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  • loicdtx · 4 ✖

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  • HDF error when trying to write Dataset read with rasterio to NetCDF · 4 ✖

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id html_url issue_url node_id user created_at updated_at ▲ author_association body reactions performed_via_github_app issue
436261308 https://github.com/pydata/xarray/issues/2535#issuecomment-436261308 https://api.github.com/repos/pydata/xarray/issues/2535 MDEyOklzc3VlQ29tbWVudDQzNjI2MTMwOA== loicdtx 5638829 2018-11-06T13:57:52Z 2018-11-06T13:57:52Z NONE

@jhamman, yes, same error message when installing from master

 
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   HDF error when trying to write Dataset read with rasterio to NetCDF 376389539
436215439 https://github.com/pydata/xarray/issues/2535#issuecomment-436215439 https://api.github.com/repos/pydata/xarray/issues/2535 MDEyOklzc3VlQ29tbWVudDQzNjIxNTQzOQ== loicdtx 5638829 2018-11-06T11:05:39Z 2018-11-06T11:05:39Z NONE

@shoyer, below the full traceback; I installed everything with pip

mktmpenv -p python3 pip install xarray numpy netcdf4 pip install rasterio

``` Traceback (most recent call last): File "/home/loic/.virtualenvs/tmp-3caa6b25124e2f31/lib/python3.6/site-packages/xarray/backends/api.py", line 724, in to_netcdf unlimited_dims=unlimited_dims, compute=compute) File "/home/loic/.virtualenvs/tmp-3caa6b25124e2f31/lib/python3.6/site-packages/xarray/core/dataset.py", line 1179, in dump_to_store unlimited_dims=unlimited_dims) File "/home/loic/.virtualenvs/tmp-3caa6b25124e2f31/lib/python3.6/site-packages/xarray/backends/common.py", line 374, in store unlimited_dims=unlimited_dims) File "/home/loic/.virtualenvs/tmp-3caa6b25124e2f31/lib/python3.6/site-packages/xarray/backends/netCDF4_.py", line 406, in set_variables super(NetCDF4DataStore, self).set_variables(args, *kwargs) File "/home/loic/.virtualenvs/tmp-3caa6b25124e2f31/lib/python3.6/site-packages/xarray/backends/common.py", line 413, in set_variables self.writer.add(source, target) File "/home/loic/.virtualenvs/tmp-3caa6b25124e2f31/lib/python3.6/site-packages/xarray/backends/common.py", line 272, in add target[...] = source File "/home/loic/.virtualenvs/tmp-3caa6b25124e2f31/lib/python3.6/site-packages/xarray/backends/netCDF4_.py", line 48, in setitem data[key] = value File "netCDF4/_netCDF4.pyx", line 4648, in netCDF4._netCDF4.Variable.setitem File "netCDF4/_netCDF4.pyx", line 4913, in netCDF4._netCDF4.Variable._put File "netCDF4/_netCDF4.pyx", line 1754, in netCDF4._netCDF4._ensure_nc_success RuntimeError: NetCDF: HDF error

During handling of the above exception, another exception occurred:

Traceback (most recent call last): File "rasterio_reprex.py", line 41, in <module> ds.to_netcdf(nc_name) File "/home/loic/.virtualenvs/tmp-3caa6b25124e2f31/lib/python3.6/site-packages/xarray/core/dataset.py", line 1254, in to_netcdf compute=compute) File "/home/loic/.virtualenvs/tmp-3caa6b25124e2f31/lib/python3.6/site-packages/xarray/backends/api.py", line 729, in to_netcdf store.close() File "/home/loic/.virtualenvs/tmp-3caa6b25124e2f31/lib/python3.6/site-packages/xarray/backends/netCDF4_.py", line 474, in close ds.close() File "netCDF4/_netCDF4.pyx", line 2276, in netCDF4._netCDF4.Dataset.close File "netCDF4/_netCDF4.pyx", line 2260, in netCDF4._netCDF4.Dataset._close File "netCDF4/_netCDF4.pyx", line 1754, in netCDF4._netCDF4._ensure_nc_success RuntimeError: NetCDF: HDF error ```

 
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   HDF error when trying to write Dataset read with rasterio to NetCDF 376389539
436062489 https://github.com/pydata/xarray/issues/2535#issuecomment-436062489 https://api.github.com/repos/pydata/xarray/issues/2535 MDEyOklzc3VlQ29tbWVudDQzNjA2MjQ4OQ== loicdtx 5638829 2018-11-05T22:39:36Z 2018-11-05T22:39:36Z NONE

yes, that's interesting... are you using a different OS? Let me know if there's something else I can help with.

 
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   HDF error when trying to write Dataset read with rasterio to NetCDF 376389539
436053420 https://github.com/pydata/xarray/issues/2535#issuecomment-436053420 https://api.github.com/repos/pydata/xarray/issues/2535 MDEyOklzc3VlQ29tbWVudDQzNjA1MzQyMA== loicdtx 5638829 2018-11-05T22:07:16Z 2018-11-05T22:07:16Z NONE

Hi @jhamman, just tried what you suggest. Apparently it's a scipy vs netCDF4 thing; it works with scipy but not with netCDF4 on both master HEAD and the latest stable release.

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

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