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authorAndreas Sturmlechner <asturm@gentoo.org>2019-01-05 22:18:47 +0100
committerAndreas Sturmlechner <asturm@gentoo.org>2019-01-11 12:57:34 +0100
commitee4ddd95642f8e48f32d8ed4b55ea681ad0b781a (patch)
tree7324adbfba8bf4bcc29261f729042b23734c7fc3 /sci-chemistry
parentmedia-gfx/gthumb: Fix build with exiv2-0.27 (diff)
downloadgentoo-ee4ddd95642f8e48f32d8ed4b55ea681ad0b781a.tar.gz
gentoo-ee4ddd95642f8e48f32d8ed4b55ea681ad0b781a.tar.bz2
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sci-chemistry/gromacs: Drop 4.6.9999 and 5.0.{4,9999}
Declared unsupported upstream and never updated to latest point release in Gentoo. Closes: https://bugs.gentoo.org/674198 Package-Manager: Portage-2.3.54, Repoman-2.3.12 Signed-off-by: Andreas Sturmlechner <asturm@gentoo.org>
Diffstat (limited to 'sci-chemistry')
-rw-r--r--sci-chemistry/gromacs/Manifest2
-rw-r--r--sci-chemistry/gromacs/gromacs-4.6.9999.ebuild261
-rw-r--r--sci-chemistry/gromacs/gromacs-5.0.4.ebuild277
-rw-r--r--sci-chemistry/gromacs/gromacs-5.0.9999.ebuild282
-rw-r--r--sci-chemistry/gromacs/metadata.xml1
5 files changed, 0 insertions, 823 deletions
diff --git a/sci-chemistry/gromacs/Manifest b/sci-chemistry/gromacs/Manifest
index e8bd9511e66..412eb6bbdb7 100644
--- a/sci-chemistry/gromacs/Manifest
+++ b/sci-chemistry/gromacs/Manifest
@@ -3,12 +3,10 @@ DIST gromacs-2016.5.tar.gz 27369491 BLAKE2B 4a8bf1ae3e298ac2e26ec476130720dc3ef0
DIST gromacs-2018.3.tar.gz 29915626 BLAKE2B 6e6eeafecdd923a25b4a2a78a8e89f793639b57ffbd63f19d133d8474302f9a381041f138a509dadb42b36e25fe508729e860efb6b0c75cdbf01d924b0a8fd83 SHA512 3c4d6eb3942d7b54d01c94c6f6f5ae706e0f5d4f9901ea11a56fde4df97b1a9112007f2cb13feea0f19f30c89f57ae80ff53a8f5203b8cdff103aa903cd0dc8f
DIST gromacs-2018.4.tar.gz 29918276 BLAKE2B daf3f91e47bab61befee4ecd91e4885835fc5ded408462c239c824567e64b5710fb252456c6be2bf0e4ce1a2119747fca9d8fb0532286bb93d6ccdd289fe57ab SHA512 8ef0b90b2c266bb706c8fdba12e763de9c21aad197c1c71f48c06378644a734a3694172804db6c916a4974a9832b128512f2445d0b72783811e64edd22d27955
DIST gromacs-2019.tar.gz 33428725 BLAKE2B 307838a5ee1a85554d6f2ef8cd9c9dd2f3d9cacd32c534545c23483b5f3a1c7d027bfbdf224b90661cd8cd3fb85c0c99c66cbd619698245a0cb45ebd512dec5d SHA512 54b11530e8ff671461e3ae9418d991fe242957943c944798cddf6efe740eee670a562cd5201dbba68b045f4bafd3afa2dc8de27e0643c7def4e05eaf0ccb5769
-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-2016.2.tar.gz 67095329 BLAKE2B fec8a663845ad67374c8a230d1590fa9e5079460198f41cee3b788aaa1c72e8ec9dcda48bc68a594f15003d11bf6617d46cc1a09c16b7a333587b43904a16ba6 SHA512 e0aceb56d1f38a7e6ab9fdaac5063fd20c5b3a162ffb6eddd0e6dc7dff9b724bfe31363493a9437e9f9d5421a534b375960fcb31e903a4901a0fa94ed8511294
DIST regressiontests-2016.5.tar.gz 67641413 BLAKE2B 4fcd30c198f3acbbabf1104c040d9a686de49536a97dbeb14732bfa0ed3cf37aa61b1b0f45393668985b993d1f1862a8985e416af819cf9793f5964f3e4f43cc SHA512 31764fd99cc4185d61de5d4443ee482c27b13533451a24aa0e4899997ce275a63685424eafacae38b1a3ffd4ce0d5ebe02a90348953b04c104f91376f0edfdff
DIST regressiontests-2018.3.tar.gz 67857855 BLAKE2B acd7a05ae79d1b4eb47d0c68a3fec9ee19f028a5019f39c37a033f48cf6da2a468375180ad6ceca9ac4f685a8bead38550663a47d6427b51f84c32a5c810e5f0 SHA512 57980d49efe6dcc3b3d14b5913a30c68fc1de5b679ef986fec1a149c76f67139b0299c3ee2825451461294fab5f345c7ad4f42e90f8991b81aafe9c369f3ff0b
DIST regressiontests-2018.4.tar.gz 67860326 BLAKE2B 0160f701a8fa14ba4f175f4fca9894104bc5cc6aa5f02ac57200fd5a8f74a29b595df609e704cb70fcd9a03529bcf758fb4547e35557a45c0546d819c2681983 SHA512 baaac0c918684216ada5254a7c3a1f5b3ea00b1a63d6085d569095139b2a0c9de4ed330d4694f7eaedab729ed5dcea547390781b3d2f7c2ffdf02e0541a90efe
DIST regressiontests-2019.tar.gz 67597618 BLAKE2B fb950d8518cf1e28db5ebb99bdda8d269c5e43dd49a117bdaae9f00857abc7c096766fb90ff1d2d95a12a875ba2e243b707bfc81a45d07fc8b340a154cf2ad0f SHA512 081e56d052c0a0d021a8a1566f802911e261e1f2b5b2141350fe2372bcad0844042f26121167ed31a31490bd4e042068690c4905fcbc80b539686a074621fc5e
-DIST regressiontests-5.0.4.tar.gz 65193251 BLAKE2B c5e5f23adcc2639fe652bc252533307c7fda44453d506603242968bd8588c7394028b2c3c7a9252f807a050d40e8f78735e904dfe517d3db8ae962051f4826c1 SHA512 747725fa28c1c9525596bdeeb8809e45268e19036c11dac67d043aa1c51748688ca37eb6014eb7e819eb927a8b9ca2631d0ace4cdff8ed491b08c316c530ab65
DIST regressiontests-5.1.3.tar.gz 66994083 BLAKE2B 7009f65ad0138664ac84e57f8bc7cce5d18a59f99943e56b6642583120bfce279e005ac0bacd2db8904ea477a48e2b938c64de46a65fa5d08fce6009d53583c3 SHA512 486e86eb3b75bae822abe82dac4e1098aa13723bd04214021f835a2f0b847303f015a9ececc33aa5ae63d31a2eeae07e512f22464b6c0e26d1286b0781578022
diff --git a/sci-chemistry/gromacs/gromacs-4.6.9999.ebuild b/sci-chemistry/gromacs/gromacs-4.6.9999.ebuild
deleted file mode 100644
index 3fba885a492..00000000000
--- a/sci-chemistry/gromacs/gromacs-4.6.9999.ebuild
+++ /dev/null
@@ -1,261 +0,0 @@
-# Copyright 1999-2018 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=6
-
-TEST_PV="4.6.6"
-MANUAL_PV="4.6.6"
-
-CMAKE_MAKEFILE_GENERATOR="ninja"
-
-inherit bash-completion-r1 cmake-utils cuda eutils multilib readme.gentoo-r1 toolchain-funcs
-
-if [[ $PV = *9999* ]]; then
- EGIT_REPO_URI="git://git.gromacs.org/gromacs.git
- https://gerrit.gromacs.org/gromacs.git
- https://github.com/gromacs/gromacs.git
- http://repo.or.cz/r/gromacs.git"
- EGIT_BRANCH="release-4-6"
- inherit git-r3
- LIVE_DEPEND="doc? (
- app-doc/doxygen
- dev-texlive/texlive-latex
- dev-texlive/texlive-latexextra
- media-gfx/imagemagick
- sys-apps/coreutils
- )"
-else
- SRC_URI="ftp://ftp.gromacs.org/pub/${PN}/${P}.tar.gz
- doc? ( ftp://ftp.gromacs.org/pub/manual/manual-${MANUAL_PV}.pdf -> ${PN}-manual-${MANUAL_PV}.pdf )
- test? ( http://gerrit.gromacs.org/download/regressiontests-${TEST_PV}.tar.gz )"
- LIVE_DEPEND=""
- KEYWORDS="~alpha ~amd64 ~arm ~ppc64 ~sparc ~x86 ~amd64-linux ~x86-linux ~x86-macos"
-fi
-
-ACCE_IUSE="cpu_flags_x86_sse2 cpu_flags_x86_sse4_1 cpu_flags_x86_fma4 cpu_flags_x86_avx"
-
-DESCRIPTION="The ultimate molecular dynamics simulation package"
-HOMEPAGE="http://www.gromacs.org/"
-
-# see COPYING for details
-# http://repo.or.cz/w/gromacs.git/blob/HEAD:/COPYING
-# base, vmd plugins, fftpack from numpy, blas/lapck from netlib, memtestG80 library, mpi_thread lib
-LICENSE="LGPL-2.1 UoI-NCSA !mkl? ( !fftw? ( BSD ) !blas? ( BSD ) !lapack? ( BSD ) ) cuda? ( LGPL-3 ) threads? ( BSD )"
-SLOT="0/${PV}"
-IUSE="X blas cuda doc -double-precision +fftw gsl lapack mkl mpi +offensive openmp +single-precision test +threads zsh-completion ${ACCE_IUSE}"
-
-CDEPEND="
- X? (
- x11-libs/libX11
- x11-libs/libSM
- x11-libs/libICE
- )
- blas? ( virtual/blas )
- cuda? ( >=dev-util/nvidia-cuda-toolkit-4.2.9-r1 )
- fftw? ( sci-libs/fftw:3.0 )
- gsl? ( sci-libs/gsl )
- lapack? ( virtual/lapack )
- mkl? ( sci-libs/mkl )
- mpi? ( virtual/mpi )"
-DEPEND="${CDEPEND}
- virtual/pkgconfig
- ${LIVE_DEPEND}
- doc? ( app-doc/doxygen )"
-RDEPEND="${CDEPEND}"
-
-REQUIRED_USE="
- || ( single-precision double-precision )
- cuda? ( single-precision )
- mkl? ( !blas !fftw !lapack )"
-
-DOCS=( AUTHORS README )
-HTML_DOCS=( "${ED}"/usr/share/gromacs/html/ )
-
-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 [[ ${PV} != *9999 ]]; then
- default
- else
- git-r3_src_unpack
- if use doc; then
- EGIT_REPO_URI="git://git.gromacs.org/manual.git" \
- EGIT_BRANCH="release-4-6" EGIT_COMMIT="release-4-6" \
- EGIT_CHECKOUT_DIR="${WORKDIR}/manual"\
- git-r3_src_unpack
- fi
- if use test; then
- EGIT_REPO_URI="git://git.gromacs.org/regressiontests.git" \
- EGIT_BRANCH="release-4-6" EGIT_COMMIT="release-4-6" \
- 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"
-
- #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=$(usex blas)
- -DGMX_GSL=$(usex gsl)
- -DGMX_EXTERNAL_LAPACK=$(usex lapack)
- -DGMX_OPENMP=$(usex openmp)
- -DGMX_COOL_QUOTES=$(usex offensive)
- -DGMX_DEFAULT_SUFFIX=off
- -DGMX_ACCELERATION="$acce"
- -DGMXLIB="$(get_libdir)"
- -DGMX_VMD_PLUGIN_PATH="${EPREFIX}/usr/$(get_libdir)/vmd/plugins/*/molfile/"
- -DGMX_PREFIX_LIBMD=ON
- -DGMX_X86_AVX_GCC_MASKLOAD_BUG=OFF
- -DGMX_USE_GCC44_BUG_WORKAROUND=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[@]} ${p} -DGMX_MPI=OFF
- -DGMX_THREAD_MPI=$(usex threads) "${cuda[@]}" -DGMX_OPENMM=OFF
- "$(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 ${cuda} -DGMX_OPENMM=OFF
- -DGMX_BINARY_SUFFIX="_mpi${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
- use mpi || continue
- einfo "Compiling for ${x} precision with mpi"
- BUILD_DIR="${WORKDIR}/${P}_${x}_mpi"\
- cmake-utils_src_compile mdrun
- 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
- #manual can only be build after gromacs was installed once in image
- if use doc && [[ $PV = *9999* && ! -d ${WORKDIR}/manual_build ]]; then
- mycmakeargs=( -DGMXBIN="${ED}"/usr/bin -DGMXSRC="${WORKDIR}/${P}" )
- BUILD_DIR="${WORKDIR}"/manual_build \
- CMAKE_USE_DIR="${WORKDIR}/manual" cmake-utils_src_configure
- [[ ${CHOST} = *-darwin* ]] && \
- export DYLD_LIBRARY_PATH="${DYLD_LIBRARY_PATH}${DYLD_LIBRARY_PATH:+:}${ED}/usr/$(get_libdir)"
- BUILD_DIR="${WORKDIR}"/manual_build cmake-utils_src_make
- [[ ${CHOST} = *-darwin* ]] && DYLD_LIBRARY_PATH="${ED}/usr/$(get_libdir)"
- newdoc "${WORKDIR}"/manual_build/gromacs.pdf "${PN}-manual-${PV}.pdf"
- fi
- use mpi || continue
- BUILD_DIR="${WORKDIR}/${P}_${x}_mpi" \
- DESTDIR="${D}" cmake-utils_src_make install-mdrun
- done
-
- use doc && [[ $PV != *9999* ]] && dodoc "${DISTDIR}/${PN}-manual-${MANUAL_PV}.pdf"
- newbashcomp "${ED}"/usr/bin/completion.bash ${PN}
- if use zsh-completion ; then
- insinto /usr/share/zsh/site-functions
- newins "${ED}"/usr/bin/completion.zsh _${PN}
- fi
- rm -f "${ED}"usr/bin/completion.*
- rm -rf "${ED}"usr/share/gromacs/html
- rm -f "${ED}"usr/bin/g_options*
- rm -f "${ED}"usr/bin/GMXRC*
-
- 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"
- if use offensive; then
- einfo
- einfo $(g_luck)
- einfo "For more Gromacs cool quotes (gcq) add g_luck to your .bashrc"
- fi
- einfo
- readme.gentoo_print_elog
-}
diff --git a/sci-chemistry/gromacs/gromacs-5.0.4.ebuild b/sci-chemistry/gromacs/gromacs-5.0.4.ebuild
deleted file mode 100644
index ac00ea29ca7..00000000000
--- a/sci-chemistry/gromacs/gromacs-5.0.4.ebuild
+++ /dev/null
@@ -1,277 +0,0 @@
-# Copyright 1999-2018 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-CMAKE_MAKEFILE_GENERATOR="ninja"
-
-inherit bash-completion-r1 cmake-utils cuda eutils multilib readme.gentoo toolchain-funcs
-
-if [[ $PV = *9999* ]]; then
- EGIT_REPO_URI="git://git.gromacs.org/gromacs.git
- https://gerrit.gromacs.org/gromacs.git
- https://github.com/gromacs/gromacs.git
- http://repo.or.cz/r/gromacs.git"
- EGIT_BRANCH="release-5-0"
- inherit git-r3
-else
- SRC_URI="ftp://ftp.gromacs.org/pub/${PN}/${PN}-${PV/_/-}.tar.gz
- test? ( http://gerrit.gromacs.org/download/regressiontests-${PV}.tar.gz )"
- KEYWORDS="~alpha amd64 arm ppc64 ~sparc x86 ~amd64-linux ~x86-linux ~x64-macos ~x86-macos"
-fi
-
-ACCE_IUSE="cpu_flags_x86_sse2 cpu_flags_x86_sse4_1 cpu_flags_x86_fma4 cpu_flags_x86_avx cpu_flags_x86_avx2"
-
-DESCRIPTION="The ultimate molecular dynamics simulation package"
-HOMEPAGE="http://www.gromacs.org/"
-
-# see COPYING for details
-# http://repo.or.cz/w/gromacs.git/blob/HEAD:/COPYING
-# base, vmd plugins, fftpack from numpy, blas/lapck from netlib, memtestG80 library, mpi_thread lib
-LICENSE="LGPL-2.1 UoI-NCSA !mkl? ( !fftw? ( BSD ) !blas? ( BSD ) !lapack? ( BSD ) ) cuda? ( LGPL-3 ) threads? ( BSD )"
-SLOT="0/${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}_${x}_mpi" \
- cmake-utils_src_install
- done
- # drop unneeded stuff
- rm "${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 "https://dx.doi.org/10.1021/ct700301q"
- einfo
- readme.gentoo_print_elog
-}
diff --git a/sci-chemistry/gromacs/gromacs-5.0.9999.ebuild b/sci-chemistry/gromacs/gromacs-5.0.9999.ebuild
deleted file mode 100644
index bb4000f2520..00000000000
--- a/sci-chemistry/gromacs/gromacs-5.0.9999.ebuild
+++ /dev/null
@@ -1,282 +0,0 @@
-# Copyright 1999-2018 Gentoo Authors
-# 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
-
-if [[ $PV = *9999* ]]; then
- EGIT_REPO_URI="git://git.gromacs.org/gromacs.git
- https://gerrit.gromacs.org/gromacs.git
- https://github.com/gromacs/gromacs.git
- http://repo.or.cz/r/gromacs.git"
- EGIT_BRANCH="release-5-0"
- inherit git-r3
-else
- SRC_URI="ftp://ftp.gromacs.org/pub/${PN}/${PN}-${PV/_/-}.tar.gz
- test? ( http://gerrit.gromacs.org/download/regressiontests-${PV}.tar.gz )"
- KEYWORDS="~alpha ~amd64 ~arm ~ppc64 ~sparc ~x86 ~amd64-linux ~x86-linux ~x64-macos ~x86-macos"
-fi
-
-ACCE_IUSE="cpu_flags_x86_sse2 cpu_flags_x86_sse4_1 cpu_flags_x86_fma4 cpu_flags_x86_avx cpu_flags_x86_avx2"
-
-DESCRIPTION="The ultimate molecular dynamics simulation package"
-HOMEPAGE="http://www.gromacs.org/"
-
-# see COPYING for details
-# http://repo.or.cz/w/gromacs.git/blob/HEAD:/COPYING
-# base, vmd plugins, fftpack from numpy, blas/lapck from netlib, memtestG80 library, mpi_thread lib
-LICENSE="LGPL-2.1 UoI-NCSA !mkl? ( !fftw? ( BSD ) !blas? ( BSD ) !lapack? ( BSD ) ) cuda? ( LGPL-3 ) threads? ( BSD )"
-SLOT="0/${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+=(
- "${fft_opts[@]}"
- -DGMX_X11=$(usex X)
- -DGMX_EXTERNAL_BLAS=$(usex blas)
- -DGMX_EXTERNAL_LAPACK=$(usex lapack)
- -DGMX_OPENMP=$(usex openmp)
- -DGMX_COOL_QUOTES=$(usex offensive)
- -DGMX_EXTERNAL_BOOST=$(usex boost)
- -DGMX_USE_TNG=$(usex tng)
- -DGMX_BUILD_MANUAL=$(usex doc)
- -DGMX_SYMLINK_OLD_BINARY_NAMES=$(usex make-symlinks)
- -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[@]} ${p}
- -DGMX_MPI=OFF
- -DGMX_THREAD_MPI=$(usex threads)
- "${cuda[@]}"
- -DGMX_OPENMM=OFF
- "$(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 "https://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 fca9b4acc97..dce564d8220 100644
--- a/sci-chemistry/gromacs/metadata.xml
+++ b/sci-chemistry/gromacs/metadata.xml
@@ -17,7 +17,6 @@
<flag name="boost">Enable external boost library</flag>
<flag name="hwloc">Enable HWLoc lib support</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="lmfit">Use external <pkg>sci-libs/lmfit</pkg></flag>
<flag name="gmxapi">Add support for gmxapi library</flag>
<!-- acceleration optimization flags -->