`run!(simulation)` hangs when using an `OutputWriter`

[jbisits]

When running the example, run!(simulation) now freezes. I then have to exit it using control C repeatedly and get an error that looks similar to this issue,

warning: force throwing a sigint 
internal error: encountered unexpected error in runtime

There is also an old Oceananigans.jl issue where run!(simulation) hangs and looks to have been solved with package versions.

This has only appeared recently and I think (but am not completely sure) it was after upgrading packages.

[jbisits]

Turns out run!(simulation) only hangs when trying to save output. By commenting out lines 228-238 (where the output writer is setup)

    simulation.output_writers[:outputs] = save_file == :netcdf ?
                                            NetCDFOutputWriter(model, outputs; filename,
                                                            overwrite_existing = overwrite_saved_output,
                                                            schedule = TimeInterval(save_schedule),
                                                            dimensions = dims,
                                                            output_attributes = oa
                                                            ) :
                                            JLD2OutputWriter(model, outputs;
                                                            filename,
                                                            schedule = TimeInterval(save_schedule),
                                                            overwrite_existing = overwrite_saved_output)

the simulation runs fine though clearly no output is saved.

[jbisits]

@taimoorsohail

[jbisits]

Correctly runs and saves when only saving S and T tracers so must have something to do with custom outputs.

[jbisits]

It seems like the problem is with η_space. If I replace η_space with a Reduction of ϵ I can still calculate the Kolmogorov scale simply so maybe this is the best approach.