Merge remote-tracking branch 'origin/main' into ss/omip-prototype

Author: simone-silvestri

.buildkite/pipeline.yml

@@ -1,7 +1,7 @@
 agents:
   queue: new-central
   slurm_mem: 8G
-  modules: climacommon/2025_03_18
+  modules: climacommon/2025_07_30
 
 timeout_in_minutes: 1440
 

.github/workflows/ci.yml

@@ -50,7 +50,7 @@ jobs:
         env:
           TEST_GROUP: "downloading"
           ECCO_USERNAME: ${{ secrets.ECCO_USERNAME }} # To download ECCO data from the podaac website
-          ECCO_PASSWORD: ${{ secrets.ECCO_PASSWORD }} # To download ECCO data from the podaac website
+          ECCO_WEBDAV_PASSWORD: ${{ secrets.ECCO_WEBDAV_PASSWORD }} # To download ECCO data from the podaac website
       - uses: julia-actions/julia-processcoverage@v1
       - uses: codecov/codecov-action@v5
         with:
@@ -86,8 +86,8 @@ jobs:
       - uses: julia-actions/julia-runtest@v1
         env:
           TEST_GROUP: "copernicus_downloading"
-          COPERNICUSMARINE_SERVICE_USERNAME: ${{ secrets.COPERNICUSMARINE_SERVICE_USERNAME }} # To download ECCO data from the podaac website
-          COPERNICUSMARINE_SERVICE_PASSWORD: ${{ secrets.COPERNICUSMARINE_SERVICE_PASSWORD }} # To download ECCO data from the podaac website
+          COPERNICUSMARINE_SERVICE_USERNAME: ${{ secrets.COPERNICUSMARINE_SERVICE_USERNAME }}
+          COPERNICUSMARINE_SERVICE_PASSWORD: ${{ secrets.COPERNICUSMARINE_SERVICE_PASSWORD }}
       - uses: julia-actions/julia-processcoverage@v1
       - uses: codecov/codecov-action@v5
         with:
@@ -97,7 +97,7 @@ jobs:
   reactant:
     name: Reactant extension - Julia ${{ matrix.version }} - ${{ matrix.os }} - ${{ matrix.arch }} - ${{ github.event_name }}
     runs-on: ${{ matrix.os }}
-    timeout-minutes: 60
+    timeout-minutes: 80
     strategy:
       fail-fast: false
       matrix:
@@ -128,3 +128,4 @@ jobs:
         with:
           files: lcov.info
           token: ${{ secrets.CODECOV_TOKEN }}
+          

Project.toml

@@ -44,7 +44,7 @@ ClimaOceanReactantExt = "Reactant"
 Adapt = "4"
 CFTime = "0.1, 0.2"
 CUDA = "4, 5"
-ClimaSeaIce = "0.3.3"
+ClimaSeaIce = "0.3.5"
 CondaPkg = "0.2.28"
 CubicSplines = "0.2"
 DataDeps = "0.7"
@@ -55,7 +55,7 @@ JLD2 = "0.4, 0.5"
 KernelAbstractions = "0.9"
 MPI = "0.20"
 NCDatasets = "0.12, 0.13, 0.14"
-Oceananigans = "0.97.4"
+Oceananigans = "0.97.6"
 OffsetArrays = "1.14"
 PrecompileTools = "1"
 PythonCall = "0.9"
@@ -65,7 +65,7 @@ SeawaterPolynomials = "0.3.5"
 StaticArrays = "1"
 Statistics = "1.9"
 SurfaceFluxes = "0.11, 0.12"
-Thermodynamics = "0.12"
+Thermodynamics = "0.12, 0.13"
 ZipFile = "0.10"
 julia = "1.10"
 

examples/near_global_ocean_simulation.jl

@@ -105,7 +105,8 @@ radiation = Radiation(arch)
 # The number of snapshots that are loaded into memory is determined by
 # the `backend`. Here, we load 41 snapshots at a time into memory.
 
-atmosphere = JRA55PrescribedAtmosphere(arch; backend=JRA55NetCDFBackend(41))
+atmosphere = JRA55PrescribedAtmosphere(arch; backend = JRA55NetCDFBackend(41),
+                                       include_rivers_and_icebergs = false)
 
 # ## The coupled simulation
 

examples/one_degree_simulation.jl

@@ -95,7 +95,8 @@ set!(seaice.model, h=ecco_sea_ice_thickness, ℵ=ecco_sea_ice_concentration)
 
 # We force the simulation with a JRA55-do atmospheric reanalysis.
 radiation  = Radiation(arch)
-atmosphere = JRA55PrescribedAtmosphere(arch; backend=JRA55NetCDFBackend(80))
+atmosphere = JRA55PrescribedAtmosphere(arch; backend=JRA55NetCDFBackend(80),
+                                       include_rivers_and_icebergs = false)
 
 # ### Coupled simulation
 

src/DataWrangling/DataWrangling.jl

@@ -147,24 +147,27 @@ Arguments
 
 !!! info "Credential setup requirements for ECCO datasets"
 
-    For ECCO datasets, the data download requires a username and password to be provided in
-    the `ECCO_USERNAME` and `ECCO_PASSWORD` environment variables respectively. This can be
+    For ECCO datasets, the data download requires "WebDAV/Programmatic API" credentials from
+    NASA's Earthdrive. The WebDAV/Programmatic API username and password need to be provided in
+    the `ECCO_USERNAME` and `ECCO_WEBDAV_PASSWORD` environment variables respectively. This can be
     done by exporting the environment variables in the shell before running the script, or by
     launching julia with
 
     ```
-    ECCO_USERNAME=myusername ECCO_PASSWORD=mypassword julia
+    ECCO_USERNAME=myusername ECCO_WEBDAV_PASSWORD=mypassword julia
     ```
 
     or by invoking
 
     ```julia
     julia> ENV["ECCO_USERNAME"] = "myusername"
 
-    julia> ENV["ECCO_PASSWORD"] = "mypassword"
+    julia> ENV["ECCO_WEBDAV_PASSWORD"] = "mypassword"
     ```
 
-    within julia.
+    within julia. More detailed instructions for obtaining WebDAV credentials are at:
+
+        https://github.com/CliMA/ClimaOcean.jl/blob/main/src/DataWrangling/ECCO/README.md
 """
 function download_dataset end # methods specific to datasets are added within each dataset module
 function inpainted_metadata_path end

src/DataWrangling/ECCO/ECCO.jl

@@ -257,7 +257,7 @@ end
 
 function download_dataset(metadata::ECCOMetadata)
     username = get(ENV, "ECCO_USERNAME", nothing)
-    password = get(ENV, "ECCO_PASSWORD", nothing)
+    password = get(ENV, "ECCO_WEBDAV_PASSWORD", nothing)
     dir = metadata.dir
 
     # Create a temporary directory to store the .netrc file
@@ -276,14 +276,14 @@ function download_dataset(metadata::ECCOMetadata)
             if !isfile(filepath)
                 instructions_msg = "\n See ClimaOcean.jl/src/DataWrangling/ECCO/README.md for instructions."
                 if isnothing(username)
-                    msg = "Could not find the ECCO_PASSWORD environment variable. \
+                    msg = "Could not find the ECCO_USERNAME environment variable. \
                             See ClimaOcean.jl/src/DataWrangling/ECCO/README.md for instructions on obtaining \
-                            and setting your ECCO_USERNAME and ECCO_PASSWORD." * instructions_msg
+                            and setting your ECCO_USERNAME and ECCO_WEBDAV_PASSWORD." * instructions_msg
                     throw(ArgumentError(msg))
                 elseif isnothing(password)
-                    msg = "Could not find the ECCO_PASSWORD environment variable. \
+                    msg = "Could not find the ECCO_WEBDAV_PASSWORD environment variable. \
                             See ClimaOcean.jl/src/DataWrangling/ECCO/README.md for instructions on obtaining \
-                            and setting your ECCO_USERNAME and ECCO_PASSWORD." * instructions_msg
+                            and setting your ECCO_USERNAME and ECCO_WEBDAV_PASSWORD." * instructions_msg
                     throw(ArgumentError(msg))
                 end
                 @info "Downloading ECCO data: $(metadatum.name) in $(metadatum.dir)..."

src/DataWrangling/ECCO/README.md

@@ -1,6 +1,6 @@
-# Setting `ECCO_USERNAME` and `ECCO_PASSWORD` environment variables for downloading ECCO datasets
+# Setting `ECCO_USERNAME` and `ECCO_WEBDAV_PASSWORD` environment variables for downloading ECCO datasets
 
-The first step is to find the username and password for your "programmatic API" credentials on NASA's Earthdrive.
+The first step is to find the username and password for your "WebDAV/Programmatic API" credentials on NASA's Earthdrive.
 For this you have to either login or make an account via the "EARTHDATA login":
 
 > https://urs.earthdata.nasa.gov
@@ -13,19 +13,19 @@ This should produce a screen similar to the following:
 
 ![image](https://github.com/user-attachments/assets/490d9098-aece-4e9c-82d7-3ec86e833347)
 
-showing your Programmatic API credentials -- except in place of the black boxes that say `your_username` and `cRaZYpASSwORD`,
+showing your WebDAV/Programmatic API credentials -- except in place of the black boxes that say `your_username` and `cRaZYpASSwORD`,
 you should see _your_ username and password.
-Copy the content of `Username:` to the environment variable `ECCO_USERNAME` and the content of `Password` to `ECCO_PASSWORD`,
+Copy the content of `Username:` to the environment variable `ECCO_USERNAME` and the content of `Password` to `ECCO_WEBDAV_PASSWORD`,
 either in a file:
 
 ```bash
 export ECCO_USERNAME=your_username
-export ECCO_PASSWORD=cRaZYpASSwORD
+export ECCO_WEBDAV_PASSWORD=cRaZYpASSwORD
 ```
 
-or within Julia by writing
+or within Julia by
 
 ```julia
 ENV["ECCO_USERNAME"] = "your_username"
-ENV["ECCO_PASSWORD"] = "cRaZYpASSwORD"
+ENV["ECCO_WEBDAV_PASSWORD"] = "cRaZYpASSwORD"
 ```

src/OceanSeaIceModels/PrescribedAtmospheres.jl

@@ -11,7 +11,7 @@ using Oceananigans.Simulations: TimeStepWizard
 using Adapt
 using Thermodynamics.Parameters: AbstractThermodynamicsParameters
 
-import Oceananigans.TimeSteppers: time_step!
+import Oceananigans.TimeSteppers: time_step!, update_state!
 
 import Thermodynamics.Parameters:
     gas_constant,   #
@@ -353,15 +353,21 @@ function default_atmosphere_pressure(grid, times)
     return pa
 end
 
-@inline function time_step!(atmos::PrescribedAtmosphere, Δt)
-    tick!(atmos.clock, Δt)
 
+@inline function update_state!(atmos::PrescribedAtmosphere)
     time = Time(atmos.clock.time)
     ftses = extract_field_time_series(atmos)
 
     for fts in ftses
         update_field_time_series!(fts, time)
     end
+    return nothing
+end
+
+@inline function time_step!(atmos::PrescribedAtmosphere, Δt)
+    tick!(atmos.clock, Δt)
+
+    update_state!(atmos)
 
     return nothing
 end

src/OceanSimulations/ocean_simulation.jl

@@ -76,9 +76,6 @@ function default_free_surface(grid::DistributedGrid;
     return free_surface
 end
 
-default_vertical_coordinate(grid) = Oceananigans.Models.ZCoordinate()
-default_vertical_coordinate(::MutableGridOfSomeKind) = Oceananigans.Models.ZStar()
-
 function default_ocean_closure(FT=Oceananigans.defaults.FloatType)
     mixing_length = CATKEMixingLength(Cᵇ=0.01)
     turbulent_kinetic_energy_equation = CATKEEquation(Cᵂϵ=1.0)
@@ -116,7 +113,6 @@ end
                      tracer_advection = WENO(order=7),
                      equation_of_state = TEOS10EquationOfState(; reference_density),
                      boundary_conditions::NamedTuple = NamedTuple(),
-                     vertical_coordinate = default_vertical_coordinate(grid),
                      radiative_forcing = default_radiative_forcing(grid),
                      warn = true,
                      verbose = false)
@@ -140,7 +136,6 @@ function ocean_simulation(grid;
                           tracer_advection = WENO(order=7),
                           equation_of_state = TEOS10EquationOfState(; reference_density),
                           boundary_conditions::NamedTuple = NamedTuple(),
-                          vertical_coordinate = default_vertical_coordinate(grid),
                           radiative_forcing = default_radiative_forcing(grid),
                           warn = true,
                           verbose = false)
@@ -263,8 +258,7 @@ function ocean_simulation(grid;
                                               free_surface,
                                               coriolis,
                                               forcing,
-                                              boundary_conditions,
-                                              vertical_coordinate)
+                                              boundary_conditions)
 
     ocean = Simulation(ocean_model; Δt, verbose)