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Specific PCIe ports goes to CPU and not via southbridge

According to an article over at scottlowe.org, the 'the [Intel Xeon] E5 processors integrate PCI Express root ports, providing upwards of 200 Gbps of throughput. This is compared to the use of the “Southbridge” with the 5500/5600 series CPUs, which were limited to about 50 Gbps.'

Later you can read you should use specific slots on the motherboard for 10GbE PCIe NICS (and probably
other high throughput cards):
Going back to the earlier discussion about PCIe root ports being integrated into the E5 CPUs, this leads to a consideration for the placement of PCIe cards. Make sure your high-speed cards aren’t inserted in a slot that runs through the C600 chipset southbridge. Make sure that you are using Gen2 x8 slot, and make sure that the slot is actually wired to support a x8 card (some slots on some systems have a x8 connector but are only wired for x4 throughput). Johnson recommends using either LoM, slot 2, slot 3, or slot 5 for 10 GbE PCIe NICs; this will ensure direct connections to one of the CPUs and not to the southbridge chipset.

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