sci-chemistry/gromacs: drop 2025.2

Signed-off-by: Alexey Shvetsov <alexxy@gentoo.org>
This commit is contained in:
Alexey Shvetsov
2025-10-30 21:29:28 +03:00
parent 8e673b91ab
commit e1cf9cf8e7
2 changed files with 0 additions and 364 deletions

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DIST gromacs-2023.5.tar.gz 42079310 BLAKE2B e50dbe76396230f4a886280bdebcf7b131506679240e77d2a2263c3b5dbfe7ef754c4265fc04e9acad7932c7691de7f694cc23140a25d0d5be649a4120f45b0c SHA512 f3a34cf0d379d6d4964d7494af6c6617c0c092293ea38a3a248af2dd2a90cae04696d52e68126176065efc480977942b00efa441028e526e1555c7e84551fc0c
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-2024.6.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-2024.6.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

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# 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
"
[[ ${PV} = 9999 ]] && EGIT_BRANCH="main" || EGIT_BRANCH="release-${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)
# since 2025 x86-32 support was dropped
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 nnpot +offensive opencl openmp +python +single-precision test +threads +tng video_cards_intel ${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] )
nnpot? ( sci-ml/caffe2[cuda=,opencl=] )
sci-libs/lmfit:=
>=dev-cpp/muParser-2.3:=
${PYTHON_DEPS}
"
BDEPEND="${CDEPEND}
virtual/pkgconfig
clang? ( >=llvm-core/clang-6:* )
$(python_gen_cond_dep '
dev-python/sphinx[${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}]
')
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 )"
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"
local nnpot="OFF"
if use nnpot; then
nnpot="TORCH"
fi
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=$(usex build-manual)
-DGMX_USE_HDF5=off
-DGMX_HWLOC=$(usex hwloc)
-DGMX_DEFAULT_SUFFIX=off
-DGMX_BUILD_HELP=$(usex doc)
-DGMX_SIMD="$acce"
-DGMX_NNPOT="$nnpot"
-DGMX_VMD_PLUGIN_PATH="${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" )
local gpu_clusters=( "-DGMX_GPU_NB_CLUSTER_SIZE=8" )
[[ ${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" )
use video_cards_intel && gpu_clusters=( "-DGMX_GPU_NB_CLUSTER_SIZE=4" )
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[@]}"
"${gpu_clusters[@]}"
"$(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
BUILD_DIR="${WORKDIR}/${P}_${x}"\
cmake_src_compile man
if use python; then
BUILD_DIR="${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
}