(0.92.0) Make RungeKutta3 the default time-stepper for Nonhydrostatic…

…Model (#3580) * Make RK3 the default time-stepper for NonhydrostaticModel * Change regression tests to use AB2 * Fix up time stepping tests * Fix up forcings tests * Fix more tests * Fix docstrings * Fix datetime test but thats weird * Fix doctest for seawater density * update docstring * Fix docstrings * Last docstring? famous last words * Test AB2 for date tests now * Use AB2 for time-stepping tests * Update time stepper tests * Use AB2 for netcdf tests * Update NetCDF test to AB2 * Update another NetCDF test to AB2 * Bump to new version * Just cosmetic stuff * More cosmetic upgrades * oops * FT -> Ft * Fix eulers * Update pipeline.yml --------- Co-authored-by: Navid C. Constantinou <navidcy@users.noreply.github.com>
CliMA · Sep 29, 2024 · 41209a2 · 41209a2 · glwagner · Sep 29, 2024
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diff --git a/.buildkite/pipeline.yml b/.buildkite/pipeline.yml
@@ -21,6 +21,10 @@ steps:
     agents:
       queue: Oceananigans
       architecture: GPU
+    retry:
+      automatic:
+        - exit_status: 1      
+          limit: 1
 
   - label: "🏕️ initialize cpu environment"
     key: "init_cpu"
@@ -38,6 +42,10 @@ steps:
     agents:
       queue: Oceananigans
       architecture: CPU
+    retry:
+      automatic:
+        - exit_status: 1      
+          limit: 1
 
 #####
 ##### Unit tests

diff --git a/Project.toml b/Project.toml
@@ -1,7 +1,7 @@
 name = "Oceananigans"
 uuid = "9e8cae18-63c1-5223-a75c-80ca9d6e9a09"
 authors = ["Climate Modeling Alliance and contributors"]
-version = "0.91.15"
+version = "0.92.0"
 
 [deps]
 Adapt = "79e6a3ab-5dfb-504d-930d-738a2a938a0e"

diff --git a/docs/src/model_setup/boundary_conditions.md b/docs/src/model_setup/boundary_conditions.md
@@ -42,7 +42,7 @@ julia> no_slip_field_bcs = FieldBoundaryConditions(no_slip_bc);
 julia> model = NonhydrostaticModel(; grid, boundary_conditions=(u=no_slip_field_bcs, v=no_slip_field_bcs, w=no_slip_field_bcs))
 NonhydrostaticModel{CPU, RectilinearGrid}(time = 0 seconds, iteration = 0)
 ├── grid: 16×16×16 RectilinearGrid{Float64, Periodic, Bounded, Bounded} on CPU with 3×3×3 halo
-├── timestepper: QuasiAdamsBashforth2TimeStepper
+├── timestepper: RungeKutta3TimeStepper
 ├── advection scheme: Centered reconstruction order 2
 ├── tracers: ()
 ├── closure: Nothing
@@ -404,7 +404,7 @@ julia> c_bcs = FieldBoundaryConditions(top = ValueBoundaryCondition(20.0),
 julia> model = NonhydrostaticModel(grid=grid, boundary_conditions=(u=u_bcs, c=c_bcs), tracers=:c)
 NonhydrostaticModel{CPU, RectilinearGrid}(time = 0 seconds, iteration = 0)
 ├── grid: 16×16×16 RectilinearGrid{Float64, Periodic, Periodic, Bounded} on CPU with 3×3×3 halo
-├── timestepper: QuasiAdamsBashforth2TimeStepper
+├── timestepper: RungeKutta3TimeStepper
 ├── advection scheme: Centered reconstruction order 2
 ├── tracers: c
 ├── closure: Nothing

diff --git a/docs/src/model_setup/buoyancy_and_equation_of_state.md b/docs/src/model_setup/buoyancy_and_equation_of_state.md
@@ -28,7 +28,7 @@ julia> grid = RectilinearGrid(size=(8, 8, 8), extent=(1, 1, 1));
 julia> model = NonhydrostaticModel(; grid, buoyancy=nothing)
 NonhydrostaticModel{CPU, RectilinearGrid}(time = 0 seconds, iteration = 0)
 ├── grid: 8×8×8 RectilinearGrid{Float64, Periodic, Periodic, Bounded} on CPU with 3×3×3 halo
-├── timestepper: QuasiAdamsBashforth2TimeStepper
+├── timestepper: RungeKutta3TimeStepper
 ├── advection scheme: Centered reconstruction order 2
 ├── tracers: ()
 ├── closure: Nothing
@@ -43,7 +43,7 @@ The option `buoyancy = nothing` is the default for [`NonhydrostaticModel`](@ref)
 julia> model = NonhydrostaticModel(; grid)
 NonhydrostaticModel{CPU, RectilinearGrid}(time = 0 seconds, iteration = 0)
 ├── grid: 8×8×8 RectilinearGrid{Float64, Periodic, Periodic, Bounded} on CPU with 3×3×3 halo
-├── timestepper: QuasiAdamsBashforth2TimeStepper
+├── timestepper: RungeKutta3TimeStepper
 ├── advection scheme: Centered reconstruction order 2
 ├── tracers: ()
 ├── closure: Nothing
@@ -77,7 +77,7 @@ a buoyancy tracer by including `:b` in `tracers` and specifying  `buoyancy = Buo
 julia> model = NonhydrostaticModel(; grid, buoyancy=BuoyancyTracer(), tracers=:b)
 NonhydrostaticModel{CPU, RectilinearGrid}(time = 0 seconds, iteration = 0)
 ├── grid: 8×8×8 RectilinearGrid{Float64, Periodic, Periodic, Bounded} on CPU with 3×3×3 halo
-├── timestepper: QuasiAdamsBashforth2TimeStepper
+├── timestepper: RungeKutta3TimeStepper
 ├── advection scheme: Centered reconstruction order 2
 ├── tracers: b
 ├── closure: Nothing
@@ -118,7 +118,7 @@ S.I. units ``\text{m}\,\text{s}^{-2}``) and requires to add `:T` and `:S` as tra
 julia> model = NonhydrostaticModel(; grid, buoyancy=SeawaterBuoyancy(), tracers=(:T, :S))
 NonhydrostaticModel{CPU, RectilinearGrid}(time = 0 seconds, iteration = 0)
 ├── grid: 8×8×8 RectilinearGrid{Float64, Periodic, Periodic, Bounded} on CPU with 3×3×3 halo
-├── timestepper: QuasiAdamsBashforth2TimeStepper
+├── timestepper: RungeKutta3TimeStepper
 ├── advection scheme: Centered reconstruction order 2
 ├── tracers: (T, S)
 ├── closure: Nothing
@@ -157,7 +157,7 @@ SeawaterBuoyancy{Float64}:
 julia> model = NonhydrostaticModel(; grid, buoyancy, tracers=(:T, :S))
 NonhydrostaticModel{CPU, RectilinearGrid}(time = 0 seconds, iteration = 0)
 ├── grid: 8×8×8 RectilinearGrid{Float64, Periodic, Periodic, Bounded} on CPU with 3×3×3 halo
-├── timestepper: QuasiAdamsBashforth2TimeStepper
+├── timestepper: RungeKutta3TimeStepper
 ├── advection scheme: Centered reconstruction order 2
 ├── tracers: (T, S)
 ├── closure: Nothing
@@ -238,7 +238,7 @@ Buoyancy:
 julia> model = NonhydrostaticModel(; grid, buoyancy, tracers=:b)
 NonhydrostaticModel{CPU, RectilinearGrid}(time = 0 seconds, iteration = 0)
 ├── grid: 8×8×8 RectilinearGrid{Float64, Periodic, Periodic, Bounded} on CPU with 3×3×3 halo
-├── timestepper: QuasiAdamsBashforth2TimeStepper
+├── timestepper: RungeKutta3TimeStepper
 ├── advection scheme: Centered reconstruction order 2
 ├── tracers: b
 ├── closure: Nothing

diff --git a/docs/src/model_setup/lagrangian_particles.md b/docs/src/model_setup/lagrangian_particles.md
@@ -43,7 +43,7 @@ model = NonhydrostaticModel(grid=grid, particles=lagrangian_particles)
 # output
 NonhydrostaticModel{CPU, RectilinearGrid}(time = 0 seconds, iteration = 0)
 ├── grid: 10×10×10 RectilinearGrid{Float64, Periodic, Periodic, Bounded} on CPU with 3×3×3 halo
-├── timestepper: QuasiAdamsBashforth2TimeStepper
+├── timestepper: RungeKutta3TimeStepper
 ├── advection scheme: Centered reconstruction order 2
 ├── tracers: ()
 ├── closure: Nothing

diff --git a/docs/src/model_setup/tracers.md b/docs/src/model_setup/tracers.md
@@ -15,7 +15,7 @@ julia> grid = RectilinearGrid(size=(16, 16, 16), extent=(1, 1, 1));
 julia> model = NonhydrostaticModel(; grid)
 NonhydrostaticModel{CPU, RectilinearGrid}(time = 0 seconds, iteration = 0)
 ├── grid: 16×16×16 RectilinearGrid{Float64, Periodic, Periodic, Bounded} on CPU with 3×3×3 halo
-├── timestepper: QuasiAdamsBashforth2TimeStepper
+├── timestepper: RungeKutta3TimeStepper
 ├── advection scheme: Centered reconstruction order 2
 ├── tracers: ()
 ├── closure: Nothing
@@ -30,7 +30,7 @@ For example, to add conservative temperature `T` and absolute salinity `S`:
 julia> model = NonhydrostaticModel(; grid, tracers=(:T, :S))
 NonhydrostaticModel{CPU, RectilinearGrid}(time = 0 seconds, iteration = 0)
 ├── grid: 16×16×16 RectilinearGrid{Float64, Periodic, Periodic, Bounded} on CPU with 3×3×3 halo
-├── timestepper: QuasiAdamsBashforth2TimeStepper
+├── timestepper: RungeKutta3TimeStepper
 ├── advection scheme: Centered reconstruction order 2
 ├── tracers: (T, S)
 ├── closure: Nothing
@@ -65,7 +65,7 @@ An arbitrary number of tracers may be simulated. For example, to simulate
 julia> model = NonhydrostaticModel(; grid, tracers=(:T, :S, :C₁, :CO₂, :nitrogen))
 NonhydrostaticModel{CPU, RectilinearGrid}(time = 0 seconds, iteration = 0)
 ├── grid: 16×16×16 RectilinearGrid{Float64, Periodic, Periodic, Bounded} on CPU with 3×3×3 halo
-├── timestepper: QuasiAdamsBashforth2TimeStepper
+├── timestepper: RungeKutta3TimeStepper
 ├── advection scheme: Centered reconstruction order 2
 ├── tracers: (T, S, C₁, CO₂, nitrogen)
 ├── closure: Nothing

diff --git a/docs/src/simulation_tips.md b/docs/src/simulation_tips.md
@@ -232,7 +232,7 @@ julia> grid = RectilinearGrid(GPU(); size=(1, 1, 1), extent=(1, 1, 1), halo=(1,
 julia> model = NonhydrostaticModel(; grid)
 NonhydrostaticModel{GPU, RectilinearGrid}(time = 0 seconds, iteration = 0)
 ├── grid: 1×1×1 RectilinearGrid{Float64, Periodic, Periodic, Bounded} on GPU with 1×1×1 halo
-├── timestepper: QuasiAdamsBashforth2TimeStepper
+├── timestepper: RungeKutta3TimeStepper
 ├── tracers: ()
 ├── closure: Nothing
 ├── buoyancy: Nothing

diff --git a/src/BuoyancyModels/buoyancy.jl b/src/BuoyancyModels/buoyancy.jl
@@ -31,7 +31,7 @@ model = NonhydrostaticModel(; grid, buoyancy, tracers=:b)
 
 NonhydrostaticModel{CPU, RectilinearGrid}(time = 0 seconds, iteration = 0)
 ├── grid: 1×8×8 RectilinearGrid{Float64, Periodic, Periodic, Bounded} on CPU with 1×3×3 halo
-├── timestepper: QuasiAdamsBashforth2TimeStepper
+├── timestepper: RungeKutta3TimeStepper
 ├── advection scheme: Centered reconstruction order 2
 ├── tracers: b
 ├── closure: Nothing

diff --git a/src/Models/NonhydrostaticModels/nonhydrostatic_model.jl b/src/Models/NonhydrostaticModels/nonhydrostatic_model.jl
@@ -64,7 +64,7 @@ end
                                   closure = nothing,
           boundary_conditions::NamedTuple = NamedTuple(),
                                   tracers = (),
-                              timestepper = :QuasiAdamsBashforth2,
+                              timestepper = :RungeKutta3,
             background_fields::NamedTuple = NamedTuple(),
             particles::ParticlesOrNothing = nothing,
     biogeochemistry::AbstractBGCOrNothing = nothing,
@@ -95,7 +95,7 @@ Keyword arguments
   - `tracers`: A tuple of symbols defining the names of the modeled tracers, or a `NamedTuple` of
                preallocated `CenterField`s.
   - `timestepper`: A symbol that specifies the time-stepping method. Either `:QuasiAdamsBashforth2` or
-                   `:RungeKutta3`.
+                   `:RungeKutta3` (default).
   - `background_fields`: `NamedTuple` with background fields (e.g., background flow). Default: `nothing`.
   - `particles`: Lagrangian particles to be advected with the flow. Default: `nothing`.
   - `biogeochemistry`: Biogeochemical model for `tracers`.
@@ -121,7 +121,7 @@ function NonhydrostaticModel(; grid,
                              closure = nothing,
                              boundary_conditions::NamedTuple = NamedTuple(),
                              tracers = (),
-                             timestepper = :QuasiAdamsBashforth2,
+                             timestepper = :RungeKutta3,
                              background_fields::NamedTuple = NamedTuple(),
                              particles::ParticlesOrNothing = nothing,
                              biogeochemistry::AbstractBGCOrNothing = nothing,

diff --git a/src/Models/seawater_density.jl b/src/Models/seawater_density.jl
@@ -81,7 +81,7 @@ SeawaterBuoyancy{Float64}:
 julia> model = NonhydrostaticModel(; grid, buoyancy, tracers)
 NonhydrostaticModel{CPU, RectilinearGrid}(time = 0 seconds, iteration = 0)
 ├── grid: 1×1×100 RectilinearGrid{Float64, Flat, Flat, Bounded} on CPU with 0×0×3 halo
-├── timestepper: QuasiAdamsBashforth2TimeStepper
+├── timestepper: RungeKutta3TimeStepper
 ├── advection scheme: Centered reconstruction order 2
 ├── tracers: (T, S)
 ├── closure: Nothing

diff --git a/test/regression_tests/ocean_large_eddy_simulation_regression_test.jl b/test/regression_tests/ocean_large_eddy_simulation_regression_test.jl
@@ -32,6 +32,7 @@ function run_ocean_large_eddy_simulation_regression_test(arch, grid_type, closur
 
     # Model instantiation
     model = NonhydrostaticModel(; grid, closure,
+                                timestepper = :QuasiAdamsBashforth2,
                                 coriolis = FPlane(f=1e-4),
                                 buoyancy = SeawaterBuoyancy(; equation_of_state),
                                 tracers = (:T, :S),

diff --git a/test/regression_tests/rayleigh_benard_regression_test.jl b/test/regression_tests/rayleigh_benard_regression_test.jl
@@ -48,6 +48,7 @@ function run_rayleigh_benard_regression_test(arch, grid_type)
                                    bottom = BoundaryCondition(Value(), Δb))
 
     model = NonhydrostaticModel(; grid,
+                                timestepper = :QuasiAdamsBashforth2,
                                 closure = ScalarDiffusivity(ν=ν, κ=κ),
                                 tracers = (:b, :c),
                                 buoyancy = Buoyancy(model=BuoyancyTracer()),

diff --git a/test/regression_tests/thermal_bubble_regression_test.jl b/test/regression_tests/thermal_bubble_regression_test.jl
@@ -15,6 +15,7 @@ function run_thermal_bubble_regression_test(arch, grid_type)
     closure = ScalarDiffusivity(ν=4e-2, κ=4e-2)
 
     model = NonhydrostaticModel(; grid, closure,
+                                timestepper = :QuasiAdamsBashforth2,
                                 coriolis = FPlane(f=1e-4),
                                 buoyancy = SeawaterBuoyancy(),
                                 hydrostatic_pressure_anomaly = CenterField(grid),

diff --git a/test/test_boundary_conditions_integration.jl b/test/test_boundary_conditions_integration.jl
@@ -13,7 +13,7 @@ function test_boundary_condition(arch, FT, topo, side, field_name, boundary_cond
                                 buoyancy=SeawaterBuoyancy(), tracers=(:T, :S))
 
     success = try
-        time_step!(model, 1e-16, euler=true)
+        time_step!(model, 1e-16)
         true
     catch err
         @warn "test_boundary_condition errored with " * sprint(showerror, err)
@@ -61,10 +61,12 @@ function fluxes_with_diffusivity_boundary_conditions_are_correct(arch, FT)
     κₑ_bcs = FieldBoundaryConditions(grid, (Center, Center, Center), bottom=ValueBoundaryCondition(κ₀))
     model_bcs = (b=buoyancy_bcs, κₑ=(b=κₑ_bcs,))
 
-    model = NonhydrostaticModel(
-        grid=grid, tracers=:b, buoyancy=BuoyancyTracer(),
-        closure=AnisotropicMinimumDissipation(), boundary_conditions=model_bcs
-    )
+    model = NonhydrostaticModel(; grid,
+                                timestepper = :QuasiAdamsBashforth2,
+                                tracers = :b,
+                                buoyancy = BuoyancyTracer(),
+                                closure = AnisotropicMinimumDissipation(),
+                                boundary_conditions = model_bcs)
 
     b₀(x, y, z) = z * bz
     set!(model, b=b₀)