An emulator is disclosed that allows for diagnoses of failures or defects within the emulator. A map of faulty resources is generated to identify which resources should be avoided during compilation. Thus, in a transparent and automated manner, defects found during diagnostics are stored in a database of unusable emulator resources. A compiler has access to the database and compiles the design taking into account unusable resources. In another embodiment, the defects of an emulator board are stored on the emulator board itself. This allows each board to store its own maintenance information that can be used at the manufacturing site for changing defective chips. Defects stored on the board itself allow the defects to be obtained independent of a position of a board within the emulator to simplify identification of the faulty resource.