Oceananigans.jl: Multiple warnings about "incremental compilation may be fatally broken for this module"

[ali-ramadhan]

Non-fatal and easy to fix but should probably be done as these look bad to users.

The Casette warnings are non-trivial to fix according to @vchuravy so maybe supressing those warnings might work (see #366).

julia> using Oceananigans
[ Info: Precompiling Oceananigans [9e8cae18-63c1-5223-a75c-80ca9d6e9a09]
WARNING: Method definition overdub(Cassette.Context{N, M, T, P, B, H} where H<:Union{Cassette.DisableHooks, Nothing} where B<:Union{Nothing, Base.IdDict{Module, Base.Dict{Symbol, Cassette.BindingMeta}}} where P<:Cassette.AbstractPass where T<:Union{Nothing, Cassette.Tag{N, X, E} where E where X where N<:Cassette.AbstractContextName} where M where N<:Cassette.AbstractContextName, Any...) in module Cassette at /home/alir/.julia/packages/Cassette/YCOeN/src/overdub.jl:524 overwritten in module GPUifyLoops at /home/alir/.julia/packages/Cassette/YCOeN/src/overdub.jl:524.
  ** incremental compilation may be fatally broken for this module **

WARNING: Method definition recurse(Cassette.Context{N, M, T, P, B, H} where H<:Union{Cassette.DisableHooks, Nothing} where B<:Union{Nothing, Base.IdDict{Module, Base.Dict{Symbol, Cassette.BindingMeta}}} where P<:Cassette.AbstractPass where T<:Union{Nothing, Cassette.Tag{N, X, E} where E where X where N<:Cassette.AbstractContextName} where M where N<:Cassette.AbstractContextName, Any...) in module Cassette at /home/alir/.julia/packages/Cassette/YCOeN/src/overdub.jl:537 overwritten in module GPUifyLoops at /home/alir/.julia/packages/Cassette/YCOeN/src/overdub.jl:537.
  ** incremental compilation may be fatally broken for this module **

WARNING: Method definition overdub(Cassette.Context{N, M, T, P, B, H} where H<:Union{Cassette.DisableHooks, Nothing} where B<:Union{Nothing, Base.IdDict{Module, Base.Dict{Symbol, Cassette.BindingMeta}}} where P<:Cassette.AbstractPass where T<:Union{Nothing, Cassette.Tag{N, X, E} where E where X where N<:Cassette.AbstractContextName} where M where N<:Cassette.AbstractContextName, Any...) in module Cassette at /home/alir/.julia/packages/Cassette/YCOeN/src/overdub.jl:524 overwritten in module GPUifyLoops at /home/alir/.julia/packages/Cassette/YCOeN/src/overdub.jl:524.
  ** incremental compilation may be fatally broken for this module **

WARNING: Method definition recurse(Cassette.Context{N, M, T, P, B, H} where H<:Union{Cassette.DisableHooks, Nothing} where B<:Union{Nothing, Base.IdDict{Module, Base.Dict{Symbol, Cassette.BindingMeta}}} where P<:Cassette.AbstractPass where T<:Union{Nothing, Cassette.Tag{N, X, E} where E where X where N<:Cassette.AbstractContextName} where M where N<:Cassette.AbstractContextName, Any...) in module Cassette at /home/alir/.julia/packages/Cassette/YCOeN/src/overdub.jl:537 overwritten in module GPUifyLoops at /home/alir/.julia/packages/Cassette/YCOeN/src/overdub.jl:537.
  ** incremental compilation may be fatally broken for this module **

WARNING: Method definition TurbulentDiffusivities(Oceananigans.AbstractArchitecture, Oceananigans.AbstractGrid{T} where T, Any, Tuple) in module TurbulenceClosures at /home/alir/Oceananigans.jl/src/TurbulenceClosures/TurbulenceClosures.jl:151 overwritten at /home/alir/Oceananigans.jl/src/TurbulenceClosures/closure_tuples.jl:35.
  ** incremental compilation may be fatally broken for this module **

WARNING: Method definition with_tracers(Any, Tuple) in module TurbulenceClosures at /home/alir/Oceananigans.jl/src/TurbulenceClosures/TurbulenceClosures.jl:154 overwritten at /home/alir/Oceananigans.jl/src/TurbulenceClosures/closure_tuples.jl:38.
  ** incremental compilation may be fatally broken for this module **

WARNING: Method definition (::Type{Oceananigans.FPlane{FT} where FT})(Any) in module Oceananigans at /home/alir/Oceananigans.jl/src/coriolis.jl:22 overwritten at /home/alir/Oceananigans.jl/src/coriolis.jl:38.
  ** incremental compilation may be fatally broken for this module **

[vchuravy]

Try master Cassette.jl ;)

[ali-ramadhan]

That worked, thanks @vchuravy! PR incoming.

[francispoulin]

After just recently installing Oceananigans I tried using the library and got this error. I gather things still work but wanted to point out tha tthere is still a Warning on my first use. See below for details.

julia> using Oceananigans
[ Info: Precompiling Oceananigans [9e8cae18-63c1-5223-a75c-80ca9d6e9a09]
WARNING: Method definition adapt_structure(Any, OffsetArrays.OffsetArray{T, N, AA} where AA<:AbstractArray{T, N} where N where T) in module OffsetArrays at /home/fpoulin/.julia/packages/OffsetArrays/ExQCD/src/OffsetArrays.jl:486 overwritten in module Utils at /home/fpoulin/.julia/packages/Oceananigans/IbUoB/src/Utils/adapt_structure.jl:5.
  ** incremental compilation may be fatally broken for this module **

[ali-ramadhan]

Hi @francispoulin, thank you for reporting this!

I believe the warning is due to https://github.com/CliMA/Oceananigans.jl/issues/1141 which should be fixed with the next tagged release (v0.44.1), hopefully coming out a bit later today.

PS: Hi from a uWaterloo grad!

[francispoulin]

Thanks for the quick reply @ali-ramadhan . That is great that this is being fixed so soon.

Would you like me to keep this open until after I test the new release?

PS: Great to hear that UWaterloo grads are going off to do such cool things, like workong on this!

[ali-ramadhan]

Would you like me to keep this open until after I test the new release?

Just re-opened the issue in case it still persists. Feel free to close this issue once you test the new release.

I'll ping back here once v0.44.1 is out.

[francispoulin]

Great and thanks again!

[ali-ramadhan]

@francispoulin v0.44.1 was just tagged so warning should be gone now!

[francispoulin]

I agree the problem goes away. Thanks!

A different issue, when I run this should I be seeing anything? I don't so have no way to observe whether it is doing anything reasonable or not.

[ali-ramadhan]

Awesome! I'll close the issue then.

Hmmm, not sure what you're running but in general Oceananigans.jl doesn't give too much feedback (something we're hoping to improve, see #1013). If you're running things in the REPL it'll print/display what each expression returns (see below) but run! doesn't produce output or report on progress by default (perhaps it would be good to add a reasonable default).

julia> using Oceananigans

julia> grid = RegularCartesianGrid(size=(100, 100, 50), extent=(2π, 2π, 1))
RegularCartesianGrid{Float64, Periodic, Periodic, Bounded}
                   domain: x ∈ [-5.496153587253255e-18, 6.283185307179586], y ∈ [-5.496153587253255e-18, 6.283185307179586], z ∈ [-1.0, 1.7080354225002348e-17]
                 topology: (Periodic, Periodic, Bounded)
  resolution (Nx, Ny, Nz): (100, 100, 50)
   halo size (Hx, Hy, Hz): (1, 1, 1)
grid spacing (Δx, Δy, Δz): (0.06283185307179587, 0.06283185307179587, 0.02)

julia> model = IncompressibleModel(grid=grid)
IncompressibleModel{CPU, Float64}(time = 0 seconds, iteration = 0) 
├── grid: RegularCartesianGrid{Float64, Periodic, Periodic, Bounded}(Nx=100, Ny=100, Nz=50)
├── tracers: (:T, :S)
├── closure: IsotropicDiffusivity{Float64,NamedTuple{(:T, :S),Tuple{Float64,Float64}}}
├── buoyancy: SeawaterBuoyancy{Float64,LinearEquationOfState{Float64},Nothing,Nothing}
└── coriolis: Nothing

julia> simulation = Simulation(model, Δt=60, stop_time=3600)
Simulation{IncompressibleModel{CPU, Float64}}
├── Model clock: time = 0 seconds, iteration = 0 
├── Next time step (Int64): 1 minute 
├── Iteration interval: 1
├── Stop criteria: Any[Oceananigans.Simulations.iteration_limit_exceeded, Oceananigans.Simulations.stop_time_exceeded, Oceananigans.Simulations.wall_time_limit_exceeded]
├── Run time: 0 seconds, wall time limit: Inf
├── Stop time: 1 hour, stop iteration: Inf
├── Diagnostics: OrderedCollections.OrderedDict with no entries
└── Output writers: OrderedCollections.OrderedDict with no entries

julia> run!(simulation)
[ Info: Simulation is stopping. Model time 1 hour has hit or exceeded simulation stop time 1 hour.

[francispoulin]

Thanks. I get the same output but no visuals and no data saved. I will learn how to do that.

[glwagner]

@francispoulin checkout the examples (like this one) for inspiration about how to save output and plot solutions and let us know if they are helpful!

[francispoulin]

Thanks @glwagner , those examples look great!