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  • HDF error when trying to write Dataset read with rasterio to NetCDF · 8 ✖

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  • MEMBER · 8 ✖
id html_url issue_url node_id user created_at updated_at ▲ author_association body reactions performed_via_github_app issue
1468827469 https://github.com/pydata/xarray/issues/2535#issuecomment-1468827469 https://api.github.com/repos/pydata/xarray/issues/2535 IC_kwDOAMm_X85XjIdN kmuehlbauer 5821660 2023-03-14T20:53:28Z 2023-03-14T20:53:28Z MEMBER

Just a heads up, I can't reproduce this with latest packages from conda-forge for neither for xr.open_rasterio nor xr.open_dataset with engine=rasterio. Maybe the issue got resolved upstream. 

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   HDF error when trying to write Dataset read with rasterio to NetCDF 376389539
499894324 https://github.com/pydata/xarray/issues/2535#issuecomment-499894324 https://api.github.com/repos/pydata/xarray/issues/2535 MDEyOklzc3VlQ29tbWVudDQ5OTg5NDMyNA== dcherian 2448579 2019-06-07T13:55:36Z 2019-06-07T13:55:36Z MEMBER

HDF error usually means a corrupt file. Does ncdump -h work on your file?

I've found that sometimes ncdump -h will succeed but there'll still be some corrupt data which will result in an error when you try to load variable values

 
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   HDF error when trying to write Dataset read with rasterio to NetCDF 376389539
445944261 https://github.com/pydata/xarray/issues/2535#issuecomment-445944261 https://api.github.com/repos/pydata/xarray/issues/2535 MDEyOklzc3VlQ29tbWVudDQ0NTk0NDI2MQ== shoyer 1217238 2018-12-10T19:37:02Z 2018-12-10T19:37:02Z MEMBER

This looks like a binary incompatibility issue with wheels for rasterio and netCDF4 on PyPI.

Good alternatives (for now) would be building from source or using conda-forge.

 
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   HDF error when trying to write Dataset read with rasterio to NetCDF 376389539
436257224 https://github.com/pydata/xarray/issues/2535#issuecomment-436257224 https://api.github.com/repos/pydata/xarray/issues/2535 MDEyOklzc3VlQ29tbWVudDQzNjI1NzIyNA== fmaussion 10050469 2018-11-06T13:45:34Z 2018-11-06T13:45:34Z MEMBER

I can reproduce this on my machine - also linux. This is going to be hard to track down though. 

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   HDF error when trying to write Dataset read with rasterio to NetCDF 376389539
436254011 https://github.com/pydata/xarray/issues/2535#issuecomment-436254011 https://api.github.com/repos/pydata/xarray/issues/2535 MDEyOklzc3VlQ29tbWVudDQzNjI1NDAxMQ== jhamman 2443309 2018-11-06T13:34:30Z 2018-11-06T13:34:30Z MEMBER

Is this the same error you get with xarray/master?

 
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   HDF error when trying to write Dataset read with rasterio to NetCDF 376389539
436132832 https://github.com/pydata/xarray/issues/2535#issuecomment-436132832 https://api.github.com/repos/pydata/xarray/issues/2535 MDEyOklzc3VlQ29tbWVudDQzNjEzMjgzMg== shoyer 1217238 2018-11-06T05:09:37Z 2018-11-06T05:09:37Z MEMBER

Exactly what error message do you see?

 
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   HDF error when trying to write Dataset read with rasterio to NetCDF 376389539
436054649 https://github.com/pydata/xarray/issues/2535#issuecomment-436054649 https://api.github.com/repos/pydata/xarray/issues/2535 MDEyOklzc3VlQ29tbWVudDQzNjA1NDY0OQ== jhamman 2443309 2018-11-05T22:11:11Z 2018-11-05T22:11:36Z MEMBER

Interesting. I'm not seeing any difference when using scipy or netcdf4 or h5netcdf.

(by the way, thank you for the reproducible example)

 
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   HDF error when trying to write Dataset read with rasterio to NetCDF 376389539
436017050 https://github.com/pydata/xarray/issues/2535#issuecomment-436017050 https://api.github.com/repos/pydata/xarray/issues/2535 MDEyOklzc3VlQ29tbWVudDQzNjAxNzA1MA== jhamman 2443309 2018-11-05T20:07:29Z 2018-11-05T20:07:29Z MEMBER

@loicdtx - thanks for the report. I just tried this using xarray master and didn't get an error. So, you could try that and see if that works. Since our last release, we've had a fairly significant refactor of the IO backends in xarray.

 
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   HDF error when trying to write Dataset read with rasterio to NetCDF 376389539

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