When you implement Hard Memory Controller (HMC) in Cyclone® V devices in Quartus® II software version 11.1SP2, the mem_ck and mem_ck_n pins do not show up in the pin planner.
Device Family: Cyclone® V GX
Type: Answers, Errata
Area: EMIF, Intellectual Property
IP Product: DDR2 SDRAM Controller MegaCore supporting UniPHY
This issue has been fixed in the Quartus II software version 12.0.