gentoo resync : 21.01.2018

2 files changed, 275 insertions, 0 deletions

diff --git a/sci-chemistry/gromacs/Manifest b/sci-chemistry/gromacs/Manifest
index 1051ed59a63c..a366b73cb338 100644
--- a/sci-chemistry/gromacs/Manifest
+++ b/sci-chemistry/gromacs/Manifest
@@ -4,6 +4,7 @@ DIST gromacs-2016.3.tar.gz 27342692 BLAKE2B 3bea357cb672f41dda68c0d4291c06e2ab8b
 DIST gromacs-2016.4.tar.gz 27368706 BLAKE2B 2a176812fe2a097d72c7148ff5ed4ed7209279cf439af6a969c3aba81157c59a4d9af34d19c7b1da088b0a4ab981b489b84446afbcaf64b20724bda1dc3560ff SHA512 69661d2a7a8a5259be277de35e2baa4b688d1f7bef225fc7d733a9b00c6ee135dcbad517c7c9f751121647c2fbd085f2c9cdf22dbd941c7ebc5d3b09e7e08f1f
 DIST gromacs-2016.tar.gz 27321561 BLAKE2B cdcf0aa5ac36981e736fd2ecc2f641e99f40146d829c88e5ff973c7b7c3c1ab920f7822c336e9eea87a8605362e723d7477dd07f9154c8a38476a3f6c391d6aa SHA512 756771baaa85a1d16e7d5b8e4c96bbd1c04c7acdc536a253886cff186316330f06d60d206a0159efb15f47f161c779d3757dc5dbceab8c097241c1382d376201
 DIST gromacs-2018-rc1.tar.gz 29863602 BLAKE2B 1b8146198aef435d74c57b5a6e42b8107416896fed71444830baf4368604c1b35326a77815c5125e1610a9765cf1d5d51d3a69a04d3679f7c1f3618598258c0a SHA512 f2a56a2d3ce6efd170f22d66dbb9418ae59257aff27853037570d0939582df947c7558aa652626dd911ee22c037ab0cb1b340b5008bc8f40d27d90883100d375
+DIST gromacs-2018.tar.gz 29855797 BLAKE2B ff7bfd6a11d8d0fba2a0da405eb264504e18d820179eee234fd2c6e0d6a001aabd601c8a695e14b6d290fbca2253f3fc760a72c6fcaf566f88bb3675612f0bfb SHA512 95c464ec4a0c95b5e7b30571e9693f6be1bce4cd3d6f7d7eeee0f0cd9b8ad43dda4dbb8568e9502706a01d1621f288711227a935060ce524871e6521d53eb902
 DIST gromacs-5.0.4.tar.gz 26342095 BLAKE2B 27a2483e23533ad627114c0005fa0d49a311b359c31aed6378bdd768c9dda03c3b19f11d961f0bd3b82a1711737d4b7dce13cad5fc56d058dd0110fe21421ee3 SHA512 bc62b623bf71dcaa948aaf7563a3d3afa973da0702062848a20323db202e862dcee413197dacd1472866ccb40fce7709e283177b1c6c49514064f23e6c46b5ee
 DIST gromacs-5.1.3.tar.gz 27095702 BLAKE2B b7fd8fa10e8c4f4368ac551338c59374dc35f85c9fdae5d64eec62929b8f04ea724a084959b3618cd8a151bf3e0a0c84c8f75de953722effca82a4928941ce73 SHA512 9ab26e1b2268f8d567b89b2d99d0b75b937b28edceaec56d17ca3243c76faa31255ffc0c45d762c7c693fe500b00e36ad43b80572d1d7f92dc87f9d2d98c0ba6
 DIST regressiontests-2016.1.tar.gz 67094518 BLAKE2B 3ae0132e246f2abcf77495bff69adb32bfe98063a824cc408279fb43022ca5e8e07afaee08f3a255657b8cdfd21ba2ff4cc428c2c3d21958ba5149ce745d436c SHA512 fc01c802d81400373a147171881f3b7b9309402e8ffb08287ba393aefbb701ba93bbe0b9549ff6fa264a8befbba445c2d2c7450633063a724f78ec8ca81ae8c9
@@ -12,6 +13,7 @@ DIST regressiontests-2016.3.tar.gz 67093968 BLAKE2B a644bbd2a0398c1d84f61809a9f4
 DIST regressiontests-2016.4.tar.gz 67643648 BLAKE2B 767c3b0ca1002e6ca68fc3346b7164cca3beaa52f9b1c70672b64cf80427cab045e4d924d0b67a4fe4c76e3a1c0a803964e278d2a9b14b87a555f98dd78525d3 SHA512 367438b897a05e1cc0dcd1d3872fb6a0e9ff6b1146e9448d941d6517dce789f0c478d20cf0a4f3565070f132dc88872441aadb8b499f59efa0e1e4a6dd6a7135
 DIST regressiontests-2016.tar.gz 66908712 BLAKE2B 3039b5b46bf99dc2e34a61ed0f47f7355087c260bd1accc119f9ed99bb03c4645d05df41e301cfc6a6de6a9a369b2bf4e01a54852100577e40605e091bbe24e8 SHA512 59902c1973c33ea8f003f21a737dc7cc64da3258112322eedc9834b53628134a6817d5ee5b3950c9bfd97a3a0580aef88ddef0609ef2c58693c96c7575651e01
 DIST regressiontests-2018-rc1.tar.gz 67866295 BLAKE2B 1936a4a14d3011e426e0f057d803339a8324e10d087d56f93dc7a497250a973c6b19ed2691b4641d12b7f13de01dbe36a9903a4e10e3792b842319e42ad0331a SHA512 feccf48d6af84abf350e5ad829c600f86b8e8e4f4f3378c34b209daa30965e3f68751058f12bdbb228da6b4ccd0a72c8191956ec5bd184f190000a9c97e581a9
+DIST regressiontests-2018.tar.gz 67858633 BLAKE2B 21fe5ca9ad682873c616d6ac46e1408d646ab4620498bd63f94f2719354ea38e3b2ee81330629038e320229079802705393b049d9fbdd91612a54a043a98fbcd SHA512 95d4085bd7d60cd1a40dde25d7a770e549f17f69771a63eb55e95e5735b29ebe76dbfebd5452542fede984e9b3ce0339c166aeb9a42754d36be87b43b6d6b1ec
 DIST regressiontests-5.0.4.tar.gz 65193251 BLAKE2B c5e5f23adcc2639fe652bc252533307c7fda44453d506603242968bd8588c7394028b2c3c7a9252f807a050d40e8f78735e904dfe517d3db8ae962051f4826c1 SHA512 747725fa28c1c9525596bdeeb8809e45268e19036c11dac67d043aa1c51748688ca37eb6014eb7e819eb927a8b9ca2631d0ace4cdff8ed491b08c316c530ab65
 DIST regressiontests-5.1.3.tar.gz 66994083 BLAKE2B 7009f65ad0138664ac84e57f8bc7cce5d18a59f99943e56b6642583120bfce279e005ac0bacd2db8904ea477a48e2b938c64de46a65fa5d08fce6009d53583c3 SHA512 486e86eb3b75bae822abe82dac4e1098aa13723bd04214021f835a2f0b847303f015a9ececc33aa5ae63d31a2eeae07e512f22464b6c0e26d1286b0781578022
 EBUILD gromacs-2016.1.ebuild 7987 BLAKE2B 45d8b50b3ee54c8c701eb8c6533c1dc7d680eb0f5c40cdf1a75e81b59bd2d603b4235f6e4942e40211b748b7cf8239c90f8d613b20bdc44fca48d23f9c45ae14 SHA512 ce2b0d2730e87831a517468033cada7097ba431d8a60dcef77a04c9e05bf4cfacb6eb500a5196e378f4c69e5020f8e9f871eac6e61dd2776834aee006ecb167f
@@ -21,6 +23,7 @@ EBUILD gromacs-2016.4.ebuild 7987 BLAKE2B 45d8b50b3ee54c8c701eb8c6533c1dc7d680eb
 EBUILD gromacs-2016.9999.ebuild 7987 BLAKE2B 45d8b50b3ee54c8c701eb8c6533c1dc7d680eb0f5c40cdf1a75e81b59bd2d603b4235f6e4942e40211b748b7cf8239c90f8d613b20bdc44fca48d23f9c45ae14 SHA512 ce2b0d2730e87831a517468033cada7097ba431d8a60dcef77a04c9e05bf4cfacb6eb500a5196e378f4c69e5020f8e9f871eac6e61dd2776834aee006ecb167f
 EBUILD gromacs-2016.ebuild 7968 BLAKE2B c0ba44661dce5ccda3c2378fad57e88ca90d15cb1914d6214ee4559e8ebd6c6c700624b32abf168a4a653cc5794fac9fab71024a9b7bc5464d404d768ac74ef1 SHA512 3ca5d4ae9b01a106b279bc828e42366a017b9517a450b773b944c6d12dce64199e3a80d280e4c475c637c70009a1a0fd1ca74f99b03f08067a10d9e9ad450d8f
 EBUILD gromacs-2018.9999.ebuild 7899 BLAKE2B 8053de4c12e2201d37e8d0a077d33fc0b103b79d73379488c46bc638ba763b55ebf69ae53180ffd850e4b860fc03a1c3ec57049f1b257e04e0322ed482afcd51 SHA512 734710474160c6a55206b332e5370bd9e2d0092aed19c4c1ccab7f5d9567eac2a47d163a50aa607f8c7e8e2ccc6eadeb9b394e9f638ac85eafe5f74ced68fd02
+EBUILD gromacs-2018.ebuild 7899 BLAKE2B f70665f54e2103275dbf7466d15c15ce41593264bb768b542a49eebd76b1764871ac9b82e9eacee5db1a413cac8863a6e87d751cdb2196ff5a431a096c7f6f3f SHA512 3cb7bab30e822420e308b15af997f01ab3ce3072ddefc752d5f0d314040f699febcd804d983cf9af160d1388b38a62e81c9ee6fc7a6647a5d7e199262b3afec9
 EBUILD gromacs-2018_rc1.ebuild 7899 BLAKE2B 8053de4c12e2201d37e8d0a077d33fc0b103b79d73379488c46bc638ba763b55ebf69ae53180ffd850e4b860fc03a1c3ec57049f1b257e04e0322ed482afcd51 SHA512 734710474160c6a55206b332e5370bd9e2d0092aed19c4c1ccab7f5d9567eac2a47d163a50aa607f8c7e8e2ccc6eadeb9b394e9f638ac85eafe5f74ced68fd02
 EBUILD gromacs-4.6.9999.ebuild 8110 BLAKE2B dd8ac9cbc4abfcc75a3a188c59cdbe5111f363404ff5a787f64b05d4bd411deebb50f172f09963800ed87997788b2e678617805e65a523bed19aa6ef18fe2b96 SHA512 2206e257f0b29b6f3a90c5d7739079b9add3e04f2a3acbd58c814811b389b5d51b3594815a94529d1de43deb380504029c302d18fc16d63a81c92727254e863e
 EBUILD gromacs-5.0.4.ebuild 8429 BLAKE2B c06c423365fa79befd5a4f0b6314e77b96d983c84df776ce84fddc79d35ce735d856d1184e5913af0c8cd3a0c4e9087110af9bd4402e2bce1f014e64a8a585a7 SHA512 d1e91cc25c5f90bd0fbad15060cae9c8bf1235ca45a2b72521b3a4f5f091bdd7d32ec2e6ff2bb22cd3fe165092f11a24ea148ae8000b8517f0b8671f6c2af6f2
diff --git a/sci-chemistry/gromacs/gromacs-2018.ebuild b/sci-chemistry/gromacs/gromacs-2018.ebuild
new file mode 100644
index 000000000000..11f2b2483a38
--- /dev/null
+++ b/sci-chemistry/gromacs/gromacs-2018.ebuild
@@ -0,0 +1,272 @@
+# Copyright 1999-2018 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=6
+
+CMAKE_MAKEFILE_GENERATOR="ninja"
+
+inherit bash-completion-r1 cmake-utils cuda eutils multilib readme.gentoo-r1 toolchain-funcs xdg-utils
+
+if [[ $PV = *9999* ]]; then
+	EGIT_REPO_URI="git://git.gromacs.org/gromacs.git
+		https://gerrit.gromacs.org/gromacs.git
+		https://github.com/gromacs/gromacs.git
+		http://repo.or.cz/r/gromacs.git"
+	[[ $PV = 9999 ]] && EGIT_BRANCH="master" || EGIT_BRANCH="release-${PV:0:4}"
+	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 cuda +doc -double-precision +fftw +hwloc lapack mkl mpi +offensive opencl openmp +single-precision test +threads +tng ${ACCE_IUSE}"
+
+CDEPEND="
+	X? (
+		x11-libs/libX11
+		x11-libs/libSM
+		x11-libs/libICE
+		)
+	blas? ( virtual/blas )
+	cuda? ( >=dev-util/nvidia-cuda-toolkit-4.2.9-r1 )
+	opencl? ( virtual/opencl )
+	fftw? ( sci-libs/fftw:3.0 )
+	hwloc? ( sys-apps/hwloc )
+	lapack? ( virtual/lapack )
+	mkl? ( sci-libs/mkl )
+	mpi? ( virtual/mpi )
+	"
+DEPEND="${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 )
+	cuda? ( !opencl )
+	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
+
+	xdg_environment_reset #591952
+
+	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+=(
+		"${fft_opts[@]}"
+		-DGMX_X11=$(usex X)
+		-DGMX_EXTERNAL_BLAS=$(usex blas)
+		-DGMX_EXTERNAL_LAPACK=$(usex lapack)
+		-DGMX_OPENMP=$(usex openmp)
+		-DGMX_COOL_QUOTES=$(usex offensive)
+		-DGMX_USE_TNG=$(usex tng)
+		-DGMX_BUILD_MANUAL=$(usex doc)
+		-DGMX_HWLOC=$(usex hwloc)
+		-DGMX_DEFAULT_SUFFIX=off
+		-DGMX_SIMD="$acce"
+		-DGMX_LIB_INSTALL_DIR="$(get_libdir)"
+		-DGMX_VMD_PLUGIN_PATH="${EPREFIX}/usr/$(get_libdir)/vmd/plugins/*/molfile/"
+		-DBUILD_TESTING=$(usex test)
+		-DGMX_BUILD_UNITTESTS=$(usex test)
+		${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" )
+		local opencl=( "-DGMX_USE_OPENCL=OFF" )
+		use opencl && opencl=( "-DGMX_USE_OPENCL=ON" ) cuda=( "-DGMX_GPU=ON" )
+		mycmakeargs=(
+			${mycmakeargs_pre[@]} ${p}
+			-DGMX_MPI=OFF
+			-DGMX_THREAD_MPI=$(usex threads)
+			"${opencl[@]}"
+			"${cuda[@]}"
+			"$(use test && echo -DREGRESSIONTEST_PATH="${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  "https://dx.doi.org/10.1021/ct700301q"
+	einfo
+	readme.gentoo_print_elog
+}