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id node_id number title user state locked assignee milestone comments created_at updated_at ▲ closed_at author_association active_lock_reason draft pull_request body reactions performed_via_github_app state_reason repo type
614785886 MDU6SXNzdWU2MTQ3ODU4ODY= 4046 automatic chunking of zarr archive apatlpo 11750960 open 0     3 2020-05-08T14:42:00Z 2023-01-18T21:54:42Z   CONTRIBUTOR      

I store data in a zarr archive that is not chunked and the resulting zarr archive is chunked. This may be as simple usage question. I don't know how to turn this behavior off.

Code sample

Here is minimal example that reproduces the issue:

python ds = xr.DataArray(np.ones((200,800))).rename('foo').to_dataset() print('Initial chunks = {}'.format(ds.foo.chunks)) ds.to_zarr('test.zarr', mode='w') print('zarr archives contains: {}'.format(os.listdir('test.zarr/foo'))) ds = xr.open_zarr('test.zarr') print('Final chunks = {}'.format(ds.foo.chunks)) returns: Initial chunks = None zarr archives contains: ['.zarray', '.zattrs', '0.0', '0.1', '1.0', '1.1'] Final chunks = ((100, 100), (400, 400))

Expected Output

I would expect the archive to not to be chunked.

Versions

Output of <tt>xr.show_versions()</tt> INSTALLED VERSIONS ------------------ commit: None python: 3.7.6 | packaged by conda-forge | (default, Mar 23 2020, 23:03:20) [GCC 7.3.0] python-bits: 64 OS: Linux OS-release: 3.12.53-60.30-default machine: x86_64 processor: x86_64 byteorder: little LC_ALL: None LANG: en_US.UTF-8 LOCALE: en_US.UTF-8 libhdf5: 1.10.5 libnetcdf: 4.7.4 xarray: 0.15.2.dev29+g6048356 pandas: 1.0.3 numpy: 1.18.1 scipy: 1.4.1 netCDF4: 1.5.3 pydap: None h5netcdf: None h5py: None Nio: None zarr: 2.4.0 cftime: 1.1.1.2 nc_time_axis: None PseudoNetCDF: None rasterio: None cfgrib: None iris: None bottleneck: None dask: 2.13.0 distributed: 2.13.0 matplotlib: 3.2.1 cartopy: 0.17.0 seaborn: 0.10.0 numbagg: None pint: None setuptools: 46.1.3.post20200325 pip: 20.0.2 conda: None pytest: None IPython: 7.13.0 sphinx: None 
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     xarray 13221727 issue
283518232 MDU6SXNzdWUyODM1MTgyMzI= 1795 open_mfdataset concat_dim chunk apatlpo 11750960 open 0     2 2017-12-20T10:34:58Z 2020-01-07T16:19:39Z   CONTRIBUTOR      

open_mfdataset does not allow chunking along concat_dim.

As a result if specific chunking is sought along that dimension by the user it may be best not to pass chunks at the open_mfdataset stage and rechunk variables afterwards. This would be the case for example if chunks are large across files but small within files: https://github.com/apatlpo/lops-array/blob/master/sandbox/natl60_tseries_debug.ipynb

I believe this is difficult to anticipate for new users (like me).

Couldn't this be specified in the documentation of open_mfdataset?

 
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     xarray 13221727 issue

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