diff --git a/Project.toml b/Project.toml index 6278fff0..d235b73e 100644 --- a/Project.toml +++ b/Project.toml @@ -5,7 +5,9 @@ version = "1.2.0" [deps] ChunkSplitters = "ae650224-84b6-46f8-82ea-d812ca08434e" +ExactOptimalTransport = "24df6009-d856-477c-ac5c-91f668376b31" HDF5 = "f67ccb44-e63f-5c2f-98bd-6dc0ccc4ba2f" +HiGHS = "87dc4568-4c63-4d18-b0c0-bb2238e4078b" LinearAlgebra = "37e2e46d-f89d-539d-b4ee-838fcccc9c8e" MPI = "da04e1cc-30fd-572f-bb4f-1f8673147195" OpenMPI_jll = "fe0851c0-eecd-5654-98d4-656369965a5c" @@ -13,6 +15,7 @@ PDMats = "90014a1f-27ba-587c-ab20-58faa44d9150" Random = "9a3f8284-a2c9-5f02-9a11-845980a1fd5c" Statistics = "10745b16-79ce-11e8-11f9-7d13ad32a3b2" StructArrays = "09ab397b-f2b6-538f-b94a-2f83cf4a842a" +SuiteSparse_jll = "bea87d4a-7f5b-5778-9afe-8cc45184846c" Test = "8dfed614-e22c-5e08-85e1-65c5234f0b40" TimerOutputs = "a759f4b9-e2f1-59dc-863e-4aeb61b1ea8f" YAML = "ddb6d928-2868-570f-bddf-ab3f9cf99eb6" diff --git a/benchmark/Manifest-v1.11.toml b/benchmark/Manifest-v1.11.toml deleted file mode 100644 index ab6e46cd..00000000 --- a/benchmark/Manifest-v1.11.toml +++ /dev/null @@ -1,1579 +0,0 @@ -# This file is machine-generated - editing it directly is not advised - -[[AbstractFFTs]] -deps = ["LinearAlgebra"] -git-tree-sha1 = "d92ad398961a3ed262d8bf04a1a2b8340f915fef" -uuid = "621f4979-c628-5d54-868e-fcf4e3e8185c" -version = "1.5.0" - - [AbstractFFTs.extensions] - AbstractFFTsChainRulesCoreExt = "ChainRulesCore" - AbstractFFTsTestExt = "Test" - - [AbstractFFTs.weakdeps] - ChainRulesCore = "d360d2e6-b24c-11e9-a2a3-2a2ae2dbcce4" - Test = "8dfed614-e22c-5e08-85e1-65c5234f0b40" - -[[AbstractTrees]] -git-tree-sha1 = "2d9c9a55f9c93e8887ad391fbae72f8ef55e1177" -uuid = "1520ce14-60c1-5f80-bbc7-55ef81b5835c" -version = "0.4.5" - -[[AliasTables]] -deps = ["PtrArrays", "Random"] -git-tree-sha1 = "9876e1e164b144ca45e9e3198d0b689cadfed9ff" -uuid = "66dad0bd-aa9a-41b7-9441-69ab47430ed8" -version = "1.1.3" - -[[ArgTools]] -uuid = "0dad84c5-d112-42e6-8d28-ef12dabb789f" -version = "1.1.2" - -[[Arpack]] -deps = ["Arpack_jll", "Libdl", "LinearAlgebra", "Logging"] -git-tree-sha1 = "9b9b347613394885fd1c8c7729bfc60528faa436" -uuid = "7d9fca2a-8960-54d3-9f78-7d1dccf2cb97" -version = "0.5.4" - -[[Arpack_jll]] -deps = ["Artifacts", "CompilerSupportLibraries_jll", "JLLWrappers", "Libdl", "OpenBLAS_jll", "Pkg"] -git-tree-sha1 = "5ba6c757e8feccf03a1554dfaf3e26b3cfc7fd5e" -uuid = "68821587-b530-5797-8361-c406ea357684" -version = "3.5.1+1" - -[[Artifacts]] -uuid = "56f22d72-fd6d-98f1-02f0-08ddc0907c33" -version = "1.11.0" - -[[Base64]] -uuid = "2a0f44e3-6c83-55bd-87e4-b1978d98bd5f" -version = "1.11.0" - -[[BenchmarkCI]] -deps = ["Base64", "BenchmarkTools", "CpuId", "Dates", "GitHub", "JSON", "LinearAlgebra", "Logging", "Markdown", "Pkg", "PkgBenchmark", "Setfield", "Tar", "UnPack", "Zstd_jll"] -git-tree-sha1 = "41eef9519b5ba56f2bad6b594d6c54b847268a30" -uuid = "20533458-34a3-403d-a444-e18f38190b5b" -version = "0.1.9" - -[[BenchmarkTools]] -deps = ["JSON", "Logging", "Printf", "Profile", "Statistics", "UUIDs"] -git-tree-sha1 = "f1dff6729bc61f4d49e140da1af55dcd1ac97b2f" -uuid = "6e4b80f9-dd63-53aa-95a3-0cdb28fa8baf" -version = "1.5.0" - -[[BitFlags]] -git-tree-sha1 = "0691e34b3bb8be9307330f88d1a3c3f25466c24d" -uuid = "d1d4a3ce-64b1-5f1a-9ba4-7e7e69966f35" -version = "0.1.9" - -[[Bzip2_jll]] -deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] -git-tree-sha1 = "8873e196c2eb87962a2048b3b8e08946535864a1" -uuid = "6e34b625-4abd-537c-b88f-471c36dfa7a0" -version = "1.0.8+2" - -[[Cairo_jll]] -deps = ["Artifacts", "Bzip2_jll", "CompilerSupportLibraries_jll", "Fontconfig_jll", "FreeType2_jll", "Glib_jll", "JLLWrappers", "LZO_jll", "Libdl", "Pixman_jll", "Xorg_libXext_jll", "Xorg_libXrender_jll", "Zlib_jll", "libpng_jll"] -git-tree-sha1 = "009060c9a6168704143100f36ab08f06c2af4642" -uuid = "83423d85-b0ee-5818-9007-b63ccbeb887a" -version = "1.18.2+1" - -[[ChunkSplitters]] -git-tree-sha1 = "397b871ff701290cc122cca06af61c5bdf9f5605" -uuid = "ae650224-84b6-46f8-82ea-d812ca08434e" -version = "3.1.0" - -[[CodecZlib]] -deps = ["TranscodingStreams", "Zlib_jll"] -git-tree-sha1 = "bce6804e5e6044c6daab27bb533d1295e4a2e759" -uuid = "944b1d66-785c-5afd-91f1-9de20f533193" -version = "0.7.6" - -[[ColorSchemes]] -deps = ["ColorTypes", "ColorVectorSpace", "Colors", "FixedPointNumbers", "PrecompileTools", "Random"] -git-tree-sha1 = "c785dfb1b3bfddd1da557e861b919819b82bbe5b" -uuid = "35d6a980-a343-548e-a6ea-1d62b119f2f4" -version = "3.27.1" - -[[ColorTypes]] -deps = ["FixedPointNumbers", "Random"] -git-tree-sha1 = "c7acce7a7e1078a20a285211dd73cd3941a871d6" -uuid = "3da002f7-5984-5a60-b8a6-cbb66c0b333f" -version = "0.12.0" -weakdeps = ["StyledStrings"] - - [ColorTypes.extensions] - StyledStringsExt = "StyledStrings" - -[[ColorVectorSpace]] -deps = ["ColorTypes", "FixedPointNumbers", "LinearAlgebra", "Requires", "Statistics", "TensorCore"] -git-tree-sha1 = "8b3b6f87ce8f65a2b4f857528fd8d70086cd72b1" -uuid = "c3611d14-8923-5661-9e6a-0046d554d3a4" -version = "0.11.0" -weakdeps = ["SpecialFunctions"] - - [ColorVectorSpace.extensions] - SpecialFunctionsExt = "SpecialFunctions" - -[[Colors]] -deps = ["ColorTypes", "FixedPointNumbers", "Reexport"] -git-tree-sha1 = "64e15186f0aa277e174aa81798f7eb8598e0157e" -uuid = "5ae59095-9a9b-59fe-a467-6f913c188581" -version = "0.13.0" - -[[Compat]] -deps = ["TOML", "UUIDs"] -git-tree-sha1 = "8ae8d32e09f0dcf42a36b90d4e17f5dd2e4c4215" -uuid = "34da2185-b29b-5c13-b0c7-acf172513d20" -version = "4.16.0" -weakdeps = ["Dates", "LinearAlgebra"] - - [Compat.extensions] - CompatLinearAlgebraExt = "LinearAlgebra" - -[[CompilerSupportLibraries_jll]] -deps = ["Artifacts", "Libdl"] -uuid = "e66e0078-7015-5450-92f7-15fbd957f2ae" -version = "1.1.1+0" - -[[ConcurrentUtilities]] -deps = ["Serialization", "Sockets"] -git-tree-sha1 = "ea32b83ca4fefa1768dc84e504cc0a94fb1ab8d1" -uuid = "f0e56b4a-5159-44fe-b623-3e5288b988bb" -version = "2.4.2" - -[[ConstructionBase]] -git-tree-sha1 = "76219f1ed5771adbb096743bff43fb5fdd4c1157" -uuid = "187b0558-2788-49d3-abe0-74a17ed4e7c9" -version = "1.5.8" - - [ConstructionBase.extensions] - ConstructionBaseIntervalSetsExt = "IntervalSets" - ConstructionBaseLinearAlgebraExt = "LinearAlgebra" - ConstructionBaseStaticArraysExt = "StaticArrays" - - [ConstructionBase.weakdeps] - IntervalSets = "8197267c-284f-5f27-9208-e0e47529a953" - LinearAlgebra = "37e2e46d-f89d-539d-b4ee-838fcccc9c8e" - StaticArrays = "90137ffa-7385-5640-81b9-e52037218182" - -[[Contour]] -git-tree-sha1 = "439e35b0b36e2e5881738abc8857bd92ad6ff9a8" -uuid = "d38c429a-6771-53c6-b99e-75d170b6e991" -version = "0.6.3" - -[[CpuId]] -deps = ["Markdown"] -git-tree-sha1 = "fcbb72b032692610bfbdb15018ac16a36cf2e406" -uuid = "adafc99b-e345-5852-983c-f28acb93d879" -version = "0.3.1" - -[[DataAPI]] -git-tree-sha1 = "abe83f3a2f1b857aac70ef8b269080af17764bbe" -uuid = "9a962f9c-6df0-11e9-0e5d-c546b8b5ee8a" -version = "1.16.0" - -[[DataStructures]] -deps = ["Compat", "InteractiveUtils", "OrderedCollections"] -git-tree-sha1 = "1d0a14036acb104d9e89698bd408f63ab58cdc82" -uuid = "864edb3b-99cc-5e75-8d2d-829cb0a9cfe8" -version = "0.18.20" - -[[DataValueInterfaces]] -git-tree-sha1 = "bfc1187b79289637fa0ef6d4436ebdfe6905cbd6" -uuid = "e2d170a0-9d28-54be-80f0-106bbe20a464" -version = "1.0.0" - -[[Dates]] -deps = ["Printf"] -uuid = "ade2ca70-3891-5945-98fb-dc099432e06a" -version = "1.11.0" - -[[Dbus_jll]] -deps = ["Artifacts", "Expat_jll", "JLLWrappers", "Libdl"] -git-tree-sha1 = "fc173b380865f70627d7dd1190dc2fce6cc105af" -uuid = "ee1fde0b-3d02-5ea6-8484-8dfef6360eab" -version = "1.14.10+0" - -[[DelimitedFiles]] -deps = ["Mmap"] -git-tree-sha1 = "9e2f36d3c96a820c678f2f1f1782582fcf685bae" -uuid = "8bb1440f-4735-579b-a4ab-409b98df4dab" -version = "1.9.1" - -[[Distributed]] -deps = ["Random", "Serialization", "Sockets"] -uuid = "8ba89e20-285c-5b6f-9357-94700520ee1b" -version = "1.11.0" - -[[Distributions]] -deps = ["AliasTables", "FillArrays", "LinearAlgebra", "PDMats", "Printf", "QuadGK", "Random", "SpecialFunctions", "Statistics", "StatsAPI", "StatsBase", "StatsFuns"] -git-tree-sha1 = "3101c32aab536e7a27b1763c0797dba151b899ad" -uuid = "31c24e10-a181-5473-b8eb-7969acd0382f" -version = "0.25.113" - - [Distributions.extensions] - DistributionsChainRulesCoreExt = "ChainRulesCore" - DistributionsDensityInterfaceExt = "DensityInterface" - DistributionsTestExt = "Test" - - [Distributions.weakdeps] - ChainRulesCore = "d360d2e6-b24c-11e9-a2a3-2a2ae2dbcce4" - DensityInterface = "b429d917-457f-4dbc-8f4c-0cc954292b1d" - Test = "8dfed614-e22c-5e08-85e1-65c5234f0b40" - -[[DocStringExtensions]] -deps = ["LibGit2"] -git-tree-sha1 = "2fb1e02f2b635d0845df5d7c167fec4dd739b00d" -uuid = "ffbed154-4ef7-542d-bbb7-c09d3a79fcae" -version = "0.9.3" - -[[Downloads]] -deps = ["ArgTools", "FileWatching", "LibCURL", "NetworkOptions"] -uuid = "f43a241f-c20a-4ad4-852c-f6b1247861c6" -version = "1.6.0" - -[[EpollShim_jll]] -deps = ["Artifacts", "JLLWrappers", "Libdl"] -git-tree-sha1 = "8e9441ee83492030ace98f9789a654a6d0b1f643" -uuid = "2702e6a9-849d-5ed8-8c21-79e8b8f9ee43" -version = "0.0.20230411+0" - -[[ExceptionUnwrapping]] -deps = ["Test"] -git-tree-sha1 = "dcb08a0d93ec0b1cdc4af184b26b591e9695423a" -uuid = "460bff9d-24e4-43bc-9d9f-a8973cb893f4" -version = "0.1.10" - -[[Expat_jll]] -deps = ["Artifacts", "JLLWrappers", "Libdl"] -git-tree-sha1 = "cc5231d52eb1771251fbd37171dbc408bcc8a1b6" -uuid = "2e619515-83b5-522b-bb60-26c02a35a201" -version = "2.6.4+0" - -[[ExprTools]] -git-tree-sha1 = "27415f162e6028e81c72b82ef756bf321213b6ec" -uuid = "e2ba6199-217a-4e67-a87a-7c52f15ade04" -version = "0.1.10" - -[[FFMPEG]] -deps = ["FFMPEG_jll"] -git-tree-sha1 = "53ebe7511fa11d33bec688a9178fac4e49eeee00" -uuid = "c87230d0-a227-11e9-1b43-d7ebe4e7570a" -version = "0.4.2" - -[[FFMPEG_jll]] -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 = "4.4.4+1" - -[[FFTW]] -deps = ["AbstractFFTs", "FFTW_jll", "LinearAlgebra", "MKL_jll", "Preferences", "Reexport"] -git-tree-sha1 = "4820348781ae578893311153d69049a93d05f39d" -uuid = "7a1cc6ca-52ef-59f5-83cd-3a7055c09341" -version = "1.8.0" - -[[FFTW_jll]] -deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] -git-tree-sha1 = "4d81ed14783ec49ce9f2e168208a12ce1815aa25" -uuid = "f5851436-0d7a-5f13-b9de-f02708fd171a" -version = "3.3.10+1" - -[[FastGaussQuadrature]] -deps = ["LinearAlgebra", "SpecialFunctions", "StaticArrays"] -git-tree-sha1 = "fd923962364b645f3719855c88f7074413a6ad92" -uuid = "442a2c76-b920-505d-bb47-c5924d526838" -version = "1.0.2" - -[[FileWatching]] -uuid = "7b1f6079-737a-58dc-b8bc-7a2ca5c1b5ee" -version = "1.11.0" - 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- -[[libblastrampoline_jll]] -deps = ["Artifacts", "Libdl"] -uuid = "8e850b90-86db-534c-a0d3-1478176c7d93" -version = "5.11.0+0" - -[[libdecor_jll]] -deps = ["Artifacts", "Dbus_jll", "JLLWrappers", "Libdl", "Libglvnd_jll", "Pango_jll", "Wayland_jll", "xkbcommon_jll"] -git-tree-sha1 = "9bf7903af251d2050b467f76bdbe57ce541f7f4f" -uuid = "1183f4f0-6f2a-5f1a-908b-139f9cdfea6f" -version = "0.2.2+0" - -[[libevdev_jll]] -deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] -git-tree-sha1 = "141fe65dc3efabb0b1d5ba74e91f6ad26f84cc22" -uuid = "2db6ffa8-e38f-5e21-84af-90c45d0032cc" -version = "1.11.0+0" - -[[libfdk_aac_jll]] -deps = ["Artifacts", "JLLWrappers", "Libdl"] -git-tree-sha1 = "8a22cf860a7d27e4f3498a0fe0811a7957badb38" -uuid = "f638f0a6-7fb0-5443-88ba-1cc74229b280" -version = "2.0.3+0" - -[[libinput_jll]] -deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg", "eudev_jll", "libevdev_jll", "mtdev_jll"] -git-tree-sha1 = "ad50e5b90f222cfe78aa3d5183a20a12de1322ce" -uuid = 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-[[oneTBB_jll]] -deps = ["Artifacts", "JLLWrappers", "Libdl"] -git-tree-sha1 = "7d0ea0f4895ef2f5cb83645fa689e52cb55cf493" -uuid = "1317d2d5-d96f-522e-a858-c73665f53c3e" -version = "2021.12.0+0" - -[[p7zip_jll]] -deps = ["Artifacts", "Libdl"] -uuid = "3f19e933-33d8-53b3-aaab-bd5110c3b7a0" -version = "17.4.0+2" - -[[x264_jll]] -deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] -git-tree-sha1 = "4fea590b89e6ec504593146bf8b988b2c00922b2" -uuid = "1270edf5-f2f9-52d2-97e9-ab00b5d0237a" -version = "2021.5.5+0" - -[[x265_jll]] -deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] -git-tree-sha1 = "ee567a171cce03570d77ad3a43e90218e38937a9" -uuid = "dfaa095f-4041-5dcd-9319-2fabd8486b76" -version = "3.5.0+0" - -[[xkbcommon_jll]] -deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg", "Wayland_jll", "Wayland_protocols_jll", "Xorg_libxcb_jll", "Xorg_xkeyboard_config_jll"] -git-tree-sha1 = "9c304562909ab2bab0262639bd4f444d7bc2be37" -uuid = "d8fb68d0-12a3-5cfd-a85a-d49703b185fd" -version = "1.4.1+1" diff --git a/benchmark/Manifest.toml b/benchmark/Manifest.toml index 49d875f4..cb25a868 100644 --- a/benchmark/Manifest.toml +++ b/benchmark/Manifest.toml @@ -1,8 +1,8 @@ # This file is machine-generated - editing it directly is not advised -julia_version = "1.10.4" +julia_version = "1.10.10" manifest_format = "2.0" -project_hash = "cec505300ec6a2cea80149f24ed06e6311223663" +project_hash = "f4354a6ef34f268e40fe7011215e1982346058d9" [[deps.AbstractFFTs]] deps = ["LinearAlgebra"] @@ -58,10 +58,10 @@ uuid = "20533458-34a3-403d-a444-e18f38190b5b" version = "0.1.9" [[deps.BenchmarkTools]] -deps = ["JSON", "Logging", "Printf", "Profile", "Statistics", "UUIDs"] -git-tree-sha1 = "f1dff6729bc61f4d49e140da1af55dcd1ac97b2f" +deps = ["Compat", "JSON", "Logging", "Printf", "Profile", "Statistics", "UUIDs"] +git-tree-sha1 = "e38fbc49a620f5d0b660d7f543db1009fe0f8336" uuid = "6e4b80f9-dd63-53aa-95a3-0cdb28fa8baf" -version = "1.5.0" +version = "1.6.0" [[deps.BitFlags]] git-tree-sha1 = "0691e34b3bb8be9307330f88d1a3c3f25466c24d" @@ -69,67 +69,39 @@ uuid = "d1d4a3ce-64b1-5f1a-9ba4-7e7e69966f35" version = "0.1.9" [[deps.Bzip2_jll]] -deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] -git-tree-sha1 = "8873e196c2eb87962a2048b3b8e08946535864a1" +deps = ["Artifacts", "JLLWrappers", "Libdl"] +git-tree-sha1 = "1b96ea4a01afe0ea4090c5c8039690672dd13f2e" uuid = "6e34b625-4abd-537c-b88f-471c36dfa7a0" -version = "1.0.8+2" - -[[deps.Cairo_jll]] -deps = ["Artifacts", "Bzip2_jll", "CompilerSupportLibraries_jll", "Fontconfig_jll", "FreeType2_jll", "Glib_jll", "JLLWrappers", "LZO_jll", "Libdl", "Pixman_jll", "Xorg_libXext_jll", "Xorg_libXrender_jll", "Zlib_jll", "libpng_jll"] -git-tree-sha1 = "009060c9a6168704143100f36ab08f06c2af4642" -uuid = "83423d85-b0ee-5818-9007-b63ccbeb887a" -version = "1.18.2+1" +version = "1.0.9+0" [[deps.ChunkSplitters]] -git-tree-sha1 = "397b871ff701290cc122cca06af61c5bdf9f5605" +git-tree-sha1 = "63a3903063d035260f0f6eab00f517471c5dc784" uuid = "ae650224-84b6-46f8-82ea-d812ca08434e" -version = "3.1.0" +version = "3.1.2" + +[[deps.CodecBzip2]] +deps = ["Bzip2_jll", "TranscodingStreams"] +git-tree-sha1 = "84990fa864b7f2b4901901ca12736e45ee79068c" +uuid = "523fee87-0ab8-5b00-afb7-3ecf72e48cfd" +version = "0.8.5" [[deps.CodecZlib]] deps = ["TranscodingStreams", "Zlib_jll"] -git-tree-sha1 = "bce6804e5e6044c6daab27bb533d1295e4a2e759" +git-tree-sha1 = "962834c22b66e32aa10f7611c08c8ca4e20749a9" uuid = "944b1d66-785c-5afd-91f1-9de20f533193" -version = "0.7.6" - -[[deps.ColorSchemes]] -deps = ["ColorTypes", "ColorVectorSpace", "Colors", "FixedPointNumbers", "PrecompileTools", "Random"] -git-tree-sha1 = "c785dfb1b3bfddd1da557e861b919819b82bbe5b" -uuid = "35d6a980-a343-548e-a6ea-1d62b119f2f4" -version = "3.27.1" - -[[deps.ColorTypes]] -deps = ["FixedPointNumbers", "Random"] -git-tree-sha1 = "c7acce7a7e1078a20a285211dd73cd3941a871d6" -uuid = "3da002f7-5984-5a60-b8a6-cbb66c0b333f" -version = "0.12.0" - - [deps.ColorTypes.extensions] - StyledStringsExt = "StyledStrings" - - [deps.ColorTypes.weakdeps] - StyledStrings = "f489334b-da3d-4c2e-b8f0-e476e12c162b" - -[[deps.ColorVectorSpace]] -deps = ["ColorTypes", "FixedPointNumbers", "LinearAlgebra", "Requires", "Statistics", "TensorCore"] -git-tree-sha1 = "8b3b6f87ce8f65a2b4f857528fd8d70086cd72b1" -uuid = "c3611d14-8923-5661-9e6a-0046d554d3a4" -version = "0.11.0" -weakdeps = ["SpecialFunctions"] - - [deps.ColorVectorSpace.extensions] - SpecialFunctionsExt = "SpecialFunctions" - -[[deps.Colors]] -deps = ["ColorTypes", "FixedPointNumbers", "Reexport"] -git-tree-sha1 = "64e15186f0aa277e174aa81798f7eb8598e0157e" -uuid = "5ae59095-9a9b-59fe-a467-6f913c188581" -version = "0.13.0" +version = "0.7.8" + +[[deps.CommonSubexpressions]] +deps = ["MacroTools"] +git-tree-sha1 = "cda2cfaebb4be89c9084adaca7dd7333369715c5" +uuid = "bbf7d656-a473-5ed7-a52c-81e309532950" +version = "0.3.1" [[deps.Compat]] deps = ["TOML", "UUIDs"] -git-tree-sha1 = "8ae8d32e09f0dcf42a36b90d4e17f5dd2e4c4215" +git-tree-sha1 = "0037835448781bb46feb39866934e243886d756a" uuid = "34da2185-b29b-5c13-b0c7-acf172513d20" -version = "4.16.0" +version = "4.18.0" weakdeps = ["Dates", "LinearAlgebra"] [deps.Compat.extensions] @@ -142,14 +114,14 @@ version = "1.1.1+0" [[deps.ConcurrentUtilities]] deps = ["Serialization", "Sockets"] -git-tree-sha1 = "ea32b83ca4fefa1768dc84e504cc0a94fb1ab8d1" +git-tree-sha1 = "d9d26935a0bcffc87d2613ce14c527c99fc543fd" uuid = "f0e56b4a-5159-44fe-b623-3e5288b988bb" -version = "2.4.2" +version = "2.5.0" [[deps.ConstructionBase]] -git-tree-sha1 = "76219f1ed5771adbb096743bff43fb5fdd4c1157" +git-tree-sha1 = "b4b092499347b18a015186eae3042f72267106cb" uuid = "187b0558-2788-49d3-abe0-74a17ed4e7c9" -version = "1.5.8" +version = "1.6.0" [deps.ConstructionBase.extensions] ConstructionBaseIntervalSetsExt = "IntervalSets" @@ -161,11 +133,6 @@ version = "1.5.8" LinearAlgebra = "37e2e46d-f89d-539d-b4ee-838fcccc9c8e" StaticArrays = "90137ffa-7385-5640-81b9-e52037218182" -[[deps.Contour]] -git-tree-sha1 = "439e35b0b36e2e5881738abc8857bd92ad6ff9a8" -uuid = "d38c429a-6771-53c6-b99e-75d170b6e991" -version = "0.6.3" - [[deps.CpuId]] deps = ["Markdown"] git-tree-sha1 = "fcbb72b032692610bfbdb15018ac16a36cf2e406" @@ -178,10 +145,10 @@ uuid = "9a962f9c-6df0-11e9-0e5d-c546b8b5ee8a" version = "1.16.0" [[deps.DataStructures]] -deps = ["Compat", "InteractiveUtils", "OrderedCollections"] -git-tree-sha1 = "1d0a14036acb104d9e89698bd408f63ab58cdc82" +deps = ["OrderedCollections"] +git-tree-sha1 = "6c72198e6a101cccdd4c9731d3985e904ba26037" uuid = "864edb3b-99cc-5e75-8d2d-829cb0a9cfe8" -version = "0.18.20" +version = "0.19.1" [[deps.DataValueInterfaces]] git-tree-sha1 = "bfc1187b79289637fa0ef6d4436ebdfe6905cbd6" @@ -192,27 +159,47 @@ version = "1.0.0" deps = ["Printf"] uuid = "ade2ca70-3891-5945-98fb-dc099432e06a" -[[deps.Dbus_jll]] -deps = ["Artifacts", "Expat_jll", "JLLWrappers", "Libdl"] -git-tree-sha1 = "fc173b380865f70627d7dd1190dc2fce6cc105af" -uuid = "ee1fde0b-3d02-5ea6-8484-8dfef6360eab" -version = "1.14.10+0" - [[deps.DelimitedFiles]] deps = ["Mmap"] git-tree-sha1 = "9e2f36d3c96a820c678f2f1f1782582fcf685bae" uuid = "8bb1440f-4735-579b-a4ab-409b98df4dab" version = "1.9.1" +[[deps.DiffResults]] +deps = ["StaticArraysCore"] +git-tree-sha1 = "782dd5f4561f5d267313f23853baaaa4c52ea621" +uuid = "163ba53b-c6d8-5494-b064-1a9d43ac40c5" +version = "1.1.0" + +[[deps.DiffRules]] +deps = ["IrrationalConstants", "LogExpFunctions", "NaNMath", "Random", "SpecialFunctions"] +git-tree-sha1 = "23163d55f885173722d1e4cf0f6110cdbaf7e272" +uuid = "b552c78f-8df3-52c6-915a-8e097449b14b" +version = "1.15.1" + +[[deps.Distances]] +deps = ["LinearAlgebra", "Statistics", "StatsAPI"] +git-tree-sha1 = "c7e3a542b999843086e2f29dac96a618c105be1d" +uuid = "b4f34e82-e78d-54a5-968a-f98e89d6e8f7" +version = "0.10.12" + + [deps.Distances.extensions] + DistancesChainRulesCoreExt = "ChainRulesCore" + DistancesSparseArraysExt = "SparseArrays" + + [deps.Distances.weakdeps] + ChainRulesCore = "d360d2e6-b24c-11e9-a2a3-2a2ae2dbcce4" + SparseArrays = "2f01184e-e22b-5df5-ae63-d93ebab69eaf" + [[deps.Distributed]] deps = ["Random", "Serialization", "Sockets"] uuid = "8ba89e20-285c-5b6f-9357-94700520ee1b" [[deps.Distributions]] deps = ["AliasTables", "FillArrays", "LinearAlgebra", "PDMats", "Printf", "QuadGK", "Random", "SpecialFunctions", "Statistics", "StatsAPI", "StatsBase", "StatsFuns"] -git-tree-sha1 = "3101c32aab536e7a27b1763c0797dba151b899ad" +git-tree-sha1 = "3e6d038b77f22791b8e3472b7c633acea1ecac06" uuid = "31c24e10-a181-5473-b8eb-7969acd0382f" -version = "0.25.113" +version = "0.25.120" [deps.Distributions.extensions] DistributionsChainRulesCoreExt = "ChainRulesCore" @@ -225,62 +212,43 @@ version = "0.25.113" Test = "8dfed614-e22c-5e08-85e1-65c5234f0b40" [[deps.DocStringExtensions]] -deps = ["LibGit2"] -git-tree-sha1 = "2fb1e02f2b635d0845df5d7c167fec4dd739b00d" +git-tree-sha1 = "7442a5dfe1ebb773c29cc2962a8980f47221d76c" uuid = "ffbed154-4ef7-542d-bbb7-c09d3a79fcae" -version = "0.9.3" +version = "0.9.5" [[deps.Downloads]] deps = ["ArgTools", "FileWatching", "LibCURL", "NetworkOptions"] uuid = "f43a241f-c20a-4ad4-852c-f6b1247861c6" version = "1.6.0" -[[deps.EpollShim_jll]] -deps = ["Artifacts", "JLLWrappers", "Libdl"] -git-tree-sha1 = "8e9441ee83492030ace98f9789a654a6d0b1f643" -uuid = "2702e6a9-849d-5ed8-8c21-79e8b8f9ee43" -version = "0.0.20230411+0" +[[deps.ExactOptimalTransport]] +deps = ["Distances", "Distributions", "FillArrays", "LinearAlgebra", "MathOptInterface", "PDMats", "QuadGK", "SparseArrays", "StatsBase"] +git-tree-sha1 = "aca11e5cbf419be6778707f4ddc90d486bc79e92" +uuid = "24df6009-d856-477c-ac5c-91f668376b31" +version = "0.2.5" [[deps.ExceptionUnwrapping]] deps = ["Test"] -git-tree-sha1 = "dcb08a0d93ec0b1cdc4af184b26b591e9695423a" +git-tree-sha1 = "d36f682e590a83d63d1c7dbd287573764682d12a" uuid = "460bff9d-24e4-43bc-9d9f-a8973cb893f4" -version = "0.1.10" - -[[deps.Expat_jll]] -deps = ["Artifacts", "JLLWrappers", "Libdl"] -git-tree-sha1 = "cc5231d52eb1771251fbd37171dbc408bcc8a1b6" -uuid = "2e619515-83b5-522b-bb60-26c02a35a201" -version = "2.6.4+0" +version = "0.1.11" [[deps.ExprTools]] git-tree-sha1 = "27415f162e6028e81c72b82ef756bf321213b6ec" uuid = "e2ba6199-217a-4e67-a87a-7c52f15ade04" version = "0.1.10" -[[deps.FFMPEG]] -deps = ["FFMPEG_jll"] -git-tree-sha1 = "53ebe7511fa11d33bec688a9178fac4e49eeee00" -uuid = "c87230d0-a227-11e9-1b43-d7ebe4e7570a" -version = "0.4.2" - -[[deps.FFMPEG_jll]] -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 = "4.4.4+1" - [[deps.FFTW]] deps = ["AbstractFFTs", "FFTW_jll", "LinearAlgebra", "MKL_jll", "Preferences", "Reexport"] -git-tree-sha1 = "4820348781ae578893311153d69049a93d05f39d" +git-tree-sha1 = "797762812ed063b9b94f6cc7742bc8883bb5e69e" uuid = "7a1cc6ca-52ef-59f5-83cd-3a7055c09341" -version = "1.8.0" +version = "1.9.0" [[deps.FFTW_jll]] -deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] -git-tree-sha1 = "4d81ed14783ec49ce9f2e168208a12ce1815aa25" +deps = ["Artifacts", "JLLWrappers", "Libdl"] +git-tree-sha1 = "6d6219a004b8cf1e0b4dbe27a2860b8e04eba0be" uuid = "f5851436-0d7a-5f13-b9de-f02708fd171a" -version = "3.3.10+1" +version = "3.3.11+0" [[deps.FastGaussQuadrature]] deps = ["LinearAlgebra", "SpecialFunctions", "StaticArrays"] @@ -303,91 +271,31 @@ weakdeps = ["PDMats", "SparseArrays", "Statistics"] FillArraysSparseArraysExt = "SparseArrays" FillArraysStatisticsExt = "Statistics" -[[deps.FixedPointNumbers]] -deps = ["Statistics"] -git-tree-sha1 = "05882d6995ae5c12bb5f36dd2ed3f61c98cbb172" -uuid = "53c48c17-4a7d-5ca2-90c5-79b7896eea93" -version = "0.8.5" - -[[deps.Fontconfig_jll]] -deps = ["Artifacts", "Bzip2_jll", "Expat_jll", "FreeType2_jll", "JLLWrappers", "Libdl", "Libuuid_jll", "Zlib_jll"] -git-tree-sha1 = "db16beca600632c95fc8aca29890d83788dd8b23" -uuid = "a3f928ae-7b40-5064-980b-68af3947d34b" -version = "2.13.96+0" - -[[deps.Format]] -git-tree-sha1 = "9c68794ef81b08086aeb32eeaf33531668d5f5fc" -uuid = "1fa38f19-a742-5d3f-a2b9-30dd87b9d5f8" -version = "1.3.7" - -[[deps.FreeType2_jll]] -deps = ["Artifacts", "Bzip2_jll", "JLLWrappers", "Libdl", "Zlib_jll"] -git-tree-sha1 = "5c1d8ae0efc6c2e7b1fc502cbe25def8f661b7bc" -uuid = "d7e528f0-a631-5988-bf34-fe36492bcfd7" -version = "2.13.2+0" +[[deps.ForwardDiff]] +deps = ["CommonSubexpressions", "DiffResults", "DiffRules", "LinearAlgebra", "LogExpFunctions", "NaNMath", "Preferences", "Printf", "Random", "SpecialFunctions"] +git-tree-sha1 = "ce15956960057e9ff7f1f535400ffa14c92429a4" +uuid = "f6369f11-7733-5829-9624-2563aa707210" +version = "1.1.0" +weakdeps = ["StaticArrays"] -[[deps.FriBidi_jll]] -deps = ["Artifacts", "JLLWrappers", "Libdl"] -git-tree-sha1 = "1ed150b39aebcc805c26b93a8d0122c940f64ce2" -uuid = "559328eb-81f9-559d-9380-de523a88c83c" -version = "1.0.14+0" + [deps.ForwardDiff.extensions] + ForwardDiffStaticArraysExt = "StaticArrays" [[deps.Future]] deps = ["Random"] uuid = "9fa8497b-333b-5362-9e8d-4d0656e87820" -[[deps.GLFW_jll]] -deps = ["Artifacts", "JLLWrappers", "Libdl", "Libglvnd_jll", "Xorg_libXcursor_jll", "Xorg_libXi_jll", "Xorg_libXinerama_jll", "Xorg_libXrandr_jll", "libdecor_jll", "xkbcommon_jll"] -git-tree-sha1 = "532f9126ad901533af1d4f5c198867227a7bb077" -uuid = "0656b61e-2033-5cc2-a64a-77c0f6c09b89" -version = "3.4.0+1" - -[[deps.GR]] -deps = ["Artifacts", "Base64", "DelimitedFiles", "Downloads", "GR_jll", "HTTP", "JSON", "Libdl", "LinearAlgebra", "Preferences", "Printf", "Qt6Wayland_jll", "Random", "Serialization", "Sockets", "TOML", "Tar", "Test", "p7zip_jll"] -git-tree-sha1 = "ee28ddcd5517d54e417182fec3886e7412d3926f" -uuid = "28b8d3ca-fb5f-59d9-8090-bfdbd6d07a71" -version = "0.73.8" - -[[deps.GR_jll]] -deps = ["Artifacts", "Bzip2_jll", "Cairo_jll", "FFMPEG_jll", "Fontconfig_jll", "FreeType2_jll", "GLFW_jll", "JLLWrappers", "JpegTurbo_jll", "Libdl", "Libtiff_jll", "Pixman_jll", "Qt6Base_jll", "Zlib_jll", "libpng_jll"] -git-tree-sha1 = "f31929b9e67066bee48eec8b03c0df47d31a74b3" -uuid = "d2c73de3-f751-5644-a686-071e5b155ba9" -version = "0.73.8+0" - [[deps.GaussianRandomFields]] -deps = ["Arpack", "FFTW", "FastGaussQuadrature", "LinearAlgebra", "Plots", "Random", "RecipesBase", "SpecialFunctions", "Statistics", "StatsBase"] -git-tree-sha1 = "aaf37fbddc7bca5391677fb5f5082dd29442ca8f" +deps = ["Arpack", "FFTW", "FastGaussQuadrature", "LinearAlgebra", "Random", "RecipesBase", "SpecialFunctions", "Statistics", "StatsBase"] +git-tree-sha1 = "f78f66b8c88c8c99a72390296fb599057e78426d" uuid = "e4b2fa32-6e09-5554-b718-106ed5adafe9" -version = "2.2.5" - -[[deps.Gettext_jll]] -deps = ["Artifacts", "CompilerSupportLibraries_jll", "JLLWrappers", "Libdl", "Libiconv_jll", "Pkg", "XML2_jll"] -git-tree-sha1 = "9b02998aba7bf074d14de89f9d37ca24a1a0b046" -uuid = "78b55507-aeef-58d4-861c-77aaff3498b1" -version = "0.21.0+0" +version = "2.2.6" [[deps.GitHub]] deps = ["Base64", "Dates", "HTTP", "JSON", "MbedTLS", "Sockets", "SodiumSeal", "URIs"] -git-tree-sha1 = "7ee730a8484d673a8ce21d8536acfe6494475994" +git-tree-sha1 = "2501485472c50b24874cc949f0fce9bd3c4a1738" uuid = "bc5e4493-9b4d-5f90-b8aa-2b2bcaad7a26" -version = "5.9.0" - -[[deps.Glib_jll]] -deps = ["Artifacts", "Gettext_jll", "JLLWrappers", "Libdl", "Libffi_jll", "Libiconv_jll", "Libmount_jll", "PCRE2_jll", "Zlib_jll"] -git-tree-sha1 = "674ff0db93fffcd11a3573986e550d66cd4fd71f" -uuid = "7746bdde-850d-59dc-9ae8-88ece973131d" -version = "2.80.5+0" - -[[deps.Graphite2_jll]] -deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] -git-tree-sha1 = "344bf40dcab1073aca04aa0df4fb092f920e4011" -uuid = "3b182d85-2403-5c21-9c21-1e1f0cc25472" -version = "1.3.14+0" - -[[deps.Grisu]] -git-tree-sha1 = "53bb909d1151e57e2484c3d1b53e19552b887fb2" -uuid = "42e2da0e-8278-4e71-bc24-59509adca0fe" -version = "1.0.2" +version = "5.10.0" [[deps.HDF5]] deps = ["Compat", "HDF5_jll", "Libdl", "MPIPreferences", "Mmap", "Preferences", "Printf", "Random", "Requires", "UUIDs"] @@ -400,66 +308,66 @@ weakdeps = ["MPI"] MPIExt = "MPI" [[deps.HDF5_jll]] -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" +deps = ["Artifacts", "CompilerSupportLibraries_jll", "JLLWrappers", "LazyArtifacts", "LibCURL_jll", "Libdl", "MPICH_jll", "MPIPreferences", "MPItrampoline_jll", "MicrosoftMPI_jll", "OpenMPI_jll", "OpenSSL_jll", "TOML", "Zlib_jll", "libaec_jll"] +git-tree-sha1 = "e94f84da9af7ce9c6be049e9067e511e17ff89ec" uuid = "0234f1f7-429e-5d53-9886-15a909be8d59" -version = "1.14.2+1" +version = "1.14.6+0" [[deps.HTTP]] -deps = ["Base64", "CodecZlib", "ConcurrentUtilities", "Dates", "ExceptionUnwrapping", "Logging", "LoggingExtras", "MbedTLS", "NetworkOptions", "OpenSSL", "Random", "SimpleBufferStream", "Sockets", "URIs", "UUIDs"] -git-tree-sha1 = "1336e07ba2eb75614c99496501a8f4b233e9fafe" +deps = ["Base64", "CodecZlib", "ConcurrentUtilities", "Dates", "ExceptionUnwrapping", "Logging", "LoggingExtras", "MbedTLS", "NetworkOptions", "OpenSSL", "PrecompileTools", "Random", "SimpleBufferStream", "Sockets", "URIs", "UUIDs"] +git-tree-sha1 = "ed5e9c58612c4e081aecdb6e1a479e18462e041e" uuid = "cd3eb016-35fb-5094-929b-558a96fad6f3" -version = "1.10.10" - -[[deps.HarfBuzz_jll]] -deps = ["Artifacts", "Cairo_jll", "Fontconfig_jll", "FreeType2_jll", "Glib_jll", "Graphite2_jll", "JLLWrappers", "Libdl", "Libffi_jll"] -git-tree-sha1 = "401e4f3f30f43af2c8478fc008da50096ea5240f" -uuid = "2e76f6c2-a576-52d4-95c1-20adfe4de566" -version = "8.3.1+0" +version = "1.10.17" + +[[deps.HiGHS]] +deps = ["HiGHS_jll", "MathOptIIS", "MathOptInterface", "PrecompileTools", "SparseArrays"] +git-tree-sha1 = "3fae2ee8d6ea22009532d5919ff592fcbcab0ad9" +uuid = "87dc4568-4c63-4d18-b0c0-bb2238e4078b" +version = "1.19.0" + +[[deps.HiGHS_jll]] +deps = ["Artifacts", "CompilerSupportLibraries_jll", "JLLWrappers", "Libdl", "Zlib_jll"] +git-tree-sha1 = "f56d423e3f583e26ceaef08a15a270b28723c89a" +uuid = "8fd58aa0-07eb-5a78-9b36-339c94fd15ea" +version = "1.11.0+1" [[deps.Hwloc_jll]] -deps = ["Artifacts", "JLLWrappers", "Libdl"] -git-tree-sha1 = "50aedf345a709ab75872f80a2779568dc0bb461b" +deps = ["Artifacts", "JLLWrappers", "Libdl", "XML2_jll", "Xorg_libpciaccess_jll"] +git-tree-sha1 = "3d468106a05408f9f7b6f161d9e7715159af247b" uuid = "e33a78d0-f292-5ffc-b300-72abe9b543c8" -version = "2.11.2+1" +version = "2.12.2+0" [[deps.HypergeometricFunctions]] deps = ["LinearAlgebra", "OpenLibm_jll", "SpecialFunctions"] -git-tree-sha1 = "b1c2585431c382e3fe5805874bda6aea90a95de9" +git-tree-sha1 = "68c173f4f449de5b438ee67ed0c9c748dc31a2ec" uuid = "34004b35-14d8-5ef3-9330-4cdb6864b03a" -version = "0.3.25" +version = "0.3.28" [[deps.IntelOpenMP_jll]] deps = ["Artifacts", "JLLWrappers", "LazyArtifacts", "Libdl"] -git-tree-sha1 = "10bd689145d2c3b2a9844005d01087cc1194e79e" +git-tree-sha1 = "ec1debd61c300961f98064cfb21287613ad7f303" uuid = "1d5cc7b8-4909-519e-a0f8-d0f5ad9712d0" -version = "2024.2.1+0" +version = "2025.2.0+0" [[deps.InteractiveUtils]] deps = ["Markdown"] uuid = "b77e0a4c-d291-57a0-90e8-8db25a27a240" [[deps.IrrationalConstants]] -git-tree-sha1 = "630b497eafcc20001bba38a4651b327dcfc491d2" +git-tree-sha1 = "e2222959fbc6c19554dc15174c81bf7bf3aa691c" uuid = "92d709cd-6900-40b7-9082-c6be49f344b6" -version = "0.2.2" +version = "0.2.4" [[deps.IteratorInterfaceExtensions]] git-tree-sha1 = "a3f24677c21f5bbe9d2a714f95dcd58337fb2856" uuid = "82899510-4779-5014-852e-03e436cf321d" version = "1.0.0" -[[deps.JLFzf]] -deps = ["Pipe", "REPL", "Random", "fzf_jll"] -git-tree-sha1 = "39d64b09147620f5ffbf6b2d3255be3c901bec63" -uuid = "1019f520-868f-41f5-a6de-eb00f4b6a39c" -version = "0.1.8" - [[deps.JLLWrappers]] deps = ["Artifacts", "Preferences"] -git-tree-sha1 = "be3dc50a92e5a386872a493a10050136d4703f9b" +git-tree-sha1 = "0533e564aae234aff59ab625543145446d8b6ec2" uuid = "692b3bcd-3c85-4b1f-b108-f13ce0eb3210" -version = "1.6.1" +version = "1.7.1" [[deps.JSON]] deps = ["Dates", "Mmap", "Parsers", "Unicode"] @@ -467,56 +375,17 @@ git-tree-sha1 = "31e996f0a15c7b280ba9f76636b3ff9e2ae58c9a" uuid = "682c06a0-de6a-54ab-a142-c8b1cf79cde6" version = "0.21.4" -[[deps.JpegTurbo_jll]] -deps = ["Artifacts", "JLLWrappers", "Libdl"] -git-tree-sha1 = "25ee0be4d43d0269027024d75a24c24d6c6e590c" -uuid = "aacddb02-875f-59d6-b918-886e6ef4fbf8" -version = "3.0.4+0" - -[[deps.LAME_jll]] -deps = ["Artifacts", "JLLWrappers", "Libdl"] -git-tree-sha1 = "170b660facf5df5de098d866564877e119141cbd" -uuid = "c1c5ebd0-6772-5130-a774-d5fcae4a789d" -version = "3.100.2+0" - -[[deps.LERC_jll]] -deps = ["Artifacts", "JLLWrappers", "Libdl"] -git-tree-sha1 = "36bdbc52f13a7d1dcb0f3cd694e01677a515655b" -uuid = "88015f11-f218-50d7-93a8-a6af411a945d" -version = "4.0.0+0" +[[deps.JSON3]] +deps = ["Dates", "Mmap", "Parsers", "PrecompileTools", "StructTypes", "UUIDs"] +git-tree-sha1 = "411eccfe8aba0814ffa0fdf4860913ed09c34975" +uuid = "0f8b85d8-7281-11e9-16c2-39a750bddbf1" +version = "1.14.3" -[[deps.LLVMOpenMP_jll]] -deps = ["Artifacts", "JLLWrappers", "Libdl"] -git-tree-sha1 = "78211fb6cbc872f77cad3fc0b6cf647d923f4929" -uuid = "1d63c593-3942-5779-bab2-d838dc0a180e" -version = "18.1.7+0" + [deps.JSON3.extensions] + JSON3ArrowExt = ["ArrowTypes"] -[[deps.LZO_jll]] -deps = ["Artifacts", "JLLWrappers", "Libdl"] -git-tree-sha1 = "854a9c268c43b77b0a27f22d7fab8d33cdb3a731" -uuid = "dd4b983a-f0e5-5f8d-a1b7-129d4a5fb1ac" -version = "2.10.2+1" - -[[deps.LaTeXStrings]] -git-tree-sha1 = "dda21b8cbd6a6c40d9d02a73230f9d70fed6918c" -uuid = "b964fa9f-0449-5b57-a5c2-d3ea65f4040f" -version = "1.4.0" - -[[deps.Latexify]] -deps = ["Format", "InteractiveUtils", "LaTeXStrings", "MacroTools", "Markdown", "OrderedCollections", "Requires"] -git-tree-sha1 = "ce5f5621cac23a86011836badfedf664a612cee4" -uuid = "23fbe1c1-3f47-55db-b15f-69d7ec21a316" -version = "0.16.5" - - [deps.Latexify.extensions] - DataFramesExt = "DataFrames" - SparseArraysExt = "SparseArrays" - SymEngineExt = "SymEngine" - - [deps.Latexify.weakdeps] - DataFrames = "a93c6f00-e57d-5684-b7b6-d8193f3e46c0" - SparseArrays = "2f01184e-e22b-5df5-ae63-d93ebab69eaf" - SymEngine = "123dc426-2d89-5057-bbad-38513e3affd8" + [deps.JSON3.weakdeps] + ArrowTypes = "31f734f8-188a-4ce0-8406-c8a06bd891cd" [[deps.LazyArtifacts]] deps = ["Artifacts", "Pkg"] @@ -524,9 +393,9 @@ uuid = "4af54fe1-eca0-43a8-85a7-787d91b784e3" [[deps.LeftChildRightSiblingTrees]] deps = ["AbstractTrees"] -git-tree-sha1 = "fb6803dafae4a5d62ea5cab204b1e657d9737e7f" +git-tree-sha1 = "95ba48564903b43b2462318aa243ee79d81135ff" uuid = "1d6d02ad-be62-4b6b-8a6d-2f90e265016e" -version = "0.2.0" +version = "0.2.1" [[deps.LibCURL]] deps = ["LibCURL_jll", "MozillaCACerts_jll"] @@ -555,53 +424,11 @@ version = "1.11.0+1" [[deps.Libdl]] uuid = "8f399da3-3557-5675-b5ff-fb832c97cbdb" -[[deps.Libffi_jll]] -deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] -git-tree-sha1 = "0b4a5d71f3e5200a7dff793393e09dfc2d874290" -uuid = "e9f186c6-92d2-5b65-8a66-fee21dc1b490" -version = "3.2.2+1" - -[[deps.Libgcrypt_jll]] -deps = ["Artifacts", "JLLWrappers", "Libdl", "Libgpg_error_jll"] -git-tree-sha1 = "8be878062e0ffa2c3f67bb58a595375eda5de80b" -uuid = "d4300ac3-e22c-5743-9152-c294e39db1e4" -version = "1.11.0+0" - -[[deps.Libglvnd_jll]] -deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg", "Xorg_libX11_jll", "Xorg_libXext_jll"] -git-tree-sha1 = "6f73d1dd803986947b2c750138528a999a6c7733" -uuid = "7e76a0d4-f3c7-5321-8279-8d96eeed0f29" -version = "1.6.0+0" - -[[deps.Libgpg_error_jll]] -deps = ["Artifacts", "JLLWrappers", "Libdl"] -git-tree-sha1 = "c6ce1e19f3aec9b59186bdf06cdf3c4fc5f5f3e6" -uuid = "7add5ba3-2f88-524e-9cd5-f83b8a55f7b8" -version = "1.50.0+0" - [[deps.Libiconv_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl"] -git-tree-sha1 = "61dfdba58e585066d8bce214c5a51eaa0539f269" +git-tree-sha1 = "be484f5c92fad0bd8acfef35fe017900b0b73809" uuid = "94ce4f54-9a6c-5748-9c1c-f9c7231a4531" -version = "1.17.0+1" - -[[deps.Libmount_jll]] -deps = ["Artifacts", "JLLWrappers", "Libdl"] -git-tree-sha1 = "0c4f9c4f1a50d8f35048fa0532dabbadf702f81e" -uuid = "4b2f31a3-9ecc-558c-b454-b3730dcb73e9" -version = "2.40.1+0" - -[[deps.Libtiff_jll]] -deps = ["Artifacts", "JLLWrappers", "JpegTurbo_jll", "LERC_jll", "Libdl", "XZ_jll", "Zlib_jll", "Zstd_jll"] -git-tree-sha1 = "b404131d06f7886402758c9ce2214b636eb4d54a" -uuid = "89763e89-9b03-5906-acba-b20f662cd828" -version = "4.7.0+0" - -[[deps.Libuuid_jll]] -deps = ["Artifacts", "JLLWrappers", "Libdl"] -git-tree-sha1 = "5ee6203157c120d79034c748a2acba45b82b8807" -uuid = "38a345b3-de98-5d2b-a5d3-14cd9215e700" -version = "2.40.1+0" +version = "1.18.0+0" [[deps.LinearAlgebra]] deps = ["Libdl", "OpenBLAS_jll", "libblastrampoline_jll"] @@ -609,9 +436,9 @@ uuid = "37e2e46d-f89d-539d-b4ee-838fcccc9c8e" [[deps.LogExpFunctions]] deps = ["DocStringExtensions", "IrrationalConstants", "LinearAlgebra"] -git-tree-sha1 = "a2d09619db4e765091ee5c6ffe8872849de0feea" +git-tree-sha1 = "13ca9e2586b89836fd20cccf56e57e2b9ae7f38f" uuid = "2ab3a3ac-af41-5b50-aa03-7779005ae688" -version = "0.3.28" +version = "0.3.29" [deps.LogExpFunctions.extensions] LogExpFunctionsChainRulesCoreExt = "ChainRulesCore" @@ -634,15 +461,15 @@ version = "1.1.0" [[deps.MKL_jll]] deps = ["Artifacts", "IntelOpenMP_jll", "JLLWrappers", "LazyArtifacts", "Libdl", "oneTBB_jll"] -git-tree-sha1 = "f046ccd0c6db2832a9f639e2c669c6fe867e5f4f" +git-tree-sha1 = "282cadc186e7b2ae0eeadbd7a4dffed4196ae2aa" uuid = "856f044c-d86e-5d09-b602-aeab76dc8ba7" -version = "2024.2.0+0" +version = "2025.2.0+0" [[deps.MPI]] deps = ["Distributed", "DocStringExtensions", "Libdl", "MPICH_jll", "MPIPreferences", "MPItrampoline_jll", "MicrosoftMPI_jll", "OpenMPI_jll", "PkgVersion", "PrecompileTools", "Requires", "Serialization", "Sockets"] -git-tree-sha1 = "892676019c58f34e38743bc989b0eca5bce5edc5" +git-tree-sha1 = "a61ecf714d71064b766d481ef43c094d4c6e3c52" uuid = "da04e1cc-30fd-572f-bb4f-1f8673147195" -version = "0.20.22" +version = "0.20.23" [deps.MPI.extensions] AMDGPUExt = "AMDGPU" @@ -654,9 +481,9 @@ version = "0.20.22" [[deps.MPICH_jll]] deps = ["Artifacts", "CompilerSupportLibraries_jll", "Hwloc_jll", "JLLWrappers", "LazyArtifacts", "Libdl", "MPIPreferences", "TOML"] -git-tree-sha1 = "7715e65c47ba3941c502bffb7f266a41a7f54423" +git-tree-sha1 = "d72d0ecc3f76998aac04e446547259b9ae4c265f" uuid = "7cb0a576-ebde-5e09-9194-50597f1243b4" -version = "4.2.3+0" +version = "4.3.1+0" [[deps.MPIPreferences]] deps = ["Libdl", "Preferences"] @@ -666,20 +493,31 @@ version = "0.1.11" [[deps.MPItrampoline_jll]] deps = ["Artifacts", "CompilerSupportLibraries_jll", "JLLWrappers", "LazyArtifacts", "Libdl", "MPIPreferences", "TOML"] -git-tree-sha1 = "70e830dab5d0775183c99fc75e4c24c614ed7142" +git-tree-sha1 = "e214f2a20bdd64c04cd3e4ff62d3c9be7e969a59" uuid = "f1f71cc9-e9ae-5b93-9b94-4fe0e1ad3748" -version = "5.5.1+0" +version = "5.5.4+0" [[deps.MacroTools]] -deps = ["Markdown", "Random"] -git-tree-sha1 = "2fa9ee3e63fd3a4f7a9a4f4744a52f4856de82df" +git-tree-sha1 = "1e0228a030642014fe5cfe68c2c0a818f9e3f522" uuid = "1914dd2f-81c6-5fcd-8719-6d5c9610ff09" -version = "0.5.13" +version = "0.5.16" [[deps.Markdown]] deps = ["Base64"] uuid = "d6f4376e-aef5-505a-96c1-9c027394607a" +[[deps.MathOptIIS]] +deps = ["MathOptInterface"] +git-tree-sha1 = "31d4a6353ea00603104f11384aa44dd8b7162b28" +uuid = "8c4f8055-bd93-4160-a86b-a0c04941dbff" +version = "0.1.1" + +[[deps.MathOptInterface]] +deps = ["BenchmarkTools", "CodecBzip2", "CodecZlib", "DataStructures", "ForwardDiff", "JSON3", "LinearAlgebra", "MutableArithmetics", "NaNMath", "OrderedCollections", "PrecompileTools", "Printf", "SparseArrays", "SpecialFunctions", "Test"] +git-tree-sha1 = "583abfbd38f15198adde0658e1b1222ece232ae2" +uuid = "b8f27783-ece8-5eb3-8dc8-9495eed66fee" +version = "1.43.0" + [[deps.MbedTLS]] deps = ["Dates", "MbedTLS_jll", "MozillaCACerts_jll", "NetworkOptions", "Random", "Sockets"] git-tree-sha1 = "c067a280ddc25f196b5e7df3877c6b226d390aaf" @@ -691,16 +529,11 @@ deps = ["Artifacts", "Libdl"] uuid = "c8ffd9c3-330d-5841-b78e-0817d7145fa1" version = "2.28.2+1" -[[deps.Measures]] -git-tree-sha1 = "c13304c81eec1ed3af7fc20e75fb6b26092a1102" -uuid = "442fdcdd-2543-5da2-b0f3-8c86c306513e" -version = "0.3.2" - [[deps.MicrosoftMPI_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] -git-tree-sha1 = "f12a29c4400ba812841c6ace3f4efbb6dbb3ba01" +git-tree-sha1 = "bc95bf4149bf535c09602e3acdf950d9b4376227" uuid = "9237b28f-5490-5468-be7b-bb81f5f5e6cf" -version = "10.1.4+2" +version = "10.1.4+3" [[deps.Missings]] deps = ["DataAPI"] @@ -715,22 +548,22 @@ uuid = "a63ad114-7e13-5084-954f-fe012c677804" uuid = "14a3606d-f60d-562e-9121-12d972cd8159" version = "2023.1.10" +[[deps.MutableArithmetics]] +deps = ["LinearAlgebra", "SparseArrays", "Test"] +git-tree-sha1 = "491bdcdc943fcbc4c005900d7463c9f216aabf4c" +uuid = "d8a4904e-b15c-11e9-3269-09a3773c0cb0" +version = "1.6.4" + [[deps.NaNMath]] deps = ["OpenLibm_jll"] -git-tree-sha1 = "0877504529a3e5c3343c6f8b4c0381e57e4387e4" +git-tree-sha1 = "9b8215b1ee9e78a293f99797cd31375471b2bcae" uuid = "77ba4419-2d1f-58cd-9bb1-8ffee604a2e3" -version = "1.0.2" +version = "1.1.3" [[deps.NetworkOptions]] uuid = "ca575930-c2e3-43a9-ace4-1e988b2c1908" version = "1.2.0" -[[deps.Ogg_jll]] -deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] -git-tree-sha1 = "887579a3eb005446d514ab7aeac5d1d027658b8f" -uuid = "e7412a2a-1a6e-54c0-be00-318e2571c051" -version = "1.3.5+1" - [[deps.OpenBLAS_jll]] deps = ["Artifacts", "CompilerSupportLibraries_jll", "Libdl"] uuid = "4536629a-c528-5b80-bd46-f80d51c5b363" @@ -739,83 +572,55 @@ version = "0.3.23+4" [[deps.OpenLibm_jll]] deps = ["Artifacts", "Libdl"] uuid = "05823500-19ac-5b8b-9628-191a04bc5112" -version = "0.8.1+2" +version = "0.8.5+0" [[deps.OpenMPI_jll]] -deps = ["Artifacts", "CompilerSupportLibraries_jll", "Hwloc_jll", "JLLWrappers", "LazyArtifacts", "Libdl", "MPIPreferences", "TOML", "Zlib_jll"] -git-tree-sha1 = "bfce6d523861a6c562721b262c0d1aaeead2647f" +deps = ["Artifacts", "CompilerSupportLibraries_jll", "JLLWrappers", "LazyArtifacts", "Libdl", "MPIPreferences", "TOML"] +git-tree-sha1 = "21cd48e9a91fd3dfaac23701e4e338e6bca4c209" uuid = "fe0851c0-eecd-5654-98d4-656369965a5c" -version = "5.0.5+0" +version = "4.1.8+1" [[deps.OpenSSL]] deps = ["BitFlags", "Dates", "MozillaCACerts_jll", "OpenSSL_jll", "Sockets"] -git-tree-sha1 = "38cb508d080d21dc1128f7fb04f20387ed4c0af4" +git-tree-sha1 = "f1a7e086c677df53e064e0fdd2c9d0b0833e3f6e" uuid = "4d8831e6-92b7-49fb-bdf8-b643e874388c" -version = "1.4.3" +version = "1.5.0" [[deps.OpenSSL_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl"] -git-tree-sha1 = "7493f61f55a6cce7325f197443aa80d32554ba10" +git-tree-sha1 = "2ae7d4ddec2e13ad3bddf5c0796f7547cf682391" uuid = "458c3c95-2e84-50aa-8efc-19380b2a3a95" -version = "3.0.15+1" +version = "3.5.2+0" [[deps.OpenSpecFun_jll]] -deps = ["Artifacts", "CompilerSupportLibraries_jll", "JLLWrappers", "Libdl", "Pkg"] -git-tree-sha1 = "13652491f6856acfd2db29360e1bbcd4565d04f1" +deps = ["Artifacts", "CompilerSupportLibraries_jll", "JLLWrappers", "Libdl"] +git-tree-sha1 = "1346c9208249809840c91b26703912dff463d335" uuid = "efe28fd5-8261-553b-a9e1-b2916fc3738e" -version = "0.5.5+0" - -[[deps.Opus_jll]] -deps = ["Artifacts", "JLLWrappers", "Libdl"] -git-tree-sha1 = "6703a85cb3781bd5909d48730a67205f3f31a575" -uuid = "91d4177d-7536-5919-b921-800302f37372" -version = "1.3.3+0" +version = "0.5.6+0" [[deps.OrderedCollections]] -git-tree-sha1 = "dfdf5519f235516220579f949664f1bf44e741c5" +git-tree-sha1 = "05868e21324cede2207c6f0f466b4bfef6d5e7ee" uuid = "bac558e1-5e72-5ebc-8fee-abe8a469f55d" -version = "1.6.3" - -[[deps.PCRE2_jll]] -deps = ["Artifacts", "Libdl"] -uuid = "efcefdf7-47ab-520b-bdef-62a2eaa19f15" -version = "10.42.0+1" +version = "1.8.1" [[deps.PDMats]] deps = ["LinearAlgebra", "SparseArrays", "SuiteSparse"] -git-tree-sha1 = "949347156c25054de2db3b166c52ac4728cbad65" +git-tree-sha1 = "f07c06228a1c670ae4c87d1276b92c7c597fdda0" uuid = "90014a1f-27ba-587c-ab20-58faa44d9150" -version = "0.11.31" - -[[deps.Pango_jll]] -deps = ["Artifacts", "Cairo_jll", "Fontconfig_jll", "FreeType2_jll", "FriBidi_jll", "Glib_jll", "HarfBuzz_jll", "JLLWrappers", "Libdl"] -git-tree-sha1 = "e127b609fb9ecba6f201ba7ab753d5a605d53801" -uuid = "36c8627f-9965-5494-a995-c6b170f724f3" -version = "1.54.1+0" +version = "0.11.35" [[deps.Parsers]] deps = ["Dates", "PrecompileTools", "UUIDs"] -git-tree-sha1 = "8489905bcdbcfac64d1daa51ca07c0d8f0283821" +git-tree-sha1 = "7d2f8f21da5db6a806faf7b9b292296da42b2810" uuid = "69de0a69-1ddd-5017-9359-2bf0b02dc9f0" -version = "2.8.1" +version = "2.8.3" [[deps.ParticleDA]] -deps = ["ChunkSplitters", "HDF5", "LinearAlgebra", "MPI", "PDMats", "Random", "Statistics", "StructArrays", "Test", "TimerOutputs", "YAML"] +deps = ["ChunkSplitters", "ExactOptimalTransport", "HDF5", "HiGHS", "LinearAlgebra", "MPI", "OpenMPI_jll", "PDMats", "Random", "Serialization", "Statistics", "StructArrays", "SuiteSparse_jll", "Test", "TimerOutputs", "YAML"] path = ".." uuid = "61cd1fb4-f4c4-4bc8-80c6-ea5639a6ca2e" version = "1.2.0" -[[deps.Pipe]] -git-tree-sha1 = "6842804e7867b115ca9de748a0cf6b364523c16d" -uuid = "b98c9c47-44ae-5843-9183-064241ee97a0" -version = "1.3.0" - -[[deps.Pixman_jll]] -deps = ["Artifacts", "CompilerSupportLibraries_jll", "JLLWrappers", "LLVMOpenMP_jll", "Libdl"] -git-tree-sha1 = "35621f10a7531bc8fa58f74610b1bfb70a3cfc6b" -uuid = "30392449-352a-5448-841d-b1acce4e97dc" -version = "0.43.4+0" - [[deps.Pkg]] deps = ["Artifacts", "Dates", "Downloads", "FileWatching", "LibGit2", "Libdl", "Logging", "Markdown", "Printf", "REPL", "Random", "SHA", "Serialization", "TOML", "Tar", "UUIDs", "p7zip_jll"] uuid = "44cfe95a-1eb2-52ea-b672-e2afdf69b78f" @@ -823,9 +628,9 @@ version = "1.10.0" [[deps.PkgBenchmark]] deps = ["BenchmarkTools", "Dates", "InteractiveUtils", "JSON", "LibGit2", "Logging", "Pkg", "Printf", "TerminalLoggers", "UUIDs"] -git-tree-sha1 = "e4a10b7cdb7ec836850e43a4cee196f4e7b02756" +git-tree-sha1 = "dc06838e215d9c072fbdb9e9e5497d7f476ccaf5" uuid = "32113eaa-f34f-5b0d-bd6c-c81e245fc73d" -version = "0.2.12" +version = "0.2.13" [[deps.PkgVersion]] deps = ["Pkg"] @@ -833,38 +638,6 @@ git-tree-sha1 = "f9501cc0430a26bc3d156ae1b5b0c1b47af4d6da" uuid = "eebad327-c553-4316-9ea0-9fa01ccd7688" version = "0.3.3" -[[deps.PlotThemes]] -deps = ["PlotUtils", "Statistics"] -git-tree-sha1 = 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[deps.Plots.extensions] - FileIOExt = "FileIO" - GeometryBasicsExt = "GeometryBasics" - IJuliaExt = "IJulia" - ImageInTerminalExt = "ImageInTerminal" - UnitfulExt = "Unitful" - - [deps.Plots.weakdeps] - FileIO = "5789e2e9-d7fb-5bc7-8068-2c6fae9b9549" - GeometryBasics = "5c1252a2-5f33-56bf-86c9-59e7332b4326" - IJulia = "7073ff75-c697-5162-941a-fcdaad2a7d2a" - ImageInTerminal = "d8c32880-2388-543b-8c61-d9f865259254" - Unitful = "1986cc42-f94f-5a68-af5c-568840ba703d" - [[deps.PrecompileTools]] deps = ["Preferences"] git-tree-sha1 = "5aa36f7049a63a1528fe8f7c3f2113413ffd4e1f" @@ -873,9 +646,9 @@ version = "1.2.1" [[deps.Preferences]] deps = ["TOML"] -git-tree-sha1 = "9306f6085165d270f7e3db02af26a400d580f5c6" +git-tree-sha1 = "0f27480397253da18fe2c12a4ba4eb9eb208bf3d" uuid = "21216c6a-2e73-6563-6e65-726566657250" -version = "1.4.3" +version = "1.5.0" [[deps.Printf]] deps = ["Unicode"] @@ -887,44 +660,20 @@ uuid = "9abbd945-dff8-562f-b5e8-e1ebf5ef1b79" [[deps.ProgressLogging]] deps = ["Logging", "SHA", "UUIDs"] -git-tree-sha1 = "80d919dee55b9c50e8d9e2da5eeafff3fe58b539" +git-tree-sha1 = "d95ed0324b0799843ac6f7a6a85e65fe4e5173f0" uuid = "33c8b6b6-d38a-422a-b730-caa89a2f386c" -version = "0.1.4" +version = "0.1.5" [[deps.PtrArrays]] -git-tree-sha1 = "77a42d78b6a92df47ab37e177b2deac405e1c88f" +git-tree-sha1 = "1d36ef11a9aaf1e8b74dacc6a731dd1de8fd493d" uuid = "43287f4e-b6f4-7ad1-bb20-aadabca52c3d" -version = "1.2.1" - -[[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 = "492601870742dcd38f233b23c3ec629628c1d724" -uuid = "c0090381-4147-56d7-9ebc-da0b1113ec56" -version 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[deps.QuadGK.extensions] QuadGKEnzymeExt = "Enzyme" @@ -946,28 +695,16 @@ git-tree-sha1 = "5c3d09cc4f31f5fc6af001c250bf1278733100ff" uuid = "3cdcf5f2-1ef4-517c-9805-6587b60abb01" version = "1.3.4" -[[deps.RecipesPipeline]] -deps = ["Dates", "NaNMath", "PlotUtils", "PrecompileTools", "RecipesBase"] -git-tree-sha1 = "45cf9fd0ca5839d06ef333c8201714e888486342" -uuid = "01d81517-befc-4cb6-b9ec-a95719d0359c" -version = "0.6.12" - [[deps.Reexport]] git-tree-sha1 = "45e428421666073eab6f2da5c9d310d99bb12f9b" uuid = "189a3867-3050-52da-a836-e630ba90ab69" version = "1.2.2" -[[deps.RelocatableFolders]] -deps = ["SHA", "Scratch"] -git-tree-sha1 = "ffdaf70d81cf6ff22c2b6e733c900c3321cab864" -uuid = "05181044-ff0b-4ac5-8273-598c1e38db00" -version = "1.0.1" - [[deps.Requires]] deps = ["UUIDs"] -git-tree-sha1 = "838a3a4188e2ded87a4f9f184b4b0d78a1e91cb7" +git-tree-sha1 = "62389eeff14780bfe55195b7204c0d8738436d64" uuid = "ae029012-a4dd-5104-9daa-d747884805df" -version = "1.3.0" +version = "1.3.1" [[deps.Rmath]] deps = ["Random", "Rmath_jll"] @@ -985,26 +722,14 @@ version = "0.5.1+0" uuid = "ea8e919c-243c-51af-8825-aaa63cd721ce" version = "0.7.0" -[[deps.Scratch]] -deps = ["Dates"] -git-tree-sha1 = "3bac05bc7e74a75fd9cba4295cde4045d9fe2386" -uuid = "6c6a2e73-6563-6170-7368-637461726353" -version = "1.2.1" - [[deps.Serialization]] uuid = "9e88b42a-f829-5b0c-bbe9-9e923198166b" [[deps.Setfield]] deps = ["ConstructionBase", "Future", "MacroTools", "Requires"] -git-tree-sha1 = "38d88503f695eb0301479bc9b0d4320b378bafe5" +git-tree-sha1 = "d0f4c9f8630b695001003d793d1349729e2af26e" uuid = "efcf1570-3423-57d1-acb7-fd33fddbac46" -version = "0.8.2" - -[[deps.Showoff]] -deps = ["Dates", "Grisu"] -git-tree-sha1 = "91eddf657aca81df9ae6ceb20b959ae5653ad1de" -uuid = "992d4aef-0814-514b-bc4d-f2e9a6c4116f" -version = "1.0.3" +version = "0.8.3" [[deps.SimpleBufferStream]] git-tree-sha1 = "f305871d2f381d21527c770d4788c06c097c9bc1" @@ -1022,9 +747,9 @@ version = "0.1.1" [[deps.SortingAlgorithms]] deps = ["DataStructures"] -git-tree-sha1 = "66e0a8e672a0bdfca2c3f5937efb8538b9ddc085" +git-tree-sha1 = "64d974c2e6fdf07f8155b5b2ca2ffa9069b608d9" uuid = "a2af1166-a08f-5f64-846c-94a0d3cef48c" -version = "1.2.1" +version = "1.2.2" [[deps.SparseArrays]] deps = ["Libdl", "LinearAlgebra", "Random", "Serialization", "SuiteSparse_jll"] @@ -1033,9 +758,9 @@ version = "1.10.0" [[deps.SpecialFunctions]] deps = ["IrrationalConstants", "LogExpFunctions", "OpenLibm_jll", "OpenSpecFun_jll"] -git-tree-sha1 = "2f5d4697f21388cbe1ff299430dd169ef97d7e14" +git-tree-sha1 = "41852b8679f78c8d8961eeadc8f62cef861a52e3" uuid = "276daf66-3868-5448-9aa4-cd146d93841b" -version = "2.4.0" +version = "2.5.1" [deps.SpecialFunctions.extensions] SpecialFunctionsChainRulesCoreExt = "ChainRulesCore" @@ -1045,15 +770,15 @@ version = "2.4.0" [[deps.StableRNGs]] deps = ["Random"] -git-tree-sha1 = "83e6cce8324d49dfaf9ef059227f91ed4441a8e5" +git-tree-sha1 = "95af145932c2ed859b63329952ce8d633719f091" uuid = 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= ["AliasTables", "DataAPI", "DataStructures", "LinearAlgebra", "LogExpFunctions", "Missings", "Printf", "Random", "SortingAlgorithms", "SparseArrays", "Statistics", "StatsAPI"] +git-tree-sha1 = "2c962245732371acd51700dbb268af311bddd719" uuid = "2913bbd2-ae8a-5f71-8c99-4fb6c76f3a91" -version = "0.34.3" +version = "0.34.6" [[deps.StatsFuns]] deps = ["HypergeometricFunctions", "IrrationalConstants", "LogExpFunctions", "Reexport", "Rmath", "SpecialFunctions"] -git-tree-sha1 = "b423576adc27097764a90e163157bcfc9acf0f46" +git-tree-sha1 = "8e45cecc66f3b42633b8ce14d431e8e57a3e242e" uuid = "4c63d2b9-4356-54db-8cca-17b64c39e42c" -version = "1.3.2" +version = "1.5.0" [deps.StatsFuns.extensions] StatsFunsChainRulesCoreExt = "ChainRulesCore" @@ -1107,22 +832,31 @@ version = "0.3.7" [[deps.StructArrays]] deps = ["ConstructionBase", "DataAPI", "Tables"] -git-tree-sha1 = "f4dc295e983502292c4c3f951dbb4e985e35b3be" +git-tree-sha1 = "8ad2e38cbb812e29348719cc63580ec1dfeb9de4" uuid = 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"Serialization", "SparseArrays"] uuid = "4607b0f0-06f3-5cda-b6b1-a6196a1729e9" @@ -1145,21 +879,15 @@ version = "1.0.1" [[deps.Tables]] deps = ["DataAPI", "DataValueInterfaces", "IteratorInterfaceExtensions", "OrderedCollections", "TableTraits"] -git-tree-sha1 = "598cd7c1f68d1e205689b1c2fe65a9f85846f297" +git-tree-sha1 = "f2c1efbc8f3a609aadf318094f8fc5204bdaf344" uuid = "bd369af6-aec1-5ad0-b16a-f7cc5008161c" -version = "1.12.0" +version = "1.12.1" [[deps.Tar]] deps = ["ArgTools", "SHA"] uuid = "a4e569a6-e804-4fa4-b0f3-eef7a1d5b13e" version = "1.10.0" -[[deps.TensorCore]] -deps = ["LinearAlgebra"] -git-tree-sha1 = "1feb45f88d133a655e001435632f019a9a1bcdb6" -uuid = "62fd8b95-f654-4bbd-a8a5-9c27f68ccd50" -version = "0.1.1" - [[deps.TerminalLoggers]] deps = ["LeftChildRightSiblingTrees", "Logging", "Markdown", "Printf", "ProgressLogging", "UUIDs"] git-tree-sha1 = "f133fab380933d042f6796eda4e130272ba520ca" @@ -1172,9 +900,15 @@ uuid = "8dfed614-e22c-5e08-85e1-65c5234f0b40" [[deps.TimerOutputs]] deps = ["ExprTools", "Printf"] -git-tree-sha1 = "3a6f063d690135f5c1ba351412c82bae4d1402bf" +git-tree-sha1 = "3748bd928e68c7c346b52125cf41fff0de6937d0" uuid = "a759f4b9-e2f1-59dc-863e-4aeb61b1ea8f" -version = "0.5.25" +version = "0.5.29" + + [deps.TimerOutputs.extensions] + FlameGraphsExt = "FlameGraphs" + + [deps.TimerOutputs.weakdeps] + FlameGraphs = "08572546-2f56-4bcf-ba4e-bab62c3a3f89" [[deps.TranscodingStreams]] git-tree-sha1 = "0c45878dcfdcfa8480052b6ab162cdd138781742" @@ -1182,9 +916,9 @@ uuid = "3bb67fe8-82b1-5028-8e26-92a6c54297fa" version = "0.11.3" [[deps.URIs]] -git-tree-sha1 = "67db6cc7b3821e19ebe75791a9dd19c9b1188f2b" +git-tree-sha1 = "bef26fb046d031353ef97a82e3fdb6afe7f21b1a" uuid = "5c2747f8-b7ea-4ff2-ba2e-563bfd36b1d4" -version = "1.5.1" +version = "1.6.1" [[deps.UUIDs]] deps = ["Random", "SHA"] @@ -1198,222 +932,23 @@ version = "1.0.2" [[deps.Unicode]] uuid = "4ec0a83e-493e-50e2-b9ac-8f72acf5a8f5" -[[deps.UnicodeFun]] -deps = ["REPL"] 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"JLLWrappers", "Libdl"] -git-tree-sha1 = "e92a1a012a10506618f10b7047e478403a046c77" -uuid = "c5fb5394-a638-5e4d-96e5-b29de1b5cf10" -version = "1.5.0+0" +[[deps.Xorg_libpciaccess_jll]] +deps = ["Artifacts", "JLLWrappers", "Libdl", "Zlib_jll"] +git-tree-sha1 = "4909eb8f1cbf6bd4b1c30dd18b2ead9019ef2fad" +uuid = "a65dc6b1-eb27-53a1-bb3e-dea574b5389e" +version = "0.18.1+0" [[deps.YAML]] deps = ["Base64", "Dates", "Printf", "StringEncodings"] -git-tree-sha1 = "dea63ff72079443240fbd013ba006bcbc8a9ac00" +git-tree-sha1 = "2f58ac39f64b41fb812340347525be3b590cce3b" uuid = "ddb6d928-2868-570f-bddf-ab3f9cf99eb6" -version = "0.4.12" +version = "0.4.14" [[deps.Zlib_jll]] deps = ["Libdl"] @@ -1422,98 +957,26 @@ version = "1.2.13+1" [[deps.Zstd_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl"] -git-tree-sha1 = "555d1076590a6cc2fdee2ef1469451f872d8b41b" +git-tree-sha1 = "446b23e73536f84e8037f5dce465e92275f6a308" uuid = "3161d3a3-bdf6-5164-811a-617609db77b4" -version = "1.5.6+1" - -[[deps.eudev_jll]] -deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg", "gperf_jll"] -git-tree-sha1 = "431b678a28ebb559d224c0b6b6d01afce87c51ba" -uuid = "35ca27e7-8b34-5b7f-bca9-bdc33f59eb06" -version = "3.2.9+0" - -[[deps.fzf_jll]] -deps = ["Artifacts", "JLLWrappers", "Libdl"] -git-tree-sha1 = "936081b536ae4aa65415d869287d43ef3cb576b2" -uuid = "214eeab7-80f7-51ab-84ad-2988db7cef09" -version = "0.53.0+0" - -[[deps.gperf_jll]] -deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] -git-tree-sha1 = "3516a5630f741c9eecb3720b1ec9d8edc3ecc033" -uuid = "1a1c6b14-54f6-533d-8383-74cd7377aa70" -version = "3.1.1+0" +version = "1.5.7+1" [[deps.libaec_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl"] -git-tree-sha1 = "46bf7be2917b59b761247be3f317ddf75e50e997" +git-tree-sha1 = "1aa23f01927b2dac46db77a56b31088feee0a491" uuid = "477f73a3-ac25-53e9-8cc3-50b2fa2566f0" -version = "1.1.2+0" - -[[deps.libaom_jll]] -deps = ["Artifacts", "JLLWrappers", "Libdl"] -git-tree-sha1 = "1827acba325fdcdf1d2647fc8d5301dd9ba43a9d" -uuid = "a4ae2306-e953-59d6-aa16-d00cac43593b" -version = "3.9.0+0" - -[[deps.libass_jll]] -deps = ["Artifacts", "Bzip2_jll", "FreeType2_jll", "FriBidi_jll", "HarfBuzz_jll", "JLLWrappers", "Libdl", "Zlib_jll"] -git-tree-sha1 = "e17c115d55c5fbb7e52ebedb427a0dca79d4484e" -uuid = "0ac62f75-1d6f-5e53-bd7c-93b484bb37c0" -version = "0.15.2+0" +version = "1.1.4+0" [[deps.libblastrampoline_jll]] deps = ["Artifacts", "Libdl"] uuid = "8e850b90-86db-534c-a0d3-1478176c7d93" -version = "5.8.0+1" - -[[deps.libdecor_jll]] -deps = ["Artifacts", "Dbus_jll", "JLLWrappers", "Libdl", "Libglvnd_jll", "Pango_jll", "Wayland_jll", "xkbcommon_jll"] -git-tree-sha1 = "9bf7903af251d2050b467f76bdbe57ce541f7f4f" -uuid = "1183f4f0-6f2a-5f1a-908b-139f9cdfea6f" -version = "0.2.2+0" - -[[deps.libevdev_jll]] -deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] -git-tree-sha1 = "141fe65dc3efabb0b1d5ba74e91f6ad26f84cc22" -uuid = "2db6ffa8-e38f-5e21-84af-90c45d0032cc" -version = "1.11.0+0" - -[[deps.libfdk_aac_jll]] -deps = ["Artifacts", "JLLWrappers", "Libdl"] -git-tree-sha1 = "8a22cf860a7d27e4f3498a0fe0811a7957badb38" -uuid = "f638f0a6-7fb0-5443-88ba-1cc74229b280" -version = "2.0.3+0" - -[[deps.libinput_jll]] -deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg", "eudev_jll", "libevdev_jll", "mtdev_jll"] -git-tree-sha1 = "ad50e5b90f222cfe78aa3d5183a20a12de1322ce" -uuid = "36db933b-70db-51c0-b978-0f229ee0e533" -version = "1.18.0+0" - -[[deps.libpng_jll]] -deps = ["Artifacts", "JLLWrappers", "Libdl", "Zlib_jll"] -git-tree-sha1 = "b70c870239dc3d7bc094eb2d6be9b73d27bef280" -uuid = "b53b4c65-9356-5827-b1ea-8c7a1a84506f" -version = "1.6.44+0" +version = "5.11.0+0" [[deps.libsodium_jll]] -deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] -git-tree-sha1 = "f76d682d87eefadd3f165d8d9fda436464213142" +deps = ["Artifacts", "JLLWrappers", "Libdl"] +git-tree-sha1 = "011b0a7331b41c25524b64dc42afc9683ee89026" uuid = "a9144af2-ca23-56d9-984f-0d03f7b5ccf8" -version = "1.0.20+1" - -[[deps.libvorbis_jll]] -deps = ["Artifacts", "JLLWrappers", "Libdl", "Ogg_jll", "Pkg"] -git-tree-sha1 = "490376214c4721cdaca654041f635213c6165cb3" -uuid = "f27f6e37-5d2b-51aa-960f-b287f2bc3b7a" -version = "1.3.7+2" - -[[deps.mtdev_jll]] -deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] -git-tree-sha1 = "814e154bdb7be91d78b6802843f76b6ece642f11" -uuid = "009596ad-96f7-51b1-9f1b-5ce2d5e8a71e" -version = "1.1.6+0" +version = "1.0.21+0" [[deps.nghttp2_jll]] deps = ["Artifacts", "Libdl"] @@ -1522,29 +985,11 @@ version = "1.52.0+1" [[deps.oneTBB_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl"] -git-tree-sha1 = "7d0ea0f4895ef2f5cb83645fa689e52cb55cf493" +git-tree-sha1 = "d5a767a3bb77135a99e433afe0eb14cd7f6914c3" uuid = "1317d2d5-d96f-522e-a858-c73665f53c3e" -version = "2021.12.0+0" +version = "2022.0.0+0" [[deps.p7zip_jll]] deps = ["Artifacts", "Libdl"] uuid = "3f19e933-33d8-53b3-aaab-bd5110c3b7a0" version = "17.4.0+2" - -[[deps.x264_jll]] -deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] -git-tree-sha1 = "4fea590b89e6ec504593146bf8b988b2c00922b2" -uuid = "1270edf5-f2f9-52d2-97e9-ab00b5d0237a" -version = "2021.5.5+0" - -[[deps.x265_jll]] -deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] -git-tree-sha1 = "ee567a171cce03570d77ad3a43e90218e38937a9" -uuid = "dfaa095f-4041-5dcd-9319-2fabd8486b76" -version = "3.5.0+0" - -[[deps.xkbcommon_jll]] -deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg", "Wayland_jll", "Wayland_protocols_jll", "Xorg_libxcb_jll", "Xorg_xkeyboard_config_jll"] -git-tree-sha1 = "9c304562909ab2bab0262639bd4f444d7bc2be37" -uuid = "d8fb68d0-12a3-5cfd-a85a-d49703b185fd" -version = "1.4.1+1" diff --git a/benchmark/Project.toml b/benchmark/Project.toml index d0f6ac77..461ff5f5 100644 --- a/benchmark/Project.toml +++ b/benchmark/Project.toml @@ -2,6 +2,7 @@ BenchmarkCI = "20533458-34a3-403d-a444-e18f38190b5b" BenchmarkTools = "6e4b80f9-dd63-53aa-95a3-0cdb28fa8baf" ChunkSplitters = "ae650224-84b6-46f8-82ea-d812ca08434e" +Dates = "ade2ca70-3891-5945-98fb-dc099432e06a" DelimitedFiles = "8bb1440f-4735-579b-a4ab-409b98df4dab" Distributions = "31c24e10-a181-5473-b8eb-7969acd0382f" GaussianRandomFields = "e4b2fa32-6e09-5554-b718-106ed5adafe9" @@ -12,9 +13,8 @@ ParticleDA = "61cd1fb4-f4c4-4bc8-80c6-ea5639a6ca2e" PkgBenchmark = "32113eaa-f34f-5b0d-bd6c-c81e245fc73d" Random = "9a3f8284-a2c9-5f02-9a11-845980a1fd5c" StableRNGs = "860ef19b-820b-49d6-a774-d7a799459cd3" - -[sources.ParticleDA] -path = ".." +SuiteSparse_jll = "bea87d4a-7f5b-5778-9afe-8cc45184846c" +Test = "8dfed614-e22c-5e08-85e1-65c5234f0b40" [compat] BenchmarkCI = "0.1" @@ -31,3 +31,6 @@ PkgBenchmark = "0.2.10" Random = "<0.0.1, 1" StableRNGs = "1" julia = "1.7" + +[sources.ParticleDA] +path = ".." diff --git a/extra/Manifest.toml b/extra/Manifest.toml index 962affa6..33bf5744 100644 --- a/extra/Manifest.toml +++ b/extra/Manifest.toml @@ -1,203 +1,261 @@ # This file is machine-generated - editing it directly is not advised -[[Adapt]] -deps = ["LinearAlgebra"] -git-tree-sha1 = "f1b523983a58802c4695851926203b36e28f09db" -uuid = "79e6a3ab-5dfb-504d-930d-738a2a938a0e" -version = "3.3.0" +[[AbstractPlutoDingetjes]] +deps = ["Pkg"] +git-tree-sha1 = "6e1d2a35f2f90a4bc7c2ed98079b2ba09c35b83a" +uuid = "6e696c72-6542-2067-7265-42206c756150" +version = "1.3.2" + +[[AliasTables]] +deps = ["PtrArrays", "Random"] +git-tree-sha1 = "9876e1e164b144ca45e9e3198d0b689cadfed9ff" +uuid = "66dad0bd-aa9a-41b7-9441-69ab47430ed8" +version = "1.1.3" + +[[ArgTools]] +uuid = "0dad84c5-d112-42e6-8d28-ef12dabb789f" +version = "1.1.2" [[Artifacts]] -deps = ["Pkg"] -git-tree-sha1 = "c30985d8821e0cd73870b17b0ed0ce6dc44cb744" uuid = "56f22d72-fd6d-98f1-02f0-08ddc0907c33" -version = "1.3.0" +version = "1.11.0" [[Base64]] uuid = "2a0f44e3-6c83-55bd-87e4-b1978d98bd5f" +version = "1.11.0" + +[[BitFlags]] +git-tree-sha1 = "0691e34b3bb8be9307330f88d1a3c3f25466c24d" +uuid = "d1d4a3ce-64b1-5f1a-9ba4-7e7e69966f35" +version = "0.1.9" [[Blosc]] deps = ["Blosc_jll"] -git-tree-sha1 = "84cf7d0f8fd46ca6f1b3e0305b4b4a37afe50fd6" +git-tree-sha1 = "310b77648d38c223d947ff3f50f511d08690b8d5" uuid = "a74b3585-a348-5f62-a45c-50e91977d574" -version = "0.7.0" +version = "0.7.3" [[Blosc_jll]] -deps = ["Libdl", "Lz4_jll", "Pkg", "Zlib_jll", "Zstd_jll"] -git-tree-sha1 = "aa9ef39b54a168c3df1b2911e7797e4feee50fbe" +deps = ["Artifacts", "JLLWrappers", "Libdl", "Lz4_jll", "Zlib_jll", "Zstd_jll"] +git-tree-sha1 = "535c80f1c0847a4c967ea945fca21becc9de1522" uuid = "0b7ba130-8d10-5ba8-a3d6-c5182647fed9" -version = "1.14.3+1" +version = "1.21.7+0" [[Bzip2_jll]] -deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] -git-tree-sha1 = "c3598e525718abcc440f69cc6d5f60dda0a1b61e" +deps = ["Artifacts", "JLLWrappers", "Libdl"] +git-tree-sha1 = "1b96ea4a01afe0ea4090c5c8039690672dd13f2e" uuid = "6e34b625-4abd-537c-b88f-471c36dfa7a0" -version = "1.0.6+5" +version = "1.0.9+0" [[Cairo_jll]] -deps = ["Artifacts", "Bzip2_jll", "Fontconfig_jll", "FreeType2_jll", "Glib_jll", "JLLWrappers", "LZO_jll", "Libdl", "Pixman_jll", "Pkg", "Xorg_libXext_jll", "Xorg_libXrender_jll", "Zlib_jll", "libpng_jll"] -git-tree-sha1 = "e2f47f6d8337369411569fd45ae5753ca10394c6" +deps = ["Artifacts", "Bzip2_jll", "CompilerSupportLibraries_jll", "Fontconfig_jll", "FreeType2_jll", "Glib_jll", "JLLWrappers", "LZO_jll", "Libdl", "Pixman_jll", "Xorg_libXext_jll", "Xorg_libXrender_jll", "Zlib_jll", "libpng_jll"] +git-tree-sha1 = "fde3bf89aead2e723284a8ff9cdf5b551ed700e8" uuid = "83423d85-b0ee-5818-9007-b63ccbeb887a" -version = "1.16.0+6" +version = "1.18.5+0" + +[[CodecZlib]] +deps = ["TranscodingStreams", "Zlib_jll"] +git-tree-sha1 = "962834c22b66e32aa10f7611c08c8ca4e20749a9" +uuid = "944b1d66-785c-5afd-91f1-9de20f533193" +version = "0.7.8" [[ColorSchemes]] -deps = ["ColorTypes", "Colors", "FixedPointNumbers", "Random", "StaticArrays"] -git-tree-sha1 = "c8fd01e4b736013bc61b704871d20503b33ea402" +deps = ["ColorTypes", "ColorVectorSpace", "Colors", "FixedPointNumbers", "PrecompileTools", "Random"] +git-tree-sha1 = "a656525c8b46aa6a1c76891552ed5381bb32ae7b" uuid = "35d6a980-a343-548e-a6ea-1d62b119f2f4" -version = "3.12.1" +version = "3.30.0" [[ColorTypes]] deps = ["FixedPointNumbers", "Random"] -git-tree-sha1 = "024fe24d83e4a5bf5fc80501a314ce0d1aa35597" +git-tree-sha1 = "67e11ee83a43eb71ddc950302c53bf33f0690dfe" uuid = "3da002f7-5984-5a60-b8a6-cbb66c0b333f" +version = "0.12.1" +weakdeps = ["StyledStrings"] + + [ColorTypes.extensions] + StyledStringsExt = "StyledStrings" + +[[ColorVectorSpace]] +deps = ["ColorTypes", "FixedPointNumbers", "LinearAlgebra", "Requires", "Statistics", "TensorCore"] +git-tree-sha1 = "8b3b6f87ce8f65a2b4f857528fd8d70086cd72b1" +uuid = "c3611d14-8923-5661-9e6a-0046d554d3a4" version = "0.11.0" + [ColorVectorSpace.extensions] + SpecialFunctionsExt = "SpecialFunctions" + + [ColorVectorSpace.weakdeps] + SpecialFunctions = "276daf66-3868-5448-9aa4-cd146d93841b" + [[Colors]] deps = ["ColorTypes", "FixedPointNumbers", "Reexport"] -git-tree-sha1 = "417b0ed7b8b838aa6ca0a87aadf1bb9eb111ce40" +git-tree-sha1 = "37ea44092930b1811e666c3bc38065d7d87fcc74" uuid = "5ae59095-9a9b-59fe-a467-6f913c188581" -version = "0.12.8" +version = "0.13.1" [[Compat]] deps = ["Base64", "Dates", "DelimitedFiles", "Distributed", "InteractiveUtils", "LibGit2", "Libdl", "LinearAlgebra", "Markdown", "Mmap", "Pkg", "Printf", "REPL", "Random", "SHA", "Serialization", "SharedArrays", "Sockets", "SparseArrays", "Statistics", "Test", "UUIDs", "Unicode"] -git-tree-sha1 = "e4e2b39db08f967cc1360951f01e8a75ec441cab" +git-tree-sha1 = "d476eaeddfcdf0de15a67a948331c69a585495fa" uuid = "34da2185-b29b-5c13-b0c7-acf172513d20" -version = "3.30.0" +version = "3.47.0" [[CompilerSupportLibraries_jll]] -deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] -git-tree-sha1 = "8e695f735fca77e9708e795eda62afdb869cbb70" +deps = ["Artifacts", "Libdl"] uuid = "e66e0078-7015-5450-92f7-15fbd957f2ae" -version = "0.3.4+0" +version = "1.1.1+0" -[[ConstructionBase]] -deps = ["LinearAlgebra"] -git-tree-sha1 = "1dc43957fb9a1574fa1b7a449e101bd1fd3a9fb7" -uuid = "187b0558-2788-49d3-abe0-74a17ed4e7c9" -version = "1.2.1" +[[ConcurrentUtilities]] +deps = ["Serialization", "Sockets"] +git-tree-sha1 = "d9d26935a0bcffc87d2613ce14c527c99fc543fd" +uuid = "f0e56b4a-5159-44fe-b623-3e5288b988bb" +version = "2.5.0" [[Contour]] -deps = ["StaticArrays"] -git-tree-sha1 = "9f02045d934dc030edad45944ea80dbd1f0ebea7" +git-tree-sha1 = "439e35b0b36e2e5881738abc8857bd92ad6ff9a8" uuid = "d38c429a-6771-53c6-b99e-75d170b6e991" -version = "0.5.7" +version = "0.6.3" [[DataAPI]] -git-tree-sha1 = "dfb3b7e89e395be1e25c2ad6d7690dc29cc53b1d" +git-tree-sha1 = "abe83f3a2f1b857aac70ef8b269080af17764bbe" uuid = "9a962f9c-6df0-11e9-0e5d-c546b8b5ee8a" -version = "1.6.0" +version = "1.16.0" [[DataStructures]] deps = ["Compat", "InteractiveUtils", "OrderedCollections"] -git-tree-sha1 = "4437b64df1e0adccc3e5d1adbc3ac741095e4677" +git-tree-sha1 = "4e1fe97fdaed23e9dc21d4d664bea76b65fc50a0" uuid = "864edb3b-99cc-5e75-8d2d-829cb0a9cfe8" -version = "0.18.9" - -[[DataValueInterfaces]] -git-tree-sha1 = "bfc1187b79289637fa0ef6d4436ebdfe6905cbd6" -uuid = "e2d170a0-9d28-54be-80f0-106bbe20a464" -version = "1.0.0" +version = "0.18.22" [[Dates]] deps = ["Printf"] uuid = "ade2ca70-3891-5945-98fb-dc099432e06a" +version = "1.11.0" + +[[Dbus_jll]] +deps = ["Artifacts", "Expat_jll", "JLLWrappers", "Libdl"] +git-tree-sha1 = "473e9afc9cf30814eb67ffa5f2db7df82c3ad9fd" +uuid = "ee1fde0b-3d02-5ea6-8484-8dfef6360eab" +version = "1.16.2+0" [[DelimitedFiles]] deps = ["Mmap"] +git-tree-sha1 = "9e2f36d3c96a820c678f2f1f1782582fcf685bae" uuid = "8bb1440f-4735-579b-a4ab-409b98df4dab" +version = "1.9.1" [[Distributed]] deps = ["Random", "Serialization", "Sockets"] uuid = "8ba89e20-285c-5b6f-9357-94700520ee1b" +version = "1.11.0" -[[EarCut_jll]] -deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] -git-tree-sha1 = "92d8f9f208637e8d2d28c664051a00569c01493d" -uuid = "5ae413db-bbd1-5e63-b57d-d24a61df00f5" -version = "2.1.5+1" +[[DocStringExtensions]] +git-tree-sha1 = "7442a5dfe1ebb773c29cc2962a8980f47221d76c" +uuid = "ffbed154-4ef7-542d-bbb7-c09d3a79fcae" +version = "0.9.5" + +[[Downloads]] +deps = ["ArgTools", "FileWatching", "LibCURL", "NetworkOptions"] +uuid = "f43a241f-c20a-4ad4-852c-f6b1247861c6" +version = "1.6.0" + +[[EpollShim_jll]] +deps = ["Artifacts", "JLLWrappers", "Libdl"] +git-tree-sha1 = "8a4be429317c42cfae6a7fc03c31bad1970c310d" +uuid = "2702e6a9-849d-5ed8-8c21-79e8b8f9ee43" +version = "0.0.20230411+1" + +[[ExceptionUnwrapping]] +deps = ["Test"] +git-tree-sha1 = "d36f682e590a83d63d1c7dbd287573764682d12a" +uuid = "460bff9d-24e4-43bc-9d9f-a8973cb893f4" +version = "0.1.11" [[Expat_jll]] -deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] -git-tree-sha1 = "1402e52fcda25064f51c77a9655ce8680b76acf0" +deps = ["Artifacts", "JLLWrappers", "Libdl"] +git-tree-sha1 = "d55dffd9ae73ff72f1c0482454dcf2ec6c6c4a63" uuid = "2e619515-83b5-522b-bb60-26c02a35a201" -version = "2.2.7+6" 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"4.3.1+4" +version = "4.4.2+2" + +[[FileWatching]] +uuid = "7b1f6079-737a-58dc-b8bc-7a2ca5c1b5ee" +version = "1.11.0" [[FixedPointNumbers]] deps = ["Statistics"] -git-tree-sha1 = "335bfdceacc84c5cdf16aadc768aa5ddfc5383cc" +git-tree-sha1 = "05882d6995ae5c12bb5f36dd2ed3f61c98cbb172" uuid = "53c48c17-4a7d-5ca2-90c5-79b7896eea93" -version = "0.8.4" +version = "0.8.5" [[Fontconfig_jll]] -deps = ["Artifacts", "Bzip2_jll", "Expat_jll", "FreeType2_jll", "JLLWrappers", "Libdl", "Libuuid_jll", "Pkg", "Zlib_jll"] -git-tree-sha1 = "35895cf184ceaab11fd778b4590144034a167a2f" +deps = ["Artifacts", "Bzip2_jll", "Expat_jll", "FreeType2_jll", "JLLWrappers", "Libdl", "Libuuid_jll", "Zlib_jll"] +git-tree-sha1 = "301b5d5d731a0654825f1f2e906990f7141a106b" uuid = "a3f928ae-7b40-5064-980b-68af3947d34b" -version = "2.13.1+14" +version = "2.16.0+0" -[[Formatting]] -deps = ["Printf"] -git-tree-sha1 = "8339d61043228fdd3eb658d86c926cb282ae72a8" -uuid = "59287772-0a20-5a39-b81b-1366585eb4c0" -version = "0.4.2" 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"Xorg_libXrandr_jll"] -git-tree-sha1 = "a199aefead29c3c2638c3571a9993b564109d45a" +deps = ["Artifacts", "JLLWrappers", "Libdl", "Libglvnd_jll", "Xorg_libXcursor_jll", "Xorg_libXi_jll", "Xorg_libXinerama_jll", "Xorg_libXrandr_jll", "libdecor_jll", "xkbcommon_jll"] +git-tree-sha1 = "fcb0584ff34e25155876418979d4c8971243bb89" uuid = "0656b61e-2033-5cc2-a64a-77c0f6c09b89" -version = "3.3.4+0" +version = "3.4.0+2" [[GR]] -deps = ["Base64", "DelimitedFiles", "GR_jll", "HTTP", "JSON", "Libdl", "LinearAlgebra", "Pkg", "Printf", "Random", "Serialization", "Sockets", "Test", "UUIDs"] -git-tree-sha1 = "011458b83178ac913dc4eb73b229af45bdde5d83" +deps = ["Artifacts", "Base64", "DelimitedFiles", "Downloads", "GR_jll", "HTTP", "JSON", "Libdl", "LinearAlgebra", "Preferences", "Printf", "Random", "Serialization", "Sockets", "TOML", "Tar", "Test", "p7zip_jll"] +git-tree-sha1 = "ddda044ca260ee324c5fc07edb6d7cf3f0b9c350" uuid = "28b8d3ca-fb5f-59d9-8090-bfdbd6d07a71" -version = "0.57.4" +version = "0.73.5" [[GR_jll]] -deps = ["Artifacts", "Bzip2_jll", "Cairo_jll", "FFMPEG_jll", "Fontconfig_jll", "GLFW_jll", "JLLWrappers", "JpegTurbo_jll", "Libdl", "Libtiff_jll", "Pixman_jll", "Pkg", "Qt5Base_jll", "Zlib_jll", "libpng_jll"] -git-tree-sha1 = "90acee5c38f4933342fa9a3bbc483119d20e7033" +deps = ["Artifacts", "Bzip2_jll", "Cairo_jll", "FFMPEG_jll", "Fontconfig_jll", "FreeType2_jll", "GLFW_jll", "JLLWrappers", "JpegTurbo_jll", "Libdl", "Libtiff_jll", "Pixman_jll", "Qt6Base_jll", "Zlib_jll", "libpng_jll"] +git-tree-sha1 = "278e5e0f820178e8a26df3184fcb2280717c79b1" uuid = "d2c73de3-f751-5644-a686-071e5b155ba9" -version = "0.57.2+0" - -[[GeometryBasics]] -deps = ["EarCut_jll", "IterTools", "LinearAlgebra", "StaticArrays", "StructArrays", "Tables"] -git-tree-sha1 = "4136b8a5668341e58398bb472754bff4ba0456ff" -uuid = "5c1252a2-5f33-56bf-86c9-59e7332b4326" -version = "0.3.12" +version = "0.73.5+0" -[[Gettext_jll]] -deps = ["Artifacts", "JLLWrappers", "Libdl", "Libiconv_jll", "Pkg", "XML2_jll"] -git-tree-sha1 = "8c14294a079216000a0bdca5ec5a447f073ddc9d" -uuid = "78b55507-aeef-58d4-861c-77aaff3498b1" -version = "0.20.1+7" +[[GettextRuntime_jll]] +deps = ["Artifacts", "CompilerSupportLibraries_jll", "JLLWrappers", "Libdl", "Libiconv_jll"] +git-tree-sha1 = "45288942190db7c5f760f59c04495064eedf9340" +uuid = "b0724c58-0f36-5564-988d-3bb0596ebc4a" +version = "0.22.4+0" [[Glib_jll]] -deps = ["Artifacts", "Gettext_jll", "JLLWrappers", "Libdl", "Libffi_jll", "Libiconv_jll", "Libmount_jll", "PCRE_jll", "Pkg", "Zlib_jll"] -git-tree-sha1 = "04690cc5008b38ecbdfede949220bc7d9ba26397" +deps = ["Artifacts", "GettextRuntime_jll", "JLLWrappers", "Libdl", "Libffi_jll", "Libiconv_jll", "Libmount_jll", "PCRE2_jll", "Zlib_jll"] +git-tree-sha1 = "35fbd0cefb04a516104b8e183ce0df11b70a3f1a" uuid = "7746bdde-850d-59dc-9ae8-88ece973131d" -version = "2.59.0+4" +version = "2.84.3+0" + +[[Graphite2_jll]] +deps = ["Artifacts", "JLLWrappers", "Libdl"] +git-tree-sha1 = "8a6dbda1fd736d60cc477d99f2e7a042acfa46e8" +uuid = "3b182d85-2403-5c21-9c21-1e1f0cc25472" +version = "1.3.15+0" [[Grisu]] git-tree-sha1 = "53bb909d1151e57e2484c3d1b53e19552b887fb2" @@ -206,345 +264,478 @@ version = "1.0.2" [[HDF5]] deps = ["Blosc", "Compat", "HDF5_jll", "Libdl", "Mmap", "Random", "Requires"] -git-tree-sha1 = "1d18a48a037b14052ca462ea9d05dee3ac607d23" +git-tree-sha1 = "698c099c6613d7b7f151832868728f426abe698b" uuid = "f67ccb44-e63f-5c2f-98bd-6dc0ccc4ba2f" -version = "0.15.5" +version = "0.15.7" [[HDF5_jll]] deps = ["Artifacts", "JLLWrappers", "LibCURL_jll", "Libdl", "OpenSSL_jll", "Pkg", "Zlib_jll"] -git-tree-sha1 = "fd83fa0bde42e01952757f01149dd968c06c4dba" +git-tree-sha1 = "4cc2bb72df6ff40b055295fdef6d92955f9dede8" uuid = "0234f1f7-429e-5d53-9886-15a909be8d59" -version = "1.12.0+1" +version = "1.12.2+2" [[HTTP]] -deps = ["Base64", "Dates", "IniFile", "MbedTLS", "NetworkOptions", "Sockets", "URIs"] -git-tree-sha1 = "1fd26bc48f96adcdd8823f7fc300053faf3d7ba1" +deps = ["Base64", "CodecZlib", "ConcurrentUtilities", "Dates", "ExceptionUnwrapping", "Logging", "LoggingExtras", "MbedTLS", "NetworkOptions", "OpenSSL", "PrecompileTools", "Random", "SimpleBufferStream", "Sockets", "URIs", "UUIDs"] +git-tree-sha1 = "ed5e9c58612c4e081aecdb6e1a479e18462e041e" uuid = "cd3eb016-35fb-5094-929b-558a96fad6f3" -version = "0.9.9" +version = "1.10.17" + +[[HarfBuzz_jll]] +deps = ["Artifacts", "Cairo_jll", "Fontconfig_jll", "FreeType2_jll", "Glib_jll", "Graphite2_jll", "JLLWrappers", "Libdl", "Libffi_jll"] +git-tree-sha1 = "f923f9a774fcf3f5cb761bfa43aeadd689714813" +uuid = "2e76f6c2-a576-52d4-95c1-20adfe4de566" +version = "8.5.1+0" -[[IniFile]] +[[Hyperscript]] deps = ["Test"] -git-tree-sha1 = "098e4d2c533924c921f9f9847274f2ad89e018b8" -uuid = "83e8ac13-25f8-5344-8a64-a9f2b223428f" -version = "0.5.0" +git-tree-sha1 = "179267cfa5e712760cd43dcae385d7ea90cc25a4" +uuid = "47d2ed2b-36de-50cf-bf87-49c2cf4b8b91" +version = "0.0.5" + +[[HypertextLiteral]] +deps = ["Tricks"] 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"1019f520-868f-41f5-a6de-eb00f4b6a39c" +version = "0.1.11" [[JLLWrappers]] -deps = ["Preferences"] -git-tree-sha1 = "642a199af8b68253517b80bd3bfd17eb4e84df6e" +deps = ["Artifacts", "Preferences"] +git-tree-sha1 = "a007feb38b422fbdab534406aeca1b86823cb4d6" uuid = "692b3bcd-3c85-4b1f-b108-f13ce0eb3210" -version = "1.3.0" +version = "1.7.0" [[JSON]] deps = ["Dates", "Mmap", "Parsers", "Unicode"] -git-tree-sha1 = "81690084b6198a2e1da36fcfda16eeca9f9f24e4" +git-tree-sha1 = "31e996f0a15c7b280ba9f76636b3ff9e2ae58c9a" uuid = "682c06a0-de6a-54ab-a142-c8b1cf79cde6" -version = "0.21.1" +version = "0.21.4" [[JpegTurbo_jll]] -deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] -git-tree-sha1 = "9aff0587d9603ea0de2c6f6300d9f9492bbefbd3" +deps = ["Artifacts", "JLLWrappers", "Libdl"] +git-tree-sha1 = "eac1206917768cb54957c65a615460d87b455fc1" uuid = "aacddb02-875f-59d6-b918-886e6ef4fbf8" -version = "2.0.1+3" +version = "3.1.1+0" [[LAME_jll]] -deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] -git-tree-sha1 = "df381151e871f41ee86cee4f5f6fd598b8a68826" +deps = ["Artifacts", "JLLWrappers", "Libdl"] +git-tree-sha1 = "059aabebaa7c82ccb853dd4a0ee9d17796f7e1bc" uuid = "c1c5ebd0-6772-5130-a774-d5fcae4a789d" -version = "3.100.0+3" +version = "3.100.3+0" -[[LZO_jll]] +[[LERC_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] -git-tree-sha1 = "f128cd6cd05ffd6d3df0523ed99b90ff6f9b349a" +git-tree-sha1 = "bf36f528eec6634efc60d7ec062008f171071434" +uuid = "88015f11-f218-50d7-93a8-a6af411a945d" +version = "3.0.0+1" + +[[LLVMOpenMP_jll]] +deps = ["Artifacts", "JLLWrappers", "Libdl"] +git-tree-sha1 = "eb62a3deb62fc6d8822c0c4bef73e4412419c5d8" +uuid = "1d63c593-3942-5779-bab2-d838dc0a180e" +version = "18.1.8+0" + +[[LZO_jll]] +deps = ["Artifacts", "JLLWrappers", "Libdl"] +git-tree-sha1 = "1c602b1127f4751facb671441ca72715cc95938a" uuid = "dd4b983a-f0e5-5f8d-a1b7-129d4a5fb1ac" -version = "2.10.0+3" +version = "2.10.3+0" [[LaTeXStrings]] -git-tree-sha1 = 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["Artifacts", "JLLWrappers", "Libdl", "Xorg_libXext_jll", "Xorg_libXrender_jll"] +git-tree-sha1 = "aff463c82a773cb86061bce8d53a0d976854923e" uuid = "ec84b674-ba8e-5d96-8ba1-2a689ba10484" -version = "1.5.2+4" +version = "1.5.5+0" [[Xorg_libXrender_jll]] -deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg", "Xorg_libX11_jll"] -git-tree-sha1 = "19560f30fd49f4d4efbe7002a1037f8c43d43b96" +deps = ["Artifacts", "JLLWrappers", "Libdl", "Xorg_libX11_jll"] +git-tree-sha1 = "7ed9347888fac59a618302ee38216dd0379c480d" uuid = "ea2f1a96-1ddc-540d-b46f-429655e07cfa" -version = "0.9.10+4" - -[[Xorg_libpthread_stubs_jll]] -deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] -git-tree-sha1 = "6783737e45d3c59a4a4c4091f5f88cdcf0908cbb" -uuid = "14d82f49-176c-5ed1-bb49-ad3f5cbd8c74" -version = "0.1.0+3" +version = "0.9.12+0" [[Xorg_libxcb_jll]] -deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg", "XSLT_jll", "Xorg_libXau_jll", "Xorg_libXdmcp_jll", "Xorg_libpthread_stubs_jll"] -git-tree-sha1 = "daf17f441228e7a3833846cd048892861cff16d6" +deps = ["Artifacts", "JLLWrappers", "Libdl", "Xorg_libXau_jll", "Xorg_libXdmcp_jll"] +git-tree-sha1 = "bfcaf7ec088eaba362093393fe11aa141fa15422" uuid = "c7cfdc94-dc32-55de-ac96-5a1b8d977c5b" -version = "1.13.0+3" +version = "1.17.1+0" [[Xorg_libxkbfile_jll]] -deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg", "Xorg_libX11_jll"] -git-tree-sha1 = "926af861744212db0eb001d9e40b5d16292080b2" +deps = ["Artifacts", "JLLWrappers", "Libdl", "Xorg_libX11_jll"] +git-tree-sha1 = "e3150c7400c41e207012b41659591f083f3ef795" uuid = "cc61e674-0454-545c-8b26-ed2c68acab7a" -version = "1.1.0+4" +version = "1.1.3+0" + +[[Xorg_xcb_util_cursor_jll]] +deps = ["Artifacts", "JLLWrappers", "Libdl", "Xorg_xcb_util_image_jll", "Xorg_xcb_util_jll", "Xorg_xcb_util_renderutil_jll"] +git-tree-sha1 = "c5bf2dad6a03dfef57ea0a170a1fe493601603f2" +uuid = "e920d4aa-a673-5f3a-b3d7-f755a4d47c43" +version = "0.1.5+0" [[Xorg_xcb_util_image_jll]] -deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg", "Xorg_xcb_util_jll"] -git-tree-sha1 = "0fab0a40349ba1cba2c1da699243396ff8e94b97" +deps = ["Artifacts", "JLLWrappers", "Libdl", "Xorg_xcb_util_jll"] +git-tree-sha1 = "f4fc02e384b74418679983a97385644b67e1263b" uuid = "12413925-8142-5f55-bb0e-6d7ca50bb09b" -version = "0.4.0+1" +version = "0.4.1+0" [[Xorg_xcb_util_jll]] -deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg", "Xorg_libxcb_jll"] -git-tree-sha1 = "e7fd7b2881fa2eaa72717420894d3938177862d1" +deps = ["Artifacts", "JLLWrappers", "Libdl", "Xorg_libxcb_jll"] +git-tree-sha1 = "68da27247e7d8d8dafd1fcf0c3654ad6506f5f97" uuid = "2def613f-5ad1-5310-b15b-b15d46f528f5" -version = "0.4.0+1" +version = "0.4.1+0" [[Xorg_xcb_util_keysyms_jll]] -deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg", "Xorg_xcb_util_jll"] -git-tree-sha1 = "d1151e2c45a544f32441a567d1690e701ec89b00" +deps = ["Artifacts", "JLLWrappers", "Libdl", "Xorg_xcb_util_jll"] +git-tree-sha1 = "44ec54b0e2acd408b0fb361e1e9244c60c9c3dd4" uuid = "975044d2-76e6-5fbe-bf08-97ce7c6574c7" -version = "0.4.0+1" +version = "0.4.1+0" [[Xorg_xcb_util_renderutil_jll]] -deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg", "Xorg_xcb_util_jll"] -git-tree-sha1 = "dfd7a8f38d4613b6a575253b3174dd991ca6183e" +deps = ["Artifacts", "JLLWrappers", "Libdl", "Xorg_xcb_util_jll"] +git-tree-sha1 = "5b0263b6d080716a02544c55fdff2c8d7f9a16a0" uuid = "0d47668e-0667-5a69-a72c-f761630bfb7e" -version = "0.3.9+1" +version = "0.3.10+0" [[Xorg_xcb_util_wm_jll]] -deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg", "Xorg_xcb_util_jll"] -git-tree-sha1 = "e78d10aab01a4a154142c5006ed44fd9e8e31b67" +deps = ["Artifacts", "JLLWrappers", "Libdl", "Xorg_xcb_util_jll"] +git-tree-sha1 = "f233c83cad1fa0e70b7771e0e21b061a116f2763" uuid = "c22f9ab0-d5fe-5066-847c-f4bb1cd4e361" -version = "0.4.1+1" +version = "0.4.2+0" [[Xorg_xkbcomp_jll]] -deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg", "Xorg_libxkbfile_jll"] -git-tree-sha1 = "4bcbf660f6c2e714f87e960a171b119d06ee163b" +deps 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"320228915c8debb12cb434c59057290f0834dbf6" +deps = ["Libdl"] uuid = "83775a58-1f1d-513f-b197-d71354ab007a" -version = "1.2.11+18" +version = "1.2.13+1" [[Zstd_jll]] -deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] -git-tree-sha1 = "2c1332c54931e83f8f94d310fa447fd743e8d600" +deps = ["Artifacts", "JLLWrappers", "Libdl"] +git-tree-sha1 = "446b23e73536f84e8037f5dce465e92275f6a308" uuid = "3161d3a3-bdf6-5164-811a-617609db77b4" -version = "1.4.8+0" +version = "1.5.7+1" + +[[eudev_jll]] +deps = ["Artifacts", "JLLWrappers", "Libdl"] +git-tree-sha1 = "c3b0e6196d50eab0c5ed34021aaa0bb463489510" +uuid = "35ca27e7-8b34-5b7f-bca9-bdc33f59eb06" +version = "3.2.14+0" + +[[fzf_jll]] +deps = ["Artifacts", "JLLWrappers", "Libdl"] +git-tree-sha1 = "b6a34e0e0960190ac2a4363a1bd003504772d631" +uuid = "214eeab7-80f7-51ab-84ad-2988db7cef09" +version = "0.61.1+0" + +[[libaom_jll]] +deps = ["Artifacts", "JLLWrappers", "Libdl"] +git-tree-sha1 = "522c1df09d05a71785765d19c9524661234738e9" +uuid = "a4ae2306-e953-59d6-aa16-d00cac43593b" +version = "3.11.0+0" [[libass_jll]] -deps = ["Artifacts", "Bzip2_jll", "FreeType2_jll", "FriBidi_jll", "JLLWrappers", "Libdl", "Pkg", "Zlib_jll"] -git-tree-sha1 = "acc685bcf777b2202a904cdcb49ad34c2fa1880c" +deps = ["Artifacts", "Bzip2_jll", "FreeType2_jll", "FriBidi_jll", "HarfBuzz_jll", "JLLWrappers", "Libdl", "Zlib_jll"] +git-tree-sha1 = "e17c115d55c5fbb7e52ebedb427a0dca79d4484e" uuid = "0ac62f75-1d6f-5e53-bd7c-93b484bb37c0" -version = "0.14.0+4" +version = "0.15.2+0" + +[[libblastrampoline_jll]] +deps = ["Artifacts", "Libdl"] +uuid = "8e850b90-86db-534c-a0d3-1478176c7d93" +version = "5.11.0+0" + +[[libdecor_jll]] +deps = ["Artifacts", "Dbus_jll", "JLLWrappers", "Libdl", "Libglvnd_jll", "Pango_jll", "Wayland_jll", "xkbcommon_jll"] +git-tree-sha1 = "9bf7903af251d2050b467f76bdbe57ce541f7f4f" +uuid = "1183f4f0-6f2a-5f1a-908b-139f9cdfea6f" +version = "0.2.2+0" + +[[libevdev_jll]] +deps = ["Artifacts", "JLLWrappers", "Libdl"] +git-tree-sha1 = "56d643b57b188d30cccc25e331d416d3d358e557" +uuid = "2db6ffa8-e38f-5e21-84af-90c45d0032cc" +version = "1.13.4+0" [[libfdk_aac_jll]] -deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] -git-tree-sha1 = "7a5780a0d9c6864184b3a2eeeb833a0c871f00ab" +deps = ["Artifacts", "JLLWrappers", "Libdl"] +git-tree-sha1 = "646634dd19587a56ee2f1199563ec056c5f228df" uuid = "f638f0a6-7fb0-5443-88ba-1cc74229b280" -version = "0.1.6+4" +version = "2.0.4+0" + +[[libinput_jll]] +deps = ["Artifacts", "JLLWrappers", "Libdl", "eudev_jll", "libevdev_jll", "mtdev_jll"] +git-tree-sha1 = "91d05d7f4a9f67205bd6cf395e488009fe85b499" +uuid = "36db933b-70db-51c0-b978-0f229ee0e533" +version = "1.28.1+0" [[libpng_jll]] -deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg", "Zlib_jll"] -git-tree-sha1 = "6abbc424248097d69c0c87ba50fcb0753f93e0ee" +deps = ["Artifacts", "JLLWrappers", "Libdl", "Zlib_jll"] +git-tree-sha1 = "07b6a107d926093898e82b3b1db657ebe33134ec" uuid = "b53b4c65-9356-5827-b1ea-8c7a1a84506f" -version = "1.6.37+6" +version = "1.6.50+0" [[libvorbis_jll]] -deps = ["Artifacts", "JLLWrappers", "Libdl", "Ogg_jll", "Pkg"] -git-tree-sha1 = "fa14ac25af7a4b8a7f61b287a124df7aab601bcd" +deps = ["Artifacts", "JLLWrappers", "Libdl", "Ogg_jll"] +git-tree-sha1 = "11e1772e7f3cc987e9d3de991dd4f6b2602663a5" uuid = "f27f6e37-5d2b-51aa-960f-b287f2bc3b7a" -version = "1.3.6+6" +version = "1.3.8+0" + +[[mtdev_jll]] +deps = ["Artifacts", "JLLWrappers", "Libdl"] +git-tree-sha1 = "b4d631fd51f2e9cdd93724ae25b2efc198b059b1" +uuid = "009596ad-96f7-51b1-9f1b-5ce2d5e8a71e" +version = "1.1.7+0" [[nghttp2_jll]] -deps = ["Libdl", "Pkg"] -git-tree-sha1 = "8e2c44ab4d49ad9518f359ed8b62f83ba8beede4" +deps = ["Artifacts", "Libdl"] uuid = "8e850ede-7688-5339-a07c-302acd2aaf8d" -version = "1.40.0+2" +version = "1.59.0+0" + +[[p7zip_jll]] +deps = ["Artifacts", "Libdl"] +uuid = "3f19e933-33d8-53b3-aaab-bd5110c3b7a0" +version = "17.4.0+2" [[x264_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] -git-tree-sha1 = "d713c1ce4deac133e3334ee12f4adff07f81778f" +git-tree-sha1 = "4fea590b89e6ec504593146bf8b988b2c00922b2" uuid = "1270edf5-f2f9-52d2-97e9-ab00b5d0237a" -version = "2020.7.14+2" +version = "2021.5.5+0" [[x265_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] -git-tree-sha1 = "487da2f8f2f0c8ee0e83f39d13037d6bbf0a45ab" +git-tree-sha1 = "ee567a171cce03570d77ad3a43e90218e38937a9" uuid = "dfaa095f-4041-5dcd-9319-2fabd8486b76" -version = "3.0.0+3" +version = "3.5.0+0" [[xkbcommon_jll]] -deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg", "Wayland_jll", "Wayland_protocols_jll", "Xorg_libxcb_jll", "Xorg_xkeyboard_config_jll"] -git-tree-sha1 = "ece2350174195bb31de1a63bea3a41ae1aa593b6" +deps = ["Artifacts", "JLLWrappers", "Libdl", "Xorg_libxcb_jll", "Xorg_xkeyboard_config_jll"] +git-tree-sha1 = "fbf139bce07a534df0e699dbb5f5cc9346f95cc1" uuid = "d8fb68d0-12a3-5cfd-a85a-d49703b185fd" -version = "0.9.1+5" +version = "1.9.2+0" diff --git a/extra/Plot_copy_states_julia.ipynb b/extra/Plot_copy_states_julia.ipynb new file mode 100644 index 00000000..85cb9189 --- /dev/null +++ b/extra/Plot_copy_states_julia.ipynb @@ -0,0 +1,476 @@ +{ + "cells": [ + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "Before running the code blocks, run the following commands to get the kernel prepared:\n", + "```sh\n", + "julia\n", + "import Pkg\n", + "Pkg.update()\n", + "Pkg.precompile()\n", + "\n", + "using Pkg\n", + "Pkg.build(\"IJulia\")\n", + "```" + ] + }, + { + "cell_type": "code", + "execution_count": 226, + "metadata": {}, + "outputs": [], + "source": [ + "using HDF5\n", + "using Serialization\n", + "using DataFrames, Plots, Statistics\n", + "using Plots.PlotMeasures \n", + "using DataFramesMeta\n", + "using Missings\n", + "using ColorSchemes" + ] + }, + { + "cell_type": "code", + "execution_count": 227, + "metadata": {}, + "outputs": [ + { + "data": { + "text/plain": [ + "safe_max (generic function with 1 method)" + ] + }, + "execution_count": 227, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "has_data(v) = any(!ismissing, v)\n", + "safe_mean(v) = has_data(v) ? mean(skipmissing(v)) : missing\n", + "safe_std(v) = has_data(v) ? std(collect(skipmissing(v)); corrected=false) : missing\n", + "safe_min(v) = has_data(v) ? minimum(skipmissing(v)) : missing\n", + "safe_max(v) = has_data(v) ? maximum(skipmissing(v)) : missing\n" + ] + }, + { + "cell_type": "code", + "execution_count": 228, + "metadata": {}, + "outputs": [ + { + "data": { + "text/plain": [ + "rename_optimization (generic function with 1 method)" + ] + }, + "execution_count": 228, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "function rename_regime(trial)\n", + " if trial == \"1(1.0) particles\"\n", + " return \"Extreme degeneracy\"\n", + " elseif trial == \"1(0.999) particles\"\n", + " return \"High degeneracy\"\n", + " elseif trial == \"1(0.99) particles\"\n", + " return \"Near-degeneracy(0.99)\"\n", + " elseif trial == \"50%(1.0) particles\"\n", + " return \"Balanced case\"\n", + " elseif trial == \"all(1.0) particles\"\n", + " return \"Uniform case\"\n", + " end\n", + " return trial\n", + "end\n", + "\n", + "function rename_stats(metric)\n", + " if metric == \"waitall_ratio\"\n", + " return \"Waitall/Overall Time Ratio\"\n", + " elseif metric == \"overall\"\n", + " return \"Overall Time (s)\"\n", + " elseif metric == \"copy_states\"\n", + " return \"Copy States Time (s)\"\n", + " elseif metric == \"waitall_phase\"\n", + " return \"Waitall Time (s)\"\n", + " elseif metric == \"optimize_resample\"\n", + " return \"Optimise Resample (s)\"\n", + " elseif metric == \"resample_ratio\"\n", + " return \"Overhead Time Ratio\"\n", + " else\n", + " return metric\n", + " end\n", + "end\n", + "\n", + "function rename_optimization(optimization)\n", + " if optimization == \"original\"\n", + " return \"Baseline\"\n", + " elseif optimization == \"only_optimize_resampling\"\n", + " return \"Optimise Resampling Only\"\n", + " elseif optimization == \"only_dedup\"\n", + " return \"Deduplication Only\"\n", + " elseif optimization == \"dedup_threading\"\n", + " return \"Deduplication + Threading\"\n", + " elseif optimization == \"dedup_threading_optimize_resampling\"\n", + " return \"Full Optimisation\"\n", + " else\n", + " return optimization\n", + " end\n", + "end" + ] + }, + { + "cell_type": "code", + "execution_count": 229, + "metadata": {}, + "outputs": [ + { + "data": { + "text/plain": [ + "timer_dict_to_df (generic function with 3 methods)" + ] + }, + "execution_count": 229, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "\n", + "function timer_dict_to_df(timer_dict, optimization, flatten=false)\n", + " rows = []\n", + "\n", + " for (trial, ranks) in timer_dict\n", + " k, total_rank, nprt_per_rank, n_float_per_particle, perm, p = split(trial, \":\")\n", + " k = k == \"half\" ? \"50%\" : k\n", + " trial_name = \"$k($p) particles\"\n", + " for (rank, timers) in ranks\n", + " function format_row(op, metric, value)\n", + " return (\n", + " optimization = optimization,\n", + " trial = String(trial_name),\n", + " perm = String(perm),\n", + " total_rank = parse(Int, total_rank),\n", + " particle_size = n_float_per_particle,\n", + " nprt_per_rank = nprt_per_rank,\n", + " rank = string(rank),\n", + " op = String(op),\n", + " metric = String(metric),\n", + " value = value,\n", + " )\n", + " end\n", + " function recursive_push(inner_timers)\n", + " for (op, metrics) in inner_timers\n", + " if op == \"receive loop\" && flatten\n", + " for (inner_op, inner_metrics) in metrics[\"inner_timers\"]\n", + " for (metric, value) in inner_metrics\n", + " push!(rows, format_row(inner_op, metric, value))\n", + " end\n", + " end\n", + " else\n", + " push!(rows, format_row(op, \"time_s\", metrics[\"time_ns\"] / 1e9))\n", + " push!(rows, format_row(op, \"n_calls\", metrics[\"n_calls\"]))\n", + " recursive_push(metrics[\"inner_timers\"])\n", + " end\n", + " end\n", + " end\n", + " push!(rows, format_row(\"overall\", \"time_s\", timers[\"time_ns\"] / 1e9))\n", + " push!(rows, format_row(\"overall\", \"n_calls\", timers[\"n_calls\"]))\n", + " recursive_push(timers[\"inner_timers\"])\n", + " end\n", + " end\n", + " return DataFrame(rows)\n", + "end" + ] + }, + { + "cell_type": "code", + "execution_count": 230, + "metadata": {}, + "outputs": [ + { + "data": { + "text/plain": [ + "df_from_h5 (generic function with 1 method)" + ] + }, + "execution_count": 230, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "function df_from_h5(root_dir, category)\n", + " optimization = split(category, \"/\")[end]\n", + "\n", + " root = dirname(@__FILE__)\n", + " h5path(rank) = joinpath(root, \"../$(root_dir)/$(category)/\", \"all_timers_$(rank).h5\") \n", + " all_timer_dfs = DataFrame()\n", + " for rank in [2, 4, 8, 16, 32]\n", + " blob = h5open(h5path(rank)) do f\n", + " read(f, \"all_timers\")\n", + " end\n", + "\n", + " # Deserialize back into Dict{String,Dict{Int,Dict{String,Any}}}\n", + " merged_timers = deserialize(IOBuffer(blob))\n", + "\n", + " # Convert to DataFrame\n", + " timer_df = timer_dict_to_df(merged_timers, optimization)\n", + " \n", + " # Concat to all_timer_dfs\n", + " all_timer_dfs = vcat(all_timer_dfs, timer_df)\n", + " end\n", + "\n", + " wide = unstack(\n", + " all_timer_dfs,\n", + " [:optimization, :trial, :perm, :total_rank, :nprt_per_rank, :particle_size, :rank, :op],\n", + " :metric,\n", + " :value\n", + " )\n", + " # Sort by perm and trial\n", + " wide = sort!(wide, [:perm, :trial])\n", + "\n", + " rand_df = wide[wide.perm .== \"randperm\", :]\n", + " return rand_df\n", + "end" + ] + }, + { + "cell_type": "code", + "execution_count": 231, + "metadata": {}, + "outputs": [ + { + "data": { + "text/plain": [ + "widen_ops (generic function with 1 method)" + ] + }, + "execution_count": 231, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "\n", + "function widen_ops(df::DataFrame)\n", + " rename!(df, Symbol.(names(df)))\n", + "\n", + " keys = [:optimization, :trial, :perm, :total_rank, :nprt_per_rank, :particle_size, :rank]\n", + " wanted = [\"overall\",\"waitall\",\"broadcast\",\"copy states\",\"write from buffer\",\"write to buffer\", \"waitall phase\", \"buffer write-back\",\n", + " \"receive loop\",\"send loop\",\"irecv\",\"remote duplicates copy\", \"optimize resample\", \"local copy\", \"remote receive\", \"send plan\", \"receive plan\", \"local replication\", \"local replication\", \"remote replication\"]\n", + "\n", + " df2 = subset(df, :op => ByRow(in(wanted)))\n", + "\n", + " transform!(df2, :n_calls => ByRow(x -> x == 0 ? missing : x) => :n_calls)\n", + "\n", + " g = groupby(df2, vcat(keys, [:op]))\n", + " avg = combine(g,\n", + " [:time_s, :n_calls] => ((t, c) -> sum(t) / sum(c) ) => :time_s_per_call\n", + " )\n", + "\n", + " wide = unstack(avg, keys, :op, :time_s_per_call; combine=first)\n", + " rename!(wide, Symbol.(replace.(string.(names(wide)), r\"[ -]\" => \"_\")))\n", + " return wide\n", + "end" + ] + }, + { + "cell_type": "code", + "execution_count": 232, + "metadata": {}, + "outputs": [ + { + "data": { + "text/plain": [ + "stats (generic function with 1 method)" + ] + }, + "execution_count": 232, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "function stats(df_stats)\n", + " df_stats = @chain df_stats[df_stats.total_rank .> 1, :] begin\n", + " @transform(\n", + " :waitall_ratio = :waitall_phase ./ :overall,\n", + " :localcopy_ratio = :local_replication ./ :overall,\n", + " :remotedup_ratio = :remote_replication ./ :overall,\n", + " :writefrombuf_ratio = :buffer_write_back ./ :overall,\n", + " :resample_ratio = :optimize_resample ./ :overall,\n", + " )\n", + " end\n", + " return df_stats\n", + "end" + ] + }, + { + "cell_type": "code", + "execution_count": 233, + "metadata": {}, + "outputs": [ + { + "data": { + "text/plain": [ + "render_stats (generic function with 3 methods)" + ] + }, + "execution_count": 233, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "function render_stats(df, stats_to_plot=[\"overall\", \"copy_states\", \"waitall_phase\", \"waitall_ratio\"])\n", + " # Configuration for plots\n", + " trials = [\"1(1.0) particles\", \"1(0.99) particles\", \"50%(1.0) particles\", \"all(1.0) particles\"]\n", + " optimizations = unique(df.optimization)\n", + " ntrials = length(trials)\n", + " nstats = length(stats_to_plot)\n", + " n_opts = length(optimizations)\n", + "\n", + " # --- Create the individual plots for the grid ---\n", + " axes = []\n", + " for (i, trial) in enumerate(trials)\n", + " for (j, stat) in enumerate(stats_to_plot)\n", + " # Create a new plot object for this subplot\n", + " p = plot(legend=false, palette=:auto, bottom_margin=10mm)\n", + " \n", + " # --- Set conditional labels and titles ---\n", + " if i == 1\n", + " plot!(p, title = rename_stats(stat), top_margin = 10mm)\n", + " end\n", + " if j == 1\n", + " plot!(p, ylabel = rename_regime(trial), left_margin = 20mm)\n", + " end\n", + " if i == ntrials\n", + " plot!(p, xlabel = \"Total Rank\", bottom_margin = 10mm)\n", + " end\n", + "\n", + " df_filtered = df[df.trial .== trial, :]\n", + " \n", + " # --- Add each optimization as a series to the plot ---\n", + " for optimization in optimizations\n", + " sub = select(df_filtered, :optimization, :total_rank, :rank, stat => :value)\n", + " subrk = sub[sub.optimization .== optimization, :]\n", + " isempty(subrk) && continue\n", + "\n", + " # Determine if log scale should be used\n", + " use_log = stat in [\"overall\", \"copy_states\", \"waitall_phase\"]\n", + "\n", + " # Group and calculate statistics.\n", + " g = if use_log\n", + " # Add a small epsilon to avoid log(0) issues\n", + " subrk_log = @transform(subrk, :log_value = log10.(:value .+ 1e-12))\n", + " \n", + " # Calculate stats in both linear (for mean) and log (for std) space\n", + " g_linear = combine(groupby(subrk, :total_rank), :value => safe_mean => :mean)\n", + " g_log = combine(groupby(subrk_log, :total_rank), :log_value => safe_std => :std_log)\n", + " \n", + " # Join them together and return\n", + " leftjoin(g_linear, g_log, on = :total_rank)\n", + " else\n", + " combine(groupby(subrk, :total_rank),\n", + " :value => safe_mean => :mean,\n", + " :value => safe_std => :std)\n", + " end\n", + "\n", + " # Filter out rows with missing data and sort\n", + " filter!(row -> all(!ismissing, values(row)), g)\n", + " sort!(g, :total_rank)\n", + " isempty(g) && continue\n", + " \n", + " # Prepare plot variables (mean and ribbon) based on the scale\n", + " local plot_mean, ribbon_val\n", + " if use_log\n", + " plot!(p, yaxis=:log)\n", + " # Use the arithmetic mean for the central line\n", + " plot_mean = g.mean\n", + " \n", + " # Calculate the geometric standard deviation as a multiplicative factor\n", + " gstd = 10 .^ g.std_log\n", + " \n", + " # Define ribbon bounds multiplicatively around the arithmetic mean\n", + " lower_bound = plot_mean ./ gstd\n", + " upper_bound = plot_mean .* gstd\n", + " \n", + " # The ribbon is the distance from the central line\n", + " ribbon_val = (plot_mean .- lower_bound, upper_bound .- plot_mean)\n", + " else\n", + " plot_mean = g.mean\n", + " ribbon_val = g.std\n", + " end\n", + "\n", + " plot!(p, string.(g.total_rank), plot_mean,\n", + " ribbon = ribbon_val, seriestype = :path,\n", + " markersize = 4, linewidth = 1.5)\n", + " end\n", + " push!(axes, p)\n", + " end\n", + " end\n", + "\n", + " # --- Create the global legend ---\n", + " legend_labels = permutedims([rename_optimization(opt) for opt in optimizations])\n", + " legend_plot = plot(\n", + " (1:n_opts)', # Dummy data for legend entries\n", + " legend = :top,\n", + " legend_columns = -1, # Force a single horizontal row\n", + " labels = legend_labels,\n", + " framestyle = :none,\n", + " palette = :auto,\n", + " size = (1,1)\n", + " )\n", + "\n", + " # --- Combine legend and plots into the final figure ---\n", + " final_fig = plot(\n", + " legend_plot,\n", + " axes...,\n", + " layout = @layout([A{0.05h}; grid(ntrials, nstats)]),\n", + " size = (400 * nstats, 300 * ntrials)\n", + " )\n", + "\n", + " return final_fig\n", + "end" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "metadata": {}, + "outputs": [], + "source": [ + "root_dir = \"test/output29\"\n", + "original_100k_df = df_from_h5(root_dir, \"original\")\n", + "dedup_100k_df = df_from_h5(root_dir, \"only_dedup\")\n", + "dedup_threads_100k_df = df_from_h5(root_dir, \"dedup_threading\")\n", + "# op_100k_df = df_from_h5(root_dir, \"only_optimize_resampling\")\n", + "dtop_100k_df = df_from_h5(root_dir, \"dedup_threading_optimize_resampling\")\n", + "\n", + "union_df = vcat(original_100k_df, dedup_100k_df, dedup_threads_100k_df, dtop_100k_df)\n", + "union_df = widen_ops(union_df)\n", + "union_df = stats(union_df)\n", + "render_stats(union_df)" + ] + } + ], + "metadata": { + "kernelspec": { + "display_name": "Julia 1.11.5", + "language": "julia", + "name": "julia-1.11" + }, + "language_info": { + "file_extension": ".jl", + "mimetype": "application/julia", + "name": "julia", + "version": "1.11.5" + } + }, + "nbformat": 4, + "nbformat_minor": 2 +} diff --git a/extra/Project.toml b/extra/Project.toml index f5896477..ae957020 100644 --- a/extra/Project.toml +++ b/extra/Project.toml @@ -1,4 +1,5 @@ [deps] +ColorSchemes = "35d6a980-a343-548e-a6ea-1d62b119f2f4" HDF5 = "f67ccb44-e63f-5c2f-98bd-6dc0ccc4ba2f" Plots = "91a5bcdd-55d7-5caf-9e0b-520d859cae80" PlutoUI = "7f904dfe-b85e-4ff6-b463-dae2292396a8" diff --git a/extra/weak_scaling/kathleen_slurm_copy_states.sh b/extra/weak_scaling/kathleen_slurm_copy_states.sh new file mode 100644 index 00000000..d9487486 --- /dev/null +++ b/extra/weak_scaling/kathleen_slurm_copy_states.sh @@ -0,0 +1,19 @@ +#!/bin/bash -l +#SBATCH --job-name=ParticleDAScaling +#SBATCH --time=02:00:00 +#SBATCH --mem-per-cpu=4G +#SBATCH --cpus-per-task=40 +#SBATCH --nodes=16 +#SBATCH --ntasks-per-node=1 +#SBATCH --chdir=/home/ucabc46/exp/ParticleDA.jl +#SBATCH --output=test/slurm_log/%x-%j.out +#SBATCH --error=test/slurm_log/%x-%j.err + +export OMP_NUM_THREADS=$SLURM_CPUS_PER_TASK +export JULIA_NUM_THREADS=$OMP_NUM_THREADS + +julia --project=. -e 'using Pkg; Pkg.instantiate(); Pkg.precompile()' + +/home/ucabc46/.julia/bin/mpiexecjl -n $SLURM_NNODES\ + julia --project=. \ + /home/ucabc46/exp/ParticleDA.jl/test/mpi_optimized_copy_states.jl -t /home/ucabc46/exp/ParticleDA.jl/test/output/dedup_threading_optimize_resampling/all_timers_$SLURM_NNODES.h5 -o \ No newline at end of file diff --git a/extra/weak_scaling/kathleen_slurm_weak_scaling.sh b/extra/weak_scaling/kathleen_slurm_weak_scaling.sh new file mode 100644 index 00000000..d72f2a14 --- /dev/null +++ b/extra/weak_scaling/kathleen_slurm_weak_scaling.sh @@ -0,0 +1,17 @@ +#!/bin/bash -l +#SBATCH --job-name=ParticleDAScaling +#SBATCH --time=02:00:00 +#SBATCH --mem-per-cpu=4G +#SBATCH --nodes=4 +#SBATCH --ntasks-per-node=1 +#SBATCH --cpus-per-task=40 +#SBATCH --chdir=/home/ucabc46/exp/ParticleDA.jl +#SBATCH --output=slurm_log/%x-%j.out +#SBATCH --error=slurm_log/%x-%j.err + +export OMP_NUM_THREADS=$SLURM_CPUS_PER_TASK +export JULIA_NUM_THREADS=$OMP_NUM_THREADS + +/home/ucabc46/.julia/bin/mpiexecjl -n $SLURM_NNODES\ + julia --project=. \ + /home/ucabc46/exp/ParticleDA.jl/extra/weak_scaling/run_particleda.jl \ No newline at end of file diff --git a/extra/weak_scaling/parametersW1.yaml b/extra/weak_scaling/parametersW1.yaml index 230c6f85..695aa615 100644 --- a/extra/weak_scaling/parametersW1.yaml +++ b/extra/weak_scaling/parametersW1.yaml @@ -1,32 +1,33 @@ -# Parameter file for ParticleDA using TDAC model with Optimal Filter. -# Developer: Alex Beskos, May 2021 - -filter: - nprt: 200 - n_time_step: 250 - verbose: true - enable_timers: true - output_filename: "optimal_filter_test.h5" - +simulate_observations: + n_time_step: 51 + seed: 123 model: llw2d: - x_length: 200.0e3 - y_length: 200.0e3 - nx: 51 - ny: 51 - station_filename: "stationsW1.txt" - obs_noise_std: [0.01] - + station_filename: "/home/ucabc46/exp/ParticleDA.jl/extra/weak_scaling/stationsW1.txt" nu: 2.5 - lambda: 5.0e3 - sigma : [0.1, 10.0, 10.0] - nu_initial_state: 2.5 - lambda_initial_state: 5.0e3 - sigma_initial_state: 0.001 - - n_integration_step: 10 - time_step: 5.0 - peak_height: 30.0 - peak_position: [1e4,1e4] + sigma: 0.01 + nx: 51 + n_integration_step: 16 + x_length: 200000.0 + peak_position: + - 10000.0 + - 10000.0 + lambda_initial_state: 5000.0 + obs_noise_std: + - 0.0025 + padding: 0 + lambda: 5000.0 + ny: 51 + y_length: 200000.0 + sigma_initial_state: 0.001 + use_peak_initial_state_mean: true + observed_state_var_indices: + - 1 + time_step: 0.5 +filter: + optimize_copy_states: true + output_filename: "llw2d_filtering.h5" + nprt: 1000 + enable_timers: true diff --git a/extra/weak_scaling/run_particleda.jl b/extra/weak_scaling/run_particleda.jl index 9b12a146..9ddf2c94 100644 --- a/extra/weak_scaling/run_particleda.jl +++ b/extra/weak_scaling/run_particleda.jl @@ -1,34 +1,55 @@ using ParticleDA using TimerOutputs using MPI +using LinearAlgebra +using YAML + +# Verify BLAS implementation is OpenBLAS +@assert occursin("openblas", string(BLAS.get_config())) + +# Set size of thread pool for BLAS operations to 1 +BLAS.set_num_threads(1) # Initialise MPI MPI.Init() mpi_size = MPI.Comm_size(MPI.COMM_WORLD) -# Save some variables for later use -test_dir = joinpath(dirname(pathof(ParticleDA)), "..", "test") -module_src = joinpath(test_dir, "model", "model.jl") -input_file = joinpath(test_dir, "integration_test_1.yaml") -truth_file = "test_observations.h5" -# Instantiate the test environment -using Pkg -Pkg.activate(test_dir) -Pkg.instantiate() - # Include the sample model source code and load it -include(module_src) -using .Model +llw2d_src = joinpath(dirname(pathof(ParticleDA)), "..", "test", "models", "llw2d.jl") +include(llw2d_src) +using .LLW2d +observation_file = joinpath(dirname(pathof(ParticleDA)), "..", "extra", "weak_scaling", "test_observations.h5") +parameters_file = joinpath(dirname(pathof(ParticleDA)), "..", "extra", "weak_scaling", "parametersW1.yaml") +output_file = joinpath(dirname(pathof(ParticleDA)), "..", "extra", "weak_scaling", "llw2d_filtering.h5") +#filter_type = OptimalFilter +filter_type = BootstrapFilter +summary_stat_type = NaiveMeanSummaryStat + +my_rank = MPI.Comm_rank(MPI.COMM_WORLD) -input_dict = ParticleDA.read_input_file("parametersW1.yaml") -run_custom_params = Dict(input_dict) +println("Rank $(my_rank): # Julia threads = $(Threads.nthreads()), # BLAS threads = $(BLAS.get_num_threads())") + +if my_rank == 0 && !isfile(observation_file) + observation_sequence = simulate_observations_from_model( + LLW2d.init, parameters_file, observation_file + ) +end +if my_rank == 0 && isfile(output_file) + rm(output_file) +end + +MPI.Barrier(MPI.COMM_WORLD) -# Real run TimerOutputs.enable_debug_timings(ParticleDA) +# update parameters to enable weak scaling +parameters = YAML.load_file(parameters_file) +parameters["filter"]["nprt"] = mpi_size * 1000 +open(parameters_file, "w") do io + YAML.write(io, parameters) +end + +println("Optimized copy states enabled: ", parameters["filter"]["optimize_copy_states"]) -run_custom_params["model"]["llw2d"]["padding"]=0 -run_custom_params["filter"]["verbose"]=true -run_custom_params["filter"]["enable_timers"]=true -run_custom_params["filter"]["output_filename"]=string("weak_scaling_r",mpi_size,".h5") -run_custom_params["filter"]["nprt"]=mpi_size * 64 -ParticleDA.run_particle_filter(Model.init, run_custom_params, BootstrapFilter(), truth_file) +final_states, final_statistics = run_particle_filter( + LLW2d.init, parameters_file, observation_file, filter_type, summary_stat_type +) diff --git a/extra/weak_scaling/test_observations.h5 b/extra/weak_scaling/test_observations.h5 index 678210e2..a2a9f388 100644 Binary files a/extra/weak_scaling/test_observations.h5 and b/extra/weak_scaling/test_observations.h5 differ diff --git a/src/ParticleDA.jl b/src/ParticleDA.jl index 31de0ab4..973fd9a3 100644 --- a/src/ParticleDA.jl +++ b/src/ParticleDA.jl @@ -271,6 +271,12 @@ function run_particle_filter( @timeit_debug timer "Resample" resample!( filter_data.resampling_indices, filter_data.weights, rng ) + if filter_params.optimize_copy_states + # Optimize resampling indices to minimize data movement when copying states + @timeit_debug timer "Optimize Resample" filter_data.resampling_indices .= optimized_resample!( + filter_data.resampling_indices, my_size + ) + end else @timeit_debug timer "Gather weights" MPI.Gather!( @@ -286,7 +292,9 @@ function run_particle_filter( filter_data.copy_buffer, filter_data.resampling_indices, my_rank, - nprt_per_rank + nprt_per_rank, + timer, + filter_params.optimize_copy_states ) if filter_params.verbose diff --git a/src/params.jl b/src/params.jl index cf73d469..84625b59 100644 --- a/src/params.jl +++ b/src/params.jl @@ -17,6 +17,8 @@ Parameters for ParticleDA run. Keyword arguments: the scheduler to balance load across threads but potentially increase overheads. If simulation of the model being filtered use multiple threads then it may be beneficial to set the `n_tasks = 1` to avoid too much contention between threads. +* `optimize_copy_states::Bool`: Flag to control whether to use optimized copy_states + function that reduces the number of messages sent during resampling. """ Base.@kwdef struct FilterParameters{V<:Union{AbstractSet, AbstractVector}} master_rank::Int = 0 @@ -27,6 +29,7 @@ Base.@kwdef struct FilterParameters{V<:Union{AbstractSet, AbstractVector}} particle_save_time_indices::V = [] seed::Union{Nothing, Int} = nothing n_tasks::Int = -1 + optimize_copy_states::Bool = false end diff --git a/src/utils.jl b/src/utils.jl index 5980420c..e0f66d13 100644 --- a/src/utils.jl +++ b/src/utils.jl @@ -1,3 +1,4 @@ +using ExactOptimalTransport, HiGHS function normalized_exp!(weight::AbstractVector) weight .-= maximum(weight) @@ -5,6 +6,43 @@ function normalized_exp!(weight::AbstractVector) weight ./= sum(weight) end +# Solve an optimal transport problem to minimize the number of particles +# that need to be communicated between ranks during resampling. +function optimized_resample!(resampled_indices::AbstractVector{Int}, nrank::Int) + nprt_per_rank = length(resampled_indices) ÷ nrank + stock_queue = [Int[] for _ in 1:nrank] + + # Assign each resampled index to its corresponding rank + for resampled_idx in resampled_indices + rank = div(resampled_idx - 1, nprt_per_rank) + 1 + push!(stock_queue[rank], resampled_idx) + end + + supply_vector = Float64[length(stock_queue[rank]) for rank in 1:nrank] + demand_vector = Float64.(fill(nprt_per_rank, nrank)) + cost_matrix = ones(Float64, nrank, nrank) + for i in 1:nrank + cost_matrix[i, i] = 0 + end + + # Solve the optimal transport problem using the HiGHS solver + y = emd(supply_vector, demand_vector, cost_matrix, HiGHS.Optimizer()) + + # update resampled_indices + for i in 1:nrank + idx = 1 + for j in 1:nrank + nmove = Int(y[j, i]) + for _ in 1:nmove + resampled_indices[(i - 1) * nprt_per_rank + idx] = popfirst!(stock_queue[j]) + idx += 1 + end + end + end + return resampled_indices +end + + # Resample particles from given weights using Stochastic Universal Sampling function resample!( resampled_indices::AbstractVector{Int}, @@ -49,9 +87,15 @@ function copy_states!( buffer::AbstractMatrix{T}, resampling_indices::Vector{Int}, my_rank::Int, - nprt_per_rank::Int + nprt_per_rank::Int, + to::TimerOutputs.TimerOutput = TimerOutputs.TimerOutput(), + dedup::Bool = false ) where T + if dedup + return copy_states_dedup!(particles, buffer, resampling_indices, my_rank, nprt_per_rank, to) + end + # These are the particle indices stored on this rank particles_have = my_rank * nprt_per_rank + 1:(my_rank + 1) * nprt_per_rank @@ -66,31 +110,154 @@ function copy_states!( reqs = Vector{MPI.Request}(undef, 0) # Send particles to processes that want them - for (k,id) in enumerate(resampling_indices) - rank_wants = floor(Int, (k - 1) / nprt_per_rank) - if id in particles_have && rank_wants != my_rank - local_id = id - my_rank * nprt_per_rank - req = MPI.Isend(view(particles, :, local_id), rank_wants, id, MPI.COMM_WORLD) - push!(reqs, req) + @timeit_debug to "send loop" begin + for (k,id) in enumerate(resampling_indices) + rank_wants = floor(Int, (k - 1) / nprt_per_rank) + if id in particles_have && rank_wants != my_rank + local_id = id - my_rank * nprt_per_rank + req = MPI.Isend(view(particles, :, local_id), rank_wants, id, MPI.COMM_WORLD) + push!(reqs, req) + end + end + end + + # Receive particles this rank wants from ranks that have them + # If I already have them, just do a local copy + # Receive into a buffer so we dont accidentally overwrite stuff + @timeit_debug to "receive loop" begin + for (k,proc,id) in zip(1:nprt_per_rank, rank_has, particles_want) + if proc == my_rank + @timeit_debug to "local copy" begin + local_id = id - my_rank * nprt_per_rank + buffer[:, k] .= view(particles, :, local_id) + end + else + @timeit_debug to "remote receive" begin + req = MPI.Irecv!(view(buffer, :, k), proc, id, MPI.COMM_WORLD) + push!(reqs,req) + end + end + end + end + + # Wait for all comms to complete + @timeit_debug to "waitall phase" MPI.Waitall(reqs) + + @timeit_debug to "buffer write-back" particles .= buffer + +end + +# An optimized version of copy_states that minimizes the number of messages sent +# by deduplicating particles that need to be sent between ranks. +function copy_states_dedup!( + particles::AbstractMatrix{T}, + buffer::AbstractMatrix{T}, + resampling_indices::Vector{Int}, + my_rank::Int, + nprt_per_rank::Int, + to::TimerOutputs.TimerOutput = TimerOutputs.TimerOutput() +) where T + + # Same as copy_states + particles_have = my_rank * nprt_per_rank + 1:(my_rank + 1) * nprt_per_rank + particles_want = resampling_indices[particles_have] + reqs = Vector{MPI.Request}(undef, 0) + + # Determine which particles need to be sent where + @timeit_debug to "send plan" sends_to = _determine_sends(resampling_indices, my_rank, nprt_per_rank) + # Categorize the particles this rank wants into local copies and remote copies + @timeit_debug to "receive plan" local_copies, remote_copies = _categorize_wants(particles_want, my_rank, nprt_per_rank) + + # Send particles to processes that want them + @timeit_debug to "send loop" begin + for (dest_rank, unique_ids) in sends_to + for id in unique_ids + local_id = id - my_rank * nprt_per_rank + req = MPI.Isend(view(particles, :, local_id), dest_rank, id, MPI.COMM_WORLD) + push!(reqs, req) + end end end # Receive particles this rank wants from ranks that have them # If I already have them, just do a local copy # Receive into a buffer so we dont accidentally overwrite stuff - for (k,proc,id) in zip(1:nprt_per_rank, rank_has, particles_want) - if proc == my_rank + @timeit_debug to "receive loop" begin + for (id, buffer_indices) in remote_copies + source_rank = floor(Int, (id - 1) / nprt_per_rank) + first_k = buffer_indices[1] # Receive into the first required slot. + req = MPI.Irecv!(view(buffer, :, first_k), source_rank, id, MPI.COMM_WORLD) + push!(reqs, req) + end + end + + # Perform local copies + @timeit_debug to "local replication" begin + for (id, buffer_indices) in local_copies local_id = id - my_rank * nprt_per_rank - buffer[:, k] .= view(particles, :, local_id) - else - req = MPI.Irecv!(view(buffer, :, k), proc, id, MPI.COMM_WORLD) - push!(reqs,req) + source_view = view(particles, :, local_id) + Threads.@threads for k in buffer_indices + buffer[:, k] .= source_view + end end end # Wait for all comms to complete - MPI.Waitall(reqs) + @timeit_debug to "waitall phase" MPI.Waitall(reqs) + + # Perform remote copies for particles received from other ranks + @timeit_debug to "remote replication" begin + for (id, buffer_indices) in remote_copies + if length(buffer_indices) > 1 + source_view = view(buffer, :, buffer_indices[1]) + # TODO: threading in chunks + Threads.@threads for i in 2:length(buffer_indices) + k = buffer_indices[i] + buffer[:, k] .= source_view + end + end + end + end + + @timeit_debug to "buffer write-back" begin + Threads.@threads for j in 1:size(particles, 2) + # @views creates a non-allocating view of the column, which is faster inside a loop + @views particles[:, j] .= buffer[:, j] + end + end +end + +function _determine_sends(resampling_indices::Vector{Int}, my_rank::Int, nprt_per_rank::Int) + sends_to = Dict{Int, Set{Int}}() + for (new_idx, old_id) in enumerate(resampling_indices) + source_rank = floor(Int, (old_id - 1) / nprt_per_rank) + + if source_rank == my_rank + dest_rank = floor(Int, (new_idx - 1) / nprt_per_rank) + if dest_rank != my_rank + unique_ids_for_dest = get!(() -> Set{Int}(), sends_to, dest_rank) + push!(unique_ids_for_dest, old_id) + end + end + end + return sends_to +end - particles .= buffer +function _categorize_wants(particles_want, my_rank::Int, nprt_per_rank::Int) + local_copies = Dict{Int, Vector{Int}}() + remote_copies = Dict{Int, Vector{Int}}() + for k in 1:nprt_per_rank + id = particles_want[k] + source_rank = floor(Int, (id - 1) / nprt_per_rank) + + if source_rank == my_rank + get!(() -> Int[], local_copies, id) |> v -> push!(v, k) + else + get!(() -> Int[], remote_copies, id) |> v -> push!(v, k) + end + end + return local_copies, remote_copies end + + diff --git a/test/Project.toml b/test/Project.toml index 8b9d6b48..cc42f7d4 100644 --- a/test/Project.toml +++ b/test/Project.toml @@ -1,5 +1,6 @@ [deps] ChunkSplitters = "ae650224-84b6-46f8-82ea-d812ca08434e" +Dates = "ade2ca70-3891-5945-98fb-dc099432e06a" DelimitedFiles = "8bb1440f-4735-579b-a4ab-409b98df4dab" Distributions = "31c24e10-a181-5473-b8eb-7969acd0382f" GaussianRandomFields = "e4b2fa32-6e09-5554-b718-106ed5adafe9" @@ -9,9 +10,11 @@ MPI = "da04e1cc-30fd-572f-bb4f-1f8673147195" OrdinaryDiffEq = "1dea7af3-3e70-54e6-95c3-0bf5283fa5ed" PDMats = "90014a1f-27ba-587c-ab20-58faa44d9150" Random = "9a3f8284-a2c9-5f02-9a11-845980a1fd5c" +Serialization = "9e88b42a-f829-5b0c-bbe9-9e923198166b" StableRNGs = "860ef19b-820b-49d6-a774-d7a799459cd3" Statistics = "10745b16-79ce-11e8-11f9-7d13ad32a3b2" Test = "8dfed614-e22c-5e08-85e1-65c5234f0b40" +TimerOutputs = "a759f4b9-e2f1-59dc-863e-4aeb61b1ea8f" YAML = "ddb6d928-2868-570f-bddf-ab3f9cf99eb6" [compat] diff --git a/test/integration_test_7.yaml b/test/integration_test_7.yaml new file mode 100644 index 00000000..456caf13 --- /dev/null +++ b/test/integration_test_7.yaml @@ -0,0 +1,15 @@ +filter: + nprt: 10 + optimize_copy_states: true + +model: + llw2d: + nx: 51 + ny: 51 + n_stations_x: 4 + n_stations_y: 4 + padding: 0 + +simulate_observations: + seed: 123 + n_time_step: 10 diff --git a/test/mpi_optimized_copy_states.jl b/test/mpi_optimized_copy_states.jl new file mode 100644 index 00000000..0cf03cf3 --- /dev/null +++ b/test/mpi_optimized_copy_states.jl @@ -0,0 +1,186 @@ +using Test, ParticleDA, MPI, Random, TimerOutputs, HDF5, Serialization +TimerOutputs.enable_debug_timings(ParticleDA) + +const rng = Random.TaskLocalRNG() +Random.seed!(rng, 1234) + +build_expected_buffer(indices, r, npr, nf) = + Float64.((1:nf) .+ ((indices[r*npr .+ (1:npr)] .- 1) .* nf)') +function sample_indices(n::Int; k::Int=10, p::Float64=0.99) + @assert 1 ≤ k < n "k must be between 1 and n-1" + @assert 0.0 ≤ p ≤ 1.0 "p must be in [0,1]" + + # 1. Pick k unique “favorite” indices via a random permutation + fav = randperm(rng, n)[1:k] + + # 2. Build the complement + other = setdiff(1:n, fav) + + # 3. Decide for each of the n draws whether it comes from fav (true) or other (false) + mask = rand(rng, n) .< p # Bool vector of length n + + # 4. Preallocate result + result = Vector{Int}(undef, n) + + # 5. How many draws from each group? + na = count(mask) + nb = n - na + + # 6. Sample with replacement from each group + result[mask] .= rand(rng, fav, na) + result[.!mask] .= rand(rng, other, nb) + + return result +end + +MPI.Init() +my_rank = MPI.Comm_rank(MPI.COMM_WORLD) +my_size = MPI.Comm_size(MPI.COMM_WORLD) + +println("Number of threads available: ", Threads.nthreads()) + +n_particle_per_rank = 1000 +n_particle = n_particle_per_rank * my_size +verbose = "-v" in ARGS || "--verbose" in ARGS +output_timer = "-t" in ARGS || "--output-timer" in ARGS +if output_timer + if length(ARGS) < 2 + error("Please provide the output filename for timers.") + end + output_filename = ARGS[2] + println("Outputting timers to HDF5 file '$output_filename'") +end +# default: dedup enabled for testing +no_dedup = "-nd" in ARGS || "--no-dedup" in ARGS +println("Deduplication enabled: ", !no_dedup) +optimize_resample = "-o" in ARGS || "--optimize-resample" in ARGS +println("Optimized resampling enabled: ", optimize_resample) + +n_float_per_particle = 100000 +# total number of floats per rank +N = n_float_per_particle * n_particle_per_rank +# build & reshape in one go, then allocate a similar array +init_local_states = reshape((my_rank*N .+ (1:N)) .* 1.0, + n_float_per_particle, + n_particle_per_rank) +local_states = similar(init_local_states) + +if verbose + for i = 1:my_size + if i == my_rank + 1 + println("rank ", my_rank, ": local states: ", local_states) + end + MPI.Barrier(MPI.COMM_WORLD) + end +end + +buffer = zeros((n_float_per_particle, n_particle_per_rank)) + + +trial_sets = Dict( + "1:$my_size:$n_particle_per_rank:$n_float_per_particle:randperm:1.0" => () -> sort!(sample_indices(n_particle, k=1, p=1.0)), + "1:$my_size:$n_particle_per_rank:$n_float_per_particle:randperm:0.99" => () -> sort!(sample_indices(n_particle, k=1, p=0.99)), + "half:$my_size:$n_particle_per_rank:$n_float_per_particle:randperm:1.0" => () -> sort!(sample_indices(n_particle, k=div(n_particle, 2), p=1.0)), + "all:$my_size:$n_particle_per_rank:$n_float_per_particle:randperm:1.0" => () -> collect(1:n_particle) +) + +local_timer_dicts = Dict{String, Dict{String,Any}}() + +for (trial_name, indices_func) in trial_sets + if verbose && my_rank == 0 + println() + println("Resampling particles to indices ", indices) + println() + end + indices = collect(1:n_particle) # Placeholder for actual indices + # repeat experiment 10 times to get average time + # warm up run + println("Warm up run...") + ParticleDA.optimized_resample!(indices, my_size) + ParticleDA.copy_states!( + local_states, + buffer, + indices, + my_rank, + n_particle_per_rank + ) + println("Starting timed runs for trial '$trial_name'...") + + timer = TimerOutputs.TimerOutput("copy_states") + for _ in 1:10 + indices = collect(indices_func()) + copyto!(local_states, init_local_states) + @timeit timer "overall" begin + if optimize_resample && my_rank == 0 + @timeit timer "optimize resample" indices = ParticleDA.optimized_resample!(indices, my_size) + end + + # broadcast no matter whether we optimize or not to eliminate the overall time bias + @timeit timer "broadcast" MPI.Bcast!(indices, 0, MPI.COMM_WORLD) + + @timeit timer "copy states" ParticleDA.copy_states!( + local_states, + buffer, + indices, + my_rank, + n_particle_per_rank, + timer, + !no_dedup + ) + end + end + local_timer_dicts[trial_name] = TimerOutputs.todict(timer["overall"]) + + if verbose + for i = 1:my_size + if i == my_rank + 1 + # reconstruct expected buffer for this rank + expected = build_expected_buffer(indices, my_rank, + n_particle_per_rank, + n_float_per_particle) + + # compare + match = local_states == expected + + println("rank ", my_rank, ": local_states =") + show(stdout, "text/plain", local_states); println() + println("rank ", my_rank, ": expected =") + show(stdout, "text/plain", expected); println() + println("rank ", my_rank, ": match = ", match) + end + MPI.Barrier(MPI.COMM_WORLD) + end + end + + # build the expected buffer + expected = build_expected_buffer(indices, my_rank, + n_particle_per_rank, + n_float_per_particle) + + @test local_states == expected +end + +if output_timer + all_local = MPI.gather(local_timer_dicts, MPI.COMM_WORLD; root=0) + if my_rank == 0 + merged = Dict{String,Dict{Int,Dict{String,Any}}}() + for r in 0:my_size-1 + for (trial, tdict) in all_local[r+1] + rankmap = get!(merged, trial, Dict{Int,Dict{String,Any}}()) + rankmap[r] = tdict + end + end + + buf = IOBuffer() + serialize(buf, merged) + blob = take!(buf) # Vector{UInt8} + + h5open(output_filename, "w") do f + write(f, "all_timers", blob) + end + end +end + + +MPI.Barrier(MPI.COMM_WORLD) +MPI.Finalize() diff --git a/test/runtests.jl b/test/runtests.jl index 9d325ea3..ca742735 100644 --- a/test/runtests.jl +++ b/test/runtests.jl @@ -465,11 +465,18 @@ end @test all(resampled_indices .== 5) end +@testset "Optimized resampling unit tests" begin + indices = [1, 3, 5, 5, 5, 5] + n_rank = 3 + optimized_indices = ParticleDA.optimized_resample!(copy(indices), n_rank) + @test optimized_indices == [1, 5, 3, 5, 5, 5] +end + @testset "Integration test -- $(input_file) with $(filter_type) and $(stat_type)" for filter_type in (ParticleDA.BootstrapFilter, ParticleDA.OptimalFilter), stat_type in (ParticleDA.MeanSummaryStat, ParticleDA.MeanAndVarSummaryStat), - input_file in ["integration_test_$i.yaml" for i in 1:6] + input_file in ["integration_test_$i.yaml" for i in 1:7] observation_file_path = tempname() ParticleDA.simulate_observations_from_model( LLW2d.init, @@ -500,7 +507,7 @@ end end @testset "MPI test -- $(file)" for file in ( - "mpi_filtering.jl", "mpi_copy_states.jl", "mpi_summary_statistics.jl" + "mpi_filtering.jl", "mpi_copy_states.jl", "mpi_summary_statistics.jl", "mpi_optimized_copy_states.jl" ) julia = Base.julia_cmd() flags = ["--startup-file=no", "-q", "-t$(Base.Threads.nthreads())"]