NetCDF output writer error

[Lichriszz]

Hi,

When I try to run this example, I got an error message (see below). Can anyone help?
Thanks!

using Oceananigans, Oceananigans.OutputWriters

grid = RegularCartesianGrid(size=(16, 16, 16), extent=(1, 1, 1));

model = IncompressibleModel(grid=grid);

simulation = Simulation(model, Δt=12, stop_time=3600);

fields = Dict("u" => model.velocities.u, "T" => model.tracers.T);

simulation.output_writers[:field_writer] =
    NetCDFOutputWriter(model, fields, filename="fields.nc", time_interval=60)

**Error message:**

LoadError: UndefKeywordError: keyword argument filepath not assigned
in expression starting at /Users/lichriszz/Desktop/Research/netcdf test.jl:11
(::Core.var"#Type##kw")(::NamedTuple{(:filename, :time_interval),Tuple{String,Int64}}, ::Type{NetCDFOutputWriter}, ::IncompressibleModel{Oceananigans.TimeSteppers.QuasiAdamsBashforth2TimeStepper{Float64,NamedTuple{(:u, :v, :w, :T, :S),Tuple{Field{Face,Center,Center,OffsetArrays.OffsetArray{Float64,3,Array{Float64,3}},RegularCartesianGrid{Float64,Periodic,Periodic,Bounded,OffsetArrays.OffsetArray{Float64,1,StepRangeLen{Float64,Base.TwicePrecision{Float64},Base.TwicePrecision{Float64}}}},NamedTuple{(:x, :y, 

[Lichriszz]

Also, I don't think the initial condition is specified in this example. I am not sure how this simulation works.

[navidcy]

Hi @Lichriszz,

1. could you clarify where you got this example from?

2. can you printout your versioninfo() output?

[Lichriszz]

Hi,

Thanks for the reply.
I got the example from https://clima.github.io/OceananigansDocumentation/v0.39.0/library/#Output-writers.
And here is the version information.

Platform Info:
OS: macOS (x86_64-apple-darwin18.7.0)
CPU: Intel(R) Core(TM) i5-1038NG7 CPU @ 2.00GHz
WORD_SIZE: 64
LIBM: libopenlibm
LLVM: libLLVM-9.0.1 (ORCJIT, icelake-client)
Environment:
JULIA_NUM_THREADS = 4
JULIA_PKG_SERVER = pkg.juliahub.com
JULIA_DEPOT_PATH = /Users/lichriszz/.julia:/Applications/JuliaPro-1.5.3-1.app/Contents/Resources/julia/Contents/Resources/julia/local/share/julia:/Applications/JuliaPro-1.5.3-1.app/Contents/Resources/julia/Contents/Resources/julia/share/julia
JULIA_LOAD_PATH = /Users/lichriszz/.julia/environments/JuliaPro_v1.5.3-1:@:@v#.#:@StdLib

[navidcy]

Also output of using Pkg; Pkg.status()? :)

[Lichriszz]

Status ~/.julia/environments/JuliaPro_v1.5.3-1/Project.toml
[c52e3926] Atom v0.12.25 ⚲
[7073ff75] IJulia v1.23.1
[033835bb] JLD2 v0.3.3
[e5e0dc1b] Juno v0.8.4 ⚲
[9e8cae18] Oceananigans v0.47.1
[4722fa14] PkgAuthentication v1.1.0
[91a5bcdd] Plots v1.10.3
[44d3d7a6] Weave v0.10.6

[navidcy]

Seems like you are using Oceananigans v0.47.1 but looking at the documentation of version v0.39.0. Is this correct? Something might have changed in between the two versions...

Have a look at here: https://clima.github.io/OceananigansDocumentation/v0.47.1/library/#Output-writers
I feel the examples have been updated.

Let me know if you still have issues.

[navidcy]

[navidcy]

perhaps @ali-ramadhan or @glwagner have some more insight...

[ali-ramadhan]

@Lichriszz Sorry for the confusion.

Like @navidcy pointed out, I think we changed the name of the keyword argument from filename to filepath for NetCDFOutputWriter at some point recently but v0.47.1 should be using filepath.

Are you sure the v0.47.1 docs use filename for NetCDFOutputWriter? The examples at https://clima.github.io/OceananigansDocumentation/v0.47.1/library/#Oceananigans.OutputWriters.NetCDFOutputWriter-Tuple{Any,Any} seem to all use filepath (at least from what I can see and search).

[Lichriszz]

Oh sorry, I was looking at the wrong version. Thanks for explaining!

[ali-ramadhan]

I think Google is especially bad at linking you to the latest/current docs for Julia packages.

So many times it sent me to some ancient version of the docs so now I've started checking the version every time I open the docs from any search engine haha.

[tomchor]

I could reproduce the error here using version 0.51.0. The problem is that the keyword options for NetCDFOutputWriter have changed. You have to change your last line to:

julia> simulation.output_writers[:field_writer] =
           NetCDFOutputWriter(model, fields, filepath="fields.nc", schedule=TimeInterval(60))

Basically the gist of the example is the same between 0.39 and 0.47, but some of the keywords used changed a bit, which is why you're getting an error (and probably because you didn't notice the change, since it was very minor).

Most examples in the Oceananigans docs are routinely tested to make sure they work! So it's good to always make sure you get the examples from the version of the docs that match your installed version :)

[tomchor]

Just a note, if you want to run your example with a more recent version of Oceananigans (which I guess is advised, no?) you will also have to change the second line to

grid = RegularRectilinearGrid(size=(16, 16, 16), extent=(1, 1, 1));

to match the more recent docs, otherwise you'll run into a similar error.