commit: 8e673b91ab29e6dd5e9cb43b3fd8ccba05c9ec29
Author: Alexey Shvetsov <alexxy <AT> gentoo <DOT> org>
AuthorDate: Thu Oct 30 18:29:02 2025 +0000
Commit: Alexey Shvetsov <alexxy <AT> gentoo <DOT> org>
CommitDate: Thu Oct 30 18:29:02 2025 +0000
URL: https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=8e673b91
sci-chemistry/gromacs: drop 2024.5
Signed-off-by: Alexey Shvetsov <alexxy <AT> gentoo.org>
sci-chemistry/gromacs/Manifest | 3 -
sci-chemistry/gromacs/gromacs-2024.5.ebuild | 341 ----------------------------
2 files changed, 344 deletions(-)
diff --git a/sci-chemistry/gromacs/Manifest b/sci-chemistry/gromacs/Manifest
index e2339ece102f..d77e1e1d979c 100644
--- a/sci-chemistry/gromacs/Manifest
+++ b/sci-chemistry/gromacs/Manifest
@@ -1,15 +1,12 @@
DIST gromacs-2023.5.tar.gz 42079310 BLAKE2B
e50dbe76396230f4a886280bdebcf7b131506679240e77d2a2263c3b5dbfe7ef754c4265fc04e9acad7932c7691de7f694cc23140a25d0d5be649a4120f45b0c
SHA512
f3a34cf0d379d6d4964d7494af6c6617c0c092293ea38a3a248af2dd2a90cae04696d52e68126176065efc480977942b00efa441028e526e1555c7e84551fc0c
-DIST gromacs-2024.5.tar.gz 42353127 BLAKE2B
c1fa6bd90390c9e13f11995ea9992902e136e15f6191ed47c9eac95384f97221533509ddd2bc4908f1d36fb790aab8a068fd1c00dd6f82e440f4719092b8ea37
SHA512
cb4f6bf4a6a53fb7ee4d8ed832d514d77d21eea3e1b86eec1bf51a4b6197a30aa8d68ca61919d7921c701af365077a9c84c12ef33d5584a1bc796b25709aa7af
DIST gromacs-2024.6.tar.gz 42340289 BLAKE2B
babba3ec83e8757d95733a51eebf780a2f0cf5da2fd3b2aa9410cdfca7901955cbd63d2ed0c61fde873b4438d85ae7769afa8f3d7ee1da26571d8989c516ecd4
SHA512
eb3d06df3e5c52d3dab801e5c2134fc05ded1bca8b1955f747e4efbb2b4cd1f50680f073592a5c5d580abff0a869ffd1c19c352bc6d9b4ab40465741ed7d001a
DIST gromacs-2025.2.tar.gz 44447261 BLAKE2B
08ac9d7d0c16934c6af9f4026da49dca18676b9f0d2ced110992980bfcfda53276751300507fcf483f18235b7a134fafc55f7f5ad8229360830585963edaaa3a
SHA512
72bc5b7fe7ad13190cc05619b786b576b4dd5523e7fdfdecc5be3b64843952c5a3c6d110c1503c5630522bbc71eb1615abd3c1387bf376a65bc286bf857dd209
DIST gromacs-2025.3.tar.gz 44407119 BLAKE2B
7e7385d5a83c02cb7152f789df6b86321b9ee22d7fb53e0e69fd01ba04ec197d1b725047f5c9983595ab124f23310f926e101d12a2113472f3b2aaa53f26b661
SHA512
8151bb0f72bf51d0368e40871b68d552c58ed69c0e431601afbf5c7923e7512d2458dfb22eb7fd79cc3c464434ca94a67c99a9f71c7e6b00d7d141789712c157
DIST manual-2023.5.pdf 13579081 BLAKE2B
42f687ebcdb79bfc77aabac4fd382940c23ba27da380b8eff342c2e9255a58fc11a0458220d1f71f3c13ab1cf6fdabad00ac1bad741781d0b787899165bea2cc
SHA512
0661f166f7a8dc24b4244c0139f366832ddfc1298129df2a6e29800b5d1567318781ab547bc7e9ee54de7a62abba4996f8e3010c91d6917c248117e5711d7dbb
-DIST manual-2024.5.pdf 13693341 BLAKE2B
b2e94b845f04201734c0a3ef834d013c2e65be53614329166d3b7e4ffcdfb71f3d25a4e8d9f852c4a7570b776532b7d0f00f9f62b76b1cd7fa8567ce22d44540
SHA512
b33a6689f965cfd867daee26b88693ab0696bb49db86e4f411030f36ce924e29f9cedbf3df51e3b02a223b91aa54394144795edb632336b8aa9eb164da8d4ded
DIST manual-2024.6.pdf 13698340 BLAKE2B
7926fe0c09ab1a6027e6e5d2692e2a590ec31c061b0f3e0dd278ffc8bffe923d6342bd9f375758fe5b0ca9c7fd43a216e486c694ba8d644acceb6467aac37425
SHA512
9130bda473ddfc475f3c7a6946890189bf225609208fb9e84c81606a72d63383199ac5e05f3620e7d7f96916ee475e19528d03b4ddc4b339772af61825beec45
DIST manual-2025.2.pdf 13810777 BLAKE2B
1ce1ef4619d1972a1e4212ab5684719744da821018b1d9e1e8fed9c03265ac8f1874f42d197845ab06e8c9ef45d6362da2985fa37f6c2f82816fa4dd14a18f0c
SHA512
c48ad55c50f3cd8873affe6c28f187d62d8e0d06d204dd481d52f5ba459d1e38094656bf766b1f396673ab121ed011f3ebdbd5aca3ab5bd13ca14955748bcdc8
DIST manual-2025.3.pdf 13822608 BLAKE2B
75ea8359a33941f1d44a6c471c03e268c707cdc4717ea43c455c25c5c60b7708e68849aba8fde7872aefa93691ef0bec531b7bd9cb0376b3ddee34c24058bdb5
SHA512
e0a3016eb6fc271d617795c1595a15e234c28a8492e2b0471b705c1f597b672ec05d0bb78ff3b977140c5f525dcc72c3b082cc74aee1e4207b9f1c2593a71bb5
DIST regressiontests-2023.5.tar.gz 48619605 BLAKE2B
f2549a34750c6866f054614a00a3360a09b82306e6bd5e5b848e18cdd3a3fabaac6203c5ca734901019403225dd47e0d662838abe9a1db7d07662f1c745b8e4f
SHA512
3ccaf9db7dfba641a5e98ebff3d735cae3f679926aba443ffedec20dd6c85e67f0e9711ebad5dfa8105122d5411f5de6ded1802a7da4ddf0599657832c8c597a
-DIST regressiontests-2024.5.tar.gz 32776573 BLAKE2B
5e397b6c601132ac96b826325bd0304d5939b87f0edaa89ba84d672a9df27351f26dbc9fde39fdb7a177be2743db93198316663a39145231741d08f3268d67cf
SHA512
8594e8365f676f18f227b4d6b87fa6a1a8ceab8301302469a626380a7d29035a2cd8667b4d923b26491d3db9298d6660a9c9bde9274dfeba278dfabdb54ef424
DIST regressiontests-2024.6.tar.gz 32776894 BLAKE2B
75dbf6a6ec5a1d0848a51335a1fb2e6777361d0b823e7f88c5145c881aa819abfc2eaaae1ae438538213c09659e9512bf77b4dc2f0ee63a28a1f213f49b5a47d
SHA512
1150396a3c20b7747a4a58c22b26c0c40cf6e6f70b8daabfc71cbe00f2dce3ad1c02d89d264a7d7db3f3e7e9dd1c0b46a438d297cdeb074e50d8d6d3e916950b
DIST regressiontests-2025.2.tar.gz 32653416 BLAKE2B
03c80b5dd80d8d0ed97f7faab5b56d8d9c1416d895a26ab871b46a2588d55b97386cb0c26b29f996d8c78460971a510f59b1930219b82104ca442c6d4b32b4b0
SHA512
bf067f867fed356352e492e51ed2c6e3a2a71ce0a43a9141db806a75101c9678a7f09ba1f0e5cfb63b3af6e375ae2edd41b8f78c1b587f5884e458fe8d6fe65f
DIST regressiontests-2025.3.tar.gz 32653489 BLAKE2B
1396872d6ebe2756b02ca1a1d173edd29f4931d2b30280299723b24164e5576c14c59997c00d7919b262fb1a15083dc90541f9f7e48587090002fc7cca9e1332
SHA512
fb947dc148e21a69e1ef06258f6c2359156e4afb7c8bee9e659ea461f5e4e9fe3654bec86324e11fcd6624889490ec73cb213bf0111cf76ded966f43c1182a20
diff --git a/sci-chemistry/gromacs/gromacs-2024.5.ebuild
b/sci-chemistry/gromacs/gromacs-2024.5.ebuild
deleted file mode 100644
index 166c99a239a8..000000000000
--- a/sci-chemistry/gromacs/gromacs-2024.5.ebuild
+++ /dev/null
@@ -1,341 +0,0 @@
-# Copyright 1999-2025 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=8
-
-CMAKE_MAKEFILE_GENERATOR="ninja"
-
-PYTHON_COMPAT=( python3_{11..13} )
-
-DISTUTILS_OPTIONAL=1
-DISTUTILS_USE_PEP517=no
-DISTUTILS_SINGLE_IMPL=1
-
-inherit bash-completion-r1 cmake cuda distutils-r1 flag-o-matic
readme.gentoo-r1 toolchain-funcs xdg-utils
-
-if [[ ${PV} = *9999* ]]; then
- EGIT_REPO_URI="
- https://gitlab.com/gromacs/gromacs.git
- https://github.com/gromacs/gromacs.git
- "
- [[ ${PV} = 9999 ]] && EGIT_BRANCH="master" ||
EGIT_BRANCH="release-${PV:0:4}"
- inherit git-r3
-else
- SRC_URI="
- https://ftp.gromacs.org/gromacs/${PN}-${PV/_/-}.tar.gz
- doc? ( https://ftp.gromacs.org/manual/manual-${PV/_/-}.pdf )
- test? (
https://ftp.gromacs.org/regressiontests/regressiontests-${PV/_/-}.tar.gz )"
- # since 2022 arm support was dropped (but not arm64)
- KEYWORDS="amd64 -arm arm64 ~riscv -x86 ~amd64-linux -x86-linux
~x64-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 cpu_flags_x86_avx512f cpu_flags_arm_neon"
-
-DESCRIPTION="The ultimate molecular dynamics simulation package"
-HOMEPAGE="https://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="blas clang clang-cuda cuda +custom-cflags +doc build-manual
double-precision +fftw +gmxapi +gmxapi-legacy +hwloc lapack mkl mpi +offensive
opencl openmp +python +single-precision test +threads +tng ${ACCE_IUSE}"
-
-CDEPEND="
- blas? ( virtual/blas )
- cuda? ( >=dev-util/nvidia-cuda-toolkit-11:=[profiler] )
- opencl? ( virtual/opencl )
- openmp? (
- sys-devel/gcc[openmp]
- llvm-runtimes/clang-runtime[openmp]
- )
- fftw? ( sci-libs/fftw:3.0= )
- hwloc? ( sys-apps/hwloc:= )
- lapack? ( virtual/lapack )
- mkl? ( sci-libs/mkl )
- mpi? ( virtual/mpi[cxx] )
- sci-libs/lmfit:=
- >=dev-cpp/muParser-2.3:=
- ${PYTHON_DEPS}
- "
-BDEPEND="${CDEPEND}
- virtual/pkgconfig
- clang? ( >=llvm-core/clang-6:* )
- build-manual? (
- app-text/doxygen
- $(python_gen_cond_dep '
- dev-python/sphinx[${PYTHON_USEDEP}]
- dev-python/sphinx-copybutton[${PYTHON_USEDEP}]
- dev-python/sphinx-inline-tabs[${PYTHON_USEDEP}]
- dev-python/sphinx-argparse[${PYTHON_USEDEP}]
- dev-python/sphinxcontrib-autoprogram[${PYTHON_USEDEP}]
- ')
- media-gfx/mscgen
- media-gfx/graphviz
- dev-texlive/texlive-latex
- dev-texlive/texlive-latexextra
- media-gfx/imagemagick
- )"
-RDEPEND="${CDEPEND}"
-
-REQUIRED_USE="
- || ( single-precision double-precision )
- doc? ( !build-manual )
- cuda? ( single-precision )
- opencl? ( single-precision )
- cuda? ( !opencl )
- clang-cuda? ( clang cuda )
- mkl? ( !blas !fftw !lapack )
- ${PYTHON_REQUIRED_USE}"
-
-DOCS=( AUTHORS README )
-
-RESTRICT="!test? ( test )"
-
-PATCHES=( "${FILESDIR}/${PN}-gcc-15.patch" )
-
-if [[ ${PV} != *9999 ]]; then
- S="${WORKDIR}/${PN}-${PV/_/-}"
-fi
-
-pkg_pretend() {
- [[ ${MERGE_TYPE} != binary ]] && use openmp && tc-check-openmp
-}
-
-pkg_setup() {
- [[ ${MERGE_TYPE} != binary ]] && use openmp && tc-check-openmp
- python-single-r1_pkg_setup
-}
-
-src_unpack() {
- if [[ ${PV} != *9999 ]]; then
- default
- else
- git-r3_src_unpack
- if use test; then
-
EGIT_REPO_URI="https://gitlab.com/gromacs/gromacs-regressiontests.git"; \
- EGIT_BRANCH="${EGIT_BRANCH}" \
- EGIT_CHECKOUT_DIR="${WORKDIR}/regressiontests"\
- git-r3_src_unpack
- fi
- fi
-}
-
-src_prepare() {
- #notes/todos
- # -on apple: there is framework support
-
- xdg_environment_reset #591952
-
- # we can use clang as default
- if use clang && ! tc-is-clang ; then
- export CC=${CHOST}-clang
- export CXX=${CHOST}-clang++
- else
- tc-export CXX CC
- fi
- # clang-cuda need to filter mfpmath
- if use clang-cuda ; then
- filter-mfpmath sse
- filter-mfpmath i386
- fi
-
- cmake_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"
- if use build-manual; then
- # try to create policy for imagemagik
- mkdir -p "${HOME}"/.config/ImageMagick
- cat >> "${HOME}"/.config/ImageMagick/policy.xml <<- EOF
- <?xml version="1.0" encoding="UTF-8"?>
- <!DOCTYPE policymap [
- <!ELEMENT policymap (policy)+>
- !ATTLIST policymap xmlns CDATA #FIXED ''>
- <!ELEMENT policy EMPTY>
- <!ATTLIST policy xmlns CDATA #FIXED '' domain NMTOKEN #REQUIRED
- name NMTOKEN #IMPLIED pattern CDATA #IMPLIED rights
NMTOKEN #IMPLIED
- stealth NMTOKEN #IMPLIED value CDATA #IMPLIED>
- ]>
- <policymap>
- <policy domain="coder" rights="read | write"
pattern="PS" />
- <policy domain="coder" rights="read | write"
pattern="PS2" />
- <policy domain="coder" rights="read | write"
pattern="PS3" />
- <policy domain="coder" rights="read | write"
pattern="EPS" />
- <policy domain="coder" rights="read | write"
pattern="PDF" />
- <policy domain="coder" rights="read | write"
pattern="XPS" />
- </policymap>
- EOF
- fi
-}
-
-src_configure() {
- local mycmakeargs_pre=( ) extra fft_opts=( )
- local acce="AUTO"
-
- if use custom-cflags; then
- #go from slowest to fastest acceleration
- acce="None"
- if (use amd64 || use x86); then
- 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"
- use cpu_flags_x86_avx512f && acce="AVX_512"
- elif (use arm); then
- use cpu_flags_arm_neon && acce="ARM_NEON"
- elif (use arm64); then
- use cpu_flags_arm_neon && acce="ARM_NEON_ASIMD"
- fi
- else
- strip-flags
- fi
-
- #to create man pages, build tree binaries are executed (bug #398437)
- [[ ${CHOST} = *-darwin* ]] && \
- extra+=" -DCMAKE_BUILD_WITH_INSTALL_RPATH=OFF"
-
- if use fftw; then
- fft_opts=( -DGMX_FFT_LIBRARY=fftw3 )
- elif use mkl; then
- local bits=$(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[@]}"
- "${lmfit_opts[@]}"
- -DGMX_USE_LMFIT=EXTERNAL
- -DGMX_USE_MUPARSER=EXTERNAL
- -DGMX_EXTERNAL_BLAS=$(usex blas)
- -DGMX_EXTERNAL_LAPACK=$(usex lapack)
- -DGMX_OPENMP=$(usex openmp)
- -DGMX_COOL_QUOTES=$(usex offensive)
- -DGMX_USE_TNG=$(usex tng)
- -DGMX_BUILD_MANUAL=$(usex build-manual)
- -DGMX_HWLOC=$(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=$(usex test)
- -DPYTHON_EXECUTABLE="${EPREFIX}/usr/bin/${EPYTHON}"
- ${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 gpu=( "-DGMX_GPU=OFF" )
- [[ ${x} = "float" ]] && use cuda && gpu=( "-DGMX_GPU=CUDA" )
- [[ ${x} = "float" ]] && use clang-cuda && gpu=(
"-DGMX_GPU=CUDA" "-DGMX_CLANG_CUDA=ON" )
- use opencl && gpu=( "-DGMX_GPU=OPENCL" )
- local mycmakeargs=(
- ${mycmakeargs_pre[@]} ${p}
- -DGMX_MPI=$(usex mpi)
- -DGMX_THREAD_MPI=$(usex threads)
- -DGMXAPI=$(usex gmxapi)
- -DGMX_INSTALL_LEGACY_API=$(usex gmxapi-legacy)
- "${gpu[@]}"
- "$(use test && echo
-DREGRESSIONTEST_PATH="${WORKDIR}/${P}_${x}/tests")"
- -DGMX_BINARY_SUFFIX="${suffix}"
- -DGMX_LIBS_SUFFIX="${suffix}"
- -DGMX_PYTHON_PACKAGE=$(usex python)
- )
- BUILD_DIR="${WORKDIR}/${P}_${x}" cmake_src_configure
- [[ ${CHOST} != *-darwin* ]] || \
- sed -i '/SET(CMAKE_INSTALL_NAME_DIR/s/^/#/'
"${WORKDIR}/${P}_${x}/gentoo_rules.cmake" || die
- done
-}
-
-src_compile() {
- for x in ${GMX_DIRS}; do
- einfo "Compiling for ${x} precision"
- BUILD_DIR="${WORKDIR}/${P}_${x}"\
- cmake_src_compile
- if use python; then
- BUILD_DIR="${WORKDIR}/${P}_${x}"\
- cmake_src_compile python_packaging/all
- BUILD_DIR="${WORKDIR}/${P}" \
- distutils-r1_src_compile
- fi
- # not 100% necessary for rel ebuilds as available from website
- if use build-manual; then
- BUILD_DIR="${WORKDIR}/${P}_${x}"\
- cmake_src_compile manual
- fi
- done
-}
-
-src_test() {
- for x in ${GMX_DIRS}; do
- BUILD_DIR="${WORKDIR}/${P}_${x}"\
- cmake_src_compile check
- done
-}
-
-src_install() {
- for x in ${GMX_DIRS}; do
- BUILD_DIR="${WORKDIR}/${P}_${x}" \
- cmake_src_install
- if use python; then
- BUILD_DIR="${WORKDIR}/${P}_${x}" \
- cmake_src_install python_packaging/install
- fi
- if use build-manual; then
- newdoc "${WORKDIR}/${P}_${x}"/docs/manual/gromacs.pdf
"${PN}-manual-${PV}.pdf"
- fi
-
- if use doc; then
- if [[ ${PV} != *9999* ]]; then
- newdoc "${DISTDIR}/manual-${PV/_/-}.pdf"
"${PN}-manual-${PV}.pdf"
- fi
- fi
- done
-
- if use tng; then
- insinto /usr/include/tng
- doins src/external/tng_io/include/tng/*h
- fi
- # drop unneeded stuff
- rm "${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 gromacs related papers from list:"
- einfo "https://www.gromacs.org/articles.html";
- einfo
- readme.gentoo_print_elog
-}
