upgrade to HDF5_jll 1.14

CliMA · Nov 15, 2023 · 7915baa · 7915baa
1 parent 9078811
commit 7915baa
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Showing 5 changed files with 89 additions and 75 deletions.
diff --git a/Project.toml b/Project.toml
@@ -16,7 +16,6 @@ ForwardDiff = "f6369f11-7733-5829-9624-2563aa707210"
 GaussQuadrature = "d54b0c1a-921d-58e0-8e36-89d8069c0969"
 GilbertCurves = "88fa7841-ef32-4516-bb70-c6ec135699d9"
 HDF5 = "f67ccb44-e63f-5c2f-98bd-6dc0ccc4ba2f"
-HDF5_jll = "0234f1f7-429e-5d53-9886-15a909be8d59"
 InteractiveUtils = "b77e0a4c-d291-57a0-90e8-8db25a27a240"
 IntervalSets = "8197267c-284f-5f27-9208-e0e47529a953"
 LinearAlgebra = "37e2e46d-f89d-539d-b4ee-838fcccc9c8e"
@@ -43,7 +42,6 @@ ForwardDiff = "0.10"
 GaussQuadrature = "0.5"
 GilbertCurves = "0.1"
 HDF5 = "0.16, 0.17"
-HDF5_jll = "~1.12"
 InteractiveUtils = "1"
 IntervalSets = "0.5, 0.6, 0.7"
 LinearAlgebra = "1"

diff --git a/docs/Manifest.toml b/docs/Manifest.toml
@@ -288,7 +288,7 @@ uuid = "3a4d1b5c-c61d-41fd-a00a-5873ba7a1b0d"
 version = "0.5.6"
 
 [[deps.ClimaCore]]
-deps = ["Adapt", "BandedMatrices", "BlockArrays", "CUDA", "ClimaComms", "CubedSphere", "DataStructures", "DocStringExtensions", "ForwardDiff", "GaussQuadrature", "GilbertCurves", "HDF5", "HDF5_jll", "InteractiveUtils", "IntervalSets", "LinearAlgebra", "PkgVersion", "RecursiveArrayTools", "Requires", "RootSolvers", "SparseArrays", "Static", "StaticArrays", "Statistics", "UnPack"]
+deps = ["Adapt", "BandedMatrices", "BlockArrays", "CUDA", "ClimaComms", "CubedSphere", "DataStructures", "DocStringExtensions", "ForwardDiff", "GaussQuadrature", "GilbertCurves", "HDF5", "InteractiveUtils", "IntervalSets", "LinearAlgebra", "PkgVersion", "RecursiveArrayTools", "Requires", "RootSolvers", "SparseArrays", "Static", "StaticArrays", "Statistics", "UnPack"]
 path = ".."
 uuid = "d414da3d-4745-48bb-8d80-42e94e092884"
 version = "0.10.55"
@@ -675,10 +675,10 @@ uuid = "c87230d0-a227-11e9-1b43-d7ebe4e7570a"
 version = "0.4.1"
 
 [[deps.FFMPEG_jll]]
-deps = ["Artifacts", "Bzip2_jll", "FreeType2_jll", "FriBidi_jll", "JLLWrappers", "LAME_jll", "Libdl", "Ogg_jll", "OpenSSL_jll", "Opus_jll", "PCRE2_jll", "Pkg", "Zlib_jll", "libaom_jll", "libass_jll", "libfdk_aac_jll", "libvorbis_jll", "x264_jll", "x265_jll"]
-git-tree-sha1 = "74faea50c1d007c85837327f6775bea60b5492dd"
+deps = ["Artifacts", "Bzip2_jll", "FreeType2_jll", "FriBidi_jll", "JLLWrappers", "LAME_jll", "Libdl", "Ogg_jll", "OpenSSL_jll", "Opus_jll", "PCRE2_jll", "Zlib_jll", "libaom_jll", "libass_jll", "libfdk_aac_jll", "libvorbis_jll", "x264_jll", "x265_jll"]
+git-tree-sha1 = "466d45dc38e15794ec7d5d63ec03d776a9aff36e"
 uuid = "b22a6f82-2f65-5046-a5b2-351ab43fb4e5"
-version = "4.4.2+2"
+version = "4.4.4+1"
 
 [[deps.FFTW]]
 deps = ["AbstractFFTs", "FFTW_jll", "LinearAlgebra", "MKL_jll", "Preferences", "Reexport"]
@@ -935,10 +935,10 @@ weakdeps = ["MPI"]
     MPIExt = "MPI"
 
 [[deps.HDF5_jll]]
-deps = ["Artifacts", "JLLWrappers", "LibCURL_jll", "Libdl", "OpenSSL_jll", "Pkg", "Zlib_jll"]
-git-tree-sha1 = "4cc2bb72df6ff40b055295fdef6d92955f9dede8"
+deps = ["Artifacts", "CompilerSupportLibraries_jll", "JLLWrappers", "LLVMOpenMP_jll", "LazyArtifacts", "LibCURL_jll", "Libdl", "MPICH_jll", "MPIPreferences", "MPItrampoline_jll", "MicrosoftMPI_jll", "OpenMPI_jll", "OpenSSL_jll", "TOML", "Zlib_jll", "libaec_jll"]
+git-tree-sha1 = "38c8874692d48d5440d5752d6c74b0c6b0b60739"
 uuid = "0234f1f7-429e-5d53-9886-15a909be8d59"
-version = "1.12.2+2"
+version = "1.14.2+1"
 
 [[deps.HTTP]]
 deps = ["Base64", "CodecZlib", "ConcurrentUtilities", "Dates", "ExceptionUnwrapping", "Logging", "LoggingExtras", "MbedTLS", "NetworkOptions", "OpenSSL", "Random", "SimpleBufferStream", "Sockets", "URIs", "UUIDs"]
@@ -1611,10 +1611,10 @@ uuid = "77ba4419-2d1f-58cd-9bb1-8ffee604a2e3"
 version = "1.0.2"
 
 [[deps.NetCDF_jll]]
-deps = ["Artifacts", "HDF5_jll", "JLLWrappers", "LibCURL_jll", "Libdl", "Pkg", "XML2_jll", "Zlib_jll"]
-git-tree-sha1 = "072f8371f74c3b9e1b26679de7fbf059d45ea221"
+deps = ["Artifacts", "Bzip2_jll", "HDF5_jll", "JLLWrappers", "LibCURL_jll", "Libdl", "XML2_jll", "Zlib_jll", "Zstd_jll"]
+git-tree-sha1 = "10c612c81eaffdd6b7c28a45a554cdd9d2f40ff1"
 uuid = "7243133f-43d8-5620-bbf4-c2c921802cf3"
-version = "400.902.5+1"
+version = "400.902.208+0"
 
 [[deps.Netpbm]]
 deps = ["FileIO", "ImageCore", "ImageMetadata"]
@@ -1701,9 +1701,9 @@ version = "1.4.1"
 
 [[deps.OpenSSL_jll]]
 deps = ["Artifacts", "JLLWrappers", "Libdl"]
-git-tree-sha1 = "a12e56c72edee3ce6b96667745e6cbbe5498f200"
+git-tree-sha1 = "cc6e1927ac521b659af340e0ca45828a3ffc748f"
 uuid = "458c3c95-2e84-50aa-8efc-19380b2a3a95"
-version = "1.1.23+0"
+version = "3.0.12+0"
 
 [[deps.OpenSpecFun_jll]]
 deps = ["Artifacts", "CompilerSupportLibraries_jll", "JLLWrappers", "Libdl", "Pkg"]
@@ -1730,9 +1730,9 @@ version = "1.6.2"
 
 [[deps.OrdinaryDiffEq]]
 deps = ["ADTypes", "Adapt", "ArrayInterface", "DataStructures", "DiffEqBase", "DocStringExtensions", "ExponentialUtilities", "FastBroadcast", "FastClosures", "FiniteDiff", "ForwardDiff", "FunctionWrappersWrappers", "IfElse", "InteractiveUtils", "LineSearches", "LinearAlgebra", "LinearSolve", "Logging", "LoopVectorization", "MacroTools", "MuladdMacro", "NLsolve", "NonlinearSolve", "Polyester", "PreallocationTools", "PrecompileTools", "Preferences", "RecursiveArrayTools", "Reexport", "SciMLBase", "SciMLNLSolve", "SciMLOperators", "SimpleNonlinearSolve", "SimpleUnPack", "SparseArrays", "SparseDiffTools", "StaticArrayInterface", "StaticArrays", "TruncatedStacktraces"]
-git-tree-sha1 = "760558496b50017d10e1907244dc2c4fa4385963"
+git-tree-sha1 = "ea532499662b771442746811fa345a7ea516225c"
 uuid = "1dea7af3-3e70-54e6-95c3-0bf5283fa5ed"
-version = "6.59.0"
+version = "6.59.1"
 
 [[deps.PCRE2_jll]]
 deps = ["Artifacts", "Libdl"]
@@ -1913,10 +1913,10 @@ uuid = "21216c6a-2e73-6563-6e65-726566657250"
 version = "1.4.1"
 
 [[deps.PrettyTables]]
-deps = ["Crayons", "LaTeXStrings", "Markdown", "Printf", "Reexport", "StringManipulation", "Tables"]
-git-tree-sha1 = "6842ce83a836fbbc0cfeca0b5a4de1a4dcbdb8d1"
+deps = ["Crayons", "LaTeXStrings", "Markdown", "PrecompileTools", "Printf", "Reexport", "StringManipulation", "Tables"]
+git-tree-sha1 = "3f43c2aae6aa4a2503b05587ab74f4f6aeff9fd0"
 uuid = "08abe8d2-0d0c-5749-adfa-8a2ac140af0d"
-version = "2.2.8"
+version = "2.3.0"
 
 [[deps.Primes]]
 deps = ["IntegerMathUtils"]
@@ -1948,9 +1948,9 @@ version = "1.0.0"
 
 [[deps.Qt6Base_jll]]
 deps = ["Artifacts", "CompilerSupportLibraries_jll", "Fontconfig_jll", "Glib_jll", "JLLWrappers", "Libdl", "Libglvnd_jll", "OpenSSL_jll", "Vulkan_Loader_jll", "Xorg_libSM_jll", "Xorg_libXext_jll", "Xorg_libXrender_jll", "Xorg_libxcb_jll", "Xorg_xcb_util_cursor_jll", "Xorg_xcb_util_image_jll", "Xorg_xcb_util_keysyms_jll", "Xorg_xcb_util_renderutil_jll", "Xorg_xcb_util_wm_jll", "Zlib_jll", "libinput_jll", "xkbcommon_jll"]
-git-tree-sha1 = "7c29f0e8c575428bd84dc3c72ece5178caa67336"
+git-tree-sha1 = "37b7bb7aabf9a085e0044307e1717436117f2b3b"
 uuid = "c0090381-4147-56d7-9ebc-da0b1113ec56"
-version = "6.5.2+2"
+version = "6.5.3+1"
 
 [[deps.QuadGK]]
 deps = ["DataStructures", "LinearAlgebra"]
@@ -2450,10 +2450,10 @@ weakdeps = ["IntervalArithmetic"]
     TaylorSeriesIAExt = "IntervalArithmetic"
 
 [[deps.TempestRemap_jll]]
-deps = ["Artifacts", "HDF5_jll", "JLLWrappers", "Libdl", "NetCDF_jll", "OpenBLAS32_jll", "Pkg"]
-git-tree-sha1 = "88c3818a492ad1a94b1aa440b01eab5d133209ff"
+deps = ["Artifacts", "HDF5_jll", "JLLWrappers", "Libdl", "NetCDF_jll", "OpenBLAS32_jll"]
+git-tree-sha1 = "723112218783928a20e0d865932694acfb7a7571"
 uuid = "8573a8c5-1df0-515e-a024-abad257ee284"
-version = "2.1.6+1"
+version = "2.2.0+0"
 
 [[deps.TensorCore]]
 deps = ["LinearAlgebra"]
@@ -2822,6 +2822,12 @@ git-tree-sha1 = "51b5eeb3f98367157a7a12a1fb0aa5328946c03c"
 uuid = "9a68df92-36a6-505f-a73e-abb412b6bfb4"
 version = "0.2.3+0"
 
+[[deps.libaec_jll]]
+deps = ["Artifacts", "JLLWrappers", "Libdl"]
+git-tree-sha1 = "eddd19a8dea6b139ea97bdc8a0e2667d4b661720"
+uuid = "477f73a3-ac25-53e9-8cc3-50b2fa2566f0"
+version = "1.0.6+1"
+
 [[deps.libaom_jll]]
 deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"]
 git-tree-sha1 = "3a2ea60308f0996d26f1e5354e10c24e9ef905d4"

diff --git a/examples/Manifest.toml b/examples/Manifest.toml
@@ -254,7 +254,7 @@ uuid = "3a4d1b5c-c61d-41fd-a00a-5873ba7a1b0d"
 version = "0.5.6"
 
 [[deps.ClimaCore]]
-deps = ["Adapt", "BandedMatrices", "BlockArrays", "CUDA", "ClimaComms", "CubedSphere", "DataStructures", "DocStringExtensions", "ForwardDiff", "GaussQuadrature", "GilbertCurves", "HDF5", "HDF5_jll", "InteractiveUtils", "IntervalSets", "LinearAlgebra", "PkgVersion", "RecursiveArrayTools", "Requires", "RootSolvers", "SparseArrays", "Static", "StaticArrays", "Statistics", "UnPack"]
+deps = ["Adapt", "BandedMatrices", "BlockArrays", "CUDA", "ClimaComms", "CubedSphere", "DataStructures", "DocStringExtensions", "ForwardDiff", "GaussQuadrature", "GilbertCurves", "HDF5", "InteractiveUtils", "IntervalSets", "LinearAlgebra", "PkgVersion", "RecursiveArrayTools", "Requires", "RootSolvers", "SparseArrays", "Static", "StaticArrays", "Statistics", "UnPack"]
 path = ".."
 uuid = "d414da3d-4745-48bb-8d80-42e94e092884"
 version = "0.10.55"
@@ -606,10 +606,10 @@ uuid = "c87230d0-a227-11e9-1b43-d7ebe4e7570a"
 version = "0.4.1"
 
 [[deps.FFMPEG_jll]]
-deps = ["Artifacts", "Bzip2_jll", "FreeType2_jll", "FriBidi_jll", "JLLWrappers", "LAME_jll", "Libdl", "Ogg_jll", "OpenSSL_jll", "Opus_jll", "PCRE2_jll", "Pkg", "Zlib_jll", "libaom_jll", "libass_jll", "libfdk_aac_jll", "libvorbis_jll", "x264_jll", "x265_jll"]
-git-tree-sha1 = "74faea50c1d007c85837327f6775bea60b5492dd"
+deps = ["Artifacts", "Bzip2_jll", "FreeType2_jll", "FriBidi_jll", "JLLWrappers", "LAME_jll", "Libdl", "Ogg_jll", "OpenSSL_jll", "Opus_jll", "PCRE2_jll", "Zlib_jll", "libaom_jll", "libass_jll", "libfdk_aac_jll", "libvorbis_jll", "x264_jll", "x265_jll"]
+git-tree-sha1 = "466d45dc38e15794ec7d5d63ec03d776a9aff36e"
 uuid = "b22a6f82-2f65-5046-a5b2-351ab43fb4e5"
-version = "4.4.2+2"
+version = "4.4.4+1"
 
 [[deps.FFTW]]
 deps = ["AbstractFFTs", "FFTW_jll", "LinearAlgebra", "MKL_jll", "Preferences", "Reexport"]
@@ -830,10 +830,10 @@ weakdeps = ["MPI"]
     MPIExt = "MPI"
 
 [[deps.HDF5_jll]]
-deps = ["Artifacts", "JLLWrappers", "LibCURL_jll", "Libdl", "OpenSSL_jll", "Pkg", "Zlib_jll"]
-git-tree-sha1 = "4cc2bb72df6ff40b055295fdef6d92955f9dede8"
+deps = ["Artifacts", "CompilerSupportLibraries_jll", "JLLWrappers", "LLVMOpenMP_jll", "LazyArtifacts", "LibCURL_jll", "Libdl", "MPICH_jll", "MPIPreferences", "MPItrampoline_jll", "MicrosoftMPI_jll", "OpenMPI_jll", "OpenSSL_jll", "TOML", "Zlib_jll", "libaec_jll"]
+git-tree-sha1 = "38c8874692d48d5440d5752d6c74b0c6b0b60739"
 uuid = "0234f1f7-429e-5d53-9886-15a909be8d59"
-version = "1.12.2+2"
+version = "1.14.2+1"
 
 [[deps.HTTP]]
 deps = ["Base64", "CodecZlib", "ConcurrentUtilities", "Dates", "ExceptionUnwrapping", "Logging", "LoggingExtras", "MbedTLS", "NetworkOptions", "OpenSSL", "Random", "SimpleBufferStream", "Sockets", "URIs", "UUIDs"]
@@ -1384,10 +1384,10 @@ uuid = "77ba4419-2d1f-58cd-9bb1-8ffee604a2e3"
 version = "1.0.2"
 
 [[deps.NetCDF_jll]]
-deps = ["Artifacts", "HDF5_jll", "JLLWrappers", "LibCURL_jll", "Libdl", "Pkg", "XML2_jll", "Zlib_jll"]
-git-tree-sha1 = "072f8371f74c3b9e1b26679de7fbf059d45ea221"
+deps = ["Artifacts", "Bzip2_jll", "HDF5_jll", "JLLWrappers", "LibCURL_jll", "Libdl", "XML2_jll", "Zlib_jll", "Zstd_jll"]
+git-tree-sha1 = "10c612c81eaffdd6b7c28a45a554cdd9d2f40ff1"
 uuid = "7243133f-43d8-5620-bbf4-c2c921802cf3"
-version = "400.902.5+1"
+version = "400.902.208+0"
 
 [[deps.NetworkOptions]]
 uuid = "ca575930-c2e3-43a9-ace4-1e988b2c1908"
@@ -1451,9 +1451,9 @@ version = "1.4.1"
 
 [[deps.OpenSSL_jll]]
 deps = ["Artifacts", "JLLWrappers", "Libdl"]
-git-tree-sha1 = "a12e56c72edee3ce6b96667745e6cbbe5498f200"
+git-tree-sha1 = "cc6e1927ac521b659af340e0ca45828a3ffc748f"
 uuid = "458c3c95-2e84-50aa-8efc-19380b2a3a95"
-version = "1.1.23+0"
+version = "3.0.12+0"
 
 [[deps.OpenSpecFun_jll]]
 deps = ["Artifacts", "CompilerSupportLibraries_jll", "JLLWrappers", "Libdl", "Pkg"]
@@ -1474,9 +1474,9 @@ version = "1.6.2"
 
 [[deps.OrdinaryDiffEq]]
 deps = ["ADTypes", "Adapt", "ArrayInterface", "DataStructures", "DiffEqBase", "DocStringExtensions", "ExponentialUtilities", "FastBroadcast", "FastClosures", "FiniteDiff", "ForwardDiff", "FunctionWrappersWrappers", "IfElse", "InteractiveUtils", "LineSearches", "LinearAlgebra", "LinearSolve", "Logging", "LoopVectorization", "MacroTools", "MuladdMacro", "NLsolve", "NonlinearSolve", "Polyester", "PreallocationTools", "PrecompileTools", "Preferences", "RecursiveArrayTools", "Reexport", "SciMLBase", "SciMLNLSolve", "SciMLOperators", "SimpleNonlinearSolve", "SimpleUnPack", "SparseArrays", "SparseDiffTools", "StaticArrayInterface", "StaticArrays", "TruncatedStacktraces"]
-git-tree-sha1 = "760558496b50017d10e1907244dc2c4fa4385963"
+git-tree-sha1 = "ea532499662b771442746811fa345a7ea516225c"
 uuid = "1dea7af3-3e70-54e6-95c3-0bf5283fa5ed"
-version = "6.59.0"
+version = "6.59.1"
 
 [[deps.PCRE2_jll]]
 deps = ["Artifacts", "Libdl"]
@@ -1604,10 +1604,10 @@ uuid = "21216c6a-2e73-6563-6e65-726566657250"
 version = "1.4.1"
 
 [[deps.PrettyTables]]
-deps = ["Crayons", "LaTeXStrings", "Markdown", "Printf", "Reexport", "StringManipulation", "Tables"]
-git-tree-sha1 = "6842ce83a836fbbc0cfeca0b5a4de1a4dcbdb8d1"
+deps = ["Crayons", "LaTeXStrings", "Markdown", "PrecompileTools", "Printf", "Reexport", "StringManipulation", "Tables"]
+git-tree-sha1 = "3f43c2aae6aa4a2503b05587ab74f4f6aeff9fd0"
 uuid = "08abe8d2-0d0c-5749-adfa-8a2ac140af0d"
-version = "2.2.8"
+version = "2.3.0"
 
 [[deps.Primes]]
 deps = ["IntegerMathUtils"]
@@ -1633,9 +1633,9 @@ version = "0.1.4"
 
 [[deps.Qt6Base_jll]]
 deps = ["Artifacts", "CompilerSupportLibraries_jll", "Fontconfig_jll", "Glib_jll", "JLLWrappers", "Libdl", "Libglvnd_jll", "OpenSSL_jll", "Vulkan_Loader_jll", "Xorg_libSM_jll", "Xorg_libXext_jll", "Xorg_libXrender_jll", "Xorg_libxcb_jll", "Xorg_xcb_util_cursor_jll", "Xorg_xcb_util_image_jll", "Xorg_xcb_util_keysyms_jll", "Xorg_xcb_util_renderutil_jll", "Xorg_xcb_util_wm_jll", "Zlib_jll", "libinput_jll", "xkbcommon_jll"]
-git-tree-sha1 = "7c29f0e8c575428bd84dc3c72ece5178caa67336"
+git-tree-sha1 = "37b7bb7aabf9a085e0044307e1717436117f2b3b"
 uuid = "c0090381-4147-56d7-9ebc-da0b1113ec56"
-version = "6.5.2+2"
+version = "6.5.3+1"
 
 [[deps.QuadGK]]
 deps = ["DataStructures", "LinearAlgebra"]
@@ -2045,10 +2045,10 @@ version = "0.15.2"
     IntervalArithmetic = "d1acc4aa-44c8-5952-acd4-ba5d80a2a253"
 
 [[deps.TempestRemap_jll]]
-deps = ["Artifacts", "HDF5_jll", "JLLWrappers", "Libdl", "NetCDF_jll", "OpenBLAS32_jll", "Pkg"]
-git-tree-sha1 = "88c3818a492ad1a94b1aa440b01eab5d133209ff"
+deps = ["Artifacts", "HDF5_jll", "JLLWrappers", "Libdl", "NetCDF_jll", "OpenBLAS32_jll"]
+git-tree-sha1 = "723112218783928a20e0d865932694acfb7a7571"
 uuid = "8573a8c5-1df0-515e-a024-abad257ee284"
-version = "2.1.6+1"
+version = "2.2.0+0"
 
 [[deps.TensorCore]]
 deps = ["LinearAlgebra"]
@@ -2420,6 +2420,12 @@ git-tree-sha1 = "3516a5630f741c9eecb3720b1ec9d8edc3ecc033"
 uuid = "1a1c6b14-54f6-533d-8383-74cd7377aa70"
 version = "3.1.1+0"
 
+[[deps.libaec_jll]]
+deps = ["Artifacts", "JLLWrappers", "Libdl"]
+git-tree-sha1 = "eddd19a8dea6b139ea97bdc8a0e2667d4b661720"
+uuid = "477f73a3-ac25-53e9-8cc3-50b2fa2566f0"
+version = "1.0.6+1"
+
 [[deps.libaom_jll]]
 deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"]
 git-tree-sha1 = "3a2ea60308f0996d26f1e5354e10c24e9ef905d4"