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

[Alexey Shvetsov]

commit:     ec5a4f359119a8d3bd186f4f3a24481a0089f98c
Author:     Alexey Shvetsov <alexxy <AT> gentoo <DOT> org>
AuthorDate: Tue Dec  3 03:59:38 2013 +0000
Commit:     Alexey Shvetsov <alexxy <AT> gentoo <DOT> org>
CommitDate: Tue Dec  3 03:59:38 2013 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=ec5a4f35

Slightly update live ebuild for master branch

Package-Manager: portage-2.2.7

---
 sci-chemistry/gromacs/ChangeLog           |   3 +
 sci-chemistry/gromacs/gromacs-9999.ebuild | 280 ++++++++++++++++++------------
 2 files changed, 172 insertions(+), 111 deletions(-)

diff --git a/sci-chemistry/gromacs/ChangeLog b/sci-chemistry/gromacs/ChangeLog
index 9a16c48..fc03b04 100644
--- a/sci-chemistry/gromacs/ChangeLog
+++ b/sci-chemistry/gromacs/ChangeLog
@@ -2,6 +2,9 @@
 # Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2
 # $Header: $
 
+  03 Dec 2013; Alexey Shvetsov <alexxy@g.o> gromacs-9999.ebuild:
+  Slightly update live ebuild for master branch
+
   01 Jun 2013; Christoph Junghans <ottxor@g.o> gromacs-4.6.9999.ebuild:
   sync with gx86
 

diff --git a/sci-chemistry/gromacs/gromacs-9999.ebuild b/sci-chemistry/gromacs/gromacs-9999.ebuild
index 36a6d2d..706734c 100644
--- a/sci-chemistry/gromacs/gromacs-9999.ebuild
+++ b/sci-chemistry/gromacs/gromacs-9999.ebuild
@@ -2,28 +2,47 @@
 # Distributed under the terms of the GNU General Public License v2
 # $Header: $
 
-EAPI="5"
+EAPI=5
 
-TEST_PV="4.0.4"
+TEST_PV="5.0-beta1"
+MANUAL_PV="5.0-beta1"
 
-EGIT_REPO_URI="git://git.gromacs.org/gromacs http://repo.or.cz/r/gromacs.git"
-EGIT_BRANCH="master"
+CMAKE_MAKEFILE_GENERATOR="ninja"
 
-ACCE_IUSE="sse2 sse4_1 avx128fma avx256"
+inherit bash-completion-r1 cmake-utils cuda eutils multilib readme.gentoo toolchain-funcs
 
-#to find external blas/lapack
-CMAKE_MIN_VERSION="2.8.5-r2"
+if [[ $PV = *9999* ]]; then
+	EGIT_REPO_URI="git://git.gromacs.org/gromacs.git
+		https://gerrit.gromacs.org/gromacs.git
+		git://github.com/gromacs/gromacs.git
+		http://repo.or.cz/r/gromacs.git"
+	EGIT_BRANCH="master"
+	inherit git-2
+	LIVE_DEPEND="doc? (
+		dev-texlive/texlive-latex
+		dev-texlive/texlive-latexextra
+		media-gfx/imagemagick
+		sys-apps/coreutils
+	)"
+else
+	SRC_URI="ftp://ftp.gromacs.org/pub/${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
 
-inherit bash-completion-r1 cmake-utils eutils git-2 multilib toolchain-funcs
+ACCE_IUSE="sse2 sse4_1 avx128fma avx256"
 
 DESCRIPTION="The ultimate molecular dynamics simulation package"
 HOMEPAGE="http://www.gromacs.org/"
 
-LICENSE="GPL-2"
+# 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 ~ppc64 ~sparc ~x86 ~amd64-linux ~x86-linux"
-IUSE="X blas doc -double-precision +fftw gsl lapack mpi +single-precision  test
-+threads xml zsh-completion ${ACCE_IUSE}"
+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}"
 
 CDEPEND="
 	X? (
@@ -32,99 +51,121 @@ CDEPEND="
 		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 )
-	xml? ( dev-libs/libxml2:2 )"
+	"
 DEPEND="${CDEPEND}
-	virtual/pkgconfig"
+	virtual/pkgconfig
+	${LIVE_DEPEND}"
 RDEPEND="${CDEPEND}"
 
-RESTRICT="test"
-
-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
+REQUIRED_USE="
+	|| ( single-precision double-precision )
+	cuda? ( single-precision )
+	mkl? ( !blas !fftw !lapack )"
 
-	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 "$GMX_DIRS" ] && GMX_DIRS+=" float"
+DOCS=( AUTHORS README )
+HTML_DOCS=( "${ED}"/usr/share/gromacs/html/ )
 
-	for x in ${GMX_DIRS}; do
-		mkdir -p "${WORKDIR}/${P}_${x}" || die
-		use test && cp -r "${WORKDIR}"/gmxtest "${WORKDIR}/${P}_${x}"
-	done
+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_configure() {
-	local mycmakeargs_pre=( )
-	#from gromacs configure
-	if use fftw; then
-		mycmakeargs_pre+=("-DGMX_FFT_LIBRARY=fftw3")
+src_unpack() {
+	if [[ ${PV} != *9999 ]]; then
+		default
 	else
-		mycmakeargs_pre+=("-DGMX_FFT_LIBRARY=fftpack")
-		ewarn "WARNING: The built-in FFTPACK routines are slow."
-		ewarn "Are you sure you don\'t want to use FFTW?"
-		ewarn "It is free and much faster..."
+		git-2_src_unpack
+		if use doc; then
+			EGIT_REPO_URI="git://git.gromacs.org/manual.git" \
+			EGIT_BRANCH="release-4-6" EGIT_NOUNPACK="yes" EGIT_COMMIT="release-4-6" \
+			EGIT_SOURCEDIR="${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
+}
 
-	if [[ $(gcc-version) == "4.1" ]]; then
-		eerror "gcc 4.1 is not supported by gromacs"
-		eerror "please run test suite"
-		die
-	fi
+src_prepare() {
+	#notes/todos
+	# -on apple: there is framework support
 
-	#note for gentoo-PREFIX on apple: use --enable-apple-64bit
-
-	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
+	cmake-utils_src_prepare
+
+	use cuda && cuda_src_prepare
 
-	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."
+	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
 
-	#go from slowest to fasterest acceleration
+	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 threads GMX_THREADS)
-		$(cmake-utils_use xml GMX_XML)
+		$(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 ${GMX_DIRS}; do
@@ -132,17 +173,32 @@ src_configure() {
 		local suffix=""
 		#if we build single and double - double is suffixed
 		use double-precision && use single-precision && \
-			[ "${x}" = "double" ] && suffix="_d"
+			[[ ${x} = "double" ]] && suffix="_d"
 		local p
-		[ "${x}" = "double" ] && p="-DGMX_DOUBLE=ON" || p="-DGMX_DOUBLE=OFF"
+		[[ ${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_MPI=ON
+		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" cmake-utils_src_configure
+		BUILD_DIR="${WORKDIR}/${P}_${x}_mpi" CC="mpicc" cmake-utils_src_configure
 	done
 }
 
@@ -151,6 +207,11 @@ 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"\
@@ -160,11 +221,8 @@ src_compile() {
 
 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}"
+		BUILD_DIR="${WORKDIR}/${P}_${x}"\
+			cmake-utils_src_make check
 	done
 }
 
@@ -172,40 +230,38 @@ 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
-		#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}"
+			DESTDIR="${D}" cmake-utils_src_make install-mdrun
 	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*
-
+	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.*
-
-	# 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
-		dohtml -r "${ED}usr/share/gromacs/html/"
-		insinto /usr/share/gromacs
-		doins "admin/programs.txt"
-		ls -1 "${ED}"/usr/bin | sed -e '/_d$/d' > "${T}"/programs.list
-		doins "${T}"/programs.list
-	fi
-	rm -rf "${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
 }
 
 pkg_postinst() {
@@ -213,9 +269,11 @@ pkg_postinst() {
 	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
-	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"
+	readme.gentoo_print_elog
 }