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FieldTimeSeries support for NetCDF #3935

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#5017
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FieldTimeSeries support for NetCDF#3935
#5017
@tomchor

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@tomchor
tomchor
opened on Nov 18, 2024

@ali-ramadhan and I are interesting in expanding FieldTimeSeries to support NetCDF.

None of us is super familiar with FTS, but it seems like, for the most part, all we need would be to figure out a way to reconstruct grids based on NetCDF output and figure out how to deal with memory access if the data is PartlyInMemory. Is that correct or are there other items that we pay attention to?

For the former we can output the relevant grid parameters to file and reconstruct it in a way that's already done for JLD2 whenever the grid can't be restored directly:

Oceananigans.jl/src/OutputReaders/field_time_series.jl

Lines 489 to 529 in 82ad840

if grid isa RectilinearGrid # we can try...
@info "Initial attempt to transfer grid to $architecture failed."
@info "Attempting to reconstruct RectilinearGrid on $architecture manually..."
Nx = file["grid/Nx"]
Ny = file["grid/Ny"]
Nz = file["grid/Nz"]
Hx = file["grid/Hx"]
Hy = file["grid/Hy"]
Hz = file["grid/Hz"]
xᶠᵃᵃ = file["grid/xᶠᵃᵃ"]
yᵃᶠᵃ = file["grid/yᵃᶠᵃ"]
zᵃᵃᶠ = file["grid/zᵃᵃᶠ"]
x = file["grid/Δxᶠᵃᵃ"] isa Number ? (xᶠᵃᵃ[1], xᶠᵃᵃ[Nx+1]) : xᶠᵃᵃ
y = file["grid/Δyᵃᶠᵃ"] isa Number ? (yᵃᶠᵃ[1], yᵃᶠᵃ[Ny+1]) : yᵃᶠᵃ
z = file["grid/Δzᵃᵃᶠ"] isa Number ? (zᵃᵃᶠ[1], zᵃᵃᶠ[Nz+1]) : zᵃᵃᶠ
topo = topology(grid)
N = (Nx, Ny, Nz)
# Reduce for Flat dimensions
domain = Dict()
for (i, ξ) in enumerate((x, y, z))
if topo[i] !== Flat
if !(ξ isa Tuple)
chopped_ξ = ξ[1:N[i]+1]
else
chopped_ξ = ξ
end
sξ = (:x, :y, :z)[i]
domain[sξ] = chopped_ξ
end
end
size = Tuple(N[i] for i=1:3 if topo[i] !== Flat)
halo = Tuple((Hx, Hy, Hz)[i] for i=1:3 if topo[i] !== Flat)
RectilinearGrid(architecture; size, halo, topology=topo, domain...)
else
throw(err)
end

We were also wondering if this is worth doing over one PR and a few small ones.

cc @glwagner

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