mdrun DESTDIR="${D}"
-	done
-
-	sed -n -e '/^GMXBIN/,/^GMXDATA/p' "${ED}"/usr/bin/GMXRC.bash > "${T}/80gromacs"
-	echo "VMD_PLUGIN_PATH=${EPREFIX}/usr/$(get_libdir)/vmd/plugins/*/molfile/" >> "${T}/80gromacs"
-
-	doenvd "${T}/80gromacs"
-	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.*
-
-	# Fix typos in a couple of files.
-	sed -e "s:+0f:-f:" -i "${ED}"usr/share/gromacs/tutor/gmxdemo/demo \
-		|| die "Failed to fixup demo script."
-
-	cd "${S}"
-	dodoc AUTHORS INSTALL* README*
-	if use doc; then
-		newdoc "${DISTDIR}/gromacs-manual-${MANUAL_PV}.pdf" "manual-${MANUAL_PV}.pdf"
-		dohtml -r "${ED}usr/share/gromacs/html/"
-	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"
-	einfo
-	einfo  $(g_luck)
-	einfo  "For more Gromacs cool quotes (gcq) add g_luck to your .bashrc"
-	einfo
-	elog  "Gromacs can use sci-chemistry/vmd to read additional file formats"
-}

diff --git a/sci-chemistry/gromacs/gromacs-4.6.9999.ebuild b/sci-chemistry/gromacs/gromacs-4.6.9999.ebuild
index 5e52c9f..8bd98be 100644
--- a/sci-chemistry/gromacs/gromacs-4.6.9999.ebuild
+++ b/sci-chemistry/gromacs/gromacs-4.6.9999.ebuild
@@ -4,10 +4,12 @@
 
 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 cuda eutils multilib 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
@@ -16,10 +18,16 @@ if [[ $PV = *9999* ]]; then
 		http://repo.or.cz/r/gromacs.git"
 	EGIT_BRANCH="release-4-6"
 	inherit git-2
+	LIVE_DEPEND="doc? (
+		dev-texlive/texlive-latex
+		media-gfx/imagemagick
+		sys-apps/coreutils
+	)"
 else
 	SRC_URI="ftp://ftp.gromacs.org/pub/${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 )"
+	LIVE_DEPEND=""
 fi
 
 ACCE_IUSE="sse2 sse4_1 avx128fma avx256"
@@ -32,7 +40,7 @@ HOMEPAGE="http://www.gromacs.org/"
 #        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 ~ppc64 ~sparc ~x86 ~amd64-linux ~x86-linux ~x86-macos"
+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="
@@ -54,11 +62,7 @@ CDEPEND="
 	)"
 DEPEND="${CDEPEND}
 	virtual/pkgconfig
-	doc? (
-		dev-texlive/texlive-latex
-		media-gfx/imagemagick
-		sys-apps/coreutils
-	)"
+	${LIVE_DEPEND}"
 RDEPEND="${CDEPEND}"
 
 REQUIRED_USE="
@@ -68,7 +72,7 @@ REQUIRED_USE="
 	mkl? ( !blas !fftw !lapack )
 	!openmm" #broken, but https://gerrit.gromacs.org/#/c/2087/
 
-DOCS=( AUTHORS INSTALL.cmake README )
+DOCS=( AUTHORS README )
 HTML_DOCS=( "${ED}"/usr/share/gromacs/html/ )
 
 pkg_pretend() {
@@ -101,8 +105,7 @@ 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
 
@@ -117,9 +120,7 @@ src_prepare() {
 		done
 	fi
 
-	if use openmm; then
-		sed -i '/option.*GMX_OPENMM/s/^#//' src/contrib/CMakeLists.txt || die
-	fi
+	DOC_CONTENTS="Gromacs can use sci-chemistry/vmd to read additional file formats"
 }
 
 src_configure() {
@@ -190,6 +191,7 @@ src_configure() {
 			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
@@ -258,6 +260,8 @@ src_install() {
 	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() {
@@ -271,5 +275,5 @@ pkg_postinst() {
 		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"
+	readme.gentoo_print_elog
 }

diff --git a/sci-chemistry/gromacs/gromacs-9999.ebuild b/sci-chemistry/gromacs/gromacs-9999.ebuild
index b9af3c0..36a6d2d 100644
--- a/sci-chemistry/gromacs/gromacs-9999.ebuild
+++ b/sci-chemistry/gromacs/gromacs-9999.ebuild
@@ -18,7 +18,6 @@ inherit bash-completion-r1 cmake-utils eutils git-2 multilib toolchain-funcs
 
 DESCRIPTION="The ultimate molecular dynamics simulation package"
 HOMEPAGE="http://www.gromacs.org/"
-SRC_URI="test? ( ftp://ftp.gromacs.org/pub/tests/gmxtest-${TEST_PV}.tgz )"
 
 LICENSE="GPL-2"
 SLOT="0/${PV}"

diff --git a/sci-chemistry/gromacs/metadata.xml b/sci-chemistry/gromacs/metadata.xml
index 8a88d53..880233e 100644
--- a/sci-chemistry/gromacs/metadata.xml
+++ b/sci-chemistry/gromacs/metadata.xml
@@ -11,7 +11,6 @@
 		<flag name="double-precision">More precise calculations at the expense of speed</flag>
 		<flag name="single-precision">Single precision version of gromacs (default)</flag>
 		<!-- acceleration optimization flags -->
-		<flag name="fkernels">Enable building of Fortran Kernels for platforms that dont have assembly loops</flag>
 		<flag name="sse4_1">Enable sse4.1 acceleration</flag>
 		<flag name="avx128fma">Enable 128bit avx with fma (e.g. AMD BullDozer)</flag>
 		<flag name="avx256">Enable 256bit avx (e.g. Intel Sandy Bridge)</flag>