merged

simone-silvestri · simone-silvestri · commit d96c32b210c3 · 2025-07-22T05:36:35.000-04:00
diff --git a/.buildkite/examples_build.yml b/.buildkite/examples_build.yml
@@ -1,6 +1,6 @@
 
 env:
-  JULIA_VERSION: "1.10.9"
+  JULIA_VERSION: "1.10.10"
   JULIA_MINOR_VERSION: "1.10"
   TARTARUS_HOME: "/storage5/buildkite-agent"
   JULIA_PKG_SERVER_REGISTRY_PREFERENCE: eager
@@ -18,7 +18,7 @@ steps:
       TMPDIR: "$TARTARUS_HOME/tmp"
     command:
       - "echo '--- Instantiate project'"
-      - "$TARTARUS_HOME/julia-$JULIA_VERSION/bin/julia --color=yes -O0 --project -e 'using Pkg; Pkg.instantiate(; verbose=true); Pkg.precompile(; strict=true)'"
+      - "$TARTARUS_HOME/julia-$JULIA_VERSION/bin/julia --color=yes -O0 --project -e 'using Pkg; Pkg.add(url=\"https://github.com/CliMA/Oceananigans.jl\", rev=\"ss/fix-zstar-bc\"); Pkg.instantiate(; verbose=true); Pkg.precompile(; strict=true)'"
       # force the initialization of the CUDA runtime as it is lazily loaded by default
       - "$TARTARUS_HOME/julia-$JULIA_VERSION/bin/julia --color=yes -O0 --project -e 'using CUDA; CUDA.precompile_runtime()'"
     agents:
@@ -29,7 +29,7 @@ steps:
   - label: "Run documentation"
     key: "build_documentation"
     commands:
-      - "$TARTARUS_HOME/julia-$JULIA_VERSION/bin/julia --color=yes -O0 --project=docs/ -e 'using Pkg; Pkg.develop(PackageSpec(path=pwd())); Pkg.instantiate()'"
+      - "$TARTARUS_HOME/julia-$JULIA_VERSION/bin/julia --color=yes -O0 --project=docs/ -e 'using Pkg; Pkg.add(url=\"https://github.com/CliMA/Oceananigans.jl\", rev=\"ss/fix-zstar-bc\"); Pkg.develop(PackageSpec(path=pwd())); Pkg.instantiate(); Pkg.precompile(; strict=true)'"
       - "$TARTARUS_HOME/julia-$JULIA_VERSION/bin/julia --color=yes -O0 --project=docs/ docs/make.jl"
     agents:
       queue: ClimaOcean-docs
@@ -38,10 +38,10 @@ steps:
       TMPDIR: "$TARTARUS_HOME/tmp"
       JULIA_DEPOT_PATH: "$TARTARUS_HOME/.julia-$BUILDKITE_BUILD_NUMBER"
       JULIA_DEBUG: "Documenter"
-      # This environment variable is needed to avoid SSL verification errors when Downloads.jl 
+      # This environment variable is needed to avoid SSL verification errors when Downloads.jl
       # tries to download the bathymetry data. It should not be required so we need to fix our certificates
       # and remove this environment variable. ref: https://github.com/JuliaLang/Downloads.jl/issues/97
-      JULIA_SSL_NO_VERIFY: "**" 
+      JULIA_SSL_NO_VERIFY: "**"
 
     timeout_in_minutes: 1440
 
diff --git a/Project.toml b/Project.toml
@@ -2,7 +2,7 @@ name = "ClimaOcean"
 uuid = "0376089a-ecfe-4b0e-a64f-9c555d74d754"
 license = "MIT"
 authors = ["Climate Modeling Alliance and contributors"]
-version = "0.7.1"
+version = "0.7.2"
 
 [deps]
 Adapt = "79e6a3ab-5dfb-504d-930d-738a2a938a0e"
diff --git a/README.md b/README.md
@@ -44,6 +44,7 @@ To illustrate how `OceanSeaIceModel` works we set up a simulation on a grid with
 using Oceananigans
 using Oceananigans.Units
 using Dates
+using CUDA
 import ClimaOcean
 
 arch = GPU()
diff --git a/docs/Project.toml b/docs/Project.toml
@@ -1,7 +1,7 @@
 [deps]
 CFTime = "179af706-886a-5703-950a-314cd64e0468"
+CUDA = "052768ef-5323-5732-b1bb-66c8b64840ba"
 CairoMakie = "13f3f980-e62b-5c42-98c6-ff1f3baf88f0"
-ClimaOcean = "0376089a-ecfe-4b0e-a64f-9c555d74d754"
 DataDeps = "124859b0-ceae-595e-8997-d05f6a7a8dfe"
 Documenter = "e30172f5-a6a5-5a46-863b-614d45cd2de4"
 DocumenterCitations = "daee34ce-89f3-4625-b898-19384cb65244"
diff --git a/docs/interface_fluxes.md b/docs/interface_fluxes.md
diff --git a/docs/make.jl b/docs/make.jl
@@ -4,6 +4,16 @@ using
   DocumenterCitations,
   Literate
 
+# temporary to enforce Oceananigans to use a specific branch
+using Pkg
+Pkg.add(PackageSpec(
+    name = "Oceananigans",
+    url = "https://github.com/CliMA/Oceananigans.jl",
+    rev = "ss/fix-zstar-bc"
+))
+Pkg.resolve()
+@show Pkg.status()
+
 ENV["DATADEPS_ALWAYS_ACCEPT"] = "true"
 
 bib_filepath = joinpath(dirname(@__FILE__), "climaocean.bib")
@@ -48,7 +58,7 @@ pages = [
 
     "Vertical grids" => "vertical_grids.md",
 
-    # "Interface fluxes" => "interface_fluxes.md",
+    "Interface fluxes" => "interface_fluxes.md",
 
     "Library" => [
         "Contents"       => "library/outline.md",
diff --git a/docs/src/index.md b/docs/src/index.md
@@ -38,6 +38,8 @@ The following script implements a near-global ocean simulation initialized from
 using Oceananigans
 using Oceananigans.Units
 using Dates
+using CUDA
+
 import ClimaOcean
 
 arch = GPU()
diff --git a/examples/ecco_mixed_layer_depth.jl b/examples/ecco_mixed_layer_depth.jl
@@ -71,7 +71,7 @@ fig
 
 # And record a movie
 
-record(fig, "ecco_mld.mp4", 1:Nt-1, framerate=4) do nn
+CairoMakie.record(fig, "ecco_mld.mp4", 1:Nt-1, framerate=4) do nn
     @info "Drawing frame $nn of $Nt..."
     n[] = nn
 end
diff --git a/examples/inspect_JRA55_data.jl b/examples/inspect_JRA55_data.jl
@@ -72,7 +72,7 @@ snapshot_interval = 3hours  # JRE55 time-resolution
 rotation_period = 60days
 rotation_rate = 2π / rotation_period
 
-record(fig, "JRA55_data.mp4", 1:Nt, framerate=16) do nn
+CairoMakie.record(fig, "JRA55_data.mp4", 1:Nt, framerate=16) do nn
     @info nn/Nt
 
     n[] = nn
diff --git a/examples/near_global_ocean_simulation.jl b/examples/near_global_ocean_simulation.jl
@@ -20,6 +20,7 @@ using CairoMakie
 using CFTime
 using Dates
 using Printf
+using CUDA
 
 # ### Grid configuration
 #
@@ -36,6 +37,7 @@ Nz = 40
 
 depth = 6000meters
 z = ExponentialCoordinate(Nz, -depth)
+z = Oceananigans.Grids.MutableVerticalDiscretization(z)
 
 grid = LatitudeLongitudeGrid(arch;
                              size = (Nx, Ny, Nz),
@@ -250,7 +252,7 @@ nothing #hide
 
 # And now we make a movie:
 
-record(fig, "near_global_ocean_surface.mp4", 1:Nt, framerate = 8) do nn
+CairoMakie.record(fig, "near_global_ocean_surface.mp4", 1:Nt, framerate = 8) do nn
     n[] = nn
 end
 nothing #hide
diff --git a/examples/one_degree_simulation.jl b/examples/one_degree_simulation.jl
@@ -15,6 +15,7 @@ using Oceananigans.Units
 using Dates
 using Printf
 using Statistics
+using CUDA
 
 # ### Grid and Bathymetry
 
@@ -27,6 +28,7 @@ Nz = 40
 
 depth = 4000meters
 z = ExponentialCoordinate(Nz, -depth; scale = 0.85*depth)
+z = Oceananigans.Grids.MutableVerticalDiscretization(z)
 underlying_grid = TripolarGrid(arch; size = (Nx, Ny, Nz), halo = (5, 5, 4), z)
 
 # Next, we build bathymetry on this grid, using interpolation passes to smooth the bathymetry.
@@ -51,8 +53,8 @@ grid = ImmersedBoundaryGrid(underlying_grid, GridFittedBottom(bottom_height);
 
 eddy_closure = Oceananigans.TurbulenceClosures.IsopycnalSkewSymmetricDiffusivity(κ_skew=2e3, κ_symmetric=2e3)
 horizontal_viscosity = HorizontalScalarDiffusivity(ν=4000)
-vertical_mixing = Oceananigans.TurbulenceClosures.CATKEVerticalDiffusivity(minimum_tke=1e-6)
-
+vertical_mixing = ClimaOcean.OceanSimulations.default_ocean_closure()
+          
 # ### Ocean simulation
 # Now we bring everything together to construct the ocean simulation.
 # We use a split-explicit timestepping with 70 substeps for the barotropic
@@ -177,9 +179,9 @@ simulation.Δt = 20minutes
 simulation.stop_time = 365days
 run!(simulation)
 
-# ### A pretty movie
+# ### A movie
 #
-# We load the saved output and make a pretty movie of the simulation. First we plot a snapshot:
+# We load the saved output and make a movie of the simulation. First we plot a snapshot:
 using CairoMakie
 
 # We suffix the ocean fields with "o":
@@ -256,7 +258,7 @@ end
 # Finally, we plot a snapshot of the surface speed, temperature, and the turbulent
 # eddy kinetic energy from the CATKE vertical mixing parameterization as well as the
 # sea ice speed and the effective sea ice thickness.
-fig = Figure(size = (1200, 1200))
+fig = Figure(size=(1200, 900))
 
 title = @lift string("Global 1ᵒ ocean simulation after ", prettytime(times[$n] - times[1]))
 
@@ -292,7 +294,7 @@ nothing #hide
 
 # And now a movie:
 
-record(fig, "one_degree_global_ocean_surface.mp4", 1:Nt, framerate = 8) do nn
+CairoMakie.record(fig, "one_degree_global_ocean_surface.mp4", 1:Nt, framerate = 8) do nn
     n[] = nn
 end
 nothing #hide
diff --git a/examples/single_column_os_papa_simulation.jl b/examples/single_column_os_papa_simulation.jl
@@ -322,7 +322,7 @@ Smax = maximum(interior(S))
 Smin = minimum(interior(S))
 xlims!(axSz, Smin - 0.2, Smax + 0.2)
 
-record(fig, "single_column_profiles.mp4", 1:Nt, framerate=24) do nn
+CairoMakie.record(fig, "single_column_profiles.mp4", 1:Nt, framerate=24) do nn
     @info "Drawing frame $nn of $Nt..."
     n[] = nn
 end
diff --git a/experiments/arctic_simulation.jl b/experiments/arctic_simulation.jl
@@ -11,12 +11,11 @@ using ClimaSeaIce.SeaIceThermodynamics: IceWaterThermalEquilibrium
 using Printf
 
 using CUDA
-CUDA.device!(1)
 arch = GPU()
 
 depth = 2000meters
 Nz = 30
-z = ExponentialCoordinate(Nz, depth; scale=depth/3)
+z = ExponentialCoordinate(Nz, -depth; scale=depth/3)
 z = MutableVerticalDiscretization(z)
 
 Nx = 180 # longitudinal direction -> 250 points is about 1.5ᵒ resolution
diff --git a/experiments/one_degree_calibration/distributed_perfect_one_degree_model_calibration.jl b/experiments/one_degree_calibration/distributed_perfect_one_degree_model_calibration.jl
@@ -1,5 +1,4 @@
 using Oceananigans
-using Oceananigans.Architectures: arch_array
 using Oceananigans.Units
 using Oceananigans.Utils: WallTimeInterval
 using Oceananigans.BuoyancyFormulations: buoyancy
diff --git a/experiments/one_degree_calibration/gm_one_degree_model_calibration.jl b/experiments/one_degree_calibration/gm_one_degree_model_calibration.jl
@@ -1,5 +1,4 @@
 using Oceananigans
-using Oceananigans.Architectures: arch_array
 using Oceananigans.Units
 using Oceananigans.Grids: on_architecture
 using Oceananigans.Utils: WallTimeInterval
diff --git a/experiments/one_degree_calibration/inspect_one_degree_near_global_simulation.jl b/experiments/one_degree_calibration/inspect_one_degree_near_global_simulation.jl
@@ -126,7 +126,7 @@ Colorbar(fig[4, 4], hm_N2; vertical=true, tellheight=false, flipaxis=true, label
 
 display(fig)
 
-record(fig, "one_degree_near_global_simulation_$(closure_name).mp4", 1:Nt, framerate=24) do nn
+CairoMakie.record(fig, "one_degree_near_global_simulation_$(closure_name).mp4", 1:Nt, framerate=24) do nn
     n[] = nn
 end
 
diff --git a/experiments/one_degree_calibration/one_degree_near_global_simulation.jl b/experiments/one_degree_calibration/one_degree_near_global_simulation.jl
@@ -10,6 +10,7 @@ using Oceananigans.TurbulenceClosures.CATKEVerticalDiffusivities:
 
 #using ParameterEstimocean.Parameters: closure_with_parameters
 using JLD2
+using CUDA
 
 const years = 365days
 
@@ -147,4 +148,3 @@ simulation.Δt = 20minutes
 run!(simulation)
 
 @info "Simulation took $(prettytime(simulation.run_wall_time))."
-
diff --git a/experiments/one_degree_calibration/perfect_one_degree_model_calibration.jl b/experiments/one_degree_calibration/perfect_one_degree_model_calibration.jl
@@ -1,5 +1,4 @@
 using Oceananigans
-using Oceananigans.Architectures: arch_array
 using Oceananigans.Units
 using Oceananigans.Utils: WallTimeInterval
 using Oceananigans.BuoyancyFormulations: buoyancy
@@ -10,6 +9,7 @@ using ParameterEstimocean.Utils: map_gpus_to_ranks!
 using ParameterEstimocean.Observations: FieldTimeSeriesCollector
 using ParameterEstimocean.Parameters: closure_with_parameters
 using JLD2
+using CUDA
 
 arch = GPU()
 
diff --git a/src/OceanSeaIceModels/InterfaceComputations/interface_states.jl b/src/OceanSeaIceModels/InterfaceComputations/interface_states.jl
@@ -103,7 +103,7 @@ function WaterMoleFraction(FT=Oceananigans.defaults.FloatType)
         magnesium = SalinityConstituent{FT}(24.31, 0.05),
     )
 
-    return SeawaterComposition(water_molar_mass, salinity_constituents)
+    return WaterMoleFraction(water_molar_mass, salinity_constituents)
 end
 
 @inline function compute_water_mole_fraction(wmf::WaterMoleFraction, S)
diff --git a/src/OceanSeaIceModels/InterfaceComputations/similarity_theory_turbulent_fluxes.jl b/src/OceanSeaIceModels/InterfaceComputations/similarity_theory_turbulent_fluxes.jl
@@ -258,7 +258,7 @@ Note that the Monin--Obukhov characteristic length scale is defined
 in terms of ``b_★`` and additionally the Von Karman constant ``ϰ``,
 
 ```math
-L_★ = - u_★² / ϰ b_★ .
+L_★ = u_★² / ϰ b_★ .
 ```
 """
 @inline function buoyancy_scale(θ★, q★, ℂ, 𝒬, g)
diff --git a/src/OceanSeaIceModels/PrescribedAtmospheres.jl b/src/OceanSeaIceModels/PrescribedAtmospheres.jl
@@ -6,6 +6,7 @@ using Oceananigans.Utils: prettysummary, Time
 using Oceananigans.Fields: Center
 using Oceananigans.OutputReaders: FieldTimeSeries, update_field_time_series!, extract_field_time_series
 using Oceananigans.TimeSteppers: Clock, tick!
+using Oceananigans.Simulations: TimeStepWizard
 
 using Adapt
 using Thermodynamics.Parameters: AbstractThermodynamicsParameters
@@ -365,6 +366,8 @@ end
     return nothing
 end
 
+(wizard::TimeStepWizard)(atmos::PrescribedAtmosphere) = Inf
+
 @inline thermodynamics_parameters(atmos::Nothing) = nothing
 @inline thermodynamics_parameters(atmos::PrescribedAtmosphere) = atmos.thermodynamics_parameters
 @inline surface_layer_height(atmos::PrescribedAtmosphere) = atmos.surface_layer_height
diff --git a/src/OceanSeaIceModels/time_step_ocean_sea_ice_model.jl b/src/OceanSeaIceModels/time_step_ocean_sea_ice_model.jl
@@ -7,6 +7,7 @@ using .InterfaceComputations:
 
 using ClimaSeaIce: SeaIceModel, SeaIceThermodynamics
 using Oceananigans.Grids: φnode
+using Oceananigans.Simulations: TimeStepWizard
 
 using Printf
 
@@ -51,3 +52,22 @@ function update_state!(coupled_model::OceanSeaIceModel, callbacks=[]; compute_te
 
     return nothing
 end
+
+function (wizard::TimeStepWizard)(simulation::Simulation{<:OceanSeaIceModel}) 
+    ocean_Δt = wizard(simulation.ocean)
+    
+    sea_ice_Δt = if isnothing(simulation.sea_ice) 
+        Inf 
+    else
+        wizard(simulation.sea_ice)
+    end
+
+    atmosphere_Δt = if isnothing(simulation.atmosphere) 
+        Inf 
+    else
+        wizard(simulation.atmosphere)
+    end
+
+    return min(ocean_Δt, sea_ice_Δt, atmosphere_Δt)
+end
+
