HDF5: Update to 1.14.3 #7908
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@@ -6,28 +6,28 @@ const YGGDRASIL_DIR = "../.." | |
| include(joinpath(YGGDRASIL_DIR, "platforms", "mpi.jl")) | ||
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| name = "HDF5" | ||
| version = v"1.14.3" | ||
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| # Collection of sources required to complete build | ||
| sources = [ | ||
| ArchiveSource("https://support.hdfgroup.org/ftp/HDF5/releases/hdf5-$(version.major).$(version.minor)/hdf5-$(version)/src/hdf5-$(version).tar.bz2", | ||
| "9425f224ed75d1280bb46d6f26923dd938f9040e7eaebf57e66ec7357c08f917"), | ||
| DirectorySource("./bundled"), | ||
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| # We don't build HDF5 on Windows; instead, we use packages from msys there: | ||
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| # 32-bit Windows from https://packages.msys2.org/package/mingw-w64-i686-hdf5 | ||
| ArchiveSource("https://mirror.msys2.org/mingw/mingw32/mingw-w64-i686-hdf5-1.14.3-1-any.pkg.tar.zst", | ||
| "09c6bf048eada4d3ad945c641111e7394169aa69904e5c4dd8de5c4b41143440"; unpack_target="i686-w64-mingw32"), | ||
| ArchiveSource("https://mirror.msys2.org/mingw/mingw32/mingw-w64-i686-zlib-1.3-1-any.pkg.tar.zst", | ||
| "21bacf3a43073749a4cbdf407c7f1da92bab56c80925b1205f7c4cb289c724a1"; unpack_target="i686-w64-mingw32"), | ||
| # We need some special compiler support libraries from mingw for i686 (libgcc_s_dw2) | ||
| ArchiveSource("https://mirror.msys2.org/mingw/mingw32/mingw-w64-i686-gcc-libs-13.2.0-2-any.pkg.tar.zst", | ||
| "2dae8189318a91067cca895572b2b46183bfd2ee97a55127a84f4f418f0b32f3"; unpack_target="i686-w64-mingw32"), | ||
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| # 64-bit Windows from https://packages.msys2.org/package/mingw-w64-x86_64-hdf5 | ||
| ArchiveSource("https://mirror.msys2.org/mingw/mingw64/mingw-w64-x86_64-hdf5-1.14.3-1-any.pkg.tar.zst", | ||
| "a6a69866725504cba9212a616c8734ade54c8de7d5f42074e33a7b62c7a31428"; unpack_target="x86_64-w64-mingw32"), | ||
| ArchiveSource("https://mirror.msys2.org/mingw/mingw64/mingw-w64-x86_64-zlib-1.3-1-any.pkg.tar.zst", | ||
| "254a6c5a8a27d1b787377a3e70a39cceb200b47c5f15f4ab5bfa1431b718ef98"; unpack_target="x86_64-w64-mingw32"), | ||
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@@ -68,102 +68,10 @@ atomic_patch -p1 ${WORKSPACE}/srcdir/patches/mpi.patch | |
| # Idea: | ||
| # - provide the registered filter plugins (BZIP2, JPEG, LZF, BLOSC, MAFISC, LZ4, Bitshuffle, and ZFP) | ||
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| # Patch `configure.ac`: | ||
| atomic_patch -p1 ${WORKSPACE}/srcdir/patches/configure.ac.patch | ||
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| # Prepare the file `config.saved` that contains predetermined | ||
| # configuration information | ||
| mkdir saved | ||
| case "${target}" in | ||
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@@ -182,7 +90,6 @@ case "${target}" in | |
| i686-w64-mingw32) | ||
| # sizeof(long double) == 12 | ||
| # layout seems to be 16-bit sign+exponent and 64-bit mantissa | ||
| cp ../files/msys2-mingw32/* saved | ||
| ;; | ||
| powerpc64le-linux-*) | ||
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@@ -195,13 +102,12 @@ case "${target}" in | |
| cp ../files/debian-amd64/* saved | ||
| ;; | ||
| x86_64-*-freebsd*) | ||
| # no __float128 | ||
| cp ../files/freebsd-amd64/* saved | ||
| ;; | ||
| x86_64-w64-mingw32) | ||
| # sizeof(long double) == 16 | ||
| # layout seems to be 16-bit sign+exponent and 64-bit mantissa | ||
| cp ../files/msys2-mingw64/* saved | ||
| ;; | ||
| *) | ||
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@@ -211,6 +117,7 @@ case "${target}" in | |
| esac | ||
| cp ../files/get_config_setting saved | ||
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| env \ | ||
| HDF5_ACLOCAL=/usr/bin/aclocal \ | ||
| HDF5_AUTOHEADER=/usr/bin/autoheader \ | ||
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@@ -253,45 +160,39 @@ elif [[ ${target} == *-w64-mingw32 ]]; then | |
| fi | ||
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| # Configure MPI | ||
| if grep -q MSMPI_VER ${prefix}/include/mpi.h; then | ||
| # Microsoft MPI | ||
| if [[ ${target} == i686-* ]]; then | ||
| # 32-bit system | ||
| # Do not enable MPI; the function MPI_File_close is not defined | ||
| # in the 32-bit version of Microsoft MPI 10.1.12498.18 | ||
| : | ||
| else | ||
| # Hide static libraries | ||
| rm ${prefix}/lib/msmpi*.lib | ||
| # Make shared libraries visible | ||
| ln -s msmpi.dll ${libdir}/libmsmpi.dll | ||
| ENABLE_PARALLEL=yes | ||
| export FCFLAGS="${FCFLAGS} -I${prefix}/src -I${prefix}/include -fno-range-check" | ||
| export LIBS="-L${libdir} -lmsmpi" | ||
| fi | ||
| else | ||
| ENABLE_PARALLEL=yes | ||
| export MPITRAMPOLINE_CC="${CC}" | ||
| export MPITRAMPOLINE_CXX="${CXX}" | ||
| export MPITRAMPOLINE_FC="${FC}" | ||
| export CC=mpicc | ||
| export CXX=mpicxx | ||
| export FC=mpifort | ||
| fi | ||
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| # This is likely a bug in HDF5; see | ||
| # <https://github.com/HDFGroup/hdf5/issues/3925>. The file | ||
| # `config/freebsd` includes `config/classic-fflags` which is | ||
| # missing. This file is supposed to contain Fortran flags for the | ||
| # classic Intel compiler. | ||
| : >../config/classic-fflags | ||
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| ../configure \ | ||
| --prefix=${prefix} \ | ||
| --build=${MACHTYPE} \ | ||
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@@ -337,14 +238,15 @@ fi | |
| "$(../saved/get_config_setting H5CONFIG_F_NUM_IKIND ../saved/config.status)" \ | ||
| "$(../saved/get_config_setting H5CONFIG_F_IKIND ../saved/config.status)" | ||
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| # Patch the generated `Makefile`: | ||
| # (We could instead patch `Makefile.in`, or maybe even `Makefile.am`.) | ||
| # - HDF5 would also try to build and run `H5detect` to collect ABI information. | ||
| # We know this information, and thus can provide it manually. | ||
| # - HDF5 would try to build and run `H5make_libsettings` to collect | ||
| # build-time information. That information seems entirely optional, so | ||
| # we do mostly nothing instead. | ||
| #atomic_patch -p1 ${WORKSPACE}/srcdir/patches/src-Makefile.patch | ||
| atomic_patch -p1 ${WORKSPACE}/srcdir/patches/fortran-src-Makefile.patch | ||
| atomic_patch -p1 ${WORKSPACE}/srcdir/patches/hl-fortran-src-Makefile.patch | ||
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@@ -357,8 +259,6 @@ make install | |
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| popd | ||
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| install_license COPYING | ||
| """ | ||
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@@ -376,7 +276,7 @@ platforms = expand_cxxstring_abis(platforms) | |
| platforms = expand_gfortran_versions(platforms) | ||
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| # TODO: Don't require MPI for Windows since we're using the non-MPI msys libraries there. | ||
| platforms, platform_dependencies = MPI.augment_platforms(platforms; MPItrampoline_compat="5.3.1", OpenMPI_compat="4.1.6") | ||
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| # Avoid platforms where the MPI implementation isn't supported | ||
| # OpenMPI | ||
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@@ -421,12 +321,8 @@ products = [ | |
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| # Dependencies that must be installed before this package can be built | ||
| dependencies = [ | ||
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Comment on lines
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There was a problem hiding this comment. @giordano OpenMP was removed as a dependency. There was a problem hiding this comment. Ah, I didn't see that addressed in the comments after my comment, I missed it had been changed before! The diff was quite large 🥲 |
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| # To ensure that the correct version of libgfortran is found at runtime | ||
| Dependency(PackageSpec(name="CompilerSupportLibraries_jll", uuid="e66e0078-7015-5450-92f7-15fbd957f2ae")), | ||
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| Dependency("LibCURL_jll"), | ||
| # The msys Windows libraries require OpenSSL@3 | ||
| Dependency("OpenSSL_jll"; compat="3.0.8"), | ||
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@@ -443,4 +339,4 @@ ENV["MPITRAMPOLINE_DELAY_INIT"] = "1" | |
| # Build the tarballs, and possibly a `build.jl` as well. | ||
| # GCC 5 reports an ICE on i686-linux-gnu-libgfortran3-cxx11-mpi+mpich | ||
| build_tarballs(ARGS, name, version, sources, script, platforms, products, dependencies; | ||
| augment_platform_block, clang_use_lld=false, julia_compat="1.6", preferred_gcc_version=v"6") | ||
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I thought the idea is that we would remove this line and replace it with a
RuntimeDependency, but I'm a bit confused as well.@giordano ?
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Why replacing that line? That'd break everything. At most you want to try and change
Yggdrasil/platforms/mpi.jl
Line 82 in 4d82df7
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#6417
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Might work now with JuliaPackaging/BinaryBuilderBase.jl#304 and JuliaPackaging/BinaryBuilder.jl#1273 but haven't tried it
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I think I'm starting to follow. You're saying we need to edit
Yggdrasil/platforms/mpi.jlby perhaps reverting c4069bf.There was a problem hiding this comment.
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Only if it solves #6417 (comment)
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I'm thinking we should leave this for another pull request since fixing that will probably hit multiple recipes.
I'm good to merge this as is now if Erik is good.
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I don't think #7908 (comment) was addressed.
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@giordano That's the comment regarding OpenMP? What is unresolved there? I think we all agree that OpenMP isn't used and isn't mentioned, and since @mkitti removed the respective dependency all is good?
Apart from this: Yes, we can merge.