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  • rabernat · 3 ✖

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  • If a NetCDF file is chunked on disk, open it with compatible dask chunks · 3 ✖

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  • MEMBER · 3 ✖
id html_url issue_url node_id user created_at updated_at ▲ author_association body reactions performed_via_github_app issue
632294837 https://github.com/pydata/xarray/issues/1440#issuecomment-632294837 https://api.github.com/repos/pydata/xarray/issues/1440 MDEyOklzc3VlQ29tbWVudDYzMjI5NDgzNw== rabernat 1197350 2020-05-21T19:19:50Z 2020-05-21T19:19:50Z MEMBER

It seems to me that the there are lots of "layers" of "chunking", especially when you are talking about chunking an entire dataset,

To simplify a little bit, here we are only talking about reading a single store, i.e. one netcdf file or one zarr group. Also out of scope is the underlying storage medium (e.g. block size). 

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   If a NetCDF file is chunked on disk, open it with compatible dask chunks 233350060
632266536 https://github.com/pydata/xarray/issues/1440#issuecomment-632266536 https://api.github.com/repos/pydata/xarray/issues/1440 MDEyOklzc3VlQ29tbWVudDYzMjI2NjUzNg== rabernat 1197350 2020-05-21T18:23:13Z 2020-05-21T18:23:13Z MEMBER

Can we overload the chunks argument in open_xxx to do this? We are already adding support for chunks="auto" ...

This gets tricky, because we may want slightly different behavior depending on whether the underlying array store is chunked.

 
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   If a NetCDF file is chunked on disk, open it with compatible dask chunks 233350060
632183683 https://github.com/pydata/xarray/issues/1440#issuecomment-632183683 https://api.github.com/repos/pydata/xarray/issues/1440 MDEyOklzc3VlQ29tbWVudDYzMjE4MzY4Mw== rabernat 1197350 2020-05-21T16:13:46Z 2020-05-21T16:14:08Z MEMBER

We discussed this issue today in our pangeo coffee break. We think the following plan would be good:

  • [ ] Write a function called auto_chunk(variable) which examines a variable for the presence of a chunks attribute in encoding or within the data itself. Returns a new variable with chunked data.
  • [ ] Refactor open_zarr to call this function
  • [ ] Add it also to open_dataset to enable auto-chunking of netCDF and geotiff data

Should we have an option like chunk_size='native', or chunk_size='100MB', with chunks chosen to align with source chunks.

 
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   If a NetCDF file is chunked on disk, open it with compatible dask chunks 233350060

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