version bump

Package-Manager: portage-2.2.18/cvs/Linux x86_64
Manifest-Sign-Key: 0xC2000586

3 files changed, 301 insertions, 9 deletions

diff --git a/sci-chemistry/gromacs/ChangeLog b/sci-chemistry/gromacs/ChangeLog
index 267f62afe60b..4e0f1e9623dd 100644
--- a/sci-chemistry/gromacs/ChangeLog
+++ b/sci-chemistry/gromacs/ChangeLog
@@ -1,6 +1,11 @@
 # ChangeLog for sci-chemistry/gromacs
 # Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2
-# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/gromacs/ChangeLog,v 1.157 2015/03/08 00:02:01 ottxor Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/gromacs/ChangeLog,v 1.158 2015/06/21 13:00:24 ottxor Exp $
+
+*gromacs-5.0.5 (21 Jun 2015)
+
+  21 Jun 2015; Christoph Junghans <ottxor@gentoo.org> +gromacs-5.0.5.ebuild:
+  version bump
 
   08 Mar 2015; Christoph Junghans <ottxor@gentoo.org> -gromacs-4.6.5.ebuild,
   -gromacs-4.6.7.ebuild, metadata.xml:
diff --git a/sci-chemistry/gromacs/Manifest b/sci-chemistry/gromacs/Manifest
index 49a2d16d63f1..737c8a84057d 100644
--- a/sci-chemistry/gromacs/Manifest
+++ b/sci-chemistry/gromacs/Manifest
@@ -2,19 +2,22 @@
 Hash: SHA256
 
 DIST gromacs-5.0.4.tar.gz 26342095 SHA256 78068eeccc0b950018ddb45c41280e53c8bedae4639dca48e17c940f8896b23b SHA512 bc62b623bf71dcaa948aaf7563a3d3afa973da0702062848a20323db202e862dcee413197dacd1472866ccb40fce7709e283177b1c6c49514064f23e6c46b5ee WHIRLPOOL d8458d3d563e015e830622ae0c924e896765a6329ffe4cb1a31c7aef3c804f392d29e3f1db5617051e85058403422f7d69a160a6c7cc810564696d88f9d50bd4
+DIST gromacs-5.0.5.tar.gz 26343524 SHA256 952c9d14879a12d03362b2233e47c51385dc99325bdde5223a2942938739bf4e SHA512 b45b2da5de48b0aa272b6d8583fd717762512fbd291ac35b414d23c430bf7b6db470f64e641728658e94784de9ddcde04242cfba09ff47931e01b85b8ca8fd73 WHIRLPOOL cc1f5f60d70780f8694acb16c96634d2aa8a16ff3d52be5ed4572dd37f80d9591f8060a0256f3e0f4a55069247398b8b52ad05efed691a0ab8619bc77aa64f76
 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
 EBUILD gromacs-5.0.4-r1.ebuild 8641 SHA256 a428cf1a36cd3685a13a3d16357d256111db6ef3ec736bc833b91b35992edc0b SHA512 1aa5f9fcf46a5f69371fe5d5155c5abfa48d3ed276a85089ac0f6a61be8f18724b5871eeb77705c5d14b01fc2574ce419406819248b0000aaa628b9570b1a831 WHIRLPOOL 99a1a0407303b0ba110cb3734eb60d9662ac62f91ba6d31072df0f671da34e8a4b0ac59450088bcdcbeb0c89b3274747d51c329ab6faa4c1eb3027a346867d36
 EBUILD gromacs-5.0.4.ebuild 8543 SHA256 60341fa094c189d6ddbee1652ec91c6db4da606d63801047eccb4bf2c364a244 SHA512 7ee97c242a6f4c0fee9e7bcb0f88b9df945385658afe716a4b8bea7c54da305a45b221428e4c771b17fa7668cd603e7566c91cc22139fe7be5aca55fd649045a WHIRLPOOL f4747b3dce00aa9b0fc5aae60644aa6e51907bbc4a91b99664ac144987eb76f0535f1acaa6b597a613ac1593f85d36a4c6a32bc03c38baa752433a26a91b1e41
-MISC ChangeLog 25133 SHA256 9018ecce8e021a090069b289160dd4e35313ca843eff7edc1453666438e2b469 SHA512 e4a50566496e00a5446d43265c975f5f5ff5c137ab17c1f9a9da50bd4a907f6fd5a3ede0e821c80c9b4776e62670e884147baf07fc5c6b43a75cc48e1d726fdd WHIRLPOOL 442a3efde3de2b333a0bfb3c045737a8bad19782646fcfad88e956cbcb862d32f058193dd7ff635d430ff7e80d6a30f47db2ade46fd5a8d338488c6d41bb6836
+EBUILD gromacs-5.0.5.ebuild 8640 SHA256 af33cd3374a809f9ad1f74eb97f1cbe63a4350be1777798e969b8a2f7884156d SHA512 28970404831b33399a3a519ecc00402a0e072e6107fd44414107f53b16f8f3cd333961f60d3218be1e042e2e7017fd6f5f6473643e5345b5bd4213d2d4810f25 WHIRLPOOL 4ffe4e34e93275d79d686cdd2ee1a3b46c863719eee54afe7be648e9d49fa2326af20cf27c0511f26e43ac99feb40afedfd893ee9433b8fceed33652cb1a9e60
+MISC ChangeLog 25256 SHA256 a87d84ef8f1aee45b1c290dc8a397b66edadfb776dc6a51fd987cf1bad27bf60 SHA512 f96383b995d7226a300bec9133cf8fc62531d35ae57a116981576a4f31abc19c3217574676b9408505eae0c872ae681dcfbfd7738cd909752329679d97264bc2 WHIRLPOOL 19c59358b0fa38ba9ab349b3875e59480100c692e54b899e5e49b60db6c267ea3fb15c4b48f36ab57611c0448d6b9816825aa3a5d44d6748e4fc7d88bc0ba0bc
 MISC metadata.xml 940 SHA256 b0f42bc2bd2b0f0ed49bb188721f0c3d6304d0bac088e2a9e0011daa540dbc5c SHA512 ca71cf1f7b6fe7f039dd590686efe9e51c6638db4aea29ea886ac39d36fd262e3f3bc93c92adb2def3b55af7c014e5d8bb69af508ea9caad0036cd34192d5da8 WHIRLPOOL 158a8aab918f8bb93893c01ecf910884818316a6d729ab899ed8b8f2315a2057987dbba04c876701ca5513502112d1b33e5573ea3628764a7f5edb4e7c963513
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diff --git a/sci-chemistry/gromacs/gromacs-5.0.5.ebuild b/sci-chemistry/gromacs/gromacs-5.0.5.ebuild
new file mode 100644
index 000000000000..dc4bd9ce5865
--- /dev/null
+++ b/sci-chemistry/gromacs/gromacs-5.0.5.ebuild
@@ -0,0 +1,284 @@
+# Copyright 1999-2015 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/gromacs/gromacs-5.0.5.ebuild,v 1.1 2015/06/21 13:00:24 ottxor Exp $
+
+EAPI=5
+
+CMAKE_MAKEFILE_GENERATOR="ninja"
+
+inherit bash-completion-r1 cmake-utils cuda eutils multilib readme.gentoo toolchain-funcs
+
+if [[ $PV = *9999* ]]; then
+	EGIT_REPO_URI="git://git.gromacs.org/gromacs.git
+		https://gerrit.gromacs.org/gromacs.git
+		git://github.com/gromacs/gromacs.git
+		http://repo.or.cz/r/gromacs.git"
+	EGIT_BRANCH="release-5-0"
+	inherit git-r3
+	KEYWORDS=""
+else
+	SRC_URI="ftp://ftp.gromacs.org/pub/${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 +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 [[ ${PV} != *9999 ]]; then
+		default
+	else
+		git-r3_src_unpack
+		if use test; then
+			EGIT_REPO_URI="git://git.gromacs.org/regressiontests.git" \
+			EGIT_BRANCH="master" EGIT_COMMIT="master" \
+			EGIT_CHECKOUT_DIR="${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)
+		$(cmake-utils_use make-symlinks GMX_SYMLINK_OLD_BINARY_NAMES)
+		-DGMX_DEFAULT_SUFFIX=off
+		-DGMX_SIMD="$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
+		[[ ${CHOST} != *-darwin* ]] || \
+		  sed -i '/SET(CMAKE_INSTALL_NAME_DIR/s/^/#/' "${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
+		# generate bash completion, not 100% necessary for
+		# rel ebuilds as bundled
+		BUILD_DIR="${WORKDIR}/${P}_${x}"\
+			cmake-utils_src_compile completion
+		# not 100% necessary for rel ebuilds as available from website
+		if use doc; then
+			BUILD_DIR="${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
+		#release ebuild does this automatically
+		if [[ $PV = *9999* ]]; then
+			cp "${WORKDIR}/${P}_${x}"/src/programs/completion/gmx-completion.bash "${ED}/usr/bin" || die
+			echo "complete -o nospace -F _gmx_compl gmx" > "${ED}/usr/bin/gmx-completion-gmx.bash" || die
+		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
+	#concatenate all gmx-completion*, starting with gmx-completion.bash (fct defs)
+	#little hacckery as some gmx-completion* newlines ,so cat won't work
+	for x in "${ED}"usr/bin/gmx-completion{,?*}.bash ; do
+		echo $(<${x})
+	done > "${T}"/gmx-bashcomp || die
+	newbashcomp "${T}"/gmx-bashcomp gmx
+	bashcomp_alias gmx mdrun
+	rm "${ED}"usr/bin/gmx-completion{,?*}.bash || die
+	if use double-precision && use single-precision; then
+		bashcomp_alias gmx gmx_d
+		bashcomp_alias gmx mdrun_d
+	fi
+	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
+}