I have this error when opening my netcdf file.
The code was working before.
How do I fix this ?
Traceback (most recent call last):
File "", line 1, in
...
File "file.py", line 71, in gather_vgt
return xr.open_dataset(filename)
File "/.../lib/python3.6/site-packages/xarray/backends/api.py", line
286, in open_dataset
autoclose=autoclose)
File "/.../lib/python3.6/site-packages/xarray/backends/netCDF4_.py",
line 275, in open
ds = opener()
File "/.../lib/python3.6/site-packages/xarray/backends/netCDF4_.py",
line 199, in _open_netcdf4_group
ds = nc4.Dataset(filename, mode=mode, **kwargs)
File "netCDF4/_netCDF4.pyx", line 2015, in
netCDF4._netCDF4.Dataset.init
File "netCDF4/_netCDF4.pyx", line 1636, in
netCDF4._netCDF4._ensure_nc_success
OSError: [Errno -101] NetCDF: HDF error: b'file.nc'
When I try to open the same netcdf file with h5py I get this error :
OSError: Unable to open file (file locking disabled on this file
system (use HDF5_USE_FILE_LOCKING environment variable to override),
errno = 38, error message = '...')
You must be in this situation :
In order to read your hdf5 or netcdf files, you need set this environment variable :
HDF5_USE_FILE_LOCKING=FALSE
For references, this was introduced in HDF5 version 1.10.1,
Added a mechanism for disabling the SWMR file locking scheme.
The file locking calls used in HDF5 1.10.0 (including patch1)
will fail when the underlying file system does not support file
locking or where locks have been disabled. To disable all file
locking operations, an environment variable named
HDF5_USE_FILE_LOCKING can be set to the five-character string
'FALSE'. This does not fundamentally change HDF5 library
operation (aside from initial file open/create, SWMR is lock-free),
but users will have to be more careful about opening files
to avoid problematic access patterns (i.e.: multiple writers) >that the file locking was designed to prevent.
Additionally, the error message that is emitted when file lock
operations set errno to ENOSYS (typical when file locking has been
disabled) has been updated to describe the problem and potential
resolution better.
(DER, 2016/10/26, HDFFV-9918)
