More general set! plus MoistureMassFractions abstraction #72

glwagner · 2025-11-05T22:01:12Z

This PR makes a few major changes:

introduce a MoistureMassFractions abstraction for representing the mass fractions of vapor, liquid, and ice.
Change the definition of the "reference state" to include the entire precomputed profile on a particular grid. This changes how MoistAirBuoyancy works with NonhydrostaticModel (previously , reference profiles were computed on-the-fly rather than precomputed)
generalizes set! for AtmosphereModel

The improvements to set! were lifted from #29

…eeze.jl into glw/better-set

codecov · 2025-11-07T19:02:05Z

Codecov Report

❌ Patch coverage is 68.32740% with 89 lines in your changes missing coverage. Please review.

Files with missing lines	Patch %	Lines
src/MoistAirBuoyancies.jl	49.62%	67 Missing ⚠️
src/AtmosphereModels/set_atmosphere_model.jl	76.92%	12 Missing ⚠️
src/Thermodynamics/reference_states.jl	79.16%	5 Missing ⚠️
src/AtmosphereModels/atmosphere_model.jl	0.00%	2 Missing ⚠️
src/AtmosphereModels/saturation_adjustment.jl	0.00%	2 Missing ⚠️
src/AtmosphereModels/anelastic_formulation.jl	95.00%	1 Missing ⚠️

📢 Thoughts on this report? Let us know!

glwagner · 2025-11-08T04:05:20Z

docs preview here: https://numericalearth.github.io/BreezeDocumentation/previews/PR72/

glwagner · 2025-11-08T14:25:54Z

After 6d97925, the bomex test started working again (that was the last of a chain of changes). Here is the latest plot (cc @mmr0)

There are a few details that got sorted in this PR, which I'll just hastily mention here, and should be documented more thoroughly in a future PR. One tricky detail for saturation adjustment is that we need to be able to calculate density, which in turn depends on the vapor mass fraction. In saturated conditions and under the assumptions of adjustment, the vapor mass fraction is given simply by the saturation specific humidity. So, using the anelastic appropriate relation for density $\rho = p_r / R^m T$ and $\rho^{v+} = p^{v+} / R^v T$ where $v+$ indicates vapor saturation, $p_r$ is reference density, $R^v$ is the vapor specific gas constant, and $R^m = q^d R^d + q^v R^v$ is the mixture gas constant, we get

$$ q^{v+} = \frac{\rho^{v+}}{\rho} = \frac{R^m}{R^v} \frac{p^{v+}}{p_r} = (1 - q^t) \frac{R^d}{R^v} \frac{p^{v+}}{p_r} + q^{v+} \frac{p^{v+}}{p_r} $$

in the last expression, we used $q^v = q^{v+}$ and $q^d = 1 - q^t$ where $q^t$ is the total moisture mass fraction --- which is known here. We then rearrange to express this in terms of $q^{v+}$ (thank goodness it was linear, haha)

$$ q^{v+} = \frac{R^d}{R^v} \frac{ \left ( 1 - q^t \right ) p^{v+}}{p_r - p^{v+}} $$

This leads to a formula that is a little elusive in the literature, but is given by Pressel et al 2015 eq 37. But there are a few errors / misstatements in that paper too, so beware.

This PR therefore adds a special routine for the "adjustment saturation specific humidity".

Another big change is how the initial guess for the iteration is generated. In the end I just used a 1 K increment. This will be subject to future investigation.

More broadly, I think we need to move on to focusing on the atmosphere model, so I will merge this. It's nice to have the Boussinesq work tied in a bow, it represents progress in Knowledge.

…eeze.jl into glw/better-set

giordano · 2025-11-08T16:18:45Z

This seems to have broken compilation of the example on GPU (tested on julia v1.10):

[ Info: Oceananigans will use 16 threads
ERROR: LoadError: GPU compilation of MethodInstance for Oceananigans.Models.NonhydrostaticModels.gpu__update_hydrostatic_pressure!(::KernelAbstractions.CompilerMetadata{Oceananigans.Utils.OffsetStaticSize{(0:65, 1:1)}, KernelAbstractions.NDIteration.DynamicCheck, Nothing, Nothing, KernelAbstractions.NDIteration.NDRange{2, KernelAbstractions.NDIteration.StaticSize{(1, 1)}, KernelAbstractions.NDIteration.StaticSize{(66, 1)}, Tuple{Int64, Int64}, Oceananigans.Utils.OffsetStaticSize{(-1, 0)}}}, ::OffsetArrays.OffsetArray{Float64, 3, CuDeviceArray{Float64, 3, 1}}, ::RectilinearGrid{Float64, Periodic, Flat, Bounded, Oceananigans.Grids.StaticVerticalDiscretization{OffsetArrays.OffsetVector{Float64, StepRangeLen{Float64, Base.TwicePrecision{Float64}, Base.TwicePrecision{Float64}, Int64}}, OffsetArrays.OffsetVector{Float64, StepRangeLen{Float64, Base.TwicePrecision{Float64}, Base.TwicePrecision{Float64}, Int64}}, Float64, Float64}, Float64, Float64, OffsetArrays.OffsetVector{Float64, StepRangeLen{Float64, Base.TwicePrecision{Float64}, Base.TwicePrecision{Float64}, Int64}}, Nothing, Nothing}, ::BuoyancyForce{MoistAirBuoyancy{ReferenceState{Float64, Field{Nothing, Nothing, Center, Nothing, RectilinearGrid{Float64, Periodic, Flat, Bounded, Oceananigans.Grids.StaticVerticalDiscretization{OffsetArrays.OffsetVector{Float64, StepRangeLen{Float64, Base.TwicePrecision{Float64}, Base.TwicePrecision{Float64}, Int64}}, OffsetArrays.OffsetVector{Float64, StepRangeLen{Float64, Base.TwicePrecision{Float64}, Base.TwicePrecision{Float64}, Int64}}, Float64, Float64}, Float64, Float64, OffsetArrays.OffsetVector{Float64, StepRangeLen{Float64, Base.TwicePrecision{Float64}, Base.TwicePrecision{Float64}, Int64}}, Nothing, GPU{CUDABackend}}, Tuple{Colon, Colon, Colon}, OffsetArrays.OffsetArray{Float64, 3, CuArray{Float64, 3, CUDA.DeviceMemory}}, Float64, FieldBoundaryConditions{Nothing, Nothing, Nothing, Nothing, Oceananigans.BoundaryConditions.NoFluxBoundaryCondition, Oceananigans.BoundaryConditions.NoFluxBoundaryCondition, Nothing, @NamedTuple{bottom_and_top::KernelAbstractions.Kernel{CUDABackend, KernelAbstractions.NDIteration.StaticSize{(1, 1)}, KernelAbstractions.NDIteration.StaticSize{(1, 1)}, typeof(Oceananigans.BoundaryConditions.gpu__fill_bottom_and_top_halo!)}, south_and_north::Nothing, west_and_east::Nothing}, @NamedTuple{bottom_and_top::Tuple{Oceananigans.BoundaryConditions.NoFluxBoundaryCondition, Oceananigans.BoundaryConditions.NoFluxBoundaryCondition}, south_and_north::Tuple{Nothing, Nothing}, west_and_east::Tuple{Nothing, Nothing}}}, Nothing, Nothing}}, ThermodynamicConstants{Float64, CondensedPhase{Float64}, CondensedPhase{Float64}}}, Oceananigans.Grids.NegativeZDirection}, ::@NamedTuple{θ::OffsetArrays.OffsetArray{Float64, 3, CuDeviceArray{Float64, 3, 1}}, qᵗ::OffsetArrays.OffsetArray{Float64, 3, CuDeviceArray{Float64, 3, 1}}}) failed
KernelError: passing non-bitstype argument

Argument 5 to your kernel function is of type BuoyancyForce{MoistAirBuoyancy{ReferenceState{Float64, Field{Nothing, Nothing, Center, Nothing, RectilinearGrid{Float64, Periodic, Flat, Bounded, Oceananigans.Grids.StaticVerticalDiscretization{OffsetArrays.OffsetVector{Float64, StepRangeLen{Float64, Base.TwicePrecision{Float64}, Base.TwicePrecision{Float64}, Int64}}, OffsetArrays.OffsetVector{Float64, StepRangeLen{Float64, Base.TwicePrecision{Float64}, Base.TwicePrecision{Float64}, Int64}}, Float64, Float64}, Float64, Float64, OffsetArrays.OffsetVector{Float64, StepRangeLen{Float64, Base.TwicePrecision{Float64}, Base.TwicePrecision{Float64}, Int64}}, Nothing, GPU{CUDABackend}}, Tuple{Colon, Colon, Colon}, OffsetArrays.OffsetArray{Float64, 3, CuArray{Float64, 3, CUDA.DeviceMemory}}, Float64, FieldBoundaryConditions{Nothing, Nothing, Nothing, Nothing, Oceananigans.BoundaryConditions.NoFluxBoundaryCondition, Oceananigans.BoundaryConditions.NoFluxBoundaryCondition, Nothing, @NamedTuple{bottom_and_top::KernelAbstractions.Kernel{CUDABackend, KernelAbstractions.NDIteration.StaticSize{(1, 1)}, KernelAbstractions.NDIteration.StaticSize{(1, 1)}, typeof(Oceananigans.BoundaryConditions.gpu__fill_bottom_and_top_halo!)}, south_and_north::Nothing, west_and_east::Nothing}, @NamedTuple{bottom_and_top::Tuple{Oceananigans.BoundaryConditions.NoFluxBoundaryCondition, Oceananigans.BoundaryConditions.NoFluxBoundaryCondition}, south_and_north::Tuple{Nothing, Nothing}, west_and_east::Tuple{Nothing, Nothing}}}, Nothing, Nothing}}, ThermodynamicConstants{Float64, CondensedPhase{Float64}, CondensedPhase{Float64}}}, Oceananigans.Grids.NegativeZDirection}, which is not a bitstype:
  .formulation is of type MoistAirBuoyancy{ReferenceState{Float64, Field{Nothing, Nothing, Center, Nothing, RectilinearGrid{Float64, Periodic, Flat, Bounded, Oceananigans.Grids.StaticVerticalDiscretization{OffsetArrays.OffsetVector{Float64, StepRangeLen{Float64, Base.TwicePrecision{Float64}, Base.TwicePrecision{Float64}, Int64}}, OffsetArrays.OffsetVector{Float64, StepRangeLen{Float64, Base.TwicePrecision{Float64}, Base.TwicePrecision{Float64}, Int64}}, Float64, Float64}, Float64, Float64, OffsetArrays.OffsetVector{Float64, StepRangeLen{Float64, Base.TwicePrecision{Float64}, Base.TwicePrecision{Float64}, Int64}}, Nothing, GPU{CUDABackend}}, Tuple{Colon, Colon, Colon}, OffsetArrays.OffsetArray{Float64, 3, CuArray{Float64, 3, CUDA.DeviceMemory}}, Float64, FieldBoundaryConditions{Nothing, Nothing, Nothing, Nothing, Oceananigans.BoundaryConditions.NoFluxBoundaryCondition, Oceananigans.BoundaryConditions.NoFluxBoundaryCondition, Nothing, @NamedTuple{bottom_and_top::KernelAbstractions.Kernel{CUDABackend, KernelAbstractions.NDIteration.StaticSize{(1, 1)}, KernelAbstractions.NDIteration.StaticSize{(1, 1)}, typeof(Oceananigans.BoundaryConditions.gpu__fill_bottom_and_top_halo!)}, south_and_north::Nothing, west_and_east::Nothing}, @NamedTuple{bottom_and_top::Tuple{Oceananigans.BoundaryConditions.NoFluxBoundaryCondition, Oceananigans.BoundaryConditions.NoFluxBoundaryCondition}, south_and_north::Tuple{Nothing, Nothing}, west_and_east::Tuple{Nothing, Nothing}}}, Nothing, Nothing}}, ThermodynamicConstants{Float64, CondensedPhase{Float64}, CondensedPhase{Float64}}} which is not isbits.
    .reference_state is of type ReferenceState{Float64, Field{Nothing, Nothing, Center, Nothing, RectilinearGrid{Float64, Periodic, Flat, Bounded, Oceananigans.Grids.StaticVerticalDiscretization{OffsetArrays.OffsetVector{Float64, StepRangeLen{Float64, Base.TwicePrecision{Float64}, Base.TwicePrecision{Float64}, Int64}}, OffsetArrays.OffsetVector{Float64, StepRangeLen{Float64, Base.TwicePrecision{Float64}, Base.TwicePrecision{Float64}, Int64}}, Float64, Float64}, Float64, Float64, OffsetArrays.OffsetVector{Float64, StepRangeLen{Float64, Base.TwicePrecision{Float64}, Base.TwicePrecision{Float64}, Int64}}, Nothing, GPU{CUDABackend}}, Tuple{Colon, Colon, Colon}, OffsetArrays.OffsetArray{Float64, 3, CuArray{Float64, 3, CUDA.DeviceMemory}}, Float64, FieldBoundaryConditions{Nothing, Nothing, Nothing, Nothing, Oceananigans.BoundaryConditions.NoFluxBoundaryCondition, Oceananigans.BoundaryConditions.NoFluxBoundaryCondition, Nothing, @NamedTuple{bottom_and_top::KernelAbstractions.Kernel{CUDABackend, KernelAbstractions.NDIteration.StaticSize{(1, 1)}, KernelAbstractions.NDIteration.StaticSize{(1, 1)}, typeof(Oceananigans.BoundaryConditions.gpu__fill_bottom_and_top_halo!)}, south_and_north::Nothing, west_and_east::Nothing}, @NamedTuple{bottom_and_top::Tuple{Oceananigans.BoundaryConditions.NoFluxBoundaryCondition, Oceananigans.BoundaryConditions.NoFluxBoundaryCondition}, south_and_north::Tuple{Nothing, Nothing}, west_and_east::Tuple{Nothing, Nothing}}}, Nothing, Nothing}} which is not isbits.
      .pressure is of type Field{Nothing, Nothing, Center, Nothing, RectilinearGrid{Float64, Periodic, Flat, Bounded, Oceananigans.Grids.StaticVerticalDiscretization{OffsetArrays.OffsetVector{Float64, StepRangeLen{Float64, Base.TwicePrecision{Float64}, Base.TwicePrecision{Float64}, Int64}}, OffsetArrays.OffsetVector{Float64, StepRangeLen{Float64, Base.TwicePrecision{Float64}, Base.TwicePrecision{Float64}, Int64}}, Float64, Float64}, Float64, Float64, OffsetArrays.OffsetVector{Float64, StepRangeLen{Float64, Base.TwicePrecision{Float64}, Base.TwicePrecision{Float64}, Int64}}, Nothing, GPU{CUDABackend}}, Tuple{Colon, Colon, Colon}, OffsetArrays.OffsetArray{Float64, 3, CuArray{Float64, 3, CUDA.DeviceMemory}}, Float64, FieldBoundaryConditions{Nothing, Nothing, Nothing, Nothing, Oceananigans.BoundaryConditions.NoFluxBoundaryCondition, Oceananigans.BoundaryConditions.NoFluxBoundaryCondition, Nothing, @NamedTuple{bottom_and_top::KernelAbstractions.Kernel{CUDABackend, KernelAbstractions.NDIteration.StaticSize{(1, 1)}, KernelAbstractions.NDIteration.StaticSize{(1, 1)}, typeof(Oceananigans.BoundaryConditions.gpu__fill_bottom_and_top_halo!)}, south_and_north::Nothing, west_and_east::Nothing}, @NamedTuple{bottom_and_top::Tuple{Oceananigans.BoundaryConditions.NoFluxBoundaryCondition, Oceananigans.BoundaryConditions.NoFluxBoundaryCondition}, south_and_north::Tuple{Nothing, Nothing}, west_and_east::Tuple{Nothing, Nothing}}}, Nothing, Nothing} which is not isbits.
        .data is of type OffsetArrays.OffsetArray{Float64, 3, CuArray{Float64, 3, CUDA.DeviceMemory}} which is not isbits.
          .parent is of type CuArray{Float64, 3, CUDA.DeviceMemory} which is not isbits.
            .data is of type GPUArrays.DataRef{CUDA.Managed{CUDA.DeviceMemory}} which is not isbits.
              .rc is of type GPUArrays.RefCounted{CUDA.Managed{CUDA.DeviceMemory}} which is not isbits.
                .obj is of type CUDA.Managed{CUDA.DeviceMemory} which is not isbits.
                  .stream is of type CuStream which is not isbits.
                    .ctx is of type Union{Nothing, CuContext} which is not isbits.
                .finalizer is of type Any which is not isbits.
                .count is of type Base.Threads.Atomic{Int64} which is not isbits.
        .boundary_conditions is of type FieldBoundaryConditions{Nothing, Nothing, Nothing, Nothing, Oceananigans.BoundaryConditions.NoFluxBoundaryCondition, Oceananigans.BoundaryConditions.NoFluxBoundaryCondition, Nothing, @NamedTuple{bottom_and_top::KernelAbstractions.Kernel{CUDABackend, KernelAbstractions.NDIteration.StaticSize{(1, 1)}, KernelAbstractions.NDIteration.StaticSize{(1, 1)}, typeof(Oceananigans.BoundaryConditions.gpu__fill_bottom_and_top_halo!)}, south_and_north::Nothing, west_and_east::Nothing}, @NamedTuple{bottom_and_top::Tuple{Oceananigans.BoundaryConditions.NoFluxBoundaryCondition, Oceananigans.BoundaryConditions.NoFluxBoundaryCondition}, south_and_north::Tuple{Nothing, Nothing}, west_and_east::Tuple{Nothing, Nothing}}} which is not isbits.
      .density is of type Field{Nothing, Nothing, Center, Nothing, RectilinearGrid{Float64, Periodic, Flat, Bounded, Oceananigans.Grids.StaticVerticalDiscretization{OffsetArrays.OffsetVector{Float64, StepRangeLen{Float64, Base.TwicePrecision{Float64}, Base.TwicePrecision{Float64}, Int64}}, OffsetArrays.OffsetVector{Float64, StepRangeLen{Float64, Base.TwicePrecision{Float64}, Base.TwicePrecision{Float64}, Int64}}, Float64, Float64}, Float64, Float64, OffsetArrays.OffsetVector{Float64, StepRangeLen{Float64, Base.TwicePrecision{Float64}, Base.TwicePrecision{Float64}, Int64}}, Nothing, GPU{CUDABackend}}, Tuple{Colon, Colon, Colon}, OffsetArrays.OffsetArray{Float64, 3, CuArray{Float64, 3, CUDA.DeviceMemory}}, Float64, FieldBoundaryConditions{Nothing, Nothing, Nothing, Nothing, Oceananigans.BoundaryConditions.NoFluxBoundaryCondition, Oceananigans.BoundaryConditions.NoFluxBoundaryCondition, Nothing, @NamedTuple{bottom_and_top::KernelAbstractions.Kernel{CUDABackend, KernelAbstractions.NDIteration.StaticSize{(1, 1)}, KernelAbstractions.NDIteration.StaticSize{(1, 1)}, typeof(Oceananigans.BoundaryConditions.gpu__fill_bottom_and_top_halo!)}, south_and_north::Nothing, west_and_east::Nothing}, @NamedTuple{bottom_and_top::Tuple{Oceananigans.BoundaryConditions.NoFluxBoundaryCondition, Oceananigans.BoundaryConditions.NoFluxBoundaryCondition}, south_and_north::Tuple{Nothing, Nothing}, west_and_east::Tuple{Nothing, Nothing}}}, Nothing, Nothing} which is not isbits.
        .data is of type OffsetArrays.OffsetArray{Float64, 3, CuArray{Float64, 3, CUDA.DeviceMemory}} which is not isbits.
          .parent is of type CuArray{Float64, 3, CUDA.DeviceMemory} which is not isbits.
            .data is of type GPUArrays.DataRef{CUDA.Managed{CUDA.DeviceMemory}} which is not isbits.
              .rc is of type GPUArrays.RefCounted{CUDA.Managed{CUDA.DeviceMemory}} which is not isbits.
                .obj is of type CUDA.Managed{CUDA.DeviceMemory} which is not isbits.
                  .stream is of type CuStream which is not isbits.
                    .ctx is of type Union{Nothing, CuContext} which is not isbits.
                .finalizer is of type Any which is not isbits.
                .count is of type Base.Threads.Atomic{Int64} which is not isbits.
        .boundary_conditions is of type FieldBoundaryConditions{Nothing, Nothing, Nothing, Nothing, Oceananigans.BoundaryConditions.NoFluxBoundaryCondition, Oceananigans.BoundaryConditions.NoFluxBoundaryCondition, Nothing, @NamedTuple{bottom_and_top::KernelAbstractions.Kernel{CUDABackend, KernelAbstractions.NDIteration.StaticSize{(1, 1)}, KernelAbstractions.NDIteration.StaticSize{(1, 1)}, typeof(Oceananigans.BoundaryConditions.gpu__fill_bottom_and_top_halo!)}, south_and_north::Nothing, west_and_east::Nothing}, @NamedTuple{bottom_and_top::Tuple{Oceananigans.BoundaryConditions.NoFluxBoundaryCondition, Oceananigans.BoundaryConditions.NoFluxBoundaryCondition}, south_and_north::Tuple{Nothing, Nothing}, west_and_east::Tuple{Nothing, Nothing}}} which is not isbits.


Only bitstypes, which are "plain data" types that are immutable
and contain no references to other values, can be used in GPU kernels.
For more information, see the `Base.isbitstype` function.

glwagner · 2025-11-08T17:10:03Z

This seems to have broken compilation of the example on GPU (tested on julia v1.10):

[ Info: Oceananigans will use 16 threads
ERROR: LoadError: GPU compilation of MethodInstance for Oceananigans.Models.NonhydrostaticModels.gpu__update_hydrostatic_pressure!(::KernelAbstractions.CompilerMetadata{Oceananigans.Utils.OffsetStaticSize{(0:65, 1:1)}, KernelAbstractions.NDIteration.DynamicCheck, Nothing, Nothing, KernelAbstractions.NDIteration.NDRange{2, KernelAbstractions.NDIteration.StaticSize{(1, 1)}, KernelAbstractions.NDIteration.StaticSize{(66, 1)}, Tuple{Int64, Int64}, Oceananigans.Utils.OffsetStaticSize{(-1, 0)}}}, ::OffsetArrays.OffsetArray{Float64, 3, CuDeviceArray{Float64, 3, 1}}, ::RectilinearGrid{Float64, Periodic, Flat, Bounded, Oceananigans.Grids.StaticVerticalDiscretization{OffsetArrays.OffsetVector{Float64, StepRangeLen{Float64, Base.TwicePrecision{Float64}, Base.TwicePrecision{Float64}, Int64}}, OffsetArrays.OffsetVector{Float64, StepRangeLen{Float64, Base.TwicePrecision{Float64}, Base.TwicePrecision{Float64}, Int64}}, Float64, Float64}, Float64, Float64, OffsetArrays.OffsetVector{Float64, StepRangeLen{Float64, Base.TwicePrecision{Float64}, Base.TwicePrecision{Float64}, Int64}}, Nothing, Nothing}, ::BuoyancyForce{MoistAirBuoyancy{ReferenceState{Float64, Field{Nothing, Nothing, Center, Nothing, RectilinearGrid{Float64, Periodic, Flat, Bounded, Oceananigans.Grids.StaticVerticalDiscretization{OffsetArrays.OffsetVector{Float64, StepRangeLen{Float64, Base.TwicePrecision{Float64}, Base.TwicePrecision{Float64}, Int64}}, OffsetArrays.OffsetVector{Float64, StepRangeLen{Float64, Base.TwicePrecision{Float64}, Base.TwicePrecision{Float64}, Int64}}, Float64, Float64}, Float64, Float64, OffsetArrays.OffsetVector{Float64, StepRangeLen{Float64, Base.TwicePrecision{Float64}, Base.TwicePrecision{Float64}, Int64}}, Nothing, GPU{CUDABackend}}, Tuple{Colon, Colon, Colon}, OffsetArrays.OffsetArray{Float64, 3, CuArray{Float64, 3, CUDA.DeviceMemory}}, Float64, FieldBoundaryConditions{Nothing, Nothing, Nothing, Nothing, Oceananigans.BoundaryConditions.NoFluxBoundaryCondition, Oceananigans.BoundaryConditions.NoFluxBoundaryCondition, Nothing, @NamedTuple{bottom_and_top::KernelAbstractions.Kernel{CUDABackend, KernelAbstractions.NDIteration.StaticSize{(1, 1)}, KernelAbstractions.NDIteration.StaticSize{(1, 1)}, typeof(Oceananigans.BoundaryConditions.gpu__fill_bottom_and_top_halo!)}, south_and_north::Nothing, west_and_east::Nothing}, @NamedTuple{bottom_and_top::Tuple{Oceananigans.BoundaryConditions.NoFluxBoundaryCondition, Oceananigans.BoundaryConditions.NoFluxBoundaryCondition}, south_and_north::Tuple{Nothing, Nothing}, west_and_east::Tuple{Nothing, Nothing}}}, Nothing, Nothing}}, ThermodynamicConstants{Float64, CondensedPhase{Float64}, CondensedPhase{Float64}}}, Oceananigans.Grids.NegativeZDirection}, ::@NamedTuple{θ::OffsetArrays.OffsetArray{Float64, 3, CuDeviceArray{Float64, 3, 1}}, qᵗ::OffsetArrays.OffsetArray{Float64, 3, CuDeviceArray{Float64, 3, 1}}}) failed
KernelError: passing non-bitstype argument

Argument 5 to your kernel function is of type BuoyancyForce{MoistAirBuoyancy{ReferenceState{Float64, Field{Nothing, Nothing, Center, Nothing, RectilinearGrid{Float64, Periodic, Flat, Bounded, Oceananigans.Grids.StaticVerticalDiscretization{OffsetArrays.OffsetVector{Float64, StepRangeLen{Float64, Base.TwicePrecision{Float64}, Base.TwicePrecision{Float64}, Int64}}, OffsetArrays.OffsetVector{Float64, StepRangeLen{Float64, Base.TwicePrecision{Float64}, Base.TwicePrecision{Float64}, Int64}}, Float64, Float64}, Float64, Float64, OffsetArrays.OffsetVector{Float64, StepRangeLen{Float64, Base.TwicePrecision{Float64}, Base.TwicePrecision{Float64}, Int64}}, Nothing, GPU{CUDABackend}}, Tuple{Colon, Colon, Colon}, OffsetArrays.OffsetArray{Float64, 3, CuArray{Float64, 3, CUDA.DeviceMemory}}, Float64, FieldBoundaryConditions{Nothing, Nothing, Nothing, Nothing, Oceananigans.BoundaryConditions.NoFluxBoundaryCondition, Oceananigans.BoundaryConditions.NoFluxBoundaryCondition, Nothing, @NamedTuple{bottom_and_top::KernelAbstractions.Kernel{CUDABackend, KernelAbstractions.NDIteration.StaticSize{(1, 1)}, KernelAbstractions.NDIteration.StaticSize{(1, 1)}, typeof(Oceananigans.BoundaryConditions.gpu__fill_bottom_and_top_halo!)}, south_and_north::Nothing, west_and_east::Nothing}, @NamedTuple{bottom_and_top::Tuple{Oceananigans.BoundaryConditions.NoFluxBoundaryCondition, Oceananigans.BoundaryConditions.NoFluxBoundaryCondition}, south_and_north::Tuple{Nothing, Nothing}, west_and_east::Tuple{Nothing, Nothing}}}, Nothing, Nothing}}, ThermodynamicConstants{Float64, CondensedPhase{Float64}, CondensedPhase{Float64}}}, Oceananigans.Grids.NegativeZDirection}, which is not a bitstype:
  .formulation is of type MoistAirBuoyancy{ReferenceState{Float64, Field{Nothing, Nothing, Center, Nothing, RectilinearGrid{Float64, Periodic, Flat, Bounded, Oceananigans.Grids.StaticVerticalDiscretization{OffsetArrays.OffsetVector{Float64, StepRangeLen{Float64, Base.TwicePrecision{Float64}, Base.TwicePrecision{Float64}, Int64}}, OffsetArrays.OffsetVector{Float64, StepRangeLen{Float64, Base.TwicePrecision{Float64}, Base.TwicePrecision{Float64}, Int64}}, Float64, Float64}, Float64, Float64, OffsetArrays.OffsetVector{Float64, StepRangeLen{Float64, Base.TwicePrecision{Float64}, Base.TwicePrecision{Float64}, Int64}}, Nothing, GPU{CUDABackend}}, Tuple{Colon, Colon, Colon}, OffsetArrays.OffsetArray{Float64, 3, CuArray{Float64, 3, CUDA.DeviceMemory}}, Float64, FieldBoundaryConditions{Nothing, Nothing, Nothing, Nothing, Oceananigans.BoundaryConditions.NoFluxBoundaryCondition, Oceananigans.BoundaryConditions.NoFluxBoundaryCondition, Nothing, @NamedTuple{bottom_and_top::KernelAbstractions.Kernel{CUDABackend, KernelAbstractions.NDIteration.StaticSize{(1, 1)}, KernelAbstractions.NDIteration.StaticSize{(1, 1)}, typeof(Oceananigans.BoundaryConditions.gpu__fill_bottom_and_top_halo!)}, south_and_north::Nothing, west_and_east::Nothing}, @NamedTuple{bottom_and_top::Tuple{Oceananigans.BoundaryConditions.NoFluxBoundaryCondition, Oceananigans.BoundaryConditions.NoFluxBoundaryCondition}, south_and_north::Tuple{Nothing, Nothing}, west_and_east::Tuple{Nothing, Nothing}}}, Nothing, Nothing}}, ThermodynamicConstants{Float64, CondensedPhase{Float64}, CondensedPhase{Float64}}} which is not isbits.
    .reference_state is of type ReferenceState{Float64, Field{Nothing, Nothing, Center, Nothing, RectilinearGrid{Float64, Periodic, Flat, Bounded, Oceananigans.Grids.StaticVerticalDiscretization{OffsetArrays.OffsetVector{Float64, StepRangeLen{Float64, Base.TwicePrecision{Float64}, Base.TwicePrecision{Float64}, Int64}}, OffsetArrays.OffsetVector{Float64, StepRangeLen{Float64, Base.TwicePrecision{Float64}, Base.TwicePrecision{Float64}, Int64}}, Float64, Float64}, Float64, Float64, OffsetArrays.OffsetVector{Float64, StepRangeLen{Float64, Base.TwicePrecision{Float64}, Base.TwicePrecision{Float64}, Int64}}, Nothing, GPU{CUDABackend}}, Tuple{Colon, Colon, Colon}, OffsetArrays.OffsetArray{Float64, 3, CuArray{Float64, 3, CUDA.DeviceMemory}}, Float64, FieldBoundaryConditions{Nothing, Nothing, Nothing, Nothing, Oceananigans.BoundaryConditions.NoFluxBoundaryCondition, Oceananigans.BoundaryConditions.NoFluxBoundaryCondition, Nothing, @NamedTuple{bottom_and_top::KernelAbstractions.Kernel{CUDABackend, KernelAbstractions.NDIteration.StaticSize{(1, 1)}, KernelAbstractions.NDIteration.StaticSize{(1, 1)}, typeof(Oceananigans.BoundaryConditions.gpu__fill_bottom_and_top_halo!)}, south_and_north::Nothing, west_and_east::Nothing}, @NamedTuple{bottom_and_top::Tuple{Oceananigans.BoundaryConditions.NoFluxBoundaryCondition, Oceananigans.BoundaryConditions.NoFluxBoundaryCondition}, south_and_north::Tuple{Nothing, Nothing}, west_and_east::Tuple{Nothing, Nothing}}}, Nothing, Nothing}} which is not isbits.
      .pressure is of type Field{Nothing, Nothing, Center, Nothing, RectilinearGrid{Float64, Periodic, Flat, Bounded, Oceananigans.Grids.StaticVerticalDiscretization{OffsetArrays.OffsetVector{Float64, StepRangeLen{Float64, Base.TwicePrecision{Float64}, Base.TwicePrecision{Float64}, Int64}}, OffsetArrays.OffsetVector{Float64, StepRangeLen{Float64, Base.TwicePrecision{Float64}, Base.TwicePrecision{Float64}, Int64}}, Float64, Float64}, Float64, Float64, OffsetArrays.OffsetVector{Float64, StepRangeLen{Float64, Base.TwicePrecision{Float64}, Base.TwicePrecision{Float64}, Int64}}, Nothing, GPU{CUDABackend}}, Tuple{Colon, Colon, Colon}, OffsetArrays.OffsetArray{Float64, 3, CuArray{Float64, 3, CUDA.DeviceMemory}}, Float64, FieldBoundaryConditions{Nothing, Nothing, Nothing, Nothing, Oceananigans.BoundaryConditions.NoFluxBoundaryCondition, Oceananigans.BoundaryConditions.NoFluxBoundaryCondition, Nothing, @NamedTuple{bottom_and_top::KernelAbstractions.Kernel{CUDABackend, KernelAbstractions.NDIteration.StaticSize{(1, 1)}, KernelAbstractions.NDIteration.StaticSize{(1, 1)}, typeof(Oceananigans.BoundaryConditions.gpu__fill_bottom_and_top_halo!)}, south_and_north::Nothing, west_and_east::Nothing}, @NamedTuple{bottom_and_top::Tuple{Oceananigans.BoundaryConditions.NoFluxBoundaryCondition, Oceananigans.BoundaryConditions.NoFluxBoundaryCondition}, south_and_north::Tuple{Nothing, Nothing}, west_and_east::Tuple{Nothing, Nothing}}}, Nothing, Nothing} which is not isbits.
        .data is of type OffsetArrays.OffsetArray{Float64, 3, CuArray{Float64, 3, CUDA.DeviceMemory}} which is not isbits.
          .parent is of type CuArray{Float64, 3, CUDA.DeviceMemory} which is not isbits.
            .data is of type GPUArrays.DataRef{CUDA.Managed{CUDA.DeviceMemory}} which is not isbits.
              .rc is of type GPUArrays.RefCounted{CUDA.Managed{CUDA.DeviceMemory}} which is not isbits.
                .obj is of type CUDA.Managed{CUDA.DeviceMemory} which is not isbits.
                  .stream is of type CuStream which is not isbits.
                    .ctx is of type Union{Nothing, CuContext} which is not isbits.
                .finalizer is of type Any which is not isbits.
                .count is of type Base.Threads.Atomic{Int64} which is not isbits.
        .boundary_conditions is of type FieldBoundaryConditions{Nothing, Nothing, Nothing, Nothing, Oceananigans.BoundaryConditions.NoFluxBoundaryCondition, Oceananigans.BoundaryConditions.NoFluxBoundaryCondition, Nothing, @NamedTuple{bottom_and_top::KernelAbstractions.Kernel{CUDABackend, KernelAbstractions.NDIteration.StaticSize{(1, 1)}, KernelAbstractions.NDIteration.StaticSize{(1, 1)}, typeof(Oceananigans.BoundaryConditions.gpu__fill_bottom_and_top_halo!)}, south_and_north::Nothing, west_and_east::Nothing}, @NamedTuple{bottom_and_top::Tuple{Oceananigans.BoundaryConditions.NoFluxBoundaryCondition, Oceananigans.BoundaryConditions.NoFluxBoundaryCondition}, south_and_north::Tuple{Nothing, Nothing}, west_and_east::Tuple{Nothing, Nothing}}} which is not isbits.
      .density is of type Field{Nothing, Nothing, Center, Nothing, RectilinearGrid{Float64, Periodic, Flat, Bounded, Oceananigans.Grids.StaticVerticalDiscretization{OffsetArrays.OffsetVector{Float64, StepRangeLen{Float64, Base.TwicePrecision{Float64}, Base.TwicePrecision{Float64}, Int64}}, OffsetArrays.OffsetVector{Float64, StepRangeLen{Float64, Base.TwicePrecision{Float64}, Base.TwicePrecision{Float64}, Int64}}, Float64, Float64}, Float64, Float64, OffsetArrays.OffsetVector{Float64, StepRangeLen{Float64, Base.TwicePrecision{Float64}, Base.TwicePrecision{Float64}, Int64}}, Nothing, GPU{CUDABackend}}, Tuple{Colon, Colon, Colon}, OffsetArrays.OffsetArray{Float64, 3, CuArray{Float64, 3, CUDA.DeviceMemory}}, Float64, FieldBoundaryConditions{Nothing, Nothing, Nothing, Nothing, Oceananigans.BoundaryConditions.NoFluxBoundaryCondition, Oceananigans.BoundaryConditions.NoFluxBoundaryCondition, Nothing, @NamedTuple{bottom_and_top::KernelAbstractions.Kernel{CUDABackend, KernelAbstractions.NDIteration.StaticSize{(1, 1)}, KernelAbstractions.NDIteration.StaticSize{(1, 1)}, typeof(Oceananigans.BoundaryConditions.gpu__fill_bottom_and_top_halo!)}, south_and_north::Nothing, west_and_east::Nothing}, @NamedTuple{bottom_and_top::Tuple{Oceananigans.BoundaryConditions.NoFluxBoundaryCondition, Oceananigans.BoundaryConditions.NoFluxBoundaryCondition}, south_and_north::Tuple{Nothing, Nothing}, west_and_east::Tuple{Nothing, Nothing}}}, Nothing, Nothing} which is not isbits.
        .data is of type OffsetArrays.OffsetArray{Float64, 3, CuArray{Float64, 3, CUDA.DeviceMemory}} which is not isbits.
          .parent is of type CuArray{Float64, 3, CUDA.DeviceMemory} which is not isbits.
            .data is of type GPUArrays.DataRef{CUDA.Managed{CUDA.DeviceMemory}} which is not isbits.
              .rc is of type GPUArrays.RefCounted{CUDA.Managed{CUDA.DeviceMemory}} which is not isbits.
                .obj is of type CUDA.Managed{CUDA.DeviceMemory} which is not isbits.
                  .stream is of type CuStream which is not isbits.
                    .ctx is of type Union{Nothing, CuContext} which is not isbits.
                .finalizer is of type Any which is not isbits.
                .count is of type Base.Threads.Atomic{Int64} which is not isbits.
        .boundary_conditions is of type FieldBoundaryConditions{Nothing, Nothing, Nothing, Nothing, Oceananigans.BoundaryConditions.NoFluxBoundaryCondition, Oceananigans.BoundaryConditions.NoFluxBoundaryCondition, Nothing, @NamedTuple{bottom_and_top::KernelAbstractions.Kernel{CUDABackend, KernelAbstractions.NDIteration.StaticSize{(1, 1)}, KernelAbstractions.NDIteration.StaticSize{(1, 1)}, typeof(Oceananigans.BoundaryConditions.gpu__fill_bottom_and_top_halo!)}, south_and_north::Nothing, west_and_east::Nothing}, @NamedTuple{bottom_and_top::Tuple{Oceananigans.BoundaryConditions.NoFluxBoundaryCondition, Oceananigans.BoundaryConditions.NoFluxBoundaryCondition}, south_and_north::Tuple{Nothing, Nothing}, west_and_east::Tuple{Nothing, Nothing}}} which is not isbits.


Only bitstypes, which are "plain data" types that are immutable
and contain no references to other values, can be used in GPU kernels.
For more information, see the `Base.isbitstype` function.

Ah nice, I think we need an adapt for ReferenceState

More general set! plus SpecificHumidities abstraction

885bcb5

glwagner marked this pull request as draft November 5, 2025 22:01

glwagner added 3 commits November 5, 2025 16:33

Merge branch 'main' into glw/better-set

b35e173

try to get SpecificHumidities working

cc404e2

Merge branch 'main' into glw/better-set

7de5ffa

glwagner marked this pull request as ready for review November 6, 2025 02:53

glwagner added 20 commits November 6, 2025 14:31

Merge branch 'main' into glw/better-set

344587f

reduce thermodynamic states

b7bc1a8

Merge branch 'main' into glw/better-set

c8729b8

get SpecificHumidities into docs

5a82643

Merge branch 'glw/better-set' of https://github.com/NumericalEarth/Br…

08059a8

…eeze.jl into glw/better-set

SpecificHumidities -> MassRatios

4c64ac6

humidities -> mass_ratios

2626abd

mass ratio -> specific moisture content

6b0c08e

Merge branch 'main' into glw/better-set

3f3d482

lets try "mass fractions"

00882a7

change "latent heat" to "reference latent heat"

8ee4fd3

reorganize stuff

58ffd01

cleanup

368eec1

fixing trhe reference state

5e036b8

bomex running

b50b01b

thermal bubble runss

da86b24

fix thermal bubble

6df90ba

fix tests

33d6d96

fix

4e5d9e1

use approx

0d938df

glwagner changed the title ~~More general set! plus SpecificHumidities abstraction~~ More general set! plus MoistureMassFractions abstraction Nov 7, 2025

glwagner added 2 commits November 7, 2025 11:44

more test fixes

f2e3e15

rm unused import

cdcc165

glwagner added 14 commits November 7, 2025 12:44

fix docs

a474950

fix

e7dd1ce

fix saturation adj bug

af8c21f

fix saturation adjustment solver for boussinesq model

52f06fa

fix broken imports

fb53b76

another import fix

37d3f1c

clean up

75134fd

fix docs example

c13789b

fix another saturation adj bug

502d589

add comments

894fe03

dont show iter

aadf957

fix diagnostics

ef7a83e

update saturation adj docs

ffa3a10

use rand not randn

662ddb1

glwagner added 3 commits November 7, 2025 22:39

add tests and change algorithm

6d97925

rm show methods

3ab4c2d

Merge branch 'main' into glw/better-set

9a0d31e

glwagner added 5 commits November 8, 2025 07:26

Merge branch 'main' into glw/better-set

73cf9d8

change ref from chammas to pressel

9b69283

Merge branch 'glw/better-set' of https://github.com/NumericalEarth/Br…

ac9cf14

…eeze.jl into glw/better-set

fix quick start

955eac8

another fix

6b4f5f7

glwagner merged commit df066f8 into main Nov 8, 2025
8 checks passed

glwagner deleted the glw/better-set branch November 8, 2025 15:30

giordano mentioned this pull request Nov 8, 2025

[GPU] Add adapt_structure for MoistAirBuoyancy, AnelasticFormulation, and ReferenceState #94

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More general set! plus MoistureMassFractions abstraction #72

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glwagner commented Nov 5, 2025 •

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More general set! plus MoistureMassFractions abstraction #72

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