Due to a problem in the Intel® Quartus® Prime Pro Edition Software v21.3 and earlier, you might see the following error during the fitter stage when a core design partition assignment exists on a level of hierarchy that contains periphery components:
Internal Error: Sub-system: CDB_ATOM, File: /quartus/db/cdb_atom/cdb_atom_sys.cpp, Line: 3000
To work around this problem, ensure that core design partition assignments are applied to levels of hierarchy that only contain core logic.
This problem is fixed beginning with the Intel® Quartus® Prime Pro Edition Software version 22.2.