xarray can open a nc file with open_dataset, but fails to load this nc file with load

[onion5376]

What is your issue?

Recently, I have downloaded chla data from copernicus marine service, and tried to regrid it with xarray. The sad thing is that the data always goes wrong in the load phase. I have checked that variables in test dataset could be plotted normally. I do know what happen to this. Any advice is appreciated.
The test code：

import xarray as xr
ds = xr.open_dataset("chla201601.nc")
ds.load()

Test dataset:
chla201601.zip

Error information:

Details

---------------------------------------------------------------------------
RuntimeError                              Traceback (most recent call last)
Cell In[3], line 1
----> 1 ds.load()

File [/usr/miniforge3/envs/xesmf_env/lib/python3.12/site-packages/xarray/core/dataset.py:880](http://localhost:8888/usr/miniforge3/envs/xesmf_env/lib/python3.12/site-packages/xarray/core/dataset.py#line=879), in Dataset.load(self, **kwargs)
    878 for k, v in self.variables.items():
    879     if k not in lazy_data:
--> 880         v.load()
    882 return self

File [/usr/miniforge3/envs/xesmf_env/lib/python3.12/site-packages/xarray/core/variable.py:981](http://localhost:8888/usr/miniforge3/envs/xesmf_env/lib/python3.12/site-packages/xarray/core/variable.py#line=980), in Variable.load(self, **kwargs)
    964 def load(self, **kwargs):
    965     """Manually trigger loading of this variable's data from disk or a
    966     remote source into memory and return this variable.
    967 
   (...)
    979     dask.array.compute
    980     """
--> 981     self._data = to_duck_array(self._data, **kwargs)
    982     return self

File [/usr/miniforge3/envs/xesmf_env/lib/python3.12/site-packages/xarray/namedarray/pycompat.py:134](http://localhost:8888/usr/miniforge3/envs/xesmf_env/lib/python3.12/site-packages/xarray/namedarray/pycompat.py#line=133), in to_duck_array(data, **kwargs)
    131     return loaded_data
    133 if isinstance(data, ExplicitlyIndexed):
--> 134     return data.get_duck_array()  # type: ignore[no-untyped-call, no-any-return]
    135 elif is_duck_array(data):
    136     return data

File [/usr/miniforge3/envs/xesmf_env/lib/python3.12/site-packages/xarray/core/indexing.py:837](http://localhost:8888/usr/miniforge3/envs/xesmf_env/lib/python3.12/site-packages/xarray/core/indexing.py#line=836), in MemoryCachedArray.get_duck_array(self)
    836 def get_duck_array(self):
--> 837     self._ensure_cached()
    838     return self.array.get_duck_array()

File [/usr/miniforge3/envs/xesmf_env/lib/python3.12/site-packages/xarray/core/indexing.py:831](http://localhost:8888/usr/miniforge3/envs/xesmf_env/lib/python3.12/site-packages/xarray/core/indexing.py#line=830), in MemoryCachedArray._ensure_cached(self)
    830 def _ensure_cached(self):
--> 831     self.array = as_indexable(self.array.get_duck_array())

File [/usr/miniforge3/envs/xesmf_env/lib/python3.12/site-packages/xarray/core/indexing.py:788](http://localhost:8888/usr/miniforge3/envs/xesmf_env/lib/python3.12/site-packages/xarray/core/indexing.py#line=787), in CopyOnWriteArray.get_duck_array(self)
    787 def get_duck_array(self):
--> 788     return self.array.get_duck_array()

File [/usr/miniforge3/envs/xesmf_env/lib/python3.12/site-packages/xarray/core/indexing.py:651](http://localhost:8888/usr/miniforge3/envs/xesmf_env/lib/python3.12/site-packages/xarray/core/indexing.py#line=650), in LazilyIndexedArray.get_duck_array(self)
    647     array = apply_indexer(self.array, self.key)
    648 else:
    649     # If the array is not an ExplicitlyIndexedNDArrayMixin,
    650     # it may wrap a BackendArray so use its __getitem__
--> 651     array = self.array[self.key]
    653 # self.array[self.key] is now a numpy array when
    654 # self.array is a BackendArray subclass
    655 # and self.key is BasicIndexer((slice(None, None, None),))
    656 # so we need the explicit check for ExplicitlyIndexed
    657 if isinstance(array, ExplicitlyIndexed):

File [/usr/miniforge3/envs/xesmf_env/lib/python3.12/site-packages/xarray/backends/netCDF4_.py:100](http://localhost:8888/usr/miniforge3/envs/xesmf_env/lib/python3.12/site-packages/xarray/backends/netCDF4_.py#line=99), in NetCDF4ArrayWrapper.__getitem__(self, key)
     99 def __getitem__(self, key):
--> 100     return indexing.explicit_indexing_adapter(
    101         key, self.shape, indexing.IndexingSupport.OUTER, self._getitem
    102     )

File [/usr/miniforge3/envs/xesmf_env/lib/python3.12/site-packages/xarray/core/indexing.py:1015](http://localhost:8888/usr/miniforge3/envs/xesmf_env/lib/python3.12/site-packages/xarray/core/indexing.py#line=1014), in explicit_indexing_adapter(key, shape, indexing_support, raw_indexing_method)
    993 """Support explicit indexing by delegating to a raw indexing method.
    994 
    995 Outer and[/or](http://localhost:8888/or) vectorized indexers are supported by indexing a second time
   (...)
   1012 Indexing result, in the form of a duck numpy-array.
   1013 """
   1014 raw_key, numpy_indices = decompose_indexer(key, shape, indexing_support)
-> 1015 result = raw_indexing_method(raw_key.tuple)
   1016 if numpy_indices.tuple:
   1017     # index the loaded np.ndarray
   1018     indexable = NumpyIndexingAdapter(result)

File [/usr/miniforge3/envs/xesmf_env/lib/python3.12/site-packages/xarray/backends/netCDF4_.py:113](http://localhost:8888/usr/miniforge3/envs/xesmf_env/lib/python3.12/site-packages/xarray/backends/netCDF4_.py#line=112), in NetCDF4ArrayWrapper._getitem(self, key)
    111     with self.datastore.lock:
    112         original_array = self.get_array(needs_lock=False)
--> 113         array = getitem(original_array, key)
    114 except IndexError:
    115     # Catch IndexError in netCDF4 and return a more informative
    116     # error message.  This is most often called when an unsorted
    117     # indexer is used before the data is loaded from disk.
    118     msg = (
    119         "The indexing operation you are attempting to perform "
    120         "is not valid on netCDF4.Variable object. Try loading "
    121         "your data into memory first by calling .load()."
    122     )

File src[/netCDF4/_netCDF4.pyx:4981](http://localhost:8888/netCDF4/_netCDF4.pyx#line=4980), in netCDF4._netCDF4.Variable.__getitem__()

File src[/netCDF4/_netCDF4.pyx:5953](http://localhost:8888/netCDF4/_netCDF4.pyx#line=5952), in netCDF4._netCDF4.Variable._get()

File src[/netCDF4/_netCDF4.pyx:2113](http://localhost:8888/netCDF4/_netCDF4.pyx#line=2112), in netCDF4._netCDF4._ensure_nc_success()

RuntimeError: NetCDF: HDF error

Main package information:

xarray 2024.9.0
numpy 2.0.2
netCDF 4 1.7.1
h5netcdf 1.4.0
python 3.12.7

The ram information:
total used free shared buff/cache available
Mem: 8.3Gi 2.1Gi 5.3Gi 45Mi 1.2Gi 6.2Gi
Swap: 3.9Gi 0B 3.9Gi

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