sci-chemistry/gromacs: Version bump

Package-Manager: portage-2.3.0

2 files changed, 271 insertions, 0 deletions

diff --git a/sci-chemistry/gromacs/Manifest b/sci-chemistry/gromacs/Manifest
index 745e8aac96da..350f1c87f94a 100644
--- a/sci-chemistry/gromacs/Manifest
+++ b/sci-chemistry/gromacs/Manifest
@@ -3,10 +3,12 @@ DIST gromacs-5.0.5.tar.gz 26343524 SHA256 952c9d14879a12d03362b2233e47c51385dc99
 DIST gromacs-5.0.6.tar.gz 26351063 SHA256 e07e950c4cd6cb84b83b145b70a15c25338ad6a7d7d1a0a83cdbd51cad954952 SHA512 5bd11d2ab79cc94c1ecf10bb05c239f7a4aed426ba3da0e536076e5145ff854889f9f0808d87a8ce007d86fce8eff9b6a809ae5fb68478528ea405c335dbffb2 WHIRLPOOL e5898fa247016a4c52e7ddc77ba03f0d39df2b863607a79f4b88f7029a2467e22cd84a507c18b52b4015619341699bbede28939be485613ac145b499a7d0998d
 DIST gromacs-5.0.7.tar.gz 26358119 SHA256 23bc5ae28e0e274965966f0a00e44ec6ffbc28c5cd2d6b64a0aa0a2bc59472ec SHA512 612dba608fe6fd3a6fd69d1edeb97ec2975361ab44ea5219990901cecafbbe542a2c8bc6acc3f89b7fdcda77ab1b0762977ddc48cc1523155f7033e4e000660f WHIRLPOOL 26292f8751c2238f4fd9a63cb64888c2d236237dc140f08b45997b87b917b096d3d7c8451e5e0633e71cd770d7e7336dbbd3056777e290d0232a902ee4018e4b
 DIST gromacs-5.1.1.tar.gz 26551710 SHA256 9316fd0be320e2dd8c048f905df5be115e1b230c4ca4f3a7ef5892a1fc0bc212 SHA512 52404b4134cfbc867553a6b3f968500e3fc85b103abef6a7de9d0a9bf53c12ad1b908c35f9eed9376965db4a250c87cffe44d8c67247512c04ee84e7d1e07074 WHIRLPOOL 7a82e2cf6a73d4083ed4f1105dee4e392eaeb7e60e97a054a15e6a505e8a124d396005912b6c40acda53608cdd19ef2422c37b182733b4fe412e74defd7489b2
+DIST gromacs-5.1.2.tar.gz 26562718 SHA256 39d6f1d7ae8ba38cea6089da40676bfa4049a49903d21551abc030992a58f304 SHA512 ddd29bba97eaf8c32f7f5daa441c1aac85222881a9cf7757f55ef7f1a15f8f45cdc600eb90059053205d71652281c85601e107ff5928425afdb0c13e8ef1de69 WHIRLPOOL 12f217e480bd04cd0cfb68c22345cfe2cd77f9417f0f873ff61aeea734aa33d61810db4e1539cd265f1ffcf2df123353592c6176aa8dce236b64de74a97a76e0
 DIST gromacs-5.1.tar.gz 26546875 SHA256 996b6061971e11942252de36b67b5cf35f02ce14adf80db8a3f079fc686c2743 SHA512 9655bd387773fa3ab0b7316854552a63945255ef02c5d9d1f98b32213b6642532b6bed88b06354d46d0ed235d6dc39e57a987a6585fb463e5aba80f366268301 WHIRLPOOL e5b4e90897c82a016911291f14daef41aa846143eae1cf5e6b9d552afe9ecbd3663d7df6350f5edd4778fa3a479c18b22efcabd9d49e1f4c304a3d39e35eaac4
 DIST regressiontests-5.0.4.tar.gz 65193251 SHA256 89ad9bc067035ac8f340319b538c446983d937b910067e871911d7afe2ecb3f0 SHA512 747725fa28c1c9525596bdeeb8809e45268e19036c11dac67d043aa1c51748688ca37eb6014eb7e819eb927a8b9ca2631d0ace4cdff8ed491b08c316c530ab65 WHIRLPOOL e15ccab0a0beefac41aeff11e2e596e971167f1590eed159ff82c4a8e3aec1d234287be597026951904ecfe6099f30ef3bcd48f2098b9f5201bde62e15fbc4f9
 DIST regressiontests-5.0.5.tar.gz 65204335 SHA256 e48b9934de89c23a63c9adc8ba9a5aa397cf5a4d1746165d833c556d5ce54833 SHA512 1a1d1a3398ba5d3cc9f68e0f401437ccbdf3265f3ea1100b3b0d314d61ccd467ce3e8492ee09a645c5aaf9c1ca0acdf5ed6213a61bbd689833f3ca002bd5c79b WHIRLPOOL 882c9d8fa45720a5a71811db898aa33b9323bfe60340e8c4f4e2ef537f02efb531c0f3a721ead0e98bdb96f1e9d71df24d1d0faae448ab3da096c694e2a9b593
 DIST regressiontests-5.0.6.tar.gz 65203643 SHA256 fd0a2408250dfc088ac9b401bc8702b8ba398a81db56c214d55f68f838d7c079 SHA512 dec41fbaa93784fb6438887eeef9f523add06032ae9801b83c492f5924872cd9b6a17e07d61cd7d8f999193d46384112e4c8046f4b2a3c28eb0c08f11c1ad8c6 WHIRLPOOL e6a8e99abc3b59be0f246769de0ebdef528caa24b930999dfbe0167a58696a68a31d0b819d2503e312977f0ec4d1ee2acb60e8eb691fab45e608250f2dfde728
 DIST regressiontests-5.0.7.tar.gz 65204051 SHA256 831c5f52b941826842a5312e3c6cd74a6410938bc5876d3f32d53215d64fb084 SHA512 2e93c84f62772eaf6facd45db67f51f751b4fa80923c71bc4fb293b33361b1314d714020bd8d50a1d0859aeedd67ce76f593e82ef31372128cbb8555eb6446b1 WHIRLPOOL b050f80946a76e752d53ccadd378ec0869f3221706a29f87d262a46fb11941b600d27b5388a5311a4fde53d60560f907150f884212e2d49a3df4b2519d1ceb3e
 DIST regressiontests-5.1.1.tar.gz 66711961 SHA256 2d51c57c6d584c4a6637b4b546eaf4b1f1713df10fe694544a82cc208a88cd78 SHA512 df865f0c900d52463cecc5482fee1c76d0c6a7f2dcb6ec657e03d1acf5ef8c60292781e6bbd43b9ebf2aab5a91782f474cef122ef118043c47eb3579656f75a6 WHIRLPOOL dd0b16ffdbd2e6eab141d327ed8922b3f038c80d414823c8d9f2e5e52cb5b820b177ec9f7a07dd794a29371eaa287a602bbd1bde9c9e895abd30c8da14f14226
+DIST regressiontests-5.1.2.tar.gz 66704132 SHA256 3e4704308da282e2e8e2550f6acae029353bf42ede4b1eccb20b157e399f3cf7 SHA512 b53fb36d5ce00361998ca9eb2121efc0d616e628ad81bf08c7fdc2cc43929cbc2e528cdd8260036235960ad96363b496aadd345d55fc100cdf02d680b2cca996 WHIRLPOOL 0859db2e0e51d56752f17d6021c2e5f6a6b820236aff731dd18335b3bde94899985c96bbe98f62c9144d8ff88fcc7e6f3091cf78618d7734345cfe71f0f6a026
 DIST regressiontests-5.1.tar.gz 66707378 SHA256 c2d751a503d5e19962198f565edb29ea2aa67f863dce02e93b82b08a02487eca SHA512 1896f967362a1a3ae1ff13b405f4633754f97ad366c01b4b3b52368a01dae70e3b71cb171bba05c7d566fe8c3c4fcf8ce6538a6ff130143606fa2302b2e714c3 WHIRLPOOL 95b77a324a26ddc97f215ab7abc60a4d72f4fe39eaa43d14431d42d70875de71bcc9a8af90cceb4deaacead7c98e744b5200f867fb3c14bd6f2c1ff725825b8b
diff --git a/sci-chemistry/gromacs/gromacs-5.1.2.ebuild b/sci-chemistry/gromacs/gromacs-5.1.2.ebuild
new file mode 100644
index 000000000000..4fb8aae932fd
--- /dev/null
+++ b/sci-chemistry/gromacs/gromacs-5.1.2.ebuild
@@ -0,0 +1,269 @@
+# Copyright 1999-2016 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI=6
+
+CMAKE_MAKEFILE_GENERATOR="ninja"
+
+inherit bash-completion-r1 cmake-utils cuda eutils multilib readme.gentoo-r1 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"
+	[[ $PV = 9999 ]] && EGIT_BRANCH="master" || EGIT_BRANCH="release-${PV:0:1}-${PV:2:1}"
+	inherit git-r3
+	KEYWORDS=""
+else
+	SRC_URI="ftp://ftp.gromacs.org/pub/${PN}/${PN}-${PV/_/-}.tar.gz
+		test? ( http://gerrit.gromacs.org/download/regressiontests-${PV}.tar.gz )"
+	KEYWORDS="~alpha ~amd64 ~arm ~ppc64 ~sparc ~x86 ~amd64-linux ~x86-linux ~x64-macos ~x86-macos"
+fi
+
+ACCE_IUSE="cpu_flags_x86_sse2 cpu_flags_x86_sse4_1 cpu_flags_x86_fma4 cpu_flags_x86_avx cpu_flags_x86_avx2"
+
+DESCRIPTION="The ultimate molecular dynamics simulation package"
+HOMEPAGE="http://www.gromacs.org/"
+
+# see COPYING for details
+# http://repo.or.cz/w/gromacs.git/blob/HEAD:/COPYING
+#        base,    vmd plugins, fftpack from numpy,  blas/lapck from netlib,        memtestG80 library,  mpi_thread lib
+LICENSE="LGPL-2.1 UoI-NCSA !mkl? ( !fftw? ( BSD ) !blas? ( BSD ) !lapack? ( BSD ) ) cuda? ( LGPL-3 ) threads? ( BSD )"
+SLOT="0/${PV}"
+IUSE="X blas boost cuda +doc -double-precision +fftw lapack 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 [[ ${PV} != *9999 ]]; then
+		default
+	else
+		git-r3_src_unpack
+		if use test; then
+			EGIT_REPO_URI="git://git.gromacs.org/regressiontests.git" \
+			EGIT_BRANCH="${EGIT_BRANCH}" \
+			EGIT_CHECKOUT_DIR="${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 cpu_flags_x86_sse2 && acce="SSE2"
+	use cpu_flags_x86_sse4_1 && acce="SSE4.1"
+	use cpu_flags_x86_fma4 && acce="AVX_128_FMA"
+	use cpu_flags_x86_avx && acce="AVX_256"
+	use cpu_flags_x86_avx2 && acce="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)
+		$(cmake-utils_use doc GMX_BUILD_MANUAL)
+		-DGMX_DEFAULT_SUFFIX=off
+		-DGMX_SIMD="$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
+		[[ ${CHOST} != *-darwin* ]] || \
+		  sed -i '/SET(CMAKE_INSTALL_NAME_DIR/s/^/#/' "${WORKDIR}/${P}_${x}/gentoo_rules.cmake" || die
+		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
+		[[ ${CHOST} != *-darwin* ]] || \
+		  sed -i '/SET(CMAKE_INSTALL_NAME_DIR/s/^/#/' "${WORKDIR}/${P}_${x}_mpi/gentoo_rules.cmake" || die
+	done
+}
+
+src_compile() {
+	for x in ${GMX_DIRS}; do
+		einfo "Compiling for ${x} precision"
+		BUILD_DIR="${WORKDIR}/${P}_${x}"\
+			cmake-utils_src_compile
+		# not 100% necessary for rel ebuilds as available from website
+		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}_${x}"/docs/manual/gromacs.pdf "${PN}-manual-${PV}.pdf"
+		fi
+		use mpi || continue
+		BUILD_DIR="${WORKDIR}/${P}_${x}_mpi" \
+			cmake-utils_src_install
+	done
+
+	if use tng; then
+		insinto /usr/include/tng
+		doins src/external/tng_io/include/tng/*h
+	fi
+	# drop unneeded stuff
+	rm "${ED}"usr/bin/GMXRC* || die
+	for x in "${ED}"usr/bin/gmx-completion-*.bash ; do
+		local n=${x##*/gmx-completion-}
+		n="${n%.bash}"
+		cat "${ED}"usr/bin/gmx-completion.bash "$x" > "${T}/${n}" || die
+		newbashcomp "${T}"/"${n}" "${n}"
+	done
+	rm "${ED}"usr/bin/gmx-completion*.bash || die
+	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
+}