[gentoo-commits] gentoo-x86 commit in sci-chemistry/gromacs: metadata.xml gromacs-5.0.ebuild ChangeLog

[Alexey Shvetsov (alexxy)]

alexxy      14/06/30 03:24:05

  Modified:             metadata.xml ChangeLog
  Added:                gromacs-5.0.ebuild
  Log:
  [sci-chemistry/gromacs] GROMACS 5.0 finaly relesed
  
  (Portage version: 2.2.10/cvs/Linux x86_64, signed Manifest commit with key F82F92E6)

Revision  Changes    Path
1.20                 sci-chemistry/gromacs/metadata.xml

file : http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-chemistry/gromacs/metadata.xml?rev=1.20&view=markup
plain: http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-chemistry/gromacs/metadata.xml?rev=1.20&content-type=text/plain
diff : http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-chemistry/gromacs/metadata.xml?r1=1.19&r2=1.20

Index: metadata.xml
===================================================================
RCS file: /var/cvsroot/gentoo-x86/sci-chemistry/gromacs/metadata.xml,v
retrieving revision 1.19
retrieving revision 1.20
diff -u -r1.19 -r1.20
--- metadata.xml	31 Dec 2013 23:35:05 -0000	1.19
+++ metadata.xml	30 Jun 2014 03:24:04 -0000	1.20
@@ -1,21 +1,27 @@
 <?xml version="1.0" encoding="UTF-8"?>
 <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
 <pkgmetadata>
-	<herd>sci-chemistry</herd>
-	<maintainer>
-		<email>ottxor@g.o</email>
-		<name>Christoph Junghans</name>
-	</maintainer>
-	<use>
-		<flag name="cuda">Enable cuda non-bonded kernels</flag>
-		<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="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>
-		<flag name="offensive">Enable gromacs partly offensive quotes</flag>
-		<flag name="openmm">Add acceleration through <pkg>sci-libs/openmm</pkg></flag>
-		<flag name="mkl">Use <pkg>sci-libs/mkl</pkg> for fft, blas, lapack routines</flag>
-	</use>
+  <herd>sci-chemistry</herd>
+  <maintainer>
+    <email>ottxor@g.o</email>
+    <name>Christoph Junghans</name>
+  </maintainer>
+  <use>
+    <flag name="cuda">Enable cuda non-bonded kernels</flag>
+    <flag name="double-precision">More precise calculations at the expense of speed</flag>
+	<flag name="single-precision">Single precision version of gromacs (default)</flag>
+	<flag name="boost">Enable external boost library</flag>
+	<flag name="tng">Enable new trajectory format - tng</flag>
+	<flag name="make-symlinks">Create symbolic links for pre-5.0 binary names</flag>
+    <!-- acceleration optimization flags -->
+    <flag name="sse4_1">Enable sse4.1 acceleration</flag>
+	<flag name="avx128fma">Enable 128bit avx with fma (e.g. AMD BullDozer)</flag>
+	<flag name="avx_128_fma">Enable 128bit avx with fma (e.g. AMD BullDozer)</flag>
+	<flag name="avx256">Enable 256bit avx (e.g. Intel Sandy Bridge)</flag>
+	<flag name="avx_256">Enable 256bit avx (e.g. Intel Sandy Bridge)</flag>
+	<flag name="avx2_256">Enable 256bit avx2 (e.g. Intel Haswell)</flag>
+    <flag name="offensive">Enable gromacs partly offensive quotes</flag>
+    <flag name="openmm">Add acceleration through <pkg>sci-libs/openmm</pkg></flag>
+    <flag name="mkl">Use <pkg>sci-libs/mkl</pkg> for fft, blas, lapack routines</flag>
+  </use>
 </pkgmetadata>



1.140                sci-chemistry/gromacs/ChangeLog

file : http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-chemistry/gromacs/ChangeLog?rev=1.140&view=markup
plain: http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-chemistry/gromacs/ChangeLog?rev=1.140&content-type=text/plain
diff : http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-chemistry/gromacs/ChangeLog?r1=1.139&r2=1.140

Index: ChangeLog
===================================================================
RCS file: /var/cvsroot/gentoo-x86/sci-chemistry/gromacs/ChangeLog,v
retrieving revision 1.139
retrieving revision 1.140
diff -u -r1.139 -r1.140
--- ChangeLog	26 Mar 2014 21:42:49 -0000	1.139
+++ ChangeLog	30 Jun 2014 03:24:04 -0000	1.140
@@ -1,6 +1,12 @@
 # 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 1.139 2014/03/26 21:42:49 maekke Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/gromacs/ChangeLog,v 1.140 2014/06/30 03:24:04 alexxy Exp $
+
+*gromacs-5.0 (30 Jun 2014)
+
+  30 Jun 2014; Alexey Shvetsov <alexxy@g.o> +gromacs-5.0.ebuild,
+  metadata.xml:
+  [sci-chemistry/gromacs] GROMACS 5.0 finaly relesed
 
   26 Mar 2014; Markus Meier <maekke@g.o> gromacs-4.6.5.ebuild:
   arm stable, bug #496632



1.1                  sci-chemistry/gromacs/gromacs-5.0.ebuild

file : http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-chemistry/gromacs/gromacs-5.0.ebuild?rev=1.1&view=markup
plain: http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-chemistry/gromacs/gromacs-5.0.ebuild?rev=1.1&content-type=text/plain

Index: gromacs-5.0.ebuild
===================================================================
# 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.ebuild,v 1.1 2014/06/30 03:24:04 alexxy Exp $

EAPI=5

TEST_PV="5.0"

CMAKE_MAKEFILE_GENERATOR="ninja"

inherit bash-completion-r1 cmake-utils cuda eutils multilib readme.gentoo toolchain-funcs

if [[ $PV = *9999* ]]; then
	EGIT_REPO_URI="git://git.gromacs.org/gromacs.git
		https://gerrit.gromacs.org/gromacs.git
		git://github.com/gromacs/gromacs.git
		http://repo.or.cz/r/gromacs.git"
	EGIT_BRANCH="release-5-0"
	inherit git-r3
else
	SRC_URI="ftp://ftp.gromacs.org/pub/${PN}/${PN}-${PV/_/-}.tar.gz
		test? ( http://gerrit.gromacs.org/download/regressiontests-${TEST_PV}.tar.gz )"
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}"
KEYWORDS="~alpha ~amd64 ~arm ~ppc64 ~sparc ~x86 ~amd64-linux ~x86-linux ~x86-macos"
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 [[ ${PV} != *9999 ]]; then
		default
	else
		git-r3_src_unpack
		if use test; then
			EGIT_REPO_URI="git://git.gromacs.org/regressiontests.git" \
			EGIT_BRANCH="master" EGIT_NOUNPACK="yes" EGIT_COMMIT="master" \
			EGIT_SOURCEDIR="${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
		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
	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}_${x}"/manual/gromacs.pdf "${PN}-manual-${PV}.pdf"
		fi
		newbashcomp "${WORKDIR}/${P}_${x}"/src/programs/completion/gmx-completion.bash gromacs
		use mpi || continue
		BUILD_DIR="${WORKDIR}/${P}_${x}_mpi" \
			cmake-utils_src_install
	done
	# drop unneeded stuff
	rm -f "${ED}"usr/bin/gmx-completion*
	rm -f "${ED}"usr/bin/g_options*
	rm -f "${ED}"usr/bin/GMXRC*
	rm -f "${ED}"usr/$(get_libdir)/libtng*.a

	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
}