That is where it is locked I would suspect, I have never seen a PCIe ratio/multiplier option in a BIOS, however i would suppose it possible or existed on boards I never owned. Typically, the PCIe on the chipset has it's own clock, separate from the system clock. Clarksdale/Allendale have the PCIe on the CPU but also has it's own clock -- supplied by the board.
yes, that is the level of complexity, the tight integration of all the different IOs. Sux for the enthusiast, but great for the volume OEMs and system builders -- two less specifications to design two (two different clock generators and the associated traces).






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