Reading a NetCDF file stored on an NFS-based filesystem such as your HOME or PERM gets stuck.
Current versions of NetCDF using HDF5 1.10 or newer implement a file locking feature to prevent data corruption in certain cases. Unfortunately, this feature is not supported on our NFS filesystems so accessing a netCDF file may result in the program getting stuck indefinitely. There are two workarounds for this problem:
Lustre being a parallel filesystem deals with locks in a different manner. If you copy/move your NetCDF files to a Lustre-based Filesystem such as SCRATCH or HPCPERM, you should be able to work with it without experiencing the problem.
If you wish to continue using the files from your NFS-based Filesystem such as HOME or PERM, you may disable the file locking feature defining the following environment variable in your shell script or interactive sessionbefore running your program:
export HDF5_USE_FILE_LOCKING=FALSE |
Similarly, if you wish to disable it from a Python Script or Python session, you may add the following line:
os.environ['HDF5_USE_FILE_LOCKING']='FALSE' |
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