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If you have a setup in which you have 2 CPU's, and for example, each has 40 PCI lanes, could you use a motherboard with a total of 80 PCI lanes, or would you only have the 40 PCI lanes from the individual CPU.

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Depends on how the motherboard is also set up. It is certainly possible to use lanes from both CPUs.

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I think you would 40 for each cpu, with expansion cards interfacing with their respective cpu.

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