JuliaDataCubes / JuliaDataCubes/YAXArrays.jl

convert(Matrix, x') is very slow

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bug
Dominant language
Julia
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Description

convert(Matrix, x') is so slow that I haven't gotten it to finish. convert(Matrix, x) works just fine.

julia> using YAXArrays, Zarr

julia> path = "~/data/DataCube/v3.0.2/esdc-8d-0.25deg-1x720x1440-3.0.2.zarr"
"~/data/DataCube/v3.0.2/esdc-8d-0.25deg-1x720x1440-3.0.2.zarr"

julia> ds = open_dataset(path)
YAXArray Dataset
Shared Axes: 
↓ lon Sampled{Float64} -179.875:0.25:179.875 ForwardOrdered Regular Points,
→ lat Sampled{Float64} -89.875:0.25:89.875 ForwardOrdered Regular Points,
↗ Ti  Sampled{DateTime} [1979-01-05T00:00:00, …, 2021-12-31T00:00:00] ForwardOrdered Irregular Points
Variables: 
....


julia> mat = ds.air_temperature_2m[Ti = 1000]
╭──────────────────────────────╮
│ 1440×720 YAXArray{Float32,2} │
├──────────────────────────────┴──────────────────────────────────────── dims ┐
  ↓ lon Sampled{Float64} -179.875:0.25:179.875 ForwardOrdered Regular Points,
  → lat Sampled{Float64} -89.875:0.25:89.875 ForwardOrdered Regular Points
├──────────────────────────────────────────────────────
....

julia> @time convert(Matrix{Float32}, mat)
  1.809297 seconds (5.15 M allocations: 362.756 MiB, 5.92% gc time, 98.13% compilation time)
...

julia> @time convert(Matrix{Float32}, mat')

# has to be interrupted

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Research direction

Start by reproducing the Julia example with YAXArrays and Zarr, comparing convert(Matrix{Float32}, mat) with convert(Matrix{Float32}, mat'). Trace the conversion path for the transposed YAXArray and verify that the transposed conversion completes without the severe slowdown or excessive allocations shown.

Written by the indexing model from the issue text.

Assessment

Tech stack
julia
Domain
data, performance
Issue type
Bug
Difficulty
3/5
Estimated time
1-2 days
Activity status
Stale
Clarity
Mostly clear
Newbie friendliness
35/100

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