The design given with "Using High-Performance Controller II with Native Interface Design" under Altmemphy design tutorial (PDF) fails to simulate because it is missing a file in the simulation directory.
To simulate properly, copy /native_to_avalon_adaptor/source/ddr2_hpcII/ ddr2_hpcII_phy_alt_mem_phy_pll.mif to the native_to_avalon_adaptor/source/simulation/modelsim folder. The MIF file is needed to simulate any design with Altmemphy based High Performance Controller for Stratix® II series devices.