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Question: Which PCIe slot should I use for Thunderbolt AIC card?(10/1/2017) Answer: The X299 platform doesn't have a specific slot for Thunderbolt AIC card.
The Thunderbolt™ AIC card is compatible with all PCIe slots from CPU.
If PCIe slot is enabled (depends on CPU), thunderbolt will be detected under the OS.
Please see below for PCIe lanes configuration based on CPU.
If you install CPU with 44 lanes, PCIE1/PCIE2/PCIE3/PCIE5 will run at x16/x8/x16/x0 or x8/x8/x16/x8.
You can install a Thunderbolt card on PCIE1/PCIE2/PCIE3/PCIE5 slot.
If you install CPU with 28 lanes, PCIE1/PCIE2/PCIE3/PCIE5 will run at x16/x0/x8/x0 or x8/x0/x8/x8.
You can install a Thunderbolt card on PCIE1/ PCIE3/PCIE5 slot.
If you install CPU with 16 lanes, PCIE1/PCIE2/PCIE3/PCIE5 will run at x16/x0/x0/x0 or x8/x0/x4/x0.
You can install a Thunderbolt card on PCIE1/ PCIE3 slot.