Altera IP Compiler for PCI Express - Manual (Page 232)

14–12 Chapter 14: External PHYs
External PHY Constraint Support
IP Compiler for PCI Express User Guide August 2014 Altera Corporation
1 To meet timing for the external PHY in the Cyclone III family, you must avoid using
dual-purpose V
REF
pins.
If you are using an external PHY with a design that does not target a Cyclone II
device, you might need to modify the PLL instance required by some external PHYs
to function correctly.
To modify the PLL instance, follow these steps:
1. Copy the PLL source file referenced in your variation file from the
/ip/ip_compiler_for_pci_express/lib directory, where is the
directory in which you installed the IP Compiler for PCI Express, to your project
directory.
2. Use the parameter editor to edit the PLL to specify the device that the PLL uses.
3. Add the modified PLL source file to your Quartus II project.