When there are multiple external memory interfaces placed in the same I/O column and the Arria® 10 EMIF IP Diagnostics tab Calibration Debug Options parameters are not configured correctly, a Quartus® Prime software internal error message of this type may occur:
Internal Error: Sub-system: EMIF, File: /quartus/periph/emif/emif_gen6_netlist_modifier.cpp, Line: 1213
Expected only one, but found 4 atoms with SOFT_NIOS_ADDR port connected!
Configure the Diagnostics tab Calibration Debug Options for the EMIF Debug tookit, daisy chaining, and Interface ID parameters correctly for each interface.
Refer to the Arria_10_Debugging_Multiple_EMIFs wiki page for details which shows an example project containing 3 interfaces with daisy-chained EMIF Toolkit connections.
This problem is scheduled to be fixed in a future release of the Quartus Prime software.