From 4f3d6241cb43eb12362b5771a5e6cf3d11ff4353 Mon Sep 17 00:00:00 2001 From: Sam Date: Tue, 10 Dec 2024 19:23:02 +0000 Subject: [PATCH 1/3] add enzyme and mooncake to benchmark --- benchmark/Manifest.toml | 442 ++++++++++-------- benchmark/Project.toml | 3 + .../bench/EpiAwareUtils/EpiAwareUtils.jl | 3 + benchmark/bench/EpiInfModels/EpiInfModels.jl | 4 + .../bench/EpiLatentModels/EpiLatentModels.jl | 4 + benchmark/bench/EpiObsModels/EpiObsModels.jl | 4 + benchmark/make_epiaware_suite.jl | 6 +- 7 files changed, 283 insertions(+), 183 deletions(-) diff --git a/benchmark/Manifest.toml b/benchmark/Manifest.toml index 451bcb15d..1d3c75ef7 100644 --- a/benchmark/Manifest.toml +++ b/benchmark/Manifest.toml @@ -1,13 +1,13 @@ # This file is machine-generated - editing it directly is not advised -julia_version = "1.11.1" +julia_version = "1.11.2" manifest_format = "2.0" -project_hash = "9fb2e9db0221fb4b8d0c098c0ecdd8e5e0675214" +project_hash = "d327c5a9161230b71edf2c9e7aa54c25fc899ba1" [[deps.ADTypes]] -git-tree-sha1 = "30bb95a372787af850addf28ac937f1be7b79173" +git-tree-sha1 = "72af59f5b8f09faee36b4ec48e014a79210f2f4f" uuid = "47edcb42-4c32-4615-8424-f2b9edc5f35b" -version = "1.10.0" +version = "1.11.0" weakdeps = ["ChainRulesCore", "ConstructionBase", "EnzymeCore"] [deps.ADTypes.extensions] @@ -33,10 +33,10 @@ uuid = "80f14c24-f653-4e6a-9b94-39d6b0f70001" version = "5.6.0" [[deps.AbstractPPL]] -deps = ["AbstractMCMC", "Accessors", "DensityInterface", "Random"] -git-tree-sha1 = "6380a9a03a4207bac53ac310dd3a283bb4df54ef" +deps = ["AbstractMCMC", "Accessors", "DensityInterface", "JSON", "Random"] +git-tree-sha1 = "bdb19638644450ee1b0fd63740381835069d34b9" uuid = "7a57a42e-76ec-4ea3-a279-07e840d6d9cf" -version = "0.8.4" +version = "0.9.0" [[deps.AbstractTrees]] git-tree-sha1 = "2d9c9a55f9c93e8887ad391fbae72f8ef55e1177" @@ -45,9 +45,9 @@ version = "0.4.5" [[deps.Accessors]] deps = ["CompositionsBase", "ConstructionBase", "InverseFunctions", "LinearAlgebra", "MacroTools", "Markdown"] -git-tree-sha1 = "b392ede862e506d451fc1616e79aa6f4c673dab8" +git-tree-sha1 = "96bed9b1b57cf750cca50c311a197e306816a1cc" uuid = "7d9f7c33-5ae7-4f3b-8dc6-eff91059b697" -version = "0.1.38" +version = "0.1.39" [deps.Accessors.extensions] AccessorsAxisKeysExt = "AxisKeys" @@ -118,9 +118,9 @@ weakdeps = ["Libtask"] [[deps.AdvancedVI]] deps = ["ADTypes", "Bijectors", "DiffResults", "Distributions", "DistributionsAD", "DocStringExtensions", "ForwardDiff", "LinearAlgebra", "ProgressMeter", "Random", "Requires", "StatsBase", "StatsFuns", "Tracker"] -git-tree-sha1 = "d23ac9ecdf0ba3dfdd8ea22f42793fabc763afdc" +git-tree-sha1 = "187f67ab998f25208651262fee9539d845016b26" uuid = "b5ca4192-6429-45e5-a2d9-87aec30a685c" -version = "0.2.10" +version = "0.2.5" [deps.AdvancedVI.extensions] AdvancedVIEnzymeExt = ["Enzyme"] @@ -141,9 +141,9 @@ uuid = "66dad0bd-aa9a-41b7-9441-69ab47430ed8" version = "1.1.3" [[deps.ArgCheck]] -git-tree-sha1 = "a3a402a35a2f7e0b87828ccabbd5ebfbebe356b4" +git-tree-sha1 = "680b3b8759bd4c54052ada14e52355ab69e07876" uuid = "dce04be8-c92d-5529-be00-80e4d2c0e197" -version = "2.3.0" +version = "2.4.0" [[deps.ArgTools]] uuid = "0dad84c5-d112-42e6-8d28-ef12dabb789f" @@ -157,9 +157,9 @@ version = "0.4.0" [[deps.ArrayInterface]] deps = ["Adapt", "LinearAlgebra"] -git-tree-sha1 = "d60a1922358aa203019b7857a2c8c37329b8736c" +git-tree-sha1 = "d5140b60b87473df18cf4fe66382b7c3596df047" uuid = "4fba245c-0d91-5ea0-9b3e-6abc04ee57a9" -version = "7.17.0" +version = "7.17.1" [deps.ArrayInterface.extensions] ArrayInterfaceBandedMatricesExt = "BandedMatrices" @@ -189,9 +189,9 @@ version = "7.17.0" [[deps.ArrayLayouts]] deps = ["FillArrays", "LinearAlgebra"] -git-tree-sha1 = "492681bc44fac86804706ddb37da10880a2bd528" +git-tree-sha1 = "2bf6e01f453284cb61c312836b4680331ddfc44b" uuid = "4c555306-a7a7-4459-81d9-ec55ddd5c99a" -version = "1.10.4" +version = "1.11.0" weakdeps = ["SparseArrays"] [deps.ArrayLayouts.extensions] @@ -203,9 +203,19 @@ version = "1.11.0" [[deps.Atomix]] deps = ["UnsafeAtomics"] -git-tree-sha1 = "c06a868224ecba914baa6942988e2f2aade419be" +git-tree-sha1 = "c3b238aa28c1bebd4b5ea4988bebf27e9a01b72b" uuid = "a9b6321e-bd34-4604-b9c9-b65b8de01458" -version = "0.1.0" +version = "1.0.1" + + [deps.Atomix.extensions] + AtomixCUDAExt = "CUDA" + AtomixMetalExt = "Metal" + AtomixoneAPIExt = "oneAPI" + + [deps.Atomix.weakdeps] + CUDA = "052768ef-5323-5732-b1bb-66c8b64840ba" + Metal = "dde4c033-4e86-420c-a63e-0dd931031962" + oneAPI = "8f75cd03-7ff8-4ecb-9b8f-daf728133b1b" [[deps.AxisAlgorithms]] deps = ["LinearAlgebra", "Random", "SparseArrays", "WoodburyMatrices"] @@ -324,9 +334,9 @@ version = "0.6.0" [[deps.ChainRules]] deps = ["Adapt", "ChainRulesCore", "Compat", "Distributed", "GPUArraysCore", "IrrationalConstants", "LinearAlgebra", "Random", "RealDot", "SparseArrays", "SparseInverseSubset", "Statistics", "StructArrays", "SuiteSparse"] -git-tree-sha1 = "9e2503a7ac8df599cbf422af95729b2d263220f6" +git-tree-sha1 = "bcffdcaed50d3453673b852f3522404a94b50fad" uuid = "082447d4-558c-5d27-93f4-14fc19e9eca2" -version = "1.72.0" +version = "1.72.1" [[deps.ChainRulesCore]] deps = ["Compat", "LinearAlgebra"] @@ -469,9 +479,9 @@ version = "1.7.0" [[deps.DataFramesMeta]] deps = ["Chain", "DataFrames", "MacroTools", "OrderedCollections", "Reexport", "TableMetadataTools"] -git-tree-sha1 = "7042a6ad5910dc9edeae814e1110209752a1c996" +git-tree-sha1 = "21a4335f249f8b5f311d00d5e62938b50ccace4e" uuid = "1313f7d8-7da2-5740-9ea0-a2ca25f37964" -version = "0.15.3" +version = "0.15.4" [[deps.DataStructures]] deps = ["Compat", "InteractiveUtils", "OrderedCollections"] @@ -513,10 +523,10 @@ uuid = "85a47980-9c8c-11e8-2b9f-f7ca1fa99fb4" version = "0.4.3" [[deps.DiffEqBase]] -deps = ["ArrayInterface", "ConcreteStructs", "DataStructures", "DocStringExtensions", "EnumX", "EnzymeCore", "FastBroadcast", "FastClosures", "FastPower", "ForwardDiff", "FunctionWrappers", "FunctionWrappersWrappers", "LinearAlgebra", "Logging", "Markdown", "MuladdMacro", "Parameters", "PreallocationTools", "PrecompileTools", "Printf", "RecursiveArrayTools", "Reexport", "SciMLBase", "SciMLOperators", "SciMLStructures", "Setfield", "Static", "StaticArraysCore", "Statistics", "TruncatedStacktraces"] -git-tree-sha1 = "b7dbeaa770bad0980ddddf606de814cff2acb3bc" +deps = ["ArrayInterface", "ConcreteStructs", "DataStructures", "DocStringExtensions", "EnumX", "EnzymeCore", "FastBroadcast", "FastClosures", "ForwardDiff", "FunctionWrappers", "FunctionWrappersWrappers", "LinearAlgebra", "Logging", "Markdown", "MuladdMacro", "Parameters", "PreallocationTools", "PrecompileTools", "Printf", "RecursiveArrayTools", "Reexport", "SciMLBase", "SciMLOperators", "SciMLStructures", "Setfield", "Static", "StaticArraysCore", "Statistics", "Tricks", "TruncatedStacktraces"] +git-tree-sha1 = "fa7d580038451a8df4434ef5b079ac9b2d486194" uuid = "2b5f629d-d688-5b77-993f-72d75c75574e" -version = "6.160.0" +version = "6.155.1" [deps.DiffEqBase.extensions] DiffEqBaseCUDAExt = "CUDA" @@ -558,11 +568,17 @@ git-tree-sha1 = "23163d55f885173722d1e4cf0f6110cdbaf7e272" uuid = "b552c78f-8df3-52c6-915a-8e097449b14b" version = "1.15.1" +[[deps.DiffTests]] +deps = ["LinearAlgebra", "SparseArrays", "Statistics"] +git-tree-sha1 = "b92beb1933df01bf4915d3a05e54c2a0aad312c7" +uuid = "de460e47-3fe3-5279-bb4a-814414816d5d" +version = "0.1.2" + [[deps.DifferentiationInterface]] -deps = ["ADTypes", "LinearAlgebra"] -git-tree-sha1 = "0c99576d0b93df0aff1bed9d9adddef14e4e658f" +deps = ["ADTypes", "Compat", "DocStringExtensions", "FillArrays", "LinearAlgebra", "PackageExtensionCompat", "SparseArrays", "SparseMatrixColorings"] +git-tree-sha1 = "9b23f9a816790b8ab9914c3c86321a546e92cbe7" uuid = "a0c0ee7d-e4b9-4e03-894e-1c5f64a51d63" -version = "0.6.22" +version = "0.5.17" [deps.DifferentiationInterface.extensions] DifferentiationInterfaceChainRulesCoreExt = "ChainRulesCore" @@ -572,13 +588,10 @@ version = "0.6.22" DifferentiationInterfaceFiniteDiffExt = "FiniteDiff" DifferentiationInterfaceFiniteDifferencesExt = "FiniteDifferences" DifferentiationInterfaceForwardDiffExt = "ForwardDiff" - DifferentiationInterfaceMooncakeExt = "Mooncake" DifferentiationInterfacePolyesterForwardDiffExt = "PolyesterForwardDiff" DifferentiationInterfaceReverseDiffExt = "ReverseDiff" - DifferentiationInterfaceSparseArraysExt = "SparseArrays" - DifferentiationInterfaceSparseMatrixColoringsExt = "SparseMatrixColorings" - DifferentiationInterfaceStaticArraysExt = "StaticArrays" DifferentiationInterfaceSymbolicsExt = "Symbolics" + DifferentiationInterfaceTapirExt = "Tapir" DifferentiationInterfaceTrackerExt = "Tracker" DifferentiationInterfaceZygoteExt = ["Zygote", "ForwardDiff"] @@ -590,13 +603,10 @@ version = "0.6.22" FiniteDiff = "6a86dc24-6348-571c-b903-95158fe2bd41" FiniteDifferences = "26cc04aa-876d-5657-8c51-4c34ba976000" ForwardDiff = "f6369f11-7733-5829-9624-2563aa707210" - Mooncake = "da2b9cff-9c12-43a0-ae48-6db2b0edb7d6" PolyesterForwardDiff = "98d1487c-24ca-40b6-b7ab-df2af84e126b" ReverseDiff = "37e2e3b7-166d-5795-8a7a-e32c996b4267" - SparseArrays = "2f01184e-e22b-5df5-ae63-d93ebab69eaf" - SparseMatrixColorings = "0a514795-09f3-496d-8182-132a7b665d35" - StaticArrays = "90137ffa-7385-5640-81b9-e52037218182" Symbolics = "0c5d862f-8b57-4792-8d23-62f2024744c7" + Tapir = "07d77754-e150-4737-8c94-cd238a1fb45b" Tracker = "9f7883ad-71c0-57eb-9f7f-b5c9e6d3789c" Zygote = "e88e6eb3-aa80-5325-afca-941959d7151f" @@ -654,10 +664,10 @@ uuid = "f43a241f-c20a-4ad4-852c-f6b1247861c6" version = "1.6.0" [[deps.DynamicPPL]] -deps = ["ADTypes", "AbstractMCMC", "AbstractPPL", "Accessors", "BangBang", "Bijectors", "Compat", "ConstructionBase", "Distributions", "DocStringExtensions", "LinearAlgebra", "LogDensityProblems", "LogDensityProblemsAD", "MacroTools", "OrderedCollections", "Random", "Requires", "Test"] -git-tree-sha1 = "b8d3cb76b27287a0d2ef6baf8dfe23e6b911f93a" +deps = ["ADTypes", "AbstractMCMC", "AbstractPPL", "Accessors", "BangBang", "Bijectors", "Compat", "ConstructionBase", "Distributions", "DocStringExtensions", "InteractiveUtils", "LinearAlgebra", "LogDensityProblems", "LogDensityProblemsAD", "MacroTools", "OrderedCollections", "Random", "Requires", "Test"] +git-tree-sha1 = "6ff628d549699f28c507d1a9289e05c8756fa39c" uuid = "366bfd00-2699-11ea-058f-f148b4cae6d8" -version = "0.28.6" +version = "0.30.5" weakdeps = ["ChainRulesCore", "EnzymeCore", "ForwardDiff", "MCMCChains", "ReverseDiff", "ZygoteRules"] [deps.DynamicPPL.extensions] @@ -670,9 +680,9 @@ weakdeps = ["ChainRulesCore", "EnzymeCore", "ForwardDiff", "MCMCChains", "Revers [[deps.DynamicPolynomials]] deps = ["Future", "LinearAlgebra", "MultivariatePolynomials", "MutableArithmetics", "Reexport", "Test"] -git-tree-sha1 = "bbf1ace0781d9744cb697fb856bd2c3f6568dadb" +git-tree-sha1 = "9a3ae38b460449cc9e7dd0cfb059c76028724627" uuid = "7c1d4256-1411-5781-91ec-d7bc3513ac07" -version = "0.6.0" +version = "0.6.1" [[deps.Einsum]] deps = ["Compat"] @@ -691,6 +701,26 @@ git-tree-sha1 = "bdb1942cd4c45e3c678fd11569d5cccd80976237" uuid = "4e289a0a-7415-4d19-859d-a7e5c4648b56" version = "1.0.4" +[[deps.Enzyme]] +deps = ["CEnum", "EnzymeCore", "Enzyme_jll", "GPUCompiler", "LLVM", "Libdl", "LinearAlgebra", "ObjectFile", "Preferences", "Printf", "Random"] +git-tree-sha1 = "b63695bc543a45cab4f30e039c26ca3bcc6780a1" +uuid = "7da242da-08ed-463a-9acd-ee780be4f1d9" +version = "0.12.36" + + [deps.Enzyme.extensions] + EnzymeBFloat16sExt = "BFloat16s" + EnzymeChainRulesCoreExt = "ChainRulesCore" + EnzymeLogExpFunctionsExt = "LogExpFunctions" + EnzymeSpecialFunctionsExt = "SpecialFunctions" + EnzymeStaticArraysExt = "StaticArrays" + + [deps.Enzyme.weakdeps] + BFloat16s = "ab4f0b2a-ad5b-11e8-123f-65d77653426b" + ChainRulesCore = "d360d2e6-b24c-11e9-a2a3-2a2ae2dbcce4" + LogExpFunctions = "2ab3a3ac-af41-5b50-aa03-7779005ae688" + SpecialFunctions = "276daf66-3868-5448-9aa4-cd146d93841b" + StaticArrays = "90137ffa-7385-5640-81b9-e52037218182" + [[deps.EnzymeCore]] git-tree-sha1 = "8f205a601760f4798a10f138c3940f0451d95188" uuid = "f151be2c-9106-41f4-ab19-57ee4f262869" @@ -700,23 +730,33 @@ weakdeps = ["Adapt"] [deps.EnzymeCore.extensions] AdaptExt = "Adapt" +[[deps.Enzyme_jll]] +deps = ["Artifacts", "JLLWrappers", "LazyArtifacts", "Libdl", "TOML"] +git-tree-sha1 = "7fb808ef6421ea58c607657eea17caa9f03c08d0" +uuid = "7cc45869-7501-5eee-bdea-0790c847d4ef" +version = "0.0.148+0" + [[deps.EpiAware]] deps = ["ADTypes", "AbstractMCMC", "AdvancedHMC", "DataFramesMeta", "Distributions", "DocStringExtensions", "DynamicPPL", "FillArrays", "LinearAlgebra", "LogExpFunctions", "MCMCChains", "OrdinaryDiffEq", "Pathfinder", "QuadGK", "Random", "Reexport", "SparseArrays", "Statistics", "Tables", "Turing"] path = "../EpiAware" uuid = "b2eeebe4-5992-4301-9193-7ebc9f62c855" -version = "0.1.0-DEV" +version = "0.1.0" [[deps.ExceptionUnwrapping]] deps = ["Test"] -git-tree-sha1 = "dcb08a0d93ec0b1cdc4af184b26b591e9695423a" +git-tree-sha1 = "d36f682e590a83d63d1c7dbd287573764682d12a" uuid = "460bff9d-24e4-43bc-9d9f-a8973cb893f4" -version = "0.1.10" +version = "0.1.11" [[deps.ExponentialUtilities]] deps = ["Adapt", "ArrayInterface", "GPUArraysCore", "GenericSchur", "LinearAlgebra", "PrecompileTools", "Printf", "SparseArrays", "libblastrampoline_jll"] -git-tree-sha1 = "8e18940a5ba7f4ddb41fe2b79b6acaac50880a86" +git-tree-sha1 = "cae251c76f353e32d32d76fae2fea655eab652af" uuid = "d4d017d3-3776-5f7e-afef-a10c40355c18" -version = "1.26.1" +version = "1.27.0" +weakdeps = ["StaticArrays"] + + [deps.ExponentialUtilities.extensions] + ExponentialUtilitiesStaticArraysExt = "StaticArrays" [[deps.ExprTools]] git-tree-sha1 = "27415f162e6028e81c72b82ef756bf321213b6ec" @@ -763,27 +803,6 @@ git-tree-sha1 = "cbf5edddb61a43669710cbc2241bc08b36d9e660" uuid = "29a986be-02c6-4525-aec4-84b980013641" version = "2.0.4" -[[deps.FastPower]] -git-tree-sha1 = "58c3431137131577a7c379d00fea00be524338fb" -uuid = "a4df4552-cc26-4903-aec0-212e50a0e84b" -version = "1.1.1" - - [deps.FastPower.extensions] - FastPowerEnzymeExt = "Enzyme" - FastPowerForwardDiffExt = "ForwardDiff" - FastPowerMeasurementsExt = "Measurements" - FastPowerMonteCarloMeasurementsExt = "MonteCarloMeasurements" - FastPowerReverseDiffExt = "ReverseDiff" - FastPowerTrackerExt = "Tracker" - - [deps.FastPower.weakdeps] - Enzyme = "7da242da-08ed-463a-9acd-ee780be4f1d9" - ForwardDiff = "f6369f11-7733-5829-9624-2563aa707210" - Measurements = "eff96d63-e80a-5855-80a2-b1b0885c5ab7" - MonteCarloMeasurements = "0987c9cc-fe09-11e8-30f0-b96dd679fdca" - ReverseDiff = "37e2e3b7-166d-5795-8a7a-e32c996b4267" - Tracker = "9f7883ad-71c0-57eb-9f7f-b5c9e6d3789c" - [[deps.FileWatching]] uuid = "7b1f6079-737a-58dc-b8bc-7a2ca5c1b5ee" version = "1.11.0" @@ -802,9 +821,9 @@ weakdeps = ["PDMats", "SparseArrays", "Statistics"] [[deps.FiniteDiff]] deps = ["ArrayInterface", "LinearAlgebra", "Setfield"] -git-tree-sha1 = "b10bdafd1647f57ace3885143936749d61638c3b" +git-tree-sha1 = "84e3a47db33be7248daa6274b287507dd6ff84e8" uuid = "6a86dc24-6348-571c-b903-95158fe2bd41" -version = "2.26.0" +version = "2.26.2" [deps.FiniteDiff.extensions] FiniteDiffBandedMatricesExt = "BandedMatrices" @@ -879,11 +898,11 @@ git-tree-sha1 = "ec632f177c0d990e64d955ccc1b8c04c485a0950" uuid = "46192b85-c4d5-4398-a991-12ede77f4527" version = "0.1.6" -[[deps.GenericLinearAlgebra]] -deps = ["LinearAlgebra", "Printf", "Random", "libblastrampoline_jll"] -git-tree-sha1 = "c4f9c87b74aedf20920034bd4db81d0bffc527d2" -uuid = "14197337-ba66-59df-a3e3-ca00e7dcff7a" -version = "0.3.14" +[[deps.GPUCompiler]] +deps = ["ExprTools", "InteractiveUtils", "LLVM", "Libdl", "Logging", "PrecompileTools", "Preferences", "Scratch", "Serialization", "TOML", "TimerOutputs", "UUIDs"] +git-tree-sha1 = "b8c120986fce117469760119f44592ff148da93e" +uuid = "61eb1bfa-7361-4325-ad38-22787b887f55" +version = "0.27.5" [[deps.GenericSchur]] deps = ["LinearAlgebra", "Printf"] @@ -904,10 +923,10 @@ uuid = "86223c79-3864-5bf0-83f7-82e725a168b6" version = "1.12.0" [[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 = "6c22309e9a356ac1ebc5c8a217045f9bae6f8d9a" uuid = "cd3eb016-35fb-5094-929b-558a96fad6f3" -version = "1.10.10" +version = "1.10.13" [[deps.HostCPUFeatures]] deps = ["BitTwiddlingConvenienceFunctions", "IfElse", "Libdl", "Static"] @@ -1058,10 +1077,10 @@ uuid = "ef3ab10e-7fda-4108-b977-705223b18434" version = "0.6.0" [[deps.KernelAbstractions]] -deps = ["Adapt", "Atomix", "InteractiveUtils", "MacroTools", "PrecompileTools", "Requires", "StaticArrays", "UUIDs", "UnsafeAtomics", "UnsafeAtomicsLLVM"] -git-tree-sha1 = "e73a077abc7fe798fe940deabe30ef6c66bdde52" +deps = ["Adapt", "Atomix", "InteractiveUtils", "MacroTools", "PrecompileTools", "Requires", "StaticArrays", "UUIDs"] +git-tree-sha1 = "b9a838cd3028785ac23822cded5126b3da394d1a" uuid = "63c18a36-062a-441e-b654-da1e3ab1ce7c" -version = "0.9.29" +version = "0.9.31" weakdeps = ["EnzymeCore", "LinearAlgebra", "SparseArrays"] [deps.KernelAbstractions.extensions] @@ -1094,10 +1113,10 @@ uuid = "5be7bae1-8223-5378-bac3-9e7378a2f6e6" version = "0.4.1" [[deps.LLVM]] -deps = ["CEnum", "LLVMExtra_jll", "Libdl", "Preferences", "Printf", "Unicode"] -git-tree-sha1 = "d422dfd9707bec6617335dc2ea3c5172a87d5908" +deps = ["CEnum", "LLVMExtra_jll", "Libdl", "Preferences", "Printf", "Requires", "Unicode"] +git-tree-sha1 = "b351d72436ddecd27381a07c242ba27282a6c8a7" uuid = "929cbde3-209d-540e-8aea-75f648917ca0" -version = "9.1.3" +version = "9.0.0" [deps.LLVM.extensions] BFloat16sExt = "BFloat16s" @@ -1107,9 +1126,9 @@ version = "9.1.3" [[deps.LLVMExtra_jll]] deps = ["Artifacts", "JLLWrappers", "LazyArtifacts", "Libdl", "TOML"] -git-tree-sha1 = "05a8bd5a42309a9ec82f700876903abce1017dd3" +git-tree-sha1 = "f42bec1e12f42ec251541f6d0482d520a4638b17" uuid = "dad2f222-ce93-54a1-a47d-0025e8a3acab" -version = "0.0.34+0" +version = "0.0.33+0" [[deps.LRUCache]] git-tree-sha1 = "b3cc6698599b10e652832c2f23db3cab99d51b59" @@ -1155,9 +1174,9 @@ version = "0.1.17" [[deps.LazyArrays]] deps = ["ArrayLayouts", "FillArrays", "LinearAlgebra", "MacroTools", "SparseArrays"] -git-tree-sha1 = "376bc148ae72e68a08f0d5d8a69e287025a37687" +git-tree-sha1 = "f289bee714e11708df257c57514585863aa02b33" uuid = "5078a376-72f3-5289-bfd5-ec5146d43c02" -version = "2.2.2" +version = "2.3.1" [deps.LazyArrays.extensions] LazyArraysBandedMatricesExt = "BandedMatrices" @@ -1285,13 +1304,12 @@ version = "2.1.2" [[deps.LogDensityProblemsAD]] deps = ["DocStringExtensions", "LogDensityProblems"] -git-tree-sha1 = "40fd43cc5dd3fe76cf67f033b69e073207a91b7e" +git-tree-sha1 = "457e6b347a87bfcd25a9eaf44a7bd5415559582f" uuid = "996a588d-648d-4e1f-a8f0-a84b347e47b1" -version = "1.12.0" +version = "1.10.1" [deps.LogDensityProblemsAD.extensions] LogDensityProblemsADADTypesExt = "ADTypes" - LogDensityProblemsADDifferentiationInterfaceExt = ["ADTypes", "DifferentiationInterface"] LogDensityProblemsADEnzymeExt = "Enzyme" LogDensityProblemsADFiniteDifferencesExt = "FiniteDifferences" LogDensityProblemsADForwardDiffBenchmarkToolsExt = ["BenchmarkTools", "ForwardDiff"] @@ -1303,7 +1321,6 @@ version = "1.12.0" [deps.LogDensityProblemsAD.weakdeps] ADTypes = "47edcb42-4c32-4615-8424-f2b9edc5f35b" BenchmarkTools = "6e4b80f9-dd63-53aa-95a3-0cdb28fa8baf" - DifferentiationInterface = "a0c0ee7d-e4b9-4e03-894e-1c5f64a51d63" Enzyme = "7da242da-08ed-463a-9acd-ee780be4f1d9" FiniteDifferences = "26cc04aa-876d-5657-8c51-4c34ba976000" ForwardDiff = "f6369f11-7733-5829-9624-2563aa707210" @@ -1346,15 +1363,15 @@ weakdeps = ["ChainRulesCore", "ForwardDiff", "SpecialFunctions"] [[deps.MCMCChains]] deps = ["AbstractMCMC", "AxisArrays", "Dates", "Distributions", "IteratorInterfaceExtensions", "KernelDensity", "LinearAlgebra", "MCMCDiagnosticTools", "MLJModelInterface", "NaturalSort", "OrderedCollections", "PrettyTables", "Random", "RecipesBase", "Statistics", "StatsBase", "StatsFuns", "TableTraits", "Tables"] -git-tree-sha1 = "d28056379864318172ff4b7958710cfddd709339" +git-tree-sha1 = "cd7aee22384792c726e19f2a22dc060b886edded" uuid = "c7f686f2-ff18-58e9-bc7b-31028e88f75d" -version = "6.0.6" +version = "6.0.7" [[deps.MCMCDiagnosticTools]] deps = ["AbstractFFTs", "DataAPI", "DataStructures", "Distributions", "LinearAlgebra", "MLJModelInterface", "Random", "SpecialFunctions", "Statistics", "StatsBase", "StatsFuns", "Tables"] -git-tree-sha1 = "8ba8b1840d3ab5b38e7c71c23c3193bb5cbc02b5" +git-tree-sha1 = "770527473d1b929bc4a812831f34970f9c6a6ff6" uuid = "be115224-59cd-429b-ad48-344e309966f0" -version = "0.3.10" +version = "0.3.13" [[deps.MKL_jll]] deps = ["Artifacts", "IntelOpenMP_jll", "JLLWrappers", "LazyArtifacts", "Libdl", "oneTBB_jll"] @@ -1423,10 +1440,10 @@ version = "0.9.20" Test = "8dfed614-e22c-5e08-85e1-65c5234f0b40" [[deps.ManifoldsBase]] -deps = ["LinearAlgebra", "Markdown", "Printf", "Random", "Requires"] -git-tree-sha1 = "74aed86f1a52d17a82a15c3fe4cabb312f8cce48" +deps = ["LinearAlgebra", "Markdown", "Printf", "Random"] +git-tree-sha1 = "57df0b7daa74bf82d3367702e133d936c28882ff" uuid = "3362f125-f0bb-47a3-aa74-596ffd7ef2fb" -version = "0.15.21" +version = "0.15.23" [deps.ManifoldsBase.extensions] ManifoldsBasePlotsExt = "Plots" @@ -1494,10 +1511,39 @@ git-tree-sha1 = "ec4f7fbeab05d7747bdf98eb74d130a2a2ed298d" uuid = "e1d29d7a-bbdc-5cf2-9ac0-f12de2c33e28" version = "1.2.0" +[[deps.MistyClosures]] +git-tree-sha1 = "1142aefd845c608f3c70e4c202c4aae725cab67b" +uuid = "dbe65cb8-6be2-42dd-bbc5-4196aaced4f4" +version = "2.0.0" + [[deps.Mmap]] uuid = "a63ad114-7e13-5084-954f-fe012c677804" version = "1.11.0" +[[deps.Mooncake]] +deps = ["ADTypes", "ChainRules", "ChainRulesCore", "DiffRules", "DiffTests", "ExprTools", "FunctionWrappers", "Graphs", "InteractiveUtils", "LinearAlgebra", "MistyClosures", "Random", "Setfield", "Test"] +git-tree-sha1 = "c22a8a114e22589ab835663b3ad19497b5b4ab90" +uuid = "da2b9cff-9c12-43a0-ae48-6db2b0edb7d6" +version = "0.4.59" + + [deps.Mooncake.extensions] + MooncakeAllocCheckExt = "AllocCheck" + MooncakeCUDAExt = "CUDA" + MooncakeJETExt = "JET" + MooncakeLuxLibExt = "LuxLib" + MooncakeLuxLibSLEEFPiratesExtension = ["LuxLib", "SLEEFPirates"] + MooncakeNNlibExt = "NNlib" + MooncakeSpecialFunctionsExt = "SpecialFunctions" + + [deps.Mooncake.weakdeps] + AllocCheck = "9b6a8646-10ed-4001-bbdc-1d2f46dfbb1a" + CUDA = "052768ef-5323-5732-b1bb-66c8b64840ba" + JET = "c3a54625-cd67-489e-a8e7-0a5a0ff4e31b" + LuxLib = "82251201-b29d-42c6-8e01-566dec8acb11" + NNlib = "872c559c-99b0-510c-b3b7-b6c96a88d5cd" + SLEEFPirates = "476501e8-09a2-5ece-8869-fb82de89a1fa" + SpecialFunctions = "276daf66-3868-5448-9aa4-cd146d93841b" + [[deps.MozillaCACerts_jll]] uuid = "14a3606d-f60d-562e-9121-12d972cd8159" version = "2023.12.12" @@ -1515,9 +1561,9 @@ version = "0.5.7" [[deps.MutableArithmetics]] deps = ["LinearAlgebra", "SparseArrays", "Test"] -git-tree-sha1 = "90077f1e79de8c9c7c8a90644494411111f4e07b" +git-tree-sha1 = "a2710df6b0931f987530f59427441b21245d8f5e" uuid = "d8a4904e-b15c-11e9-3269-09a3773c0cb0" -version = "1.5.2" +version = "1.6.0" [[deps.NLSolversBase]] deps = ["DiffResults", "Distributed", "FiniteDiff", "ForwardDiff"] @@ -1527,9 +1573,9 @@ version = "7.8.3" [[deps.NNlib]] deps = ["Adapt", "Atomix", "ChainRulesCore", "GPUArraysCore", "KernelAbstractions", "LinearAlgebra", "Random", "Statistics"] -git-tree-sha1 = "da09a1e112fd75f9af2a5229323f01b56ec96a4c" +git-tree-sha1 = "1177f161cda2083543b9967d7ca2a3e24e721e13" uuid = "872c559c-99b0-510c-b3b7-b6c96a88d5cd" -version = "0.9.24" +version = "0.9.26" [deps.NNlib.extensions] NNlibAMDGPUExt = "AMDGPU" @@ -1619,10 +1665,16 @@ version = "3.14.0" Symbolics = "0c5d862f-8b57-4792-8d23-62f2024744c7" Zygote = "e88e6eb3-aa80-5325-afca-941959d7151f" +[[deps.ObjectFile]] +deps = ["Reexport", "StructIO"] +git-tree-sha1 = "7249afa1c4dfd86bfbcc9b28939ab6ef844f4e11" +uuid = "d8793406-e978-5875-9003-1fc021f44a92" +version = "0.4.2" + [[deps.OffsetArrays]] -git-tree-sha1 = "1a27764e945a152f7ca7efa04de513d473e9542e" +git-tree-sha1 = "39d000d9c33706b8364817d8894fae1548f40295" uuid = "6fe1bfb0-de20-5000-8ca7-80f57d26f881" -version = "1.14.1" +version = "1.14.2" weakdeps = ["Adapt"] [deps.OffsetArrays.extensions] @@ -1676,15 +1728,15 @@ version = "0.4.0" [[deps.Optimization]] deps = ["ADTypes", "ArrayInterface", "ConsoleProgressMonitor", "DocStringExtensions", "LBFGSB", "LinearAlgebra", "Logging", "LoggingExtras", "OptimizationBase", "Printf", "ProgressLogging", "Reexport", "SciMLBase", "SparseArrays", "TerminalLoggers"] -git-tree-sha1 = "0b2a631276dc92ab147535689fa43f1e22a657b8" +git-tree-sha1 = "4b59eef21418fbdf28afbe2d7e945d8efbe5057d" uuid = "7f7a1694-90dd-40f0-9382-eb1efda571ba" -version = "3.28.0" +version = "4.0.5" [[deps.OptimizationBase]] -deps = ["ADTypes", "ArrayInterface", "DocStringExtensions", "LinearAlgebra", "PDMats", "Reexport", "Requires", "SciMLBase", "SparseArrays", "SymbolicAnalysis", "SymbolicIndexingInterface", "Symbolics"] -git-tree-sha1 = "3e5e5e8cbe572200dcd94a6084a63ca68fe76279" +deps = ["ADTypes", "ArrayInterface", "DifferentiationInterface", "DocStringExtensions", "FastClosures", "LinearAlgebra", "PDMats", "Reexport", "Requires", "SciMLBase", "SparseArrays", "SparseConnectivityTracer", "SparseMatrixColorings", "SymbolicAnalysis", "SymbolicIndexingInterface", "Symbolics"] +git-tree-sha1 = "f6acffdbcd4288efaa500b495d078a677d224eb2" uuid = "bca83a33-5cc9-4baa-983d-23429ab6bcbb" -version = "1.5.0" +version = "2.0.4" [deps.OptimizationBase.extensions] OptimizationEnzymeExt = "Enzyme" @@ -1692,8 +1744,6 @@ version = "1.5.0" OptimizationForwardDiffExt = "ForwardDiff" OptimizationMTKExt = "ModelingToolkit" OptimizationReverseDiffExt = "ReverseDiff" - OptimizationSparseDiffExt = ["SparseDiffTools", "ReverseDiff"] - OptimizationTrackerExt = "Tracker" OptimizationZygoteExt = "Zygote" [deps.OptimizationBase.weakdeps] @@ -1702,20 +1752,18 @@ version = "1.5.0" ForwardDiff = "f6369f11-7733-5829-9624-2563aa707210" ModelingToolkit = "961ee093-0014-501f-94e3-6117800e7a78" ReverseDiff = "37e2e3b7-166d-5795-8a7a-e32c996b4267" - SparseDiffTools = "47a9eef4-7e08-11e9-0b38-333d64bd3804" - Tracker = "9f7883ad-71c0-57eb-9f7f-b5c9e6d3789c" Zygote = "e88e6eb3-aa80-5325-afca-941959d7151f" [[deps.OptimizationOptimJL]] -deps = ["Optim", "Optimization", "Reexport", "SparseArrays"] -git-tree-sha1 = "43870d726f883a47d158beebb1fc3c9fab1da9d6" +deps = ["Optim", "Optimization", "PrecompileTools", "Reexport", "SparseArrays"] +git-tree-sha1 = "980ec7190741db164a2923dc42d6f1e7ce2cc434" uuid = "36348300-93cb-4f02-beb5-3c3902f8871e" -version = "0.3.2" +version = "0.4.1" [[deps.OrderedCollections]] -git-tree-sha1 = "dfdf5519f235516220579f949664f1bf44e741c5" +git-tree-sha1 = "12f1439c4f986bb868acda6ea33ebc78e19b95ad" uuid = "bac558e1-5e72-5ebc-8fee-abe8a469f55d" -version = "1.6.3" +version = "1.7.0" [[deps.OrdinaryDiffEq]] deps = ["ADTypes", "Adapt", "ArrayInterface", "DataStructures", "DiffEqBase", "DocStringExtensions", "EnumX", "ExponentialUtilities", "FastBroadcast", "FastClosures", "FillArrays", "FiniteDiff", "ForwardDiff", "FunctionWrappersWrappers", "InteractiveUtils", "LineSearches", "LinearAlgebra", "LinearSolve", "Logging", "MacroTools", "MuladdMacro", "NonlinearSolve", "OrdinaryDiffEqAdamsBashforthMoulton", "OrdinaryDiffEqBDF", "OrdinaryDiffEqCore", "OrdinaryDiffEqDefault", "OrdinaryDiffEqDifferentiation", "OrdinaryDiffEqExplicitRK", "OrdinaryDiffEqExponentialRK", "OrdinaryDiffEqExtrapolation", "OrdinaryDiffEqFIRK", "OrdinaryDiffEqFeagin", "OrdinaryDiffEqFunctionMap", "OrdinaryDiffEqHighOrderRK", "OrdinaryDiffEqIMEXMultistep", "OrdinaryDiffEqLinear", "OrdinaryDiffEqLowOrderRK", "OrdinaryDiffEqLowStorageRK", "OrdinaryDiffEqNonlinearSolve", "OrdinaryDiffEqNordsieck", "OrdinaryDiffEqPDIRK", "OrdinaryDiffEqPRK", "OrdinaryDiffEqQPRK", "OrdinaryDiffEqRKN", "OrdinaryDiffEqRosenbrock", "OrdinaryDiffEqSDIRK", "OrdinaryDiffEqSSPRK", "OrdinaryDiffEqStabilizedIRK", "OrdinaryDiffEqStabilizedRK", "OrdinaryDiffEqSymplecticRK", "OrdinaryDiffEqTsit5", "OrdinaryDiffEqVerner", "Polyester", "PreallocationTools", "PrecompileTools", "Preferences", "RecursiveArrayTools", "Reexport", "SciMLBase", "SciMLOperators", "SciMLStructures", "SimpleNonlinearSolve", "SimpleUnPack", "SparseArrays", "SparseDiffTools", "Static", "StaticArrayInterface", "StaticArrays", "TruncatedStacktraces"] @@ -1736,10 +1784,10 @@ uuid = "6ad6398a-0878-4a85-9266-38940aa047c8" version = "1.1.2" [[deps.OrdinaryDiffEqCore]] -deps = ["ADTypes", "Accessors", "Adapt", "ArrayInterface", "DataStructures", "DiffEqBase", "DocStringExtensions", "EnumX", "FastBroadcast", "FastClosures", "FastPower", "FillArrays", "FunctionWrappersWrappers", "InteractiveUtils", "LinearAlgebra", "Logging", "MacroTools", "MuladdMacro", "Polyester", "PrecompileTools", "Preferences", "RecursiveArrayTools", "Reexport", "SciMLBase", "SciMLOperators", "SciMLStructures", "SimpleUnPack", "Static", "StaticArrayInterface", "StaticArraysCore", "SymbolicIndexingInterface", "TruncatedStacktraces"] -git-tree-sha1 = "6f86041d5978ce3574f022f4098e0c216e2a3395" +deps = ["ADTypes", "Adapt", "ArrayInterface", "DataStructures", "DiffEqBase", "DocStringExtensions", "EnumX", "FastBroadcast", "FastClosures", "FillArrays", "FunctionWrappersWrappers", "InteractiveUtils", "LinearAlgebra", "Logging", "MacroTools", "MuladdMacro", "Polyester", "PrecompileTools", "Preferences", "RecursiveArrayTools", "Reexport", "SciMLBase", "SciMLOperators", "SciMLStructures", "SimpleUnPack", "Static", "StaticArrayInterface", "StaticArraysCore", "TruncatedStacktraces"] +git-tree-sha1 = "5595eb94d0dd3cde2f5cf456394a1e0a61237e95" uuid = "bbf590c4-e513-4bbe-9b18-05decba2e5d8" -version = "1.10.2" +version = "1.6.0" weakdeps = ["EnzymeCore"] [deps.OrdinaryDiffEqCore.extensions] @@ -1770,16 +1818,16 @@ uuid = "e0540318-69ee-4070-8777-9e2de6de23de" version = "1.1.0" [[deps.OrdinaryDiffEqExtrapolation]] -deps = ["DiffEqBase", "FastBroadcast", "FastPower", "LinearSolve", "MuladdMacro", "OrdinaryDiffEqCore", "OrdinaryDiffEqDifferentiation", "Polyester", "RecursiveArrayTools", "Reexport"] -git-tree-sha1 = "048bcccc8f59c20d5b4ad268eef4d7d21c005a94" +deps = ["DiffEqBase", "FastBroadcast", "LinearSolve", "MuladdMacro", "OrdinaryDiffEqCore", "OrdinaryDiffEqDifferentiation", "Polyester", "RecursiveArrayTools", "Reexport"] +git-tree-sha1 = "fea595528a160ed5cade9eee217a9691b1d97714" uuid = "becaefa8-8ca2-5cf9-886d-c06f3d2bd2c4" -version = "1.2.1" +version = "1.1.0" [[deps.OrdinaryDiffEqFIRK]] -deps = ["DiffEqBase", "FastBroadcast", "FastPower", "GenericLinearAlgebra", "GenericSchur", "LinearAlgebra", "LinearSolve", "MuladdMacro", "OrdinaryDiffEqCore", "OrdinaryDiffEqDifferentiation", "OrdinaryDiffEqNonlinearSolve", "Polynomials", "RecursiveArrayTools", "Reexport", "RootedTrees", "SciMLOperators", "Symbolics"] -git-tree-sha1 = "1dcf5bebc5179c1c119a7a30f99bbb93eec02d44" +deps = ["DiffEqBase", "FastBroadcast", "LinearAlgebra", "LinearSolve", "MuladdMacro", "OrdinaryDiffEqCore", "OrdinaryDiffEqDifferentiation", "OrdinaryDiffEqNonlinearSolve", "RecursiveArrayTools", "Reexport", "SciMLOperators"] +git-tree-sha1 = "795221c662698851328cb7787965ab4a180d9468" uuid = "5960d6e9-dd7a-4743-88e7-cf307b64f125" -version = "1.3.0" +version = "1.1.1" [[deps.OrdinaryDiffEqFeagin]] deps = ["DiffEqBase", "FastBroadcast", "MuladdMacro", "OrdinaryDiffEqCore", "Polyester", "RecursiveArrayTools", "Reexport", "Static"] @@ -1825,9 +1873,9 @@ version = "1.2.1" [[deps.OrdinaryDiffEqNonlinearSolve]] deps = ["ADTypes", "ArrayInterface", "DiffEqBase", "FastBroadcast", "FastClosures", "ForwardDiff", "LinearAlgebra", "LinearSolve", "MuladdMacro", "NonlinearSolve", "OrdinaryDiffEqCore", "OrdinaryDiffEqDifferentiation", "PreallocationTools", "RecursiveArrayTools", "SciMLBase", "SciMLOperators", "SciMLStructures", "SimpleNonlinearSolve", "StaticArrays"] -git-tree-sha1 = "5e1b316555fa95892edc13f6a429ac784d0be4dd" +git-tree-sha1 = "3a3eb0b7ef3f996c468d6f8013eac9525bcfd788" uuid = "127b3ac7-2247-4354-8eb6-78cf4e7c58e8" -version = "1.2.4" +version = "1.3.0" [[deps.OrdinaryDiffEqNordsieck]] deps = ["DiffEqBase", "FastBroadcast", "LinearAlgebra", "MuladdMacro", "OrdinaryDiffEqCore", "OrdinaryDiffEqTsit5", "Polyester", "RecursiveArrayTools", "Reexport", "Static"] @@ -1939,9 +1987,9 @@ version = "2.8.1" [[deps.Pathfinder]] deps = ["ADTypes", "Distributions", "Folds", "IrrationalConstants", "LinearAlgebra", "LogDensityProblems", "LogDensityProblemsAD", "Optim", "Optimization", "OptimizationOptimJL", "PDMats", "PSIS", "ProgressLogging", "Random", "Requires", "SciMLBase", "Statistics", "StatsBase", "Transducers", "UnPack"] -git-tree-sha1 = "4207ff39e325bd90056ef58ce2584666129fbca9" +git-tree-sha1 = "f9d783f5d5524321d77610baf024eb986aa21810" uuid = "b1d3bc72-d0e7-4279-b92f-7fa5d6d2d454" -version = "0.9.5" +version = "0.9.7" [deps.Pathfinder.extensions] PathfinderDynamicHMCExt = "DynamicHMC" @@ -1984,10 +2032,10 @@ uuid = "1d0040c9-8b98-4ee7-8388-3f51789ca0ad" version = "0.2.2" [[deps.Polynomials]] -deps = ["LinearAlgebra", "RecipesBase", "Requires", "Setfield", "SparseArrays"] -git-tree-sha1 = "1a9cfb2dc2c2f1bd63f1906d72af39a79b49b736" +deps = ["LinearAlgebra", "OrderedCollections", "RecipesBase", "Requires", "Setfield", "SparseArrays"] +git-tree-sha1 = "adc25dbd4d13f148f3256b6d4743fe7e63a71c4a" uuid = "f27b6e38-b328-58d1-80ce-0feddd5e7a45" -version = "4.0.11" +version = "4.0.12" [deps.Polynomials.extensions] PolynomialsChainRulesCoreExt = "ChainRulesCore" @@ -2078,13 +2126,11 @@ deps = ["DataStructures", "LinearAlgebra"] git-tree-sha1 = "cda3b045cf9ef07a08ad46731f5a3165e56cf3da" uuid = "1fd47b50-473d-5c70-9696-f719f8f3bcdc" version = "2.11.1" +weakdeps = ["Enzyme"] [deps.QuadGK.extensions] QuadGKEnzymeExt = "Enzyme" - [deps.QuadGK.weakdeps] - Enzyme = "7da242da-08ed-463a-9acd-ee780be4f1d9" - [[deps.Quaternions]] deps = ["LinearAlgebra", "Random", "RealDot"] git-tree-sha1 = "994cc27cdacca10e68feb291673ec3a76aa2fae9" @@ -2139,9 +2185,9 @@ version = "1.3.4" [[deps.RecursiveArrayTools]] deps = ["Adapt", "ArrayInterface", "DocStringExtensions", "GPUArraysCore", "IteratorInterfaceExtensions", "LinearAlgebra", "RecipesBase", "StaticArraysCore", "Statistics", "SymbolicIndexingInterface", "Tables"] -git-tree-sha1 = "6f4dca5fd8e97087a76b7ab8384d1c3086ace0b7" +git-tree-sha1 = "32f824db4e5bab64e25a12b22483a30a6b813d08" uuid = "731186ca-8d62-57ce-b412-fbd966d074cd" -version = "3.27.3" +version = "3.27.4" [deps.RecursiveArrayTools.extensions] RecursiveArrayToolsFastBroadcastExt = "FastBroadcast" @@ -2150,6 +2196,7 @@ version = "3.27.3" RecursiveArrayToolsMonteCarloMeasurementsExt = "MonteCarloMeasurements" RecursiveArrayToolsReverseDiffExt = ["ReverseDiff", "Zygote"] RecursiveArrayToolsSparseArraysExt = ["SparseArrays"] + RecursiveArrayToolsStructArraysExt = "StructArrays" RecursiveArrayToolsTrackerExt = "Tracker" RecursiveArrayToolsZygoteExt = "Zygote" @@ -2160,6 +2207,7 @@ version = "3.27.3" MonteCarloMeasurements = "0987c9cc-fe09-11e8-30f0-b96dd679fdca" ReverseDiff = "37e2e3b7-166d-5795-8a7a-e32c996b4267" SparseArrays = "2f01184e-e22b-5df5-ae63-d93ebab69eaf" + StructArrays = "09ab397b-f2b6-538f-b94a-2f83cf4a842a" Tracker = "9f7883ad-71c0-57eb-9f7f-b5c9e6d3789c" Zygote = "e88e6eb3-aa80-5325-afca-941959d7151f" @@ -2204,23 +2252,11 @@ git-tree-sha1 = "58cdd8fb2201a6267e1db87ff148dd6c1dbd8ad8" uuid = "f50d1b31-88e8-58de-be2c-1cc44531875f" version = "0.5.1+0" -[[deps.RootedTrees]] -deps = ["LaTeXStrings", "Latexify", "LinearAlgebra", "Preferences", "RecipesBase", "Requires"] -git-tree-sha1 = "c0c464d3063e46e4128d21fd677ca575ace44fdc" -uuid = "47965b36-3f3e-11e9-0dcf-4570dfd42a8c" -version = "2.23.1" - - [deps.RootedTrees.extensions] - PlotsExt = "Plots" - - [deps.RootedTrees.weakdeps] - Plots = "91a5bcdd-55d7-5caf-9e0b-520d859cae80" - [[deps.Roots]] deps = ["Accessors", "CommonSolve", "Printf"] -git-tree-sha1 = "3a7c7e5c3f015415637f5debdf8a674aa2c979c4" +git-tree-sha1 = "8e3694d669323cdfb560e344dc872b984de23b71" uuid = "f2b01f46-fcfa-551c-844a-d8ac1e96c665" -version = "2.2.1" +version = "2.2.2" [deps.Roots.extensions] RootsChainRulesCoreExt = "ChainRulesCore" @@ -2265,9 +2301,9 @@ version = "0.1.1" [[deps.SciMLBase]] deps = ["ADTypes", "Accessors", "ArrayInterface", "CommonSolve", "ConstructionBase", "Distributed", "DocStringExtensions", "EnumX", "Expronicon", "FunctionWrappersWrappers", "IteratorInterfaceExtensions", "LinearAlgebra", "Logging", "Markdown", "PrecompileTools", "Preferences", "Printf", "RecipesBase", "RecursiveArrayTools", "Reexport", "RuntimeGeneratedFunctions", "SciMLOperators", "SciMLStructures", "StaticArraysCore", "Statistics", "SymbolicIndexingInterface"] -git-tree-sha1 = "cacc7bc54bab8749b1fc1032c4911fe80cffb959" +git-tree-sha1 = "87e054302a94a2d087f918ad50b0290977db67e6" uuid = "0bca4576-84f4-4d90-8ffe-ffa030f20462" -version = "2.61.0" +version = "2.67.0" [deps.SciMLBase.extensions] SciMLBaseChainRulesCoreExt = "ChainRulesCore" @@ -2301,15 +2337,21 @@ weakdeps = ["SparseArrays", "StaticArraysCore"] [[deps.SciMLStructures]] deps = ["ArrayInterface"] -git-tree-sha1 = "25514a6f200219cd1073e4ff23a6324e4a7efe64" +git-tree-sha1 = "0444a37a25fab98adbd90baa806ee492a3af133a" uuid = "53ae85a6-f571-4167-b2af-e1d143709226" -version = "1.5.0" +version = "1.6.1" [[deps.ScientificTypesBase]] git-tree-sha1 = "a8e18eb383b5ecf1b5e6fc237eb39255044fd92b" uuid = "30f210dd-8aff-4c5f-94ba-8e64358c1161" version = "3.0.0" +[[deps.Scratch]] +deps = ["Dates"] +git-tree-sha1 = "3bac05bc7e74a75fd9cba4295cde4045d9fe2386" +uuid = "6c6a2e73-6563-6170-7368-637461726353" +version = "1.2.1" + [[deps.SentinelArrays]] deps = ["Dates", "Random"] git-tree-sha1 = "d0553ce4031a081cc42387a9b9c8441b7d99f32d" @@ -2338,9 +2380,9 @@ version = "1.2.0" [[deps.SimpleNonlinearSolve]] deps = ["ADTypes", "ArrayInterface", "ConcreteStructs", "DiffEqBase", "DiffResults", "DifferentiationInterface", "FastClosures", "FiniteDiff", "ForwardDiff", "LinearAlgebra", "MaybeInplace", "PrecompileTools", "Reexport", "SciMLBase", "Setfield", "StaticArraysCore"] -git-tree-sha1 = "44021f3efc023be3871195d8ad98b865001a2fa1" +git-tree-sha1 = "97a7e10717bd27e600ba55da9d90a5628c1a403b" uuid = "727e6d20-b764-4bd8-a329-72de5adea6c7" -version = "1.12.3" +version = "1.12.2" weakdeps = ["ChainRulesCore", "ReverseDiff", "Tracker", "Zygote"] [deps.SimpleNonlinearSolve.extensions] @@ -2387,11 +2429,31 @@ deps = ["Libdl", "LinearAlgebra", "Random", "Serialization", "SuiteSparse_jll"] uuid = "2f01184e-e22b-5df5-ae63-d93ebab69eaf" version = "1.11.0" +[[deps.SparseConnectivityTracer]] +deps = ["ADTypes", "DocStringExtensions", "FillArrays", "LinearAlgebra", "Random", "SparseArrays"] +git-tree-sha1 = "010b3c44301805d1ede9159f449a351d61172aa6" +uuid = "9f842d2f-2579-4b1d-911e-f412cf18a3f5" +version = "0.6.9" + + [deps.SparseConnectivityTracer.extensions] + SparseConnectivityTracerDataInterpolationsExt = "DataInterpolations" + SparseConnectivityTracerLogExpFunctionsExt = "LogExpFunctions" + SparseConnectivityTracerNNlibExt = "NNlib" + SparseConnectivityTracerNaNMathExt = "NaNMath" + SparseConnectivityTracerSpecialFunctionsExt = "SpecialFunctions" + + [deps.SparseConnectivityTracer.weakdeps] + DataInterpolations = "82cc6244-b520-54b8-b5a6-8a565e85f1d0" + LogExpFunctions = "2ab3a3ac-af41-5b50-aa03-7779005ae688" + NNlib = "872c559c-99b0-510c-b3b7-b6c96a88d5cd" + NaNMath = "77ba4419-2d1f-58cd-9bb1-8ffee604a2e3" + SpecialFunctions = "276daf66-3868-5448-9aa4-cd146d93841b" + [[deps.SparseDiffTools]] -deps = ["ADTypes", "Adapt", "ArrayInterface", "Compat", "DataStructures", "FiniteDiff", "ForwardDiff", "Graphs", "LinearAlgebra", "PackageExtensionCompat", "Random", "Reexport", "SciMLOperators", "Setfield", "SparseArrays", "StaticArrayInterface", "StaticArrays", "UnPack", "VertexSafeGraphs"] -git-tree-sha1 = "b906758c107b049b6b71599b9f928d9b14e5554a" +deps = ["ADTypes", "Adapt", "ArrayInterface", "Compat", "DataStructures", "FiniteDiff", "ForwardDiff", "Graphs", "LinearAlgebra", "PackageExtensionCompat", "Random", "Reexport", "SciMLOperators", "Setfield", "SparseArrays", "StaticArrayInterface", "StaticArrays", "Tricks", "UnPack", "VertexSafeGraphs"] +git-tree-sha1 = "c9e5d7ee75cf6a1ca3a22c9a6a4ef451792cf62b" uuid = "47a9eef4-7e08-11e9-0b38-333d64bd3804" -version = "2.23.0" +version = "2.20.0" [deps.SparseDiffTools.extensions] SparseDiffToolsEnzymeExt = "Enzyme" @@ -2413,6 +2475,18 @@ git-tree-sha1 = "52962839426b75b3021296f7df242e40ecfc0852" uuid = "dc90abb0-5640-4711-901d-7e5b23a2fada" version = "0.1.2" +[[deps.SparseMatrixColorings]] +deps = ["ADTypes", "DataStructures", "DocStringExtensions", "LinearAlgebra", "Random", "SparseArrays"] +git-tree-sha1 = "76b44c879661552d64f382acf66faa29ab56b3d9" +uuid = "0a514795-09f3-496d-8182-132a7b665d35" +version = "0.4.10" + + [deps.SparseMatrixColorings.extensions] + SparseMatrixColoringsColorsExt = "Colors" + + [deps.SparseMatrixColorings.weakdeps] + Colors = "5ae59095-9a9b-59fe-a467-6f913c188581" + [[deps.Sparspak]] deps = ["Libdl", "LinearAlgebra", "Logging", "OffsetArrays", "Printf", "SparseArrays", "Test"] git-tree-sha1 = "342cf4b449c299d8d1ceaf00b7a49f4fbc7940e7" @@ -2532,6 +2606,11 @@ weakdeps = ["Adapt", "GPUArraysCore", "SparseArrays", "StaticArrays"] StructArraysSparseArraysExt = "SparseArrays" StructArraysStaticArraysExt = "StaticArrays" +[[deps.StructIO]] +git-tree-sha1 = "c581be48ae1cbf83e899b14c07a807e1787512cc" +uuid = "53d494c1-5632-5724-8f4c-31dff12d585f" +version = "0.3.1" + [[deps.SuiteSparse]] deps = ["Libdl", "LinearAlgebra", "Serialization", "SparseArrays"] uuid = "4607b0f0-06f3-5cda-b6b1-a6196a1729e9" @@ -2549,9 +2628,9 @@ version = "0.3.0" [[deps.SymbolicIndexingInterface]] deps = ["Accessors", "ArrayInterface", "RuntimeGeneratedFunctions", "StaticArraysCore"] -git-tree-sha1 = "6c6761e08bf5a270905cdd065be633abfa1b155b" +git-tree-sha1 = "8db233b54917e474165d582bef2244fa040e0a56" uuid = "2efcf032-c050-4f8e-a9bb-153293bab1f5" -version = "0.3.35" +version = "0.3.36" [[deps.SymbolicLimits]] deps = ["SymbolicUtils"] @@ -2575,9 +2654,9 @@ version = "3.7.2" [[deps.Symbolics]] deps = ["ADTypes", "ArrayInterface", "Bijections", "CommonWorldInvalidations", "ConstructionBase", "DataStructures", "DiffRules", "Distributions", "DocStringExtensions", "DomainSets", "DynamicPolynomials", "IfElse", "LaTeXStrings", "Latexify", "Libdl", "LinearAlgebra", "LogExpFunctions", "MacroTools", "Markdown", "NaNMath", "PrecompileTools", "Primes", "RecipesBase", "Reexport", "RuntimeGeneratedFunctions", "SciMLBase", "Setfield", "SparseArrays", "SpecialFunctions", "StaticArraysCore", "SymbolicIndexingInterface", "SymbolicLimits", "SymbolicUtils", "TermInterface"] -git-tree-sha1 = "24e006074ef13894ed23d006f55e6082998c9035" +git-tree-sha1 = "ce9c95fc859007747a4faf10166201e0b10d4313" uuid = "0c5d862f-8b57-4792-8d23-62f2024744c7" -version = "6.19.0" +version = "6.22.0" [deps.Symbolics.extensions] SymbolicsForwardDiffExt = "ForwardDiff" @@ -2653,9 +2732,9 @@ version = "0.5.2" [[deps.TimerOutputs]] deps = ["ExprTools", "Printf"] -git-tree-sha1 = "3a6f063d690135f5c1ba351412c82bae4d1402bf" +git-tree-sha1 = "d7298ebdfa1654583468a487e8e83fae9d72dac3" uuid = "a759f4b9-e2f1-59dc-863e-4aeb61b1ea8f" -version = "0.5.25" +version = "0.5.26" [[deps.Tracker]] deps = ["Adapt", "ChainRulesCore", "DiffRules", "ForwardDiff", "Functors", "LinearAlgebra", "LogExpFunctions", "MacroTools", "NNlib", "NaNMath", "Optimisers", "Printf", "Random", "Requires", "SpecialFunctions", "Statistics"] @@ -2700,6 +2779,11 @@ git-tree-sha1 = "be986ad9dac14888ba338c2554dcfec6939e1393" uuid = "d5829a12-d9aa-46ab-831f-fb7c9ab06edf" version = "0.2.1" +[[deps.Tricks]] +git-tree-sha1 = "7822b97e99a1672bfb1b49b668a6d46d58d8cbcb" +uuid = "410a4b4d-49e4-4fbc-ab6d-cb71b17b3775" +version = "0.1.9" + [[deps.TruncatedStacktraces]] deps = ["InteractiveUtils", "MacroTools", "Preferences"] git-tree-sha1 = "ea3e54c2bdde39062abf5a9758a23735558705e1" @@ -2707,10 +2791,10 @@ uuid = "781d530d-4396-4725-bb49-402e4bee1e77" version = "1.4.0" [[deps.Turing]] -deps = ["ADTypes", "AbstractMCMC", "Accessors", "AdvancedHMC", "AdvancedMH", "AdvancedPS", "AdvancedVI", "BangBang", "Bijectors", "Compat", "DataStructures", "Distributions", "DistributionsAD", "DocStringExtensions", "DynamicPPL", "EllipticalSliceSampling", "ForwardDiff", "Libtask", "LinearAlgebra", "LogDensityProblems", "LogDensityProblemsAD", "MCMCChains", "NamedArrays", "Optimization", "OptimizationOptimJL", "OrderedCollections", "Printf", "Random", "Reexport", "Requires", "SciMLBase", "SpecialFunctions", "Statistics", "StatsAPI", "StatsBase", "StatsFuns"] -git-tree-sha1 = "f69f33f7862a66674c279fe9b86b457a96767e35" +deps = ["ADTypes", "AbstractMCMC", "Accessors", "AdvancedHMC", "AdvancedMH", "AdvancedPS", "AdvancedVI", "BangBang", "Bijectors", "Compat", "DataStructures", "Distributions", "DistributionsAD", "DocStringExtensions", "DynamicPPL", "EllipticalSliceSampling", "ForwardDiff", "Libtask", "LinearAlgebra", "LogDensityProblems", "LogDensityProblemsAD", "MCMCChains", "NamedArrays", "Optimization", "OptimizationOptimJL", "OrderedCollections", "Printf", "Random", "Reexport", "SciMLBase", "SpecialFunctions", "Statistics", "StatsAPI", "StatsBase", "StatsFuns"] +git-tree-sha1 = "3453ab63621f1a06df04d995da2eb6fcd422617c" uuid = "fce5fe82-541a-59a6-adf8-730c64b5f9a0" -version = "0.34.1" +version = "0.35.1" [deps.Turing.extensions] TuringDynamicHMCExt = "DynamicHMC" @@ -2722,9 +2806,9 @@ version = "0.34.1" [[deps.TuringBenchmarking]] deps = ["ADTypes", "AbstractMCMC", "BenchmarkTools", "DynamicPPL", "ForwardDiff", "LinearAlgebra", "LogDensityProblems", "LogDensityProblemsAD", "PrettyTables", "Requires", "ReverseDiff", "Zygote"] -git-tree-sha1 = "b512c8ab665cb6396f19533b6960cc3e0fc4d556" +git-tree-sha1 = "2421fcac17d8f62c02e9c95c60968faa72ef95d8" uuid = "0db1332d-5c25-4deb-809f-459bc696f94f" -version = "0.5.5" +version = "0.5.6" [deps.TuringBenchmarking.extensions] TuringBenchmarkingBridgeStanExt = "BridgeStan" @@ -2753,9 +2837,9 @@ version = "1.11.0" [[deps.Unitful]] deps = ["Dates", "LinearAlgebra", "Random"] -git-tree-sha1 = "d95fe458f26209c66a187b1114df96fd70839efd" +git-tree-sha1 = "01915bfcd62be15329c9a07235447a89d588327c" uuid = "1986cc42-f94f-5a68-af5c-568840ba703d" -version = "1.21.0" +version = "1.21.1" weakdeps = ["ConstructionBase", "InverseFunctions"] [deps.Unitful.extensions] @@ -2773,12 +2857,6 @@ git-tree-sha1 = "6331ac3440856ea1988316b46045303bef658278" uuid = "013be700-e6cd-48c3-b4a1-df204f14c38f" version = "0.2.1" -[[deps.UnsafeAtomicsLLVM]] -deps = ["LLVM", "UnsafeAtomics"] -git-tree-sha1 = "2d17fabcd17e67d7625ce9c531fb9f40b7c42ce4" -uuid = "d80eeb9a-aca5-4d75-85e5-170c8b632249" -version = "0.2.1" - [[deps.VectorizationBase]] deps = ["ArrayInterface", "CPUSummary", "HostCPUFeatures", "IfElse", "LayoutPointers", "Libdl", "LinearAlgebra", "SIMDTypes", "Static", "StaticArrayInterface"] git-tree-sha1 = "4ab62a49f1d8d9548a1c8d1a75e5f55cf196f64e" diff --git a/benchmark/Project.toml b/benchmark/Project.toml index 88dcf30da..025ed9897 100644 --- a/benchmark/Project.toml +++ b/benchmark/Project.toml @@ -1,9 +1,12 @@ [deps] +ADTypes = "47edcb42-4c32-4615-8424-f2b9edc5f35b" BenchmarkCI = "20533458-34a3-403d-a444-e18f38190b5b" BenchmarkTools = "6e4b80f9-dd63-53aa-95a3-0cdb28fa8baf" Distributions = "31c24e10-a181-5473-b8eb-7969acd0382f" DynamicPPL = "366bfd00-2699-11ea-058f-f148b4cae6d8" +Enzyme = "7da242da-08ed-463a-9acd-ee780be4f1d9" EpiAware = "b2eeebe4-5992-4301-9193-7ebc9f62c855" +Mooncake = "da2b9cff-9c12-43a0-ae48-6db2b0edb7d6" PkgBenchmark = "32113eaa-f34f-5b0d-bd6c-c81e245fc73d" Turing = "fce5fe82-541a-59a6-adf8-730c64b5f9a0" TuringBenchmarking = "0db1332d-5c25-4deb-809f-459bc696f94f" diff --git a/benchmark/bench/EpiAwareUtils/EpiAwareUtils.jl b/benchmark/bench/EpiAwareUtils/EpiAwareUtils.jl index 6cb6d967d..0b1ebc99f 100644 --- a/benchmark/bench/EpiAwareUtils/EpiAwareUtils.jl +++ b/benchmark/bench/EpiAwareUtils/EpiAwareUtils.jl @@ -1,6 +1,9 @@ module BenchEpiAwareUtils using BenchmarkTools, EpiAware.EpiAwareUtils +using ADTypes, Mooncake, Enzyme + +Enzyme.API.runtimeActivity!(true) suite = BenchmarkGroup() diff --git a/benchmark/bench/EpiInfModels/EpiInfModels.jl b/benchmark/bench/EpiInfModels/EpiInfModels.jl index 0d9ca5f1e..11a580eb6 100644 --- a/benchmark/bench/EpiInfModels/EpiInfModels.jl +++ b/benchmark/bench/EpiInfModels/EpiInfModels.jl @@ -1,6 +1,10 @@ module BenchEpiInfModels using BenchmarkTools, TuringBenchmarking, EpiAware, Distributions +using ADTypes, Mooncake, Enzyme + +Enzyme.API.runtimeActivity!(true) + suite = BenchmarkGroup() include("../../make_epiaware_suite.jl") diff --git a/benchmark/bench/EpiLatentModels/EpiLatentModels.jl b/benchmark/bench/EpiLatentModels/EpiLatentModels.jl index b90fb0285..f6e119d12 100644 --- a/benchmark/bench/EpiLatentModels/EpiLatentModels.jl +++ b/benchmark/bench/EpiLatentModels/EpiLatentModels.jl @@ -1,6 +1,10 @@ module BenchEpiLatentModels using BenchmarkTools, TuringBenchmarking, EpiAware, DynamicPPL +using ADTypes, Mooncake, Enzyme + +Enzyme.API.runtimeActivity!(true) + suite = BenchmarkGroup() include("../../make_epiaware_suite.jl") diff --git a/benchmark/bench/EpiObsModels/EpiObsModels.jl b/benchmark/bench/EpiObsModels/EpiObsModels.jl index 73d8f180e..3f49d7943 100644 --- a/benchmark/bench/EpiObsModels/EpiObsModels.jl +++ b/benchmark/bench/EpiObsModels/EpiObsModels.jl @@ -1,6 +1,10 @@ module BenchEpiObsModels using BenchmarkTools, TuringBenchmarking, EpiAware, DynamicPPL +using ADTypes, Mooncake, Enzyme + +Enzyme.API.runtimeActivity!(true) + suite = BenchmarkGroup() include("../../make_epiaware_suite.jl") diff --git a/benchmark/make_epiaware_suite.jl b/benchmark/make_epiaware_suite.jl index 58d5ec297..11fe9bcd7 100644 --- a/benchmark/make_epiaware_suite.jl +++ b/benchmark/make_epiaware_suite.jl @@ -2,7 +2,11 @@ A custom wrapper for the `TuringBenchmarking.make_turing_suite` that adds EpiAware specific defaults. """ function make_epiaware_suite(model; check = true, - adbackends = [:forwarddiff, :reversediff, :reversediff_compiled]) + adbackends = [ + :forwarddiff, :reversediff, :reversediff_compiled, + ADTypes.AutoMooncake(config = nothing), + ADTypes.AutoEnzyme() + ]) suite = prefix_warnings( () -> TuringBenchmarking.make_turing_suite( model; check = check, adbackends = adbackends), From 14e68a9f8cefc85f507ed28ed6031d5e1d641428 Mon Sep 17 00:00:00 2001 From: Sam Date: Tue, 10 Dec 2024 19:38:09 +0000 Subject: [PATCH 2/3] also try injecting Mooncake and Enzyme into case studies --- EpiAware/docs/Project.toml | 2 ++ .../src/showcase/replications/chatzilena-2019/index.jl | 6 +++--- .../docs/src/showcase/replications/mishra-2020/index.jl | 7 +++++-- 3 files changed, 10 insertions(+), 5 deletions(-) diff --git a/EpiAware/docs/Project.toml b/EpiAware/docs/Project.toml index 76b276e49..ff27d90d8 100644 --- a/EpiAware/docs/Project.toml +++ b/EpiAware/docs/Project.toml @@ -8,9 +8,11 @@ DataFramesMeta = "1313f7d8-7da2-5740-9ea0-a2ca25f37964" Distributions = "31c24e10-a181-5473-b8eb-7969acd0382f" Documenter = "e30172f5-a6a5-5a46-863b-614d45cd2de4" DynamicPPL = "366bfd00-2699-11ea-058f-f148b4cae6d8" +Enzyme = "7da242da-08ed-463a-9acd-ee780be4f1d9" EpiAware = "b2eeebe4-5992-4301-9193-7ebc9f62c855" LinearAlgebra = "37e2e46d-f89d-539d-b4ee-838fcccc9c8e" LogExpFunctions = "2ab3a3ac-af41-5b50-aa03-7779005ae688" +Mooncake = "da2b9cff-9c12-43a0-ae48-6db2b0edb7d6" OrdinaryDiffEq = "1dea7af3-3e70-54e6-95c3-0bf5283fa5ed" PairPlots = "43a3c2be-4208-490b-832a-a21dcd55d7da" Pluto = "c3e4b0f8-55cb-11ea-2926-15256bba5781" diff --git a/EpiAware/docs/src/showcase/replications/chatzilena-2019/index.jl b/EpiAware/docs/src/showcase/replications/chatzilena-2019/index.jl index 7363732cd..3c117f511 100644 --- a/EpiAware/docs/src/showcase/replications/chatzilena-2019/index.jl +++ b/EpiAware/docs/src/showcase/replications/chatzilena-2019/index.jl @@ -31,7 +31,7 @@ using CSV, DataFramesMeta #Data wrangling using CairoMakie, PairPlots # ╔═╡ 14641441-dbea-4fdf-88e0-64a57da60ef7 -using ReverseDiff #Automatic differentiation backend +using ADTypes, Mooncake #Automatic differentiation backend # ╔═╡ a0d91258-8ab5-4adc-98f2-8f17b4bd685c begin #Date utility and set Random seed @@ -591,7 +591,7 @@ Starting from the initial guess, the MAP point is calculated rapidly in one pass # ╔═╡ 6796ae76-bc2d-4895-ba0a-5e2c23c50dfb map_fit_stoch_mdl = maximum_a_posteriori(stochastic_mdl; - adtype = AutoReverseDiff(), + adtype = AutoMooncake(config = nothing), initial_params = initial_guess ) @@ -603,7 +603,7 @@ Now we can run NUTS, sampling 1000 posterior draws per chain for 4 chains. # ╔═╡ 156272d7-56c4-4ac4-bf3e-7882f4edc144 chn2 = sample( stochastic_mdl, - NUTS(; adtype = AutoReverseDiff(true)), + NUTS(; adtype = AutoMooncake(config = nothing)), MCMCThreads(), 1000, 4; initial_params = fill(map_fit_stoch_mdl.values.array, 4) ) diff --git a/EpiAware/docs/src/showcase/replications/mishra-2020/index.jl b/EpiAware/docs/src/showcase/replications/mishra-2020/index.jl index 1a7453b9b..50dd0c119 100644 --- a/EpiAware/docs/src/showcase/replications/mishra-2020/index.jl +++ b/EpiAware/docs/src/showcase/replications/mishra-2020/index.jl @@ -28,7 +28,10 @@ using CSV, DataFramesMeta #Data wrangling using CairoMakie, PairPlots, TimeSeries #Plotting backend # ╔═╡ 97b5374e-7653-4b3b-98eb-d8f73aa30580 -using ReverseDiff #Automatic differentiation backend +begin + using ADTypes, Enzyme #Automatic differentiation backend + Enzyme.API.runtimeActivity!(true) +end # ╔═╡ 1642dbda-4915-4e29-beff-bca592f3ec8d begin #Date utility and set Random seed @@ -391,7 +394,7 @@ num_threads = min(10, Threads.nthreads()) inference_method = EpiMethod( pre_sampler_steps = [ManyPathfinder(nruns = 4, maxiters = 100)], sampler = NUTSampler( - adtype = AutoReverseDiff(compile = true), + adtype = AutoEnzyme(), ndraws = 2000, nchains = num_threads, mcmc_parallel = MCMCThreads()) From 0c244b855573a460480087ea483664e8c4661c6a Mon Sep 17 00:00:00 2001 From: Sam Date: Tue, 10 Dec 2024 19:54:14 +0000 Subject: [PATCH 3/3] use as keyword --- .../docs/src/showcase/replications/chatzilena-2019/index.jl | 4 ++-- EpiAware/docs/src/showcase/replications/mishra-2020/index.jl | 2 +- benchmark/make_epiaware_suite.jl | 2 +- 3 files changed, 4 insertions(+), 4 deletions(-) diff --git a/EpiAware/docs/src/showcase/replications/chatzilena-2019/index.jl b/EpiAware/docs/src/showcase/replications/chatzilena-2019/index.jl index 3c117f511..d85cdd78b 100644 --- a/EpiAware/docs/src/showcase/replications/chatzilena-2019/index.jl +++ b/EpiAware/docs/src/showcase/replications/chatzilena-2019/index.jl @@ -591,7 +591,7 @@ Starting from the initial guess, the MAP point is calculated rapidly in one pass # ╔═╡ 6796ae76-bc2d-4895-ba0a-5e2c23c50dfb map_fit_stoch_mdl = maximum_a_posteriori(stochastic_mdl; - adtype = AutoMooncake(config = nothing), + adtype = ADTypes.AutoMooncake(; config = nothing), initial_params = initial_guess ) @@ -603,7 +603,7 @@ Now we can run NUTS, sampling 1000 posterior draws per chain for 4 chains. # ╔═╡ 156272d7-56c4-4ac4-bf3e-7882f4edc144 chn2 = sample( stochastic_mdl, - NUTS(; adtype = AutoMooncake(config = nothing)), + NUTS(; adtype = ADTypes.AutoMooncake(; config = nothing)), MCMCThreads(), 1000, 4; initial_params = fill(map_fit_stoch_mdl.values.array, 4) ) diff --git a/EpiAware/docs/src/showcase/replications/mishra-2020/index.jl b/EpiAware/docs/src/showcase/replications/mishra-2020/index.jl index 50dd0c119..05ea0f11b 100644 --- a/EpiAware/docs/src/showcase/replications/mishra-2020/index.jl +++ b/EpiAware/docs/src/showcase/replications/mishra-2020/index.jl @@ -394,7 +394,7 @@ num_threads = min(10, Threads.nthreads()) inference_method = EpiMethod( pre_sampler_steps = [ManyPathfinder(nruns = 4, maxiters = 100)], sampler = NUTSampler( - adtype = AutoEnzyme(), + adtype = ADTypes.AutoEnzyme(), ndraws = 2000, nchains = num_threads, mcmc_parallel = MCMCThreads()) diff --git a/benchmark/make_epiaware_suite.jl b/benchmark/make_epiaware_suite.jl index 11fe9bcd7..9b3c329dd 100644 --- a/benchmark/make_epiaware_suite.jl +++ b/benchmark/make_epiaware_suite.jl @@ -4,7 +4,7 @@ function make_epiaware_suite(model; check = true, adbackends = [ :forwarddiff, :reversediff, :reversediff_compiled, - ADTypes.AutoMooncake(config = nothing), + ADTypes.AutoMooncake(; config = nothing), ADTypes.AutoEnzyme() ]) suite = prefix_warnings(