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  • NetCDF: Attempting netcdf-4 operation on netcdf-3 file · 4 ✖
id html_url issue_url node_id user created_at updated_at ▲ author_association body reactions performed_via_github_app issue
1485155675 https://github.com/pydata/xarray/issues/5515#issuecomment-1485155675 https://api.github.com/repos/pydata/xarray/issues/5515 IC_kwDOAMm_X85Yha1b kmuehlbauer 5821660 2023-03-27T13:59:40Z 2023-03-27T13:59:40Z MEMBER

Late to the party. If this is still an issue for you @mickaellalande, MODIS data can also be read using engine="rasterio" (needs rioxarray).

```python In [1]: import xarray as xr ...: with xr.open_dataset('source/MODIS/MOD10C1.A2000055.061.2020037182124.hdf', engine="rasterio") as ds: ...: display(ds) ...: <xarray.Dataset> Dimensions: (band: 1, x: 7200, y: 3600) Coordinates: * band (band) int64 1 * x (x) float64 -180.0 -179.9 -179.9 ... 179.9 180.0 * y (y) float64 89.97 89.92 89.88 ... -89.93 -89.98 spatial_ref int64 ... Data variables: Day_CMG_Snow_Cover (band, y, x) float32 ... Day_CMG_Clear_Index (band, y, x) float32 ... Day_CMG_Cloud_Obscured (band, y, x) float32 ... Snow_Spatial_QA (band, y, x) float32 ... Attributes: (12/50) ALGORITHMPACKAGEACCEPTANCEDATE: 09-2013 ALGORITHMPACKAGEMATURITYCODE: Normal ALGORITHMPACKAGENAME: MOD_PR10C1 ALGORITHMPACKAGEVERSION: 6 ASSOCIATEDINSTRUMENTSHORTNAME.1: MODIS ASSOCIATEDPLATFORMSHORTNAME.1: Terra ... ... SNOWCOVERPERCENT: 28 SOUTHBOUNDINGCOORDINATE: -90.0 SPSOPARAMETERS: none VERSIONID: 61 WESTBOUNDINGCOORDINATE: -180.0 ZONEIDENTIFIER: Other Grid System

```

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  NetCDF: Attempting netcdf-4 operation on netcdf-3 file 928381010
867821781 https://github.com/pydata/xarray/issues/5515#issuecomment-867821781 https://api.github.com/repos/pydata/xarray/issues/5515 MDEyOklzc3VlQ29tbWVudDg2NzgyMTc4MQ== shoyer 1217238 2021-06-24T17:30:07Z 2021-06-24T17:30:07Z MEMBER

OK, so the (misleading) error message here is ultimately coming from the underlying netCDF library, not Xarray.

Inspecting these files, it looks like they are HDF4 files, not netCDF3. We haven't really tested HDF4 files much with Xarray, but it would be nice to support them.

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  NetCDF: Attempting netcdf-4 operation on netcdf-3 file 928381010
867405472 https://github.com/pydata/xarray/issues/5515#issuecomment-867405472 https://api.github.com/repos/pydata/xarray/issues/5515 MDEyOklzc3VlQ29tbWVudDg2NzQwNTQ3Mg== mickaellalande 20254164 2021-06-24T07:24:35Z 2021-06-24T14:37:51Z CONTRIBUTOR

```pytb

RuntimeError Traceback (most recent call last) <ipython-input-4-db5c6cefdcdc> in <module> ----> 1 xr.open_dataset(root_data_path+'/MODIS/MOD10C1_Terra/MOD10C1.A2000055.061.2020037182124.hdf')

~/miniconda3/envs/phd_v3/lib/python3.8/site-packages/xarray/backends/api.py in open_dataset(filename_or_obj, group, decode_cf, mask_and_scale, decode_times, autoclose, concat_characters, decode_coords, engine, chunks, lock, cache, drop_variables, backend_kwargs, use_cftime, decode_timedelta) 543 544 with close_on_error(store): --> 545 ds = maybe_decode_store(store) 546 547 # Ensure source filename always stored in dataset object (GH issue #2550)

~/miniconda3/envs/phd_v3/lib/python3.8/site-packages/xarray/backends/api.py in maybe_decode_store(store, lock) 449 450 def maybe_decode_store(store, lock=False): --> 451 ds = conventions.decode_cf( 452 store, 453 mask_and_scale=mask_and_scale,

~/miniconda3/envs/phd_v3/lib/python3.8/site-packages/xarray/conventions.py in decode_cf(obj, concat_characters, mask_and_scale, decode_times, decode_coords, drop_variables, use_cftime, decode_timedelta) 578 encoding = obj.encoding 579 elif isinstance(obj, AbstractDataStore): --> 580 vars, attrs = obj.load() 581 extra_coords = set() 582 file_obj = obj

~/miniconda3/envs/phd_v3/lib/python3.8/site-packages/xarray/backends/common.py in load(self) 121 """ 122 variables = FrozenDict( --> 123 (_decode_variable_name(k), v) for k, v in self.get_variables().items() 124 ) 125 attributes = FrozenDict(self.get_attrs())

~/miniconda3/envs/phd_v3/lib/python3.8/site-packages/xarray/backends/netCDF4_.py in get_variables(self) 397 398 def get_variables(self): --> 399 dsvars = FrozenDict( 400 (k, self.open_store_variable(k, v)) for k, v in self.ds.variables.items() 401 )

~/miniconda3/envs/phd_v3/lib/python3.8/site-packages/xarray/core/utils.py in FrozenDict(args, kwargs) 436 437 def FrozenDict(args, kwargs) -> Frozen: --> 438 return Frozen(dict(*args, kwargs)) 439 440

~/miniconda3/envs/phd_v3/lib/python3.8/site-packages/xarray/backends/netCDF4_.py in <genexpr>(.0) 398 def get_variables(self): 399 dsvars = FrozenDict( --> 400 (k, self.open_store_variable(k, v)) for k, v in self.ds.variables.items() 401 ) 402 return dsvars

~/miniconda3/envs/phd_v3/lib/python3.8/site-packages/xarray/backends/netCDF4_.py in open_store_variable(self, name, var) 374 # netCDF4 specific encoding; save _FillValue for later 375 encoding = {} --> 376 filters = var.filters() 377 if filters is not None: 378 encoding.update(filters)

netCDF4/_netCDF4.pyx in netCDF4._netCDF4.Variable.filters()

netCDF4/_netCDF4.pyx in netCDF4._netCDF4._ensure_nc_success()

RuntimeError: NetCDF: Attempting netcdf-4 operation on netcdf-3 file ```

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  NetCDF: Attempting netcdf-4 operation on netcdf-3 file 928381010
866968227 https://github.com/pydata/xarray/issues/5515#issuecomment-866968227 https://api.github.com/repos/pydata/xarray/issues/5515 MDEyOklzc3VlQ29tbWVudDg2Njk2ODIyNw== shoyer 1217238 2021-06-23T16:03:58Z 2021-06-23T16:03:58Z MEMBER

could you kindly share the full error traceback?

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  NetCDF: Attempting netcdf-4 operation on netcdf-3 file 928381010

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