commit: 9c844e558978a158283c37f50bc25c37f9e6efeb
Author: Alexey Shvetsov <alexxy <AT> gentoo <DOT> org>
AuthorDate: Fri Mar 21 10:04:33 2025 +0000
Commit: Alexey Shvetsov <alexxy <AT> gentoo <DOT> org>
CommitDate: Fri Mar 21 10:04:33 2025 +0000
URL: https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=9c844e55
sci-chemistry/gromacs: drop 2024.3
Signed-off-by: Alexey Shvetsov <alexxy <AT> gentoo.org>
sci-chemistry/gromacs/Manifest | 3 -
sci-chemistry/gromacs/gromacs-2024.3.ebuild | 341 ----------------------------
2 files changed, 344 deletions(-)
diff --git a/sci-chemistry/gromacs/Manifest b/sci-chemistry/gromacs/Manifest
index c32796338fae..65370d97cbb4 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-2024.3.tar.gz 42373103 BLAKE2B
f45af72ecdf119b423d98b84818eaca1aa2e3f43eaf1aff7435de2a5891079a880f19a654627ee2f43e3a38c9dcfa0638bc6eb6da201b3c9ce89b2dc32fc683b
SHA512
13f23e581c2b63f6262e8359e7bed6a1a5f3164047ea38d2b6a44bcd2b20b61332705167435fe2ad30fe6f24f8ab49b982388550cdecb49167e4156e36286d3d
DIST gromacs-2024.5.tar.gz 42353127 BLAKE2B
c1fa6bd90390c9e13f11995ea9992902e136e15f6191ed47c9eac95384f97221533509ddd2bc4908f1d36fb790aab8a068fd1c00dd6f82e440f4719092b8ea37
SHA512
cb4f6bf4a6a53fb7ee4d8ed832d514d77d21eea3e1b86eec1bf51a4b6197a30aa8d68ca61919d7921c701af365077a9c84c12ef33d5584a1bc796b25709aa7af
DIST gromacs-2025.0.tar.gz 44417653 BLAKE2B
9fb55c6c5c842faefe1811e8e2da558cae2564d81767da13fab9f23f674d6451700885269cd25d70caae6a7553d8b6fd885922bb74976e6bc9a7251e01ce696b
SHA512
0d3b2684827f6f9223a954fa5df408c2e7fbe2e61f6aef2d9a8b6bdd614045ed08a08d3229f3203064dc0c6b747de1b36449afc2de0b7da7300199bbcc2be77f
DIST gromacs-2025.1.tar.gz 44415202 BLAKE2B
aff5ef4a1d75134573b14722007685c14f2c1195caed80ce3eaed074492aea535e290b25fc63e0479ff1ed296ffbc7985ed296b442fedb6ede8a6cbb780edeba
SHA512
6affc4c36621528686e36a9f6008b82c1b552a4308a35b45e70129cb93de378f1c54473b1b8ee1a741c9ecdce963d28bc3746261f2a1a1f410733cbe0c583240
DIST manual-2023.5.pdf 13579081 BLAKE2B
42f687ebcdb79bfc77aabac4fd382940c23ba27da380b8eff342c2e9255a58fc11a0458220d1f71f3c13ab1cf6fdabad00ac1bad741781d0b787899165bea2cc
SHA512
0661f166f7a8dc24b4244c0139f366832ddfc1298129df2a6e29800b5d1567318781ab547bc7e9ee54de7a62abba4996f8e3010c91d6917c248117e5711d7dbb
-DIST manual-2024.3.pdf 13676383 BLAKE2B
fa5b310ee8977c525781492c70a18d40f8842f5fa43831ad0283c033f39968ba98e74ea618a4a9c25d88c3ed694071327220617b17f316ba2f29777c3edc95ca
SHA512
8dd09913b89213a6673a5f5e3462fb963d1f30d68e0d58b846b7e2cf2f73baacb14fabab6591b680849607f4ca617cf288899729939b2c32021b4ee5ba06835f
DIST manual-2024.5.pdf 13693341 BLAKE2B
b2e94b845f04201734c0a3ef834d013c2e65be53614329166d3b7e4ffcdfb71f3d25a4e8d9f852c4a7570b776532b7d0f00f9f62b76b1cd7fa8567ce22d44540
SHA512
b33a6689f965cfd867daee26b88693ab0696bb49db86e4f411030f36ce924e29f9cedbf3df51e3b02a223b91aa54394144795edb632336b8aa9eb164da8d4ded
DIST manual-2025.0.pdf 13801499 BLAKE2B
0b7a542680b3204e345a0a28a3abb8218d1d24389f0187f0bac6106b166087448382bf31abefc4d8579928f94ba52d309810ac3e66227f44db7030fb45018b49
SHA512
e16068e3357771a40970b17e8ad81407dff9e1621c7d35bb388cf74b80e0f4e7aea7069f08fe17c34eb83517dbf095efe3a96949f30a7c214a4b5d2c09ec7f1c
DIST manual-2025.1.pdf 13805396 BLAKE2B
f625b33e9b412c8a4343c7830defe331d1cc12233b3eca4f296a814d09552f15d59dc0052938b0e6ab96af623ee942059cb86e7488411bcefea454518b604c0f
SHA512
de1abb1ac66f5f0e4f9238dfa7a2f0f44b4fc565d4527d508294dcce35858da32bf1ec9fce623d2d1a9b4c851a6c45cb44ac973ba0d53e56d1a6bc3225a3e2fc
DIST regressiontests-2023.5.tar.gz 48619605 BLAKE2B
f2549a34750c6866f054614a00a3360a09b82306e6bd5e5b848e18cdd3a3fabaac6203c5ca734901019403225dd47e0d662838abe9a1db7d07662f1c745b8e4f
SHA512
3ccaf9db7dfba641a5e98ebff3d735cae3f679926aba443ffedec20dd6c85e67f0e9711ebad5dfa8105122d5411f5de6ded1802a7da4ddf0599657832c8c597a
-DIST regressiontests-2024.3.tar.gz 32776961 BLAKE2B
6a74977a396f8e82f7aba7a384cc840275b86d470597a4bbb93e97f1c13cd8fcf6d86ab26bdd4a89464b863954c9ed7dbd49af095e821573845f7bda43c2b90b
SHA512
1c4afbbca82c9b9ad371713ef5e7e093ca766f25f6fbda55c79ea1aecb2f0a06bdb042d3c8a86e3d9bf9e8b8091244827dbff544f66037ffa56b0bcb341a9d2c
DIST regressiontests-2024.5.tar.gz 32776573 BLAKE2B
5e397b6c601132ac96b826325bd0304d5939b87f0edaa89ba84d672a9df27351f26dbc9fde39fdb7a177be2743db93198316663a39145231741d08f3268d67cf
SHA512
8594e8365f676f18f227b4d6b87fa6a1a8ceab8301302469a626380a7d29035a2cd8667b4d923b26491d3db9298d6660a9c9bde9274dfeba278dfabdb54ef424
DIST regressiontests-2025.0.tar.gz 32653708 BLAKE2B
38d4fb66c33da1f16a8d1ed66841c9eecce900f24d8c5c7f7c26df43f35c431db9745ac1f195af7572439184a4f1d1f099f81e0a843b3ffbe6e8df0371d3bb31
SHA512
925a392926794af9067c7c385daafbd6b36b0f138d6a2354f23652b2a8f750bb9268b14d9d67579cfbacbc88543790317ec56e095bdccd9e0ed80fb9a39fd439
DIST regressiontests-2025.1.tar.gz 32653610 BLAKE2B
8301571cc10631ffa88999c56b2a30dec0543d49515193eced776ee13e10a6efa60a618100a486002b9c6deaddc0d17abd8b611cbdc49ee4dea91f722c1b73de
SHA512
e104f35f83e3afeea1b47e9f54a277330a4774962ca572a0694fda49c1e8752aa80c834786eaa3d23adeee938af1203d5eb7f06134f702e500b452f580bb4701
diff --git a/sci-chemistry/gromacs/gromacs-2024.3.ebuild
b/sci-chemistry/gromacs/gromacs-2024.3.ebuild
deleted file mode 100644
index d57a37462c1d..000000000000
--- a/sci-chemistry/gromacs/gromacs-2024.3.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..12} )
-
-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-core/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
-}
