issues: 323333361
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| id | node_id | number | title | user | state | locked | assignee | milestone | comments | created_at | updated_at | closed_at | author_association | active_lock_reason | draft | pull_request | body | reactions | performed_via_github_app | state_reason | repo | type |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 323333361 | MDU6SXNzdWUzMjMzMzMzNjE= | 2132 | to_netcdf - RuntimeError: NetCDF: HDF error | 11750960 | closed | 0 | 3 | 2018-05-15T18:31:49Z | 2018-05-16T19:50:52Z | 2018-05-16T18:52:59Z | CONTRIBUTOR | I am trying to store data to a netcdf file, and have issues: Data is created according to: ```python import numpy as np import xarray as xr i = np.arange(4320) j = np.arange(4320) face = np.arange(13) v = xr.DataArray(np.random.randn(face.size, j.size, i.size), \ coords={'i': i, 'j': j, 'face': face}, dims=['face','j','i']) ``` The following works:
But this does not work:
with the following error message:
```
---------------------------------------------------------------------------
RuntimeError Traceback (most recent call last)
~/.miniconda3/envs/equinox/lib/python3.6/site-packages/xarray/backends/api.py in to_netcdf(dataset, path_or_file, mode, format, group, engine, writer, encoding, unlimited_dims)
656 dataset.dump_to_store(store, sync=sync, encoding=encoding,
--> 657 unlimited_dims=unlimited_dims)
658 if path_or_file is None:
~/.miniconda3/envs/equinox/lib/python3.6/site-packages/xarray/core/dataset.py in dump_to_store(self, store, encoder, sync, encoding, unlimited_dims)
1073 store.store(variables, attrs, check_encoding,
-> 1074 unlimited_dims=unlimited_dims)
1075 if sync:
~/.miniconda3/envs/equinox/lib/python3.6/site-packages/xarray/backends/common.py in store(self, variables, attributes, check_encoding_set, unlimited_dims)
362 self.set_variables(variables, check_encoding_set,
--> 363 unlimited_dims=unlimited_dims)
364
~/.miniconda3/envs/equinox/lib/python3.6/site-packages/xarray/backends/netCDF4_.py in set_variables(self, *args, **kwargs)
353 with self.ensure_open(autoclose=False):
--> 354 super(NetCDF4DataStore, self).set_variables(*args, **kwargs)
355
~/.miniconda3/envs/equinox/lib/python3.6/site-packages/xarray/backends/common.py in set_variables(self, variables, check_encoding_set, unlimited_dims)
401
--> 402 self.writer.add(source, target)
403
~/.miniconda3/envs/equinox/lib/python3.6/site-packages/xarray/backends/common.py in add(self, source, target)
264 else:
--> 265 target[...] = source
266
~/.miniconda3/envs/equinox/lib/python3.6/site-packages/xarray/backends/netCDF4_.py in __setitem__(self, key, value)
46 data = self.get_array()
---> 47 data[key] = value
48
netCDF4/_netCDF4.pyx in netCDF4._netCDF4.Variable.__setitem__()
netCDF4/_netCDF4.pyx in netCDF4._netCDF4.Variable._put()
netCDF4/_netCDF4.pyx in netCDF4._netCDF4._ensure_nc_success()
RuntimeError: NetCDF: HDF error
During handling of the above exception, another exception occurred:
RuntimeError Traceback (most recent call last)
<ipython-input-4-9da9ecadc6a6> in <module>()
2 if os.path.isfile(file_out):
3 os.remove(file_out)
----> 4 v.to_netcdf(file_out)
~/.miniconda3/envs/equinox/lib/python3.6/site-packages/xarray/core/dataarray.py in to_netcdf(self, *args, **kwargs)
1515 dataset = self.to_dataset()
1516
-> 1517 return dataset.to_netcdf(*args, **kwargs)
1518
1519 def to_dict(self):
~/.miniconda3/envs/equinox/lib/python3.6/site-packages/xarray/core/dataset.py in to_netcdf(self, path, mode, format, group, engine, encoding, unlimited_dims)
1135 return to_netcdf(self, path, mode, format=format, group=group,
1136 engine=engine, encoding=encoding,
-> 1137 unlimited_dims=unlimited_dims)
1138
1139 def to_zarr(self, store=None, mode='w-', synchronizer=None, group=None,
~/.miniconda3/envs/equinox/lib/python3.6/site-packages/xarray/backends/api.py in to_netcdf(dataset, path_or_file, mode, format, group, engine, writer, encoding, unlimited_dims)
660 finally:
661 if sync and isinstance(path_or_file, basestring):
--> 662 store.close()
663
664 if not sync:
~/.miniconda3/envs/equinox/lib/python3.6/site-packages/xarray/backends/netCDF4_.py in close(self)
419 ds = find_root(self.ds)
420 if ds._isopen:
--> 421 ds.close()
422 self._isopen = False
netCDF4/_netCDF4.pyx in netCDF4._netCDF4.Dataset.close()
netCDF4/_netCDF4.pyx in netCDF4._netCDF4.Dataset._close()
netCDF4/_netCDF4.pyx in netCDF4._netCDF4._ensure_nc_success()
RuntimeError: NetCDF: HDF error
```
The following may of some use:
Output of
|
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completed | 13221727 | issue |