Install missing header

Package-Manager: portage-2.2.18/cvs/Linux x86_64
Manifest-Sign-Key: 0xB9D4F231BD1558AB!

diff --git a/sci-chemistry/gromacs/ChangeLog b/sci-chemistry/gromacs/ChangeLog
index f427475736e96766712c2c7f80a58143ef454f2f..c415376982ed12e3d6c1c42f850b0f1a88b7b349 100644 (file)
--- a/sci-chemistry/gromacs/ChangeLog
+++ b/sci-chemistry/gromacs/ChangeLog
@@ -1,6 +1,12 @@
 # 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 1.155 2015/02/26 19:04:02 maekke Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/gromacs/ChangeLog,v 1.156 2015/03/06 09:42:31 jlec Exp $
+
+*gromacs-5.0.4-r1 (06 Mar 2015)
+
+  06 Mar 2015; Justin Lecher <jlec@gentoo.org> +gromacs-5.0.4-r1.ebuild,
+  metadata.xml:
+  Install missing header
 
   26 Feb 2015; Markus Meier <maekke@gentoo.org> gromacs-5.0.4.ebuild:
   arm stable, bug #538370

diff --git a/sci-chemistry/gromacs/Manifest b/sci-chemistry/gromacs/Manifest
index 013d3aa1fa74396956e2f98c799613b6931b2e22..1cd2ec0a3175fd0cc45aa3dfa4944802f3e7d535 100644 (file)
--- a/sci-chemistry/gromacs/Manifest
+++ b/sci-chemistry/gromacs/Manifest
@@ -1,5 +1,5 @@
 -----BEGIN PGP SIGNED MESSAGE-----
-Hash: SHA256
+Hash: SHA512
 
 DIST gromacs-4.6.5.tar.gz 10991576 SHA256 a7242f315963a111e87fd28795696b1e818ac97479788356c4f73a04e9cdef09 SHA512 6ebb3ef74cf9ef2a749bdad6ce7c2deca607ef3b04cab3ce0be25ac1e7c69b3716761a66b5214642b82a96571e488d8a7bffda651840e56d95c14ba099cc1e0c WHIRLPOOL e639f0d1256173dafe8ba1231d46596f23a29b5ab97883600673b078e2927492dd473834398cd9fd864eb3d529ef853c2592d0b2c5ebb18ebb25ca171568aa72
 DIST gromacs-4.6.7.tar.gz 11031209 SHA256 6afb1837e363192043de34b188ca3cf83db6bd189601f2001a1fc5b0b2a214d9 SHA512 8472aa06e2050b469dac4c3a0b039014fa45055cdc550226605d90abec6956830ad2a1b634d10529fbf2e55e686a497e689dd165333bef7fe89b193227fa98e5 WHIRLPOOL 221b3d4e5ce6505edb5badc0e14391e6861cb7efad108b8b6eeaed435df6df15bc3580e52f18007c98e987b02a7d003381400d8adca246dc47c680954dcfe25a
@@ -11,13 +11,26 @@ DIST regressiontests-4.6.7.tar.gz 44036109 SHA256 afe433fb40860392970851d9c317e6
 DIST regressiontests-5.0.4.tar.gz 65193251 SHA256 89ad9bc067035ac8f340319b538c446983d937b910067e871911d7afe2ecb3f0 SHA512 747725fa28c1c9525596bdeeb8809e45268e19036c11dac67d043aa1c51748688ca37eb6014eb7e819eb927a8b9ca2631d0ace4cdff8ed491b08c316c530ab65 WHIRLPOOL e15ccab0a0beefac41aeff11e2e596e971167f1590eed159ff82c4a8e3aec1d234287be597026951904ecfe6099f30ef3bcd48f2098b9f5201bde62e15fbc4f9
 EBUILD gromacs-4.6.5.ebuild 9100 SHA256 628ea5b483e04eeb8bf537688010753d14db95ddbf606e13bbc14671a108a76e SHA512 3b08dd9ee120ac90ef665646a4f0711aa7da853e3e18b5e06775a5b0cedad892c2fe2786ebf86212bd8b2c5dbce0a2c68fbed00491d2ac8b73f0a996546ad54b WHIRLPOOL 8816588c2c09b72c864f1913318391e8150ca105209f279a5cdc770ad03fadebdfbf86101e2dfb6a6b0a8837a6ae0b86b0c7d6afcf331d3555f3de44d23bcea2
 EBUILD gromacs-4.6.7.ebuild 9168 SHA256 d3b867e887b205912a8456163301c81e7dc3a712a7c4408a97c783d8d0aa86f3 SHA512 367b93a3f34bb64beb63d7cad8d09a22306315b6db185af87df28f1f99e6cdb05d6d7c96a03d572784cca1452461e4f8c798556b125bb3ddf51ee3158c753134 WHIRLPOOL c67e62f3d9c113b8a97310d40c4780ad6818164a42525f56cf5dfeea92616c8007218668b9fc20601c57fff0a1bb2025754f29a116f863e3413ceb5df8bff8c9
+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 24855 SHA256 faf41f7085bca569cf09d647f85587de3630ea8d864cd482edea38594191c215 SHA512 19e544357b5dc57ad6e55005667ed34afcd4c584f77fc786dc18926d8dcdffbad595b919450a8da54939eb71bd43b725053617ed512f23283880275d76d03f5b WHIRLPOOL 8d661dab0bb6fa1855dd95f0adec0a4c123a36de01380e54295b923ac94b0a34749504297907b049ded64541cbeaae222f31d09cdae78134970dc047cfb16338
-MISC metadata.xml 1011 SHA256 8633825abc15609e9eb9fffe9f0f52a373caf14b0c42260b6c60c3ab98cc2d87 SHA512 39fee165790042b503413d56475a9c732e2f43039774bdacf38a4a75e469f64a4fc584e78bbb5bf248191c8d9fe7ce94f02ebb4a60c94719f77cd1d795758dfa WHIRLPOOL e81831950496b723955b6e2b11384786ef0a4a5c33172c1a6826af84af0b3203d66e5c0a270969d413bc464e9adaac3eb600f94c2b8d2225f95f2773f4cf0d3a
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diff --git a/sci-chemistry/gromacs/gromacs-5.0.4-r1.ebuild b/sci-chemistry/gromacs/gromacs-5.0.4-r1.ebuild
new file mode 100644 (file)
index 0000000..030d75c
--- /dev/null
+++ b/sci-chemistry/gromacs/gromacs-5.0.4-r1.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-5.0.4-r1.ebuild,v 1.1 2015/03/06 09:42:31 jlec 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
+}

diff --git a/sci-chemistry/gromacs/metadata.xml b/sci-chemistry/gromacs/metadata.xml
index 8a5c7453f0ad4298c974b8015c6920b5455592dc..264aca065256a2fb9120936471390ab3aa5d5bab 100644 (file)
--- a/sci-chemistry/gromacs/metadata.xml
+++ b/sci-chemistry/gromacs/metadata.xml
@@ -9,10 +9,10 @@
   <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>
+    <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="offensive">Enable gromacs partly offensive quotes</flag>
     <flag name="openmm">Add acceleration through <pkg>sci-libs/openmm</pkg></flag>