error from netCDF in cf.write
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Description
I am processing some CMIP6 data on Jasmin (making time-means). I get the following error. I realise that you probably need more background to diagnose it, but perhaps it's obvious from this much information? As a result of the error, the file is not properly written, just the start of it.
Thanks. Jonathan
Traceback (most recent call last):
File "/home/users/jonathan/bin/grouptime", line 97, in <module>
cf.write(n,ofile)
File "/apps/jasmin/jaspy/miniforge_envs/jaspy3.12/mf3-25.3.0-3/envs/jaspy3.12-mf3-25.3.0-3-v20250704/lib/python3.12/site-packages/cfdm/read_write/write.py", line 826, in __new__
netcdf.write(
File "/apps/jasmin/jaspy/miniforge_envs/jaspy3.12/mf3-25.3.0-3/envs/jaspy3.12-mf3-25.3.0-3-v20250704/lib/python3.12/site-packages/cfdm/decorators.py", line 171, in verbose_override_wrapper
return method_with_verbose_kwarg(*args, **kwargs)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/apps/jasmin/jaspy/miniforge_envs/jaspy3.12/mf3-25.3.0-3/envs/jaspy3.12-mf3-25.3.0-3-v20250704/lib/python3.12/site-packages/cfdm/read_write/netcdf/netcdfwrite.py", line 5232, in write
self._file_io_iteration(
File "/apps/jasmin/jaspy/miniforge_envs/jaspy3.12/mf3-25.3.0-3/envs/jaspy3.12-mf3-25.3.0-3-v20250704/lib/python3.12/site-packages/cfdm/read_write/netcdf/netcdfwrite.py", line 5478, in _file_io_iteration
self._write_global_attributes(fields)
File "/apps/jasmin/jaspy/miniforge_envs/jaspy3.12/mf3-25.3.0-3/envs/jaspy3.12-mf3-25.3.0-3-v20250704/lib/python3.12/site-packages/cfdm/read_write/netcdf/netcdfwrite.py", line 4610, in _write_global_attributes
g["netcdf"].setncattr(
File "src/netCDF4/_netCDF4.pyx", line 3087, in netCDF4._netCDF4.Dataset.setncattr
File "src/netCDF4/_netCDF4.pyx", line 1858, in netCDF4._netCDF4._set_att
File "src/netCDF4/_netCDF4.pyx", line 6733, in netCDF4._netCDF4._strencode
UnicodeEncodeError: 'utf-8' codec can't encode characters in position 61-63: surrogates not allowed
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Research direction
Start with cfdm/read_write/netcdf/netcdfwrite.py at _write_global_attributes and the netCDF4 Dataset.setncattr call shown in the traceback. Reproduce cf.write in the reported Python environment and identify which global attribute contains the invalid surrogate characters. Done means the affected data can be written without the UnicodeEncodeError and the behavior is covered by an appropriate regression test.
Written by the indexing model from the issue text.
Assessment
- Tech stack
- python
- Domain
- data
- Issue type
- Bug
- Difficulty
- 3/5
- Estimated time
- 1-2 days
- Activity status
- Quiet
- Clarity
- Needs clarification
- Newbie friendliness
- 45/100