Merge branch 'main' into ep/modify_dycoms_rf02

Author: ericmpham

.buildkite/Manifest-v1.11.toml

@@ -5,9 +5,9 @@ manifest_format = "2.0"
 project_hash = "04945e2a7116cfacb2d57340f477dbe23e208227"
 
 [[deps.ADTypes]]
-git-tree-sha1 = "7927b9af540ee964cc5d1b73293f1eb0b761a3a1"
+git-tree-sha1 = "60665b326b75db6517939d0e1875850bc4a54368"
 uuid = "47edcb42-4c32-4615-8424-f2b9edc5f35b"
-version = "1.16.0"
+version = "1.17.0"
 weakdeps = ["ChainRulesCore", "ConstructionBase", "EnzymeCore"]
 
     [deps.ADTypes.extensions]
@@ -153,9 +153,9 @@ version = "0.1.7"
 
 [[deps.Atomix]]
 deps = ["UnsafeAtomics"]
-git-tree-sha1 = "b5bb4dc6248fde467be2a863eb8452993e74d402"
+git-tree-sha1 = "29bb0eb6f578a587a49da16564705968667f5fa8"
 uuid = "a9b6321e-bd34-4604-b9c9-b65b8de01458"
-version = "1.1.1"
+version = "1.1.2"
 
     [deps.Atomix.extensions]
     AtomixCUDAExt = "CUDA"
@@ -285,10 +285,10 @@ uuid = "4e9b3aee-d8a1-5a3d-ad8b-7d824db253f0"
 version = "1.0.1+0"
 
 [[deps.CUDA]]
-deps = ["AbstractFFTs", "Adapt", "BFloat16s", "CEnum", "CUDA_Driver_jll", "CUDA_Runtime_Discovery", "CUDA_Runtime_jll", "Crayons", "DataFrames", "ExprTools", "GPUArrays", "GPUCompiler", "GPUToolbox", "KernelAbstractions", "LLVM", "LLVMLoopInfo", "LazyArtifacts", "Libdl", "LinearAlgebra", "Logging", "NVTX", "Preferences", "PrettyTables", "Printf", "Random", "Random123", "RandomNumbers", "Reexport", "Requires", "SparseArrays", "StaticArrays", "Statistics", "demumble_jll"]
-git-tree-sha1 = "b8ae59258f3d96ce75a00f9229e719356eb929d6"
+deps = ["AbstractFFTs", "Adapt", "BFloat16s", "CEnum", "CUDA_Compiler_jll", "CUDA_Driver_jll", "CUDA_Runtime_Discovery", "CUDA_Runtime_jll", "Crayons", "DataFrames", "ExprTools", "GPUArrays", "GPUCompiler", "GPUToolbox", "KernelAbstractions", "LLVM", "LLVMLoopInfo", "LazyArtifacts", "Libdl", "LinearAlgebra", "Logging", "NVTX", "Preferences", "PrettyTables", "Printf", "Random", "Random123", "RandomNumbers", "Reexport", "Requires", "SparseArrays", "StaticArrays", "Statistics", "demumble_jll"]
+git-tree-sha1 = "27f69b3923e58730f0a71396070e9114fc0bba40"
 uuid = "052768ef-5323-5732-b1bb-66c8b64840ba"
-version = "5.8.2"
+version = "5.8.3"
 
     [deps.CUDA.extensions]
     ChainRulesCoreExt = "ChainRulesCore"
@@ -302,23 +302,29 @@ version = "5.8.2"
     SparseMatricesCSR = "a0a7dd2c-ebf4-11e9-1f05-cf50bc540ca1"
     SpecialFunctions = "276daf66-3868-5448-9aa4-cd146d93841b"
 
+[[deps.CUDA_Compiler_jll]]
+deps = ["Artifacts", "CUDA_Driver_jll", "JLLWrappers", "LazyArtifacts", "Libdl", "TOML"]
+git-tree-sha1 = "fdb9ddf3e08e2aca4c84b3252df2dea046caadee"
+uuid = "d1e2174e-dfdc-576e-b43e-73b79eb1aca8"
+version = "0.2.0+1"
+
 [[deps.CUDA_Driver_jll]]
 deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"]
-git-tree-sha1 = "18afa851ed10552e6df25dfaa7ef450104ae73d4"
+git-tree-sha1 = "12621de83838b5ce6a185050db5a184f4540679b"
 uuid = "4ee394cb-3365-5eb0-8335-949819d2adfc"
-version = "0.13.1+0"
+version = "13.0.0+0"
 
 [[deps.CUDA_Runtime_Discovery]]
 deps = ["Libdl"]
-git-tree-sha1 = "33576c7c1b2500f8e7e6baa082e04563203b3a45"
+git-tree-sha1 = "f9a521f52d236fe49f1028d69e549e7f2644bb72"
 uuid = "1af6417a-86b4-443c-805f-a4643ffb695f"
-version = "0.3.5"
+version = "1.0.0"
 
 [[deps.CUDA_Runtime_jll]]
 deps = ["Artifacts", "CUDA_Driver_jll", "JLLWrappers", "LazyArtifacts", "Libdl", "TOML"]
-git-tree-sha1 = "b5c173a64f9f4224a82fdc26fda8614cb2ecfa27"
+git-tree-sha1 = "cc727d90c9769db27945219f9ba149dbddc74f06"
 uuid = "76a88914-d11a-5bdc-97e0-2f5a05c973a2"
-version = "0.17.1+0"
+version = "0.19.0+0"
 
 [[deps.Cairo]]
 deps = ["Cairo_jll", "Colors", "Glib_jll", "Graphics", "Libdl", "Pango_jll"]
@@ -340,9 +346,9 @@ version = "1.18.5+0"
 
 [[deps.ChainRulesCore]]
 deps = ["Compat", "LinearAlgebra"]
-git-tree-sha1 = "06ee8d1aa558d2833aa799f6f0b31b30cada405f"
+git-tree-sha1 = "e4c6a16e77171a5f5e25e9646617ab1c276c5607"
 uuid = "d360d2e6-b24c-11e9-a2a3-2a2ae2dbcce4"
-version = "1.25.2"
+version = "1.26.0"
 weakdeps = ["SparseArrays"]
 
     [deps.ChainRulesCore.extensions]
@@ -366,7 +372,7 @@ version = "0.5.19"
 deps = ["Adapt", "ArgParse", "Artifacts", "AtmosphericProfilesLibrary", "ClimaComms", "ClimaCore", "ClimaDiagnostics", "ClimaInterpolations", "ClimaParams", "ClimaTimeSteppers", "ClimaUtilities", "CloudMicrophysics", "Dates", "ForwardDiff", "Insolation", "Interpolations", "LazyArtifacts", "LazyBroadcast", "LinearAlgebra", "Logging", "NCDatasets", "NVTX", "NullBroadcasts", "RRTMGP", "Random", "SciMLBase", "SparseMatrixColorings", "StaticArrays", "Statistics", "SurfaceFluxes", "Thermodynamics", "UnrolledUtilities", "YAML"]
 path = ".."
 uuid = "b2c96348-7fb7-4fe0-8da9-78d88439e717"
-version = "0.31.1"
+version = "0.31.2"
 
 [[deps.ClimaComms]]
 deps = ["Adapt", "Logging", "LoggingExtras"]
@@ -381,9 +387,9 @@ weakdeps = ["CUDA", "MPI"]
 
 [[deps.ClimaCore]]
 deps = ["Adapt", "BandedMatrices", "BlockArrays", "ClimaComms", "CubedSphere", "DataStructures", "ForwardDiff", "GaussQuadrature", "GilbertCurves", "HDF5", "InteractiveUtils", "IntervalSets", "KrylovKit", "LazyBroadcast", "LinearAlgebra", "MultiBroadcastFusion", "NVTX", "PkgVersion", "RecursiveArrayTools", "RootSolvers", "SparseArrays", "StaticArrays", "Statistics", "UnrolledUtilities"]
-git-tree-sha1 = "b2fbb5a52601005cf4e7547032d5bf371a2f4a69"
+git-tree-sha1 = "f9c4a2b43410bff9f33301eeb7664350014ce593"
 uuid = "d414da3d-4745-48bb-8d80-42e94e092884"
-version = "0.14.38"
+version = "0.14.39"
 weakdeps = ["CUDA", "Krylov"]
 
     [deps.ClimaCore.extensions]
@@ -442,9 +448,9 @@ weakdeps = ["BenchmarkTools", "CUDA", "OrderedCollections", "PrettyTables", "Sta
 
 [[deps.ClimaUtilities]]
 deps = ["Artifacts", "ClimaComms", "Dates"]
-git-tree-sha1 = "4402148693a5096c28cb09e544ce92b049b33e41"
+git-tree-sha1 = "fe1a7b3143f11c017118d3c99f067a09cb622f81"
 uuid = "b3f4f4ca-9299-4f7f-bd9b-81e1242a7513"
-version = "0.1.25"
+version = "0.1.26"
 weakdeps = ["Adapt", "CUDA", "ClimaCore", "ClimaCoreTempestRemap", "Interpolations", "NCDatasets"]
 
     [deps.ClimaUtilities.extensions]
@@ -638,9 +644,9 @@ version = "1.9.1"
 
 [[deps.DiffEqBase]]
 deps = ["ArrayInterface", "ConcreteStructs", "DataStructures", "DocStringExtensions", "EnumX", "EnzymeCore", "FastBroadcast", "FastClosures", "FastPower", "FunctionWrappers", "FunctionWrappersWrappers", "LinearAlgebra", "Logging", "Markdown", "MuladdMacro", "Parameters", "PrecompileTools", "Printf", "RecursiveArrayTools", "Reexport", "SciMLBase", "SciMLOperators", "SciMLStructures", "Setfield", "Static", "StaticArraysCore", "Statistics", "SymbolicIndexingInterface", "TruncatedStacktraces"]
-git-tree-sha1 = "803ea1b97e06d9f4b0da348589d451c5a456e9f4"
+git-tree-sha1 = "1b1e070e57681d1176d99a5ec455717e24686612"
 uuid = "2b5f629d-d688-5b77-993f-72d75c75574e"
-version = "6.182.1"
+version = "6.183.2"
 
     [deps.DiffEqBase.extensions]
     DiffEqBaseCUDAExt = "CUDA"
@@ -690,9 +696,9 @@ version = "1.15.1"
 
 [[deps.DiskArrays]]
 deps = ["ConstructionBase", "LRUCache", "Mmap", "OffsetArrays"]
-git-tree-sha1 = "16d93ff95ecc421463eaefd694e6746bb1c0919e"
+git-tree-sha1 = "bfde0790720fcac006a3d62149309a685fc3aa13"
 uuid = "3c3547ce-8d99-4f5e-a174-61eb10b00ae3"
-version = "0.4.14"
+version = "0.4.15"
 
 [[deps.Distributed]]
 deps = ["Random", "Serialization", "Sockets"]
@@ -961,9 +967,10 @@ uuid = "61eb1bfa-7361-4325-ad38-22787b887f55"
 version = "1.6.1"
 
 [[deps.GPUToolbox]]
-git-tree-sha1 = "15d8b0f5a6dca9bf8c02eeaf6687660dafa638d0"
+deps = ["LLVM"]
+git-tree-sha1 = "5bfe837129bf49e2e049b4f1517546055cc16a93"
 uuid = "096a3bc2-3ced-46d0-87f4-dd12716f4bfc"
-version = "0.2.0"
+version = "0.3.0"
 
 [[deps.GaussQuadrature]]
 deps = ["SpecialFunctions"]
@@ -1241,9 +1248,9 @@ version = "1.0.0"
 
 [[deps.JET]]
 deps = ["CodeTracking", "InteractiveUtils", "JuliaInterpreter", "JuliaSyntax", "LoweredCodeUtils", "MacroTools", "Pkg", "PrecompileTools", "Preferences", "Test"]
-git-tree-sha1 = "c5bc131290ca461230634d6a44a69f3c9a8d8577"
+git-tree-sha1 = "c5afee875b8daa022c09cda641c314c325e7d545"
 uuid = "c3a54625-cd67-489e-a8e7-0a5a0ff4e31b"
-version = "0.9.19"
+version = "0.9.20"
 
     [deps.JET.extensions]
     JETCthulhuExt = "Cthulhu"
@@ -1530,9 +1537,9 @@ version = "2.10.0"
 
 [[deps.LittleCMS_jll]]
 deps = ["Artifacts", "JLLWrappers", "JpegTurbo_jll", "Libdl", "Libtiff_jll"]
-git-tree-sha1 = "fa7fd067dca76cadd880f1ca937b4f387975a9f5"
+git-tree-sha1 = "8e6a74641caf3b84800f2ccd55dc7ab83893c10b"
 uuid = "d3a379c0-f9a3-5b72-a4c0-6bf4d2e8af0f"
-version = "2.16.0+0"
+version = "2.17.0+0"
 
 [[deps.LogExpFunctions]]
 deps = ["DocStringExtensions", "IrrationalConstants", "LinearAlgebra"]
@@ -1958,6 +1965,22 @@ git-tree-sha1 = "7dbfb7f61c3aa5def7b7dad3fa344c1c2858a83b"
 uuid = "9c32591e-4766-534b-9725-b71a8799265b"
 version = "24.6.0+0"
 
+[[deps.PreallocationTools]]
+deps = ["Adapt", "ArrayInterface", "PrecompileTools"]
+git-tree-sha1 = "520070df581845686c8c488b6dadce6b2c316856"
+uuid = "d236fae5-4411-538c-8e31-a6e3d9e00b46"
+version = "0.4.32"
+
+    [deps.PreallocationTools.extensions]
+    PreallocationToolsForwardDiffExt = "ForwardDiff"
+    PreallocationToolsReverseDiffExt = "ReverseDiff"
+    PreallocationToolsSparseConnectivityTracerExt = "SparseConnectivityTracer"
+
+    [deps.PreallocationTools.weakdeps]
+    ForwardDiff = "f6369f11-7733-5829-9624-2563aa707210"
+    ReverseDiff = "37e2e3b7-166d-5795-8a7a-e32c996b4267"
+    SparseConnectivityTracer = "9f842d2f-2579-4b1d-911e-f412cf18a3f5"
+
 [[deps.PrecompileCI]]
 deps = ["ClimaAtmos", "ClimaComms", "ClimaCore", "ClimaParams", "PrecompileTools"]
 path = "PrecompileCI"
@@ -1972,9 +1995,9 @@ 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.PrettyTables]]
 deps = ["Crayons", "LaTeXStrings", "Markdown", "PrecompileTools", "Printf", "Reexport", "StringManipulation", "Tables"]
@@ -2173,10 +2196,10 @@ uuid = "94e857df-77ce-4151-89e5-788b33177be4"
 version = "0.1.0"
 
 [[deps.SciMLBase]]
-deps = ["ADTypes", "Accessors", "Adapt", "ArrayInterface", "CommonSolve", "ConstructionBase", "Distributed", "DocStringExtensions", "EnumX", "FunctionWrappersWrappers", "IteratorInterfaceExtensions", "LinearAlgebra", "Logging", "Markdown", "Moshi", "PrecompileTools", "Preferences", "Printf", "RecipesBase", "RecursiveArrayTools", "Reexport", "RuntimeGeneratedFunctions", "SciMLOperators", "SciMLStructures", "StaticArraysCore", "Statistics", "SymbolicIndexingInterface"]
-git-tree-sha1 = "c056c723b68700fec386dfde8c577089df720c8e"
+deps = ["ADTypes", "Accessors", "Adapt", "ArrayInterface", "CommonSolve", "ConstructionBase", "Distributed", "DocStringExtensions", "EnumX", "FunctionWrappersWrappers", "IteratorInterfaceExtensions", "LinearAlgebra", "Logging", "Markdown", "Moshi", "PreallocationTools", "PrecompileTools", "Preferences", "Printf", "RecipesBase", "RecursiveArrayTools", "Reexport", "RuntimeGeneratedFunctions", "SciMLOperators", "SciMLStructures", "StaticArraysCore", "Statistics", "SymbolicIndexingInterface"]
+git-tree-sha1 = "4041803a2ec7b65fecf0596fe5dd4ef3111b0f2a"
 uuid = "0bca4576-84f4-4d90-8ffe-ffa030f20462"
-version = "2.108.0"
+version = "2.111.0"
 
     [deps.SciMLBase.extensions]
     SciMLBaseChainRulesCoreExt = "ChainRulesCore"
@@ -2201,9 +2224,9 @@ version = "2.108.0"
 
 [[deps.SciMLOperators]]
 deps = ["Accessors", "ArrayInterface", "DocStringExtensions", "LinearAlgebra", "MacroTools"]
-git-tree-sha1 = "7d3a1519dc4d433a6b20035eaff20bde8be77c66"
+git-tree-sha1 = "aea915a39b547c48a18ee041120db1ae8df5a691"
 uuid = "c0aeaf25-5076-4817-a8d5-81caf7dfa961"
-version = "1.4.0"
+version = "1.5.0"
 weakdeps = ["SparseArrays", "StaticArraysCore"]
 
     [deps.SciMLOperators.extensions]
@@ -2478,10 +2501,14 @@ weakdeps = ["ClimaParams"]
     CreateParametersExt = "ClimaParams"
 
 [[deps.SymbolicIndexingInterface]]
-deps = ["Accessors", "ArrayInterface", "PrettyTables", "RuntimeGeneratedFunctions", "StaticArraysCore"]
-git-tree-sha1 = "59ca6eddaaa9849e7de9fd1153b6faf0b1db7b80"
+deps = ["Accessors", "ArrayInterface", "RuntimeGeneratedFunctions", "StaticArraysCore"]
+git-tree-sha1 = "93104ca226670c0cb92ba8bc6998852ad55a2d4c"
 uuid = "2efcf032-c050-4f8e-a9bb-153293bab1f5"
-version = "0.3.42"
+version = "0.3.43"
+weakdeps = ["PrettyTables"]
+
+    [deps.SymbolicIndexingInterface.extensions]
+    SymbolicIndexingInterfacePrettyTablesExt = "PrettyTables"
 
 [[deps.TOML]]
 deps = ["Dates"]

NEWS.md

@@ -4,6 +4,9 @@ ClimaAtmos.jl Release Notes
 main
 -------
 
+v0.31.2
+-------
+
 ### Add RWP diagnostic
 PR [#3946](https://github.com/CliMA/ClimaAtmos.jl/pull/3946) adds rainwater path diagnostic variable.
 

Project.toml

@@ -1,7 +1,7 @@
 name = "ClimaAtmos"
 uuid = "b2c96348-7fb7-4fe0-8da9-78d88439e717"
 authors = ["Climate Modeling Alliance"]
-version = "0.31.1"
+version = "0.31.2"
 
 [deps]
 Adapt = "79e6a3ab-5dfb-504d-930d-738a2a938a0e"

config/longrun_configs/longrun_aquaplanet_allsky_progedmf_0M.yml

@@ -1,7 +1,9 @@
 implicit_sgs_advection: true
 implicit_sgs_mass_flux: true
+implicit_sgs_entr_detr: true
+implicit_sgs_nh_pressure: true
 max_newton_iters_ode: 3
-dt: "20secs"
+dt: "30secs"
 t_end: "60days"
 dt_save_state_to_disk: "30days"
 moist: "equil"

toml/longrun_aquaplanet_progedmf.toml

@@ -4,6 +4,9 @@ value = 40000.0
 [zd_viscous]
 value = 40000.0
 
+[alpha_rayleigh_sgs_tracer]
+value = 1e-3
+
 [precipitation_timescale]
 value = 600