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Fix docs + examples (#466)
* fix one issue * one bugfix * using Dates * another bugfix * Clean up one degree simulation (#460) * Update one_degree_simulation.jl * Update make.jl * Update one_degree_simulation.jl * One degree example enhancement (#362) * drop ActiveCellEnstrophyConserving * bump patch release * fix typo + no x/y labels in figs * Update one_degree_simulation.jl * hotfix to change * Fixes docs that don't build on `main` (#388) * infer FT in SimilarityTheoryFluxes from ocean_grid * homogenize compats * drop ClimaOcean * better continents plot * fix papa * minor text formatting * code alignment + spaces, not tab * Implement sea-ice ocean stress (#453) * add sea-ice ocean stress * last index * add this * add a clock * add the arctic * add the metadatum * thos works! * bugfix * Update experiments/arctic_simulation.jl * Update src/OceanSeaIceModels/InterfaceComputations/sea_ice_ocean_fluxes.jl * add a test * remember the allowscalar * more testing * fix test * fix tests * Update test/test_surface_fluxes.jl * Update test/test_surface_fluxes.jl --------- Co-authored-by: Navid C. Constantinou <[email protected]> --------- Co-authored-by: Simone Silvestri <[email protected]> * back to zstar * maybe zstar has too many parameters * updates * dont worry about skipping passes (its buggy) * niceness * Update one_degree_simulation.jl * Update examples_build.yml * tweak one degree * try without restoring * Update one_degree_simulation.jl * Update one_degree_simulation.jl * point buildkite to tartarus * clean up * update * Update examples/one_degree_simulation.jl * use the right julia * minor * fix * reenable plotting * rm duplicate visible devices * Update make.jl * add convenience first_date(dataset) * fixes in docs * fixes in docs * clarify linear tapered polar mask * put restoring back * fix * rm u-forcing * Update examples/one_degree_simulation.jl * fix bug from merge main * go back to 1deg * 100 levels * Update one_degree_simulation.jl * Update metadata.jl * Update one_degree_simulation.jl * Update one_degree_simulation.jl * Update one_degree_simulation.jl * Update one_degree_simulation.jl * Update one_degree_simulation.jl * Update one_degree_simulation.jl * workin on example * seems to work * rm arctic night * comment back in animation * run 1/4 degree on GPU * Update make.jl * Update metadata.jl * fix docs rendering * undo changes to Bathymetry.jl since tests were failing --------- Co-authored-by: Simone Silvestri <[email protected]> Co-authored-by: Navid C. Constantinou <[email protected]>
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‎.buildkite/examples_build.yml‎

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agents:
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queue: new-central
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slurm_mem: 8G
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modules: climacommon/2024_10_10
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slurm_time: 48:00:00
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env:
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JULIA_LOAD_PATH: "${JULIA_LOAD_PATH}:${BUILDKITE_BUILD_CHECKOUT_PATH}/.buildkite"
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OPENBLAS_NUM_THREADS: 1
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OMPI_MCA_opal_warn_on_missing_libcuda: 0
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JULIA_VERSION: "1.10.9"
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JULIA_MINOR_VERSION: "1.10"
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TARTARUS_HOME: "/storage5/buildkite-agent"
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JULIA_PKG_SERVER_REGISTRY_PREFERENCE: eager
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JULIA_NUM_PRECOMPILE_TASKS: 8
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JULIA_NUM_THREADS: 8
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CUDA_VISIBLE_DEVICES: "2" # Device for building ClimaOcean docs
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steps:
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- label: "initialize"
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key: "init"
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env:
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JULIA_DEPOT_PATH: "$TARTARUS_HOME/.julia-$BUILDKITE_BUILD_NUMBER"
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TEST_GROUP: "init"
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JULIA_BINDIR: "$TARTARUS_HOME/julia-$JULIA_VERSION/bin"
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TMPDIR: "$TARTARUS_HOME/tmp"
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command:
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- "echo '--- Instantiate project'"
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- "julia --project -e 'using Pkg; Pkg.instantiate(; verbose=true); Pkg.precompile(; strict=true)'"
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- "$TARTARUS_HOME/julia-$JULIA_VERSION/bin/julia --color=yes -O0 --project -e 'using Pkg; Pkg.instantiate(; verbose=true); Pkg.precompile(; strict=true)'"
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# force the initialization of the CUDA runtime as it is lazily loaded by default
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- "julia --project -e 'using CUDA; CUDA.precompile_runtime()'"
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- "$TARTARUS_HOME/julia-$JULIA_VERSION/bin/julia --color=yes -O0 --project -e 'using CUDA; CUDA.precompile_runtime()'"
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agents:
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slurm_mem: 120G
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slurm_gpus: 1
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slurm_cpus_per_task: 8
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queue: ClimaOcean-docs
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- wait
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- label: "Run documentation"
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key: "build_documentation"
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commands:
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- "julia --color=yes --project=docs/ -e 'using Pkg; Pkg.instantiate(); Pkg.develop(PackageSpec(path=pwd()))'"
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- "julia --color=yes --project=docs/ docs/make.jl"
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- "$TARTARUS_HOME/julia-$JULIA_VERSION/bin/julia --color=yes -O0 --project=docs/ -e 'using Pkg; Pkg.develop(PackageSpec(path=pwd())); Pkg.instantiate()'"
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- "$TARTARUS_HOME/julia-$JULIA_VERSION/bin/julia --color=yes -O0 --project=docs/ docs/make.jl"
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agents:
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slurm_mem: 120G
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slurm_gpus: 1
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slurm_cpus_per_task: 8
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slurm_ntasks: 1
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slurm_gpus_per_task: 1
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slurm_time: 48:00:00
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queue: ClimaOcean-docs
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env:
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TMPDIR: "$TARTARUS_HOME/tmp"
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JULIA_DEPOT_PATH: "$TARTARUS_HOME/.julia-$BUILDKITE_BUILD_NUMBER"
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JULIA_DEBUG: "Documenter"
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# This environment variable is needed to avoid SSL verification errors when Downloads.jl
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# tries to download the bathymetry data. It should not be required so we need to fix our certificates

‎docs/make.jl‎

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@@ -14,8 +14,8 @@ const OUTPUT_DIR = joinpath(@__DIR__, "src/literated")
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to_be_literated = [
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# "ecco_inspect_temperature_salinity.jl",
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"generate_bathymetry.jl",
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"generate_surface_fluxes.jl",
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# "generate_bathymetry.jl",
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# "generate_surface_fluxes.jl",
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"single_column_os_papa_simulation.jl",
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"one_degree_simulation.jl",
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# "mediterranean_simulation_with_ecco_restoring.jl",
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"Examples" => [
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# "Inspect ECCO2 data" => "literated/ecco_inspect_temperature_salinity.md",
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"Generate bathymetry" => "literated/generate_bathymetry.md",
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"Surface fluxes" => "literated/generate_surface_fluxes.md",
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# "Generate bathymetry" => "literated/generate_bathymetry.md",
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# "Surface fluxes" => "literated/generate_surface_fluxes.md",
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"Single-column simulation" => "literated/single_column_os_papa_simulation.md",
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# "Mediterranean simulation with ECCO restoring" => "literated/mediterranean_simulation_with_ecco_restoring.md",
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"One-degree Ocean simulation" => "literated/one_degree_simulation.md",

‎docs/src/library/internals.md‎

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Public = false
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```
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## InitialConditions
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```@autodocs
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Public = false
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```
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## EN4
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```@autodocs
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Modules = [ClimaOcean.EN4]
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Public = false
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```
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## JRA55
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```@autodocs
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```@autodocs
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Modules = [ClimaOcean.VerticalGrids]
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Private = false
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Public = false
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```
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## OceanSeaIceModels
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```@autodocs
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Modules = [ClimaOcean.OceanSeaIceModels]
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Private = false
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Public = false
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```
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## CrossRealmFluxes
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## InterfaceComputations
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```@autodocs
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Modules = [ClimaOcean.OceanSeaIceModels.CrossRealmFluxes]
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Private = false
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Modules = [ClimaOcean.OceanSeaIceModels.InterfaceComputations]
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Public = false
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```

‎docs/src/library/public.md‎

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Private = false
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```
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## EN4
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```@autodocs
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Modules = [ClimaOcean.EN4]
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Private = false
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```
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## JRA55
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```@autodocs
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Modules = [ClimaOcean.Bathymetry]
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Private = false
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```
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## VerticalGrids
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```@autodocs
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Modules = [ClimaOcean.VerticalGrids]
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Private = false
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```
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## OceanSeaIceModels
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```@autodocs
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Modules = [ClimaOcean.OceanSeaIceModels]
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Private = false
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```
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## InterfaceComputations
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```@autodocs
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Modules = [ClimaOcean.OceanSeaIceModels.InterfaceComputations]
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Private = false
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```

‎examples/arctic_night.jl‎

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‎examples/generate_surface_fluxes.jl‎

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using ClimaOcean.JRA55
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using ClimaOcean.OceanSimulations
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using Oceananigans
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using Dates
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using CairoMakie
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# # Computing fluxes on the ECCO2 grid
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# We visualize the bottom height of the ECCO grid using CairoMakie.
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fig = Figure()
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ax = Axis(fig[1, 1])
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heatmap!(ax, interior(grid.immersed_boundary.bottom_height, :, :, 1))
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save("ECCO_continents.png", fig) #hide
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fig, ax, hm = heatmap(grid.immersed_boundary.bottom_height)
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Colorbar(fig[1, 2], hm, height = Relative(3/4), label = "Depth (m)")
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save("ECCO_continents.png", fig)
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# ![](ECCO_continents.png)
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coupled_model = OceanSeaIceModel(ocean; atmosphere, radiation=Radiation(eltype))
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# # Now that the surface fluxes are computed, we can extract and visualize them.
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# # The turbulent fluxes are stored in `coupled_modelinterfaces.atmosphere_ocean_interface.fluxes`.
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# Now that the surface fluxes are computed, we can extract and visualize them.
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# The turbulent fluxes are stored in `coupled_model.interfaces.atmosphere_ocean_interface.fluxes`.
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fluxes = coupled_model.interfaces.atmosphere_ocean_interface.fluxes
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fluxes = coupled_model.interfaces.atmosphere_ocean_interface.fluxes
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λ, φ, z = nodes(fluxes.sensible_heat)
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fig = Figure(size = (800, 800), fontsize = 15)
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ax = Axis(fig[3, 1], title = "Water vapor flux (kg m⁻² s⁻¹)", xlabel = "Longitude", ylabel = "Latitude")
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heatmap!(ax, λ, φ, interior(fluxes.water_vapor, :, :, 1); colormap = :bwr)
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save("fluxes.png", fig)
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save("surface_fluxes.png", fig)
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# ![](fluxes.png)
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# ![](surface_fluxes.png)

‎examples/idealized_single_column_simulation.jl‎

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using Oceananigans
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using Oceananigans.Units
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using SeawaterPolynomials
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using Dates
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# Ocean state parameters
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T₀ = 0 # Surface temperature, ᵒC

‎examples/near_global_ocean_simulation.jl‎

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# # Near-global ocean simulation
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#
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# This example sets up and runs a near-global ocean simulation using the Oceananigans.jl and
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# ClimaOcean.jl. The simulation covers latitudes from 75°S to 75°N with a horizontal
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# ClimaOcean.jl. The simulation covers latitudes from 75°S to 75°N, with a horizontal
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# resolution of 1/4 degree and 40 vertical levels.
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#
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# The simulation's results are visualized with the CairoMakie.jl package.
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# Finally, we specify the architecture for the simulation, which in this case is a GPU.
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arch = GPU()
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Nx = 1440
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Ny = 600
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Nz = 40
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#
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# We use `regrid_bathymetry` to derive the bottom height from ETOPO1 data.
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# To smooth the interpolated data we use 5 interpolation passes. We also fill in
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# (i) all the minor enclosed basins except the 3 largest `major_basins`, as well as
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# (ii) regions that are shallower than `minimum_depth`.
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# * all the minor enclosed basins except the 3 largest `major_basins`, as well as
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# * regions that are shallower than `minimum_depth`.
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bottom_height = regrid_bathymetry(grid;
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minimum_depth = 10meters,

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