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authorAlexey Shvetsov <alexxy@gentoo.org>2019-10-02 13:07:31 +0300
committerAlexey Shvetsov <alexxy@gentoo.org>2019-10-02 13:07:31 +0300
commit50ecd80e60a5e09e9684840980b027c029bd5e50 (patch)
tree2b3321f6c5ef2c3f46e246a3be6b3cbed2840235 /sci-chemistry
parentsys-fs/f2fs-tools: Version bump (v1.13.0) (diff)
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sci-chemistry/gromacs: Drop old
Package-Manager: Portage-2.3.76, Repoman-2.3.16 Signed-off-by: Alexey Shvetsov <alexxy@gentoo.org>
Diffstat (limited to 'sci-chemistry')
-rw-r--r--sci-chemistry/gromacs/Manifest2
-rw-r--r--sci-chemistry/gromacs/gromacs-2018.3.ebuild270
2 files changed, 0 insertions, 272 deletions
diff --git a/sci-chemistry/gromacs/Manifest b/sci-chemistry/gromacs/Manifest
index 275cb8fb5a1..5c5fd361564 100644
--- a/sci-chemistry/gromacs/Manifest
+++ b/sci-chemistry/gromacs/Manifest
@@ -1,8 +1,6 @@
-DIST gromacs-2018.3.tar.gz 29915626 BLAKE2B 6e6eeafecdd923a25b4a2a78a8e89f793639b57ffbd63f19d133d8474302f9a381041f138a509dadb42b36e25fe508729e860efb6b0c75cdbf01d924b0a8fd83 SHA512 3c4d6eb3942d7b54d01c94c6f6f5ae706e0f5d4f9901ea11a56fde4df97b1a9112007f2cb13feea0f19f30c89f57ae80ff53a8f5203b8cdff103aa903cd0dc8f
DIST gromacs-2018.7.tar.gz 29912662 BLAKE2B 0714b28ec2443f3201275fc2fa6db1202a059161362134d4de03a900a3a67fe9d31ba8c058d5ee971198fecd69379fcd389f03d25c61f50b8460c43ba5c564d5 SHA512 fbc3b847b70b1396f412b8f4a1b977268651f8d53a222dcf6349fe563ff6319e096484209a24351e382bc9162a949b3900591f5b469c32dd9effeb894f03c172
DIST gromacs-2019.2.tar.gz 33437869 BLAKE2B bebe4942688dace148856d4491b687b8e0fd2c86d7fbd9eecdb46824d316a0fc3854464ecafa79d8db92327ee8467be204b050c11f1e71132184efd812c3bf09 SHA512 da7ff24e8485774e22d1c2464fbe64675c3305ef0e21a3d17e363201031952e5d4a9b81f572d5284fb6f2596ed99daf62fe78d653387d9d714274f46bc750183
DIST gromacs-2019.3.tar.gz 33441419 BLAKE2B 79319dd23982c65c7c4d8e5f633cef0c7fd99a38a4e0cc9030a3ffb0fdfc07a4fbfbcfa942896f23a143b747e044fae645498a3e6992497d1f1a7d966f80b2b0 SHA512 de9f54d095b45ea7efd1043f83a40f6c778a6e3e2067a01f48d1ce843d68d226061933ca28a3edb635b795a8ddd5ef9deb8ed1114aa3235bc8039db8ff7d0218
-DIST regressiontests-2018.3.tar.gz 67857855 BLAKE2B acd7a05ae79d1b4eb47d0c68a3fec9ee19f028a5019f39c37a033f48cf6da2a468375180ad6ceca9ac4f685a8bead38550663a47d6427b51f84c32a5c810e5f0 SHA512 57980d49efe6dcc3b3d14b5913a30c68fc1de5b679ef986fec1a149c76f67139b0299c3ee2825451461294fab5f345c7ad4f42e90f8991b81aafe9c369f3ff0b
DIST regressiontests-2018.7.tar.gz 67856738 BLAKE2B 955ae8b5e74f90fec704cf41fbd00bd8c09d754f950551fe0adfcd407db6fdb4491a3815149ea37d36c747316c79d462e823b9f6b26f2376bf90d87aad95731b SHA512 c2ff390750bd99faebcd8d5dd8ad6dbf2b00113ed888bddddf985dbf95d7f347093adb67f3c396547b3e2990de330fddb7efe83ded91a72cf97c82a1dac7e826
DIST regressiontests-2019.2.tar.gz 67643003 BLAKE2B 4178de5d62f194a81f97e442c10f123dc59c5e63f2078f7f07135709f3f6e530e0d237bf40264b285c084519d5ace75dfcbcddc16dc740c4f17233dc33542e45 SHA512 c1f25bc770d3f0a873c887d5563c1cd88179e81211b70ce6f5015696e6fa0b6931a8da7a449f2b223f3105b9e2e7eca67248e96fbfc2a7fd5fb360ba616f22ff
DIST regressiontests-2019.3.tar.gz 67640462 BLAKE2B ed6c176a144e0407be66585be5d6090c31c047498bc5f48f59685108de91f2f9ddb2d22b291a15e6ffa1db848aae19b94a79c8c3d34b1067680f759a179953dd SHA512 822e905fb488ce308eb9324d93f78106da5252c773c7941d49c6162e73bdff109aeca1f0d57216c6dd6536a4c41d80013fa1cee2f5206b0c4160a3e5b4a31315
diff --git a/sci-chemistry/gromacs/gromacs-2018.3.ebuild b/sci-chemistry/gromacs/gromacs-2018.3.ebuild
deleted file mode 100644
index fd73db9a981..00000000000
--- a/sci-chemistry/gromacs/gromacs-2018.3.ebuild
+++ /dev/null
@@ -1,270 +0,0 @@
-# Copyright 1999-2019 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 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
- https://repo.or.cz/r/gromacs.git"
- [[ $PV = 9999 ]] && EGIT_BRANCH="master" || EGIT_BRANCH="release-${PV:0:4}"
- 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="amd64 arm 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
-# https://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 ${ACCE_IUSE}"
-
-CDEPEND="
- X? (
- x11-libs/libX11
- x11-libs/libSM
- x11-libs/libICE
- )
- blas? ( virtual/blas )
- cuda? ( >=dev-util/nvidia-cuda-toolkit-4.2.9-r1 )
- opencl? ( virtual/opencl )
- fftw? ( sci-libs/fftw:3.0 )
- hwloc? ( <sys-apps/hwloc-2 )
- lapack? ( virtual/lapack )
- mkl? ( sci-libs/mkl )
- mpi? ( virtual/mpi )
- "
-DEPEND="${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_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
-}