Serialize ImmersedBoundaryGrid by converting immersed boundary functions to arrays?

[glwagner]

Right now we just punt on serializing immersed boundary grids:

Oceananigans.jl/src/OutputWriters/output_writer_utils.jl

Lines 56 to 61 in adffd0c

	function serializeproperty!(file, location, p::ImmersedBoundaryGrid)
	# Note: when we support array representations of immersed boundaries, we should save those too.
	@warn "Cannot serialize ImmersedBoundaryGrid; serializing underlying grid instead."
	file[location] = p.grid
	return nothing
	end

Mainly the issue is that we can't serialize functions. But we could convert any function-based immersed boundary implementation to an array and serialize that.

[francispoulin]

Sorry for the silly question but what does it mean to serialize a function? It sounds to me like it's going from parallel to serial but I don't think that's right.

[glwagner]

"Serialization" means "saving to disk":

https://en.wikipedia.org/wiki/Serialization

Functions can't be serialized by JLD2:

julia> using JLD2

julia> file = jldopen("test.jld2", "a+")
JLDFile /Users/gregorywagner/Projects/OceanTurbulenceParameterEstimation.jl/test.jld2 (read/write)
  (no datasets)

julia> f(x) = println("Hello world!")
f (generic function with 1 method)

julia> file["f"] = f
f (generic function with 1 method)

julia> close(file)

julia> exit()

# Restart julia
$ julia   
               _
   _       _ _(_)_     |  Documentation: https://docs.julialang.org
  (_)     | (_) (_)    |
   _ _   _| |_  __ _   |  Type "?" for help, "]?" for Pkg help.
  | | | | | | |/ _` |  |
  | | |_| | | | (_| |  |  Version 1.6.5 (2021-12-19)
 _/ |\__'_|_|_|\__'_|  |  Official https://julialang.org/ release
|__/                   |

julia> using JLD2

julia> file = jldopen("test.jld2")
JLDFile /Users/gregorywagner/Projects/OceanTurbulenceParameterEstimation.jl/test.jld2 (read-only)
 └─🔢 f

julia> f = file["f"]
┌ Warning: type Main.#f does not exist in workspace; reconstructing
└ @ JLD2 ~/.julia/packages/JLD2/b0tI9/src/data/reconstructing_datatypes.jl:364
JLD2.ReconstructedTypes.var"##Main.#f#257"()

julia> f(1)
ERROR: MethodError: objects of type JLD2.ReconstructedTypes.var"##Main.#f#257" are not callable
Stacktrace:
 [1] top-level scope
   @ REPL[5]:1

[glwagner]

I guess in our terminology "saving" is a bit more restricted than "serializing". When we "save" an object, we do it in a way that might be readable from Python or MATLAB (for example). This means that we only "save" common types like numbers, arrays, strings. Anything we output to NetCDF is "saved". When we "serialize" we might embed a Julia struct in a file. So when we serialize something we can only load it back from Julia. We can only serialize with JLD2.

[glwagner]

Done