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Looking at the specs it seems to me like maybe the both support x16, but I can't tell.
It will be fine just leave it there
according to your own link it could sit in either the top slot or the 2nd slot both the same.
Multi-GPU CFX support
2 x PCIe 3.0 x 16 (supports x 16, x8/x4)
1 x PCIe 2.0 x 16 (at x4 mode)
3 x PCIe 2.0 x 1
Multi-GPU CFX support
2 x PCIe 3.0 x 16(supports x 16, x8/x4)
1 x PCIe 2.0 x 16(at x4 mode)
3 x PCIe 2.0 x 1
Without checking the manual to identify which are which I'd install the card in the top most slot as I mentiined earlier. But it'll be fine in the other x16 slot. No need to return it if it needs to be moved. Just power PC off, remove the side panel. Touch the case to ground yourself and remove the GPU and plug it in the other slot. Really isnt a difficult task
I think PCIE_X16_2 is x4 only and PCIE_X16_1 will run at x8 if two cards are installed.
And all of that only counts for Ryzen CPUs without Vega graphics. As the integrated graphics processors come with less lanes.
I'm not confident enough in myself to change it myself, so I'll just leave it as is.
Top of this page. Click Help, then click System Information. Look at the log and see if it says PCIE 16X under Primary Bus.
I'm not sure but you are correct that the manual has a really convoluted way of describing their PCIe layout.
The part of the spec sheet says that there are two PCIe 3.0 x16 Safe Slots that "support x16, x8/x4 modes). Which, the way I read it, says single population of either slot it should be running at x16 mode. But when running a card in each slot, one will be x8 and the other in x4 modes.
Primary Bus: PCI Express 4x
Looks like it needs changed.
It's been running at x4. Is this bad for the card? Is it damaged now?