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  • to_netcdf() fails to write if input is read from netcdf3_classic · 6 ✖
id html_url issue_url node_id user created_at updated_at ▲ author_association body reactions performed_via_github_app issue
477653931 https://github.com/pydata/xarray/issues/2822#issuecomment-477653931 https://api.github.com/repos/pydata/xarray/issues/2822 MDEyOklzc3VlQ29tbWVudDQ3NzY1MzkzMQ== hellkite500 5186647 2019-03-28T15:48:04Z 2019-03-28T15:48:04Z NONE

Interesting! I wonder why using the netCDF4 python interface works fine with this scenario. It must not be using the nccopy code.

I will see if I can test a newer netcdf library. This is definitely an edge case, but thanks for providing a workaround!

The netCDF file is an excerpt from a hydrology water modeling input file. Definitely a bit of legacy workflows and files involved.

 
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   to_netcdf() fails to write if input is read from netcdf3_classic 422903285
475487497 https://github.com/pydata/xarray/issues/2822#issuecomment-475487497 https://api.github.com/repos/pydata/xarray/issues/2822 MDEyOklzc3VlQ29tbWVudDQ3NTQ4NzQ5Nw== shoyer 1217238 2019-03-22T04:08:32Z 2019-03-22T04:08:32Z MEMBER

I can reproduce this with libnetcdf 4.6.2.

It looks like this problem is associated with having a _NCProperties attribute on a netCDF3 file: ```

netCDF4.Dataset('some_netcdf_classic_file_simple.nc') <class 'netCDF4._netCDF4.Dataset'> root group (NETCDF3_CLASSIC data model, file format NETCDF3): _NCProperties: version=1|netcdflibversion=4.6.1|hdf5libversion=1.8.20 Conventions: CF-1.5 featureType: timeSeries NCO: netCDF Operators version 4.7.5 (Homepage = http://nco.sf.net, Code = http://github.com/nco/nco) nco_openmp_thread_number: 1 dimensions(sizes): feature_id(1) variables(dimensions): >i4 Q_TYPE(feature_id), >f4 lat(feature_id), >f4 lon(feature_id) groups: ```

This appears to be fixed in libnetcdf 4.6.3 (https://github.com/Unidata/netcdf-c/issues/803), if you can upgrade to that version.

In the meantime, you can manually delete the _NCProperties attribute, e.g., del data.attrs['_NCProperties']

Out of curiosity, where did this netCDF file come from?

 
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   to_netcdf() fails to write if input is read from netcdf3_classic 422903285
474907748 https://github.com/pydata/xarray/issues/2822#issuecomment-474907748 https://api.github.com/repos/pydata/xarray/issues/2822 MDEyOklzc3VlQ29tbWVudDQ3NDkwNzc0OA== hellkite500 5186647 2019-03-20T16:13:43Z 2019-03-20T16:13:43Z NONE

minimal_example.tar.gz Here is a netcdf file and the minimal code to produce AttributeError: NetCDF: String match to name in use

 
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   to_netcdf() fails to write if input is read from netcdf3_classic 422903285
474871120 https://github.com/pydata/xarray/issues/2822#issuecomment-474871120 https://api.github.com/repos/pydata/xarray/issues/2822 MDEyOklzc3VlQ29tbWVudDQ3NDg3MTEyMA== shoyer 1217238 2019-03-20T15:02:22Z 2019-03-20T15:02:22Z MEMBER

OK, in that case please provide a full example that I can run.

 
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   to_netcdf() fails to write if input is read from netcdf3_classic 422903285
474837398 https://github.com/pydata/xarray/issues/2822#issuecomment-474837398 https://api.github.com/repos/pydata/xarray/issues/2822 MDEyOklzc3VlQ29tbWVudDQ3NDgzNzM5OA== hellkite500 5186647 2019-03-20T13:50:07Z 2019-03-20T13:50:07Z NONE

with xr.open_dataset('some_netcdf_classic_file') as ds: data = ds # do something with data data.to_netcdf('some_new_file', 'w') or

``` with xr.open_dataset('some_netcdf_classic_file') as ds: data = ds.load()

do something with data

data.to_netcdf('some_new_file', 'w') ```

I just tried both of these in a minimal example and I still get the same exception. 

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   to_netcdf() fails to write if input is read from netcdf3_classic 422903285
474641356 https://github.com/pydata/xarray/issues/2822#issuecomment-474641356 https://api.github.com/repos/pydata/xarray/issues/2822 MDEyOklzc3VlQ29tbWVudDQ3NDY0MTM1Ng== shoyer 1217238 2019-03-20T00:54:34Z 2019-03-20T00:54:43Z MEMBER

When you leave the with context, the original file is automatically closed.

But something like either of these should work: with xr.open_dataset('some_netcdf_classic_file') as ds: data = ds # do something with data data.to_netcdf('some_new_file', 'w') or ``` with xr.open_dataset('some_netcdf_classic_file') as ds: data = ds.load()

do something with data

data.to_netcdf('some_new_file', 'w') ```

 
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   to_netcdf() fails to write if input is read from netcdf3_classic 422903285

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