Merge pull request #225 from OceanBioME/ali/upgrade-to-oceananigans-0…

….92.1 Update to use Oceananigans v0.92.1
OceanBioME · Oct 24, 2024 · 54cfd8a · 54cfd8a · ali-ramadhan · Oct 24, 2024
2 parents ed9520d + 93d7a95
commit 54cfd8a
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diff --git a/Manifest.toml b/Manifest.toml
@@ -1,8 +1,8 @@
 # This file is machine-generated - editing it directly is not advised
 
-julia_version = "1.10.2"
+julia_version = "1.10.5"
 manifest_format = "2.0"
-project_hash = "3c5ec406d66c67a7c97dba5d81a300057adf87ab"
+project_hash = "12da5d1eabe1dd5798ee1a29e23ad2e10e287ad8"
 
 [[deps.AbstractFFTs]]
 deps = ["LinearAlgebra"]
@@ -45,9 +45,9 @@ version = "0.1.38"
 
 [[deps.Adapt]]
 deps = ["LinearAlgebra", "Requires"]
-git-tree-sha1 = "6a55b747d1812e699320963ffde36f1ebdda4099"
+git-tree-sha1 = "d80af0733c99ea80575f612813fa6aa71022d33a"
 uuid = "79e6a3ab-5dfb-504d-930d-738a2a938a0e"
-version = "4.0.4"
+version = "4.1.0"
 weakdeps = ["StaticArrays"]
 
     [deps.Adapt.extensions]
@@ -77,15 +77,15 @@ uuid = "2a0f44e3-6c83-55bd-87e4-b1978d98bd5f"
 
 [[deps.Blosc_jll]]
 deps = ["Artifacts", "JLLWrappers", "Libdl", "Lz4_jll", "Zlib_jll", "Zstd_jll"]
-git-tree-sha1 = "19b98ee7e3db3b4eff74c5c9c72bf32144e24f10"
+git-tree-sha1 = "ef12cdd1c7fb7e1dfd6fa8fd60d4db6bc61d2f23"
 uuid = "0b7ba130-8d10-5ba8-a3d6-c5182647fed9"
-version = "1.21.5+0"
+version = "1.21.6+0"
 
 [[deps.Bzip2_jll]]
 deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"]
-git-tree-sha1 = "9e2a6b69137e6969bab0152632dcb3bc108c8bdd"
+git-tree-sha1 = "8873e196c2eb87962a2048b3b8e08946535864a1"
 uuid = "6e34b625-4abd-537c-b88f-471c36dfa7a0"
-version = "1.0.8+1"
+version = "1.0.8+2"
 
 [[deps.CEnum]]
 git-tree-sha1 = "389ad5c84de1ae7cf0e28e381131c98ea87d54fc"
@@ -168,7 +168,7 @@ weakdeps = ["Dates", "LinearAlgebra"]
 [[deps.CompilerSupportLibraries_jll]]
 deps = ["Artifacts", "Libdl"]
 uuid = "e66e0078-7015-5450-92f7-15fbd957f2ae"
-version = "1.1.0+0"
+version = "1.1.1+0"
 
 [[deps.CompositionsBase]]
 git-tree-sha1 = "802bb88cd69dfd1509f6670416bd4434015693ad"
@@ -239,9 +239,9 @@ version = "0.3.23"
 
 [[deps.Distances]]
 deps = ["LinearAlgebra", "Statistics", "StatsAPI"]
-git-tree-sha1 = "66c4c81f259586e8f002eacebc177e1fb06363b0"
+git-tree-sha1 = "c7e3a542b999843086e2f29dac96a618c105be1d"
 uuid = "b4f34e82-e78d-54a5-968a-f98e89d6e8f7"
-version = "0.10.11"
+version = "0.10.12"
 
     [deps.Distances.extensions]
     DistancesChainRulesCoreExt = "ChainRulesCore"
@@ -285,9 +285,9 @@ version = "3.3.10+1"
 
 [[deps.FileIO]]
 deps = ["Pkg", "Requires", "UUIDs"]
-git-tree-sha1 = "82d8afa92ecf4b52d78d869f038ebfb881267322"
+git-tree-sha1 = "62ca0547a14c57e98154423419d8a342dca75ca9"
 uuid = "5789e2e9-d7fb-5bc7-8068-2c6fae9b9549"
-version = "1.16.3"
+version = "1.16.4"
 
 [[deps.FileWatching]]
 uuid = "7b1f6079-737a-58dc-b8bc-7a2ca5c1b5ee"
@@ -417,15 +417,15 @@ version = "1.0.0"
 
 [[deps.JLD2]]
 deps = ["FileIO", "MacroTools", "Mmap", "OrderedCollections", "PrecompileTools", "Requires", "TranscodingStreams"]
-git-tree-sha1 = "a0746c21bdc986d0dc293efa6b1faee112c37c28"
+git-tree-sha1 = "b464b9b461ee989b435a689a4f7d870b68d467ed"
 uuid = "033835bb-8acc-5ee8-8aae-3f567f8a3819"
-version = "0.4.53"
+version = "0.5.6"
 
 [[deps.JLLWrappers]]
 deps = ["Artifacts", "Preferences"]
-git-tree-sha1 = "f389674c99bfcde17dc57454011aa44d5a260a40"
+git-tree-sha1 = "be3dc50a92e5a386872a493a10050136d4703f9b"
 uuid = "692b3bcd-3c85-4b1f-b108-f13ce0eb3210"
-version = "1.6.0"
+version = "1.6.1"
 
 [[deps.JuliaNVTXCallbacks_jll]]
 deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"]
@@ -435,9 +435,9 @@ version = "0.2.1+0"
 
 [[deps.KernelAbstractions]]
 deps = ["Adapt", "Atomix", "InteractiveUtils", "MacroTools", "PrecompileTools", "Requires", "StaticArrays", "UUIDs", "UnsafeAtomics", "UnsafeAtomicsLLVM"]
-git-tree-sha1 = "5126765c5847f74758c411c994312052eb7117ef"
+git-tree-sha1 = "04e52f596d0871fa3890170fa79cb15e481e4cd8"
 uuid = "63c18a36-062a-441e-b654-da1e3ab1ce7c"
-version = "0.9.27"
+version = "0.9.28"
 
     [deps.KernelAbstractions.extensions]
     EnzymeExt = "EnzymeCore"
@@ -450,10 +450,10 @@ version = "0.9.27"
     SparseArrays = "2f01184e-e22b-5df5-ae63-d93ebab69eaf"
 
 [[deps.LLVM]]
-deps = ["CEnum", "LLVMExtra_jll", "Libdl", "Preferences", "Printf", "Requires", "Unicode"]
-git-tree-sha1 = "4ad43cb0a4bb5e5b1506e1d1f48646d7e0c80363"
+deps = ["CEnum", "LLVMExtra_jll", "Libdl", "Preferences", "Printf", "Unicode"]
+git-tree-sha1 = "d422dfd9707bec6617335dc2ea3c5172a87d5908"
 uuid = "929cbde3-209d-540e-8aea-75f648917ca0"
-version = "9.1.2"
+version = "9.1.3"
 weakdeps = ["BFloat16s"]
 
     [deps.LLVM.extensions]
@@ -486,9 +486,9 @@ weakdeps = ["Serialization"]
     SerializationExt = ["Serialization"]
 
 [[deps.LaTeXStrings]]
-git-tree-sha1 = "50901ebc375ed41dbf8058da26f9de442febbbec"
+git-tree-sha1 = "dda21b8cbd6a6c40d9d02a73230f9d70fed6918c"
 uuid = "b964fa9f-0449-5b57-a5c2-d3ea65f4040f"
-version = "1.3.1"
+version = "1.4.0"
 
 [[deps.LazyArtifacts]]
 deps = ["Artifacts", "Pkg"]
@@ -574,9 +574,9 @@ version = "0.1.11"
 
 [[deps.MPItrampoline_jll]]
 deps = ["Artifacts", "CompilerSupportLibraries_jll", "JLLWrappers", "LazyArtifacts", "Libdl", "MPIPreferences", "TOML"]
-git-tree-sha1 = "fde81c9f9c94fe5fbeaed7b3f1330305cf9a327c"
+git-tree-sha1 = "70e830dab5d0775183c99fc75e4c24c614ed7142"
 uuid = "f1f71cc9-e9ae-5b93-9b94-4fe0e1ad3748"
-version = "5.5.0+0"
+version = "5.5.1+0"
 
 [[deps.MacroTools]]
 deps = ["Markdown", "Random"]
@@ -648,9 +648,9 @@ version = "1.2.0"
 
 [[deps.Oceananigans]]
 deps = ["Adapt", "CUDA", "Crayons", "CubedSphere", "Dates", "Distances", "DocStringExtensions", "FFTW", "Glob", "IncompleteLU", "InteractiveUtils", "IterativeSolvers", "JLD2", "KernelAbstractions", "LinearAlgebra", "Logging", "MPI", "NCDatasets", "OffsetArrays", "OrderedCollections", "Pkg", "Printf", "Random", "Rotations", "SeawaterPolynomials", "SparseArrays", "Statistics", "StructArrays"]
-git-tree-sha1 = "cac4f28778a22404724ba667368f071047b513c1"
+git-tree-sha1 = "d32e4de90d49d0613c589dfa8d423b5c4f2248ca"
 uuid = "9e8cae18-63c1-5223-a75c-80ca9d6e9a09"
-version = "0.92.0"
+version = "0.92.1"
 
     [deps.Oceananigans.extensions]
     OceananigansEnzymeExt = "Enzyme"
@@ -856,9 +856,9 @@ version = "1.10.0"
 
 [[deps.StaticArrays]]
 deps = ["LinearAlgebra", "PrecompileTools", "Random", "StaticArraysCore"]
-git-tree-sha1 = "eeafab08ae20c62c44c8399ccb9354a04b80db50"
+git-tree-sha1 = "777657803913ffc7e8cc20f0fd04b634f871af8f"
 uuid = "90137ffa-7385-5640-81b9-e52037218182"
-version = "1.9.7"
+version = "1.9.8"
 
     [deps.StaticArrays.extensions]
     StaticArraysChainRulesCoreExt = "ChainRulesCore"
@@ -932,20 +932,16 @@ version = "1.10.0"
 
 [[deps.TaylorSeries]]
 deps = ["LinearAlgebra", "Markdown", "Requires", "SparseArrays"]
-git-tree-sha1 = "90c9bc500f4c5cdd235c81503ec91b2048f06423"
+git-tree-sha1 = "abc13c4d3cccd1703335ba03abdaf0dc8ecc97e2"
 uuid = "6aa5eb33-94cf-58f4-a9d0-e4b2c4fc25ea"
-version = "0.17.8"
+version = "0.17.3"
 
     [deps.TaylorSeries.extensions]
     TaylorSeriesIAExt = "IntervalArithmetic"
-    TaylorSeriesJLD2Ext = "JLD2"
-    TaylorSeriesRATExt = "RecursiveArrayTools"
     TaylorSeriesSAExt = "StaticArrays"
 
     [deps.TaylorSeries.weakdeps]
     IntervalArithmetic = "d1acc4aa-44c8-5952-acd4-ba5d80a2a253"
-    JLD2 = "033835bb-8acc-5ee8-8aae-3f567f8a3819"
-    RecursiveArrayTools = "731186ca-8d62-57ce-b412-fbd966d074cd"
     StaticArrays = "90137ffa-7385-5640-81b9-e52037218182"
 
 [[deps.Test]]
@@ -954,14 +950,14 @@ uuid = "8dfed614-e22c-5e08-85e1-65c5234f0b40"
 
 [[deps.TimerOutputs]]
 deps = ["ExprTools", "Printf"]
-git-tree-sha1 = "5a13ae8a41237cff5ecf34f73eb1b8f42fff6531"
+git-tree-sha1 = "3a6f063d690135f5c1ba351412c82bae4d1402bf"
 uuid = "a759f4b9-e2f1-59dc-863e-4aeb61b1ea8f"
-version = "0.5.24"
+version = "0.5.25"
 
 [[deps.TranscodingStreams]]
-git-tree-sha1 = "e84b3a11b9bece70d14cce63406bbc79ed3464d2"
+git-tree-sha1 = "0c45878dcfdcfa8480052b6ab162cdd138781742"
 uuid = "3bb67fe8-82b1-5028-8e26-92a6c54297fa"
-version = "0.11.2"
+version = "0.11.3"
 
 [[deps.UUIDs]]
 deps = ["Random", "SHA"]
@@ -1019,13 +1015,13 @@ version = "1.1.2+0"
 [[deps.libblastrampoline_jll]]
 deps = ["Artifacts", "Libdl"]
 uuid = "8e850b90-86db-534c-a0d3-1478176c7d93"
-version = "5.8.0+1"
+version = "5.11.0+0"
 
 [[deps.libzip_jll]]
 deps = ["Artifacts", "Bzip2_jll", "GnuTLS_jll", "JLLWrappers", "Libdl", "XZ_jll", "Zlib_jll", "Zstd_jll"]
-git-tree-sha1 = "3282b7d16ae7ac3e57ec2f3fa8fafb564d8f9f7f"
+git-tree-sha1 = "668ac0297e6bd8f4d53dfdcd3ace71f2e00f4a35"
 uuid = "337d8026-41b4-5cde-a456-74a10e5b31d1"
-version = "1.10.1+0"
+version = "1.11.1+0"
 
 [[deps.nghttp2_jll]]
 deps = ["Artifacts", "Libdl"]

diff --git a/Project.toml b/Project.toml
@@ -1,7 +1,7 @@
 name = "OceanBioME"
 uuid = "a49af516-9db8-4be4-be45-1dad61c5a376"
 authors = ["Jago Strong-Wright <[email protected]> and contributors"]
-version = "0.13.0"
+version = "0.13.1"
 
 [deps]
 Adapt = "79e6a3ab-5dfb-504d-930d-738a2a938a0e"
@@ -24,7 +24,7 @@ EnsembleKalmanProcesses = "1"
 GibbsSeaWater = "0.1"
 JLD2 = "0.4, 0.5"
 KernelAbstractions = "0.9"
-Oceananigans = "0.91.9, 0.92"
+Oceananigans = "^0.92.1"
 OffsetArrays = "1.14"
 Roots = "2"
 SeawaterPolynomials = "0.3"

diff --git a/docs/Project.toml b/docs/Project.toml
@@ -16,11 +16,11 @@ Printf = "de0858da-6303-5e67-8744-51eddeeeb8d7"
 Statistics = "10745b16-79ce-11e8-11f9-7d13ad32a3b2"
 
 [compat]
-CairoMakie = "0.11"
+CairoMakie = "0.11, 0.12"
 Documenter = "1"
 DocumenterCitations = "1"
 EnsembleKalmanProcesses = "1"
 JLD2 = "0.4"
 Literate = "≥2.9.0"
-Oceananigans = "0.91"
+Oceananigans = "^0.92.1"
 julia = "1.10"
diff --git a/src/Models/Sediments/Sediments.jl b/src/Models/Sediments/Sediments.jl
@@ -9,7 +9,7 @@ using OceanBioME: DiscreteBiogeochemistry, ContinuousBiogeochemistry, BoxModelGr
 using Oceananigans
 using Oceananigans.Architectures: device, architecture, on_architecture
 using Oceananigans.Utils: launch!
-using Oceananigans.Advection: advective_tracer_flux_z, TracerAdvection
+using Oceananigans.Advection: advective_tracer_flux_z, FluxFormAdvection
 using Oceananigans.Units: day
 using Oceananigans.Fields: ConstantField
 using Oceananigans.Biogeochemistry: biogeochemical_drift_velocity
@@ -38,13 +38,13 @@ function update_tendencies!(bgc, sediment::FlatSediment, model)
 
     launch!(arch, model.grid, :xy,
             calculate_sediment_tendencies!,
-            sediment, biogeochemistry, model.grid, 
-            sinking_advection(biogeochemistry, model.advection), 
-            required_tracers(sediment, biogeochemistry, model.tracers), 
-            required_tendencies(sediment, biogeochemistry, model.timestepper.Gⁿ), 
+            sediment, biogeochemistry, model.grid,
+            sinking_advection(biogeochemistry, model.advection),
+            required_tracers(sediment, biogeochemistry, model.tracers),
+            required_tendencies(sediment, biogeochemistry, model.timestepper.Gⁿ),
             sediment.tendencies.Gⁿ,
             model.clock.time)
-            
+
     return nothing
 end
 
@@ -72,9 +72,9 @@ end
 
 @inline advection_scheme(advection, val_tracer) = advection
 @inline advection_scheme(advection::NamedTuple, val_tracer::Val{T}) where T = advection_scheme(advection[T], val_tracer)
-@inline advection_scheme(advection::TracerAdvection, val_tracer) = advection.z
+@inline advection_scheme(advection::FluxFormAdvection, val_tracer) = advection.z
 
-@inline function sinking_flux(i, j, k, grid, advection, val_tracer::Val{T}, bgc, tracers) where T 
+@inline function sinking_flux(i, j, k, grid, advection, val_tracer::Val{T}, bgc, tracers) where T
     return - advective_tracer_flux_z(i, j, k, grid, advection_scheme(advection, val_tracer), biogeochemical_drift_velocity(bgc, val_tracer).w, tracers[T]) /
       volume(i, j, k, grid, Center(), Center(), Center())
 end

diff --git a/src/Models/Sediments/coupled_timesteppers.jl b/src/Models/Sediments/coupled_timesteppers.jl
@@ -13,14 +13,15 @@ const BGC_WITH_FLAT_SEDIMENT = Union{<:DiscreteBiogeochemistry{<:Any, <:Any, <:F
 
 # This is definitly type piracy
 @inline function ab2_step!(model::NonhydrostaticModel{<:Any, <:Any, <:Any, <:Any, <:Any, <:Any, <:Any, <:Any, <:Any, <:Any, <:Any, <:Any, <:Any, <:Any, <:Any, <:Any, <:Any, <:BGC_WITH_FLAT_SEDIMENT}, Δt)
-    workgroup, worksize = work_layout(model.grid, :xyz)
     arch = model.architecture
-    step_field_kernel! = ab2_step_field!(device(arch), workgroup, worksize)
     model_fields = prognostic_fields(model)
     χ = model.timestepper.χ
 
     for (i, field) in enumerate(model_fields)
 
+        workgroup, worksize = work_layout(model.grid, :xyz, location(field))
+        step_field_kernel! = ab2_step_field!(device(arch), workgroup, worksize)
+
         step_field_kernel!(field, Δt, χ,
                            model.timestepper.Gⁿ[i],
                            model.timestepper.G⁻[i])
@@ -40,9 +41,9 @@ const BGC_WITH_FLAT_SEDIMENT = Union{<:DiscreteBiogeochemistry{<:Any, <:Any, <:F
     sediment = model.biogeochemistry.sediment
 
     for (i, field) in enumerate(sediment_fields(sediment))
-        launch!(arch, model.grid, :xy, ab2_step_flat_field!, 
-                field, Δt, χ, 
-                sediment.tendencies.Gⁿ[i], 
+        launch!(arch, model.grid, :xy, ab2_step_flat_field!,
+                field, Δt, χ,
+                sediment.tendencies.Gⁿ[i],
                 sediment.tendencies.G⁻[i])
 
     end
@@ -61,12 +62,12 @@ end
 
     sediment = model.biogeochemistry.sediment
     arch = model.architecture
-    
+
 
     for (i, field) in enumerate(sediment_fields(sediment))
-        launch!(arch, model.grid, :xy, ab2_step_flat_field!, 
-                field, Δt, χ, 
-                sediment.tendencies.Gⁿ[i], 
+        launch!(arch, model.grid, :xy, ab2_step_flat_field!,
+                field, Δt, χ,
+                sediment.tendencies.Gⁿ[i],
                 sediment.tendencies.G⁻[i])
 
     end
@@ -83,12 +84,13 @@ end
 end
 
 function rk3_substep!(model::NonhydrostaticModel{<:Any, <:Any, <:Any, <:Any, <:Any, <:Any, <:Any, <:Any, <:Any, <:Any, <:Any, <:Any, <:Any, <:Any, <:Any, <:Any, <:Any, <:BGC_WITH_FLAT_SEDIMENT}, Δt, γⁿ, ζⁿ)
-    workgroup, worksize = work_layout(model.grid, :xyz)
     arch = model.architecture
-    substep_field_kernel! = rk3_substep_field!(device(arch), workgroup, worksize)
     model_fields = prognostic_fields(model)
 
     for (i, field) in enumerate(model_fields)
+        workgroup, worksize = work_layout(model.grid, :xyz, location(field))
+        substep_field_kernel! = rk3_substep_field!(device(arch), workgroup, worksize)
+
         substep_field_kernel!(field, Δt, γⁿ, ζⁿ,
                               model.timestepper.Gⁿ[i],
                               model.timestepper.G⁻[i])
@@ -108,9 +110,9 @@ function rk3_substep!(model::NonhydrostaticModel{<:Any, <:Any, <:Any, <:Any, <:A
     sediment = model.biogeochemistry.sediment
 
     for (i, field) in enumerate(sediment_fields(sediment))
-        launch!(arch, model.grid, :xy, rk3_step_flat_field!, 
+        launch!(arch, model.grid, :xy, rk3_step_flat_field!,
                 field, Δt, γⁿ, ζⁿ,
-                sediment.tendencies.Gⁿ[i], 
+                sediment.tendencies.Gⁿ[i],
                 sediment.tendencies.G⁻[i])
     end