Use zstar in examples (#573)

* Update one_degree_simulation.jl

* Update one_degree_simulation.jl

* try without implicit solver

* Update Project.toml

* Update near_global_ocean_simulation.jl

* Update one_degree_simulation.jl

* changes

* try it in both

* adding the correct zstar branch

* added CUDA

* Update pipeline.yml

* revert CUDA

* enforce using a specific branch

* Delete Manifest.toml

* Update Project.toml

* enforce using Oceananigans#ss/fix-zstar-bc

* drop geebrish

* enforce using Oceananigans#ss/fix-zstar-bc

* use julia v1.10.10

* precompile again

* use julia v1.10.10

* first oceananigans; then develop

* add CUDA

* using CUDA + record from Makie not CUDA

* Update one_degree_simulation.jl

* some changes

* add more stuff

* improvements

* improve

* add an equatorial single column

* possibly remove a bug?

* Update atmosphere_sea_ice_fluxes.jl

* Update atmosphere_sea_ice_fluxes.jl

* adding the correct Manifest

* remove equatorial single column

* remove manifest

* revert

* token

* Revert "token"

This reverts commit 4015bf4.

* code alignment

* drop specific branch

* drop specific branch

* fix ExponentialCoordinate args

* disambiguate ExponentialCoordinate

* drop cuda compat

* disambiguate ExponentialCoordinate

---------

Co-authored-by: Navid C. Constantinou <[email protected]>

Author: simone-silvestri

.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
@@ -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.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
 

examples/near_global_ocean_simulation.jl

@@ -38,6 +38,7 @@ Nz = 40
 
 depth = 6000meters
 z = ExponentialCoordinate(Nz, -depth, 0)
+z = Oceananigans.Grids.MutableVerticalDiscretization(z)
 
 grid = LatitudeLongitudeGrid(arch;
                              size = (Nx, Ny, Nz),

examples/one_degree_simulation.jl

@@ -28,6 +28,7 @@ Nz = 40
 
 depth = 4000meters
 z = ExponentialCoordinate(Nz, -depth, 0; 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.
@@ -51,7 +52,7 @@ grid = ImmersedBoundaryGrid(underlying_grid, GridFittedBottom(bottom_height);
 # parameterization. We also include some explicit horizontal diffusivity.
 
 eddy_closure = Oceananigans.TurbulenceClosures.IsopycnalSkewSymmetricDiffusivity(κ_skew=2e3, κ_symmetric=2e3)
-vertical_mixing = Oceananigans.TurbulenceClosures.CATKEVerticalDiffusivity(minimum_tke=1e-6)
+vertical_mixing = ClimaOcean.OceanSimulations.default_ocean_closure()
 horizontal_viscosity = HorizontalScalarDiffusivity(ν=4000)
 
 # ### Ocean simulation

experiments/arctic_simulation.jl

@@ -15,7 +15,7 @@ arch = GPU()
 
 depth = 2000meters
 Nz = 30
-z = ExponentialCoordinate(Nz, depth, 0; scale=depth/3)
+z = ExponentialCoordinate(Nz, -depth, 0; scale=depth/3)
 z = MutableVerticalDiscretization(z)
 
 Nx = 180 # longitudinal direction -> 250 points is about 1.5ᵒ resolution

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))."
-

experiments/one_degree_calibration/perfect_one_degree_model_calibration.jl

@@ -9,6 +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()
 

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)