time decoding error in reading CESM outputs (netCDF files)

[Ali]

Hi,

I am trying to use xarray to open CESM outputs in netCDF format.
Here is the error:
ValueError: unable to decode time units 'common_year since 1-1-1 0:0:0' with "calendar 'noleap'". Try opening your dataset with decode_times=False or installing cftime if it is not installed.

Apparently this is a common issue:

time decoding error with "days since" · Issue #521 · pydata/xarray

I am trying to use xray with some CESM POP model netCDF output, which supposedly follows CF-1.0 conventions. It is failing because the models time units are "'days since 0000-01-01 00:00:00". When ...

github.com

And I took their advice this way:
ds = xr.open_dataset('some_CESM_output_file.nc', decode_times=False)
ds.time_bound.attrs['calendar'] = ds.time.attrs['calendar']
ds = xr.decode_cf(ds, use_cftime=True)

However, still struggling with:
ValueError: zero not allowed as a reference year, does not exist in Julian or Gregorian calendars

I wonder if there is any trick to resolve this issue.

Thanks in advance for your suggestion,
Ali

 

[strandwg]

Hi,

I am trying to use xarray to open CESM outputs in netCDF format.
Here is the error:
ValueError: unable to decode time units 'common_year since 1-1-1 0:0:0' with "calendar 'noleap'". Try opening your dataset with decode_times=False or installing cftime if it is not installed.

Apparently this is a common issue:

time decoding error with "days since" · Issue #521 · pydata/xarray

I am trying to use xray with some CESM POP model netCDF output, which supposedly follows CF-1.0 conventions. It is failing because the models time units are "'days since 0000-01-01 00:00:00". When ...

github.com

And I took their advice this way:
ds = xr.open_dataset('some_CESM_output_file.nc', decode_times=False)
ds.time_bound.attrs['calendar'] = ds.time.attrs['calendar']
ds = xr.decode_cf(ds, use_cftime=True)

However, still struggling with:
ValueError: zero not allowed as a reference year, does not exist in Julian or Gregorian calendars

I wonder if there is any trick to resolve this issue.

Thanks in advance for your suggestion,
Ali

It appears you're looking at output from the land ice model, CISM?

 

[Ali]

It appears you're looking at output from the land ice model, CISM?

Well I am not quite sure this error is exactly related to which subdirectory. But it happened when I was trying to use xarray this way:
xr.open_mfdataset("/glade/scratch/afallah/CESM2_C4MIP/cesm2_1_0.B1850.f09_g17.CMIP6-piControl.001.uga_extension/arc/*/*/*.nc")

Even I tried to open smaller volume of data, but this also show another error!
MergeError: conflicting values for variable 'time_bnds' on objects to be combined. You can skip this check by specifying compat='override'.
xr.open_mfdataset("/glade/scratch/afallah/CESM2_C4MIP/cesm2_1_0.B1850.f09_g17.CMIP6-piControl.001.uga_extension/arc/atm/hist/*.nc")

 

[strandwg]

Well I am not quite sure this error is exactly related to which subdirectory. But it happened when I was trying to use xarray this way:
xr.open_mfdataset("/glade/scratch/afallah/CESM2_C4MIP/cesm2_1_0.B1850.f09_g17.CMIP6-piControl.001.uga_extension/arc/*/*/*.nc")

Even I tried to open smaller volume of data, but this also show another error!
MergeError: conflicting values for variable 'time_bnds' on objects to be combined. You can skip this check by specifying compat='override'.
xr.open_mfdataset("/glade/scratch/afallah/CESM2_C4MIP/cesm2_1_0.B1850.f09_g17.CMIP6-piControl.001.uga_extension/arc/atm/hist/*.nc")

The first error you noticed is from CISM output files, under glc/hist/*nc.

The second error probably comes from the "cam.i." files under atm/hist/*nc, which aren't model output history files.

 

[Ali]

The first error you noticed is from CISM output files, under glc/hist/*nc.

The second error probably comes from the "cam.i." files under atm/hist/*nc, which aren't model output history files.

The second error is actually related to xr.open_mfdataset and could be resolved by adding this part: ,compat="override", data_vars='minimal', coords='minimal'

concat_dim getting added to *all* variables of multifile datasets · Issue #2064 · pydata/xarray

Code Sample Using the following example data set: example_jan.nc #!/usr/bin/env python3 import xarray ds = xarray.open_mfdataset('example_jan.nc', concat_dim='Time') print(ds) The result from xarra...

github.com

And for the first error, I can skip glc.