I’m glad that it fixed your issue.
I don’t know what cause the HDF related error. But we have recently encountered the same error message HDF5-DIAG: Error detected in HDF5 (1.12.0) MPI-process 0: when the observation file was unintentionally removed. So, can you please double check if the path for the observation file ( under obs space.obsdatain.obsfilein key) is correct in your yaml file ? This might not be a reason for the error because the error message also said Exception: Reason: An exception occurred inside ioda while opening a variable.
The other thing is… JEDI-MPAS 1.0.0 requires IODA Version 2 format for the observation files. So I wonder which version of obs2ioda.x is used to generate your obs files: obs2ioda-v1 or obs2ioda-v2. Also please check if there is an executable bin/ioda-upgrade.x under your build directory. This executable converts the IODA V1 format into V2 format.