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H12SSL has two more PCIe x16 slots, and they are 4.0.

That is weird and should be fixed. Maybe restart or reset the BMC, powercycle the machine, or unplug the power to be sure and wait a while before powering up again. I do remember I had the same issue with a H11DSI-NT motherbeard. Also updating the BMC firmware and possibly also the motherboard...

Check the jumpers and the BIOS. There is a jumper setting to {dis,en}-able the onboard VGA. In the BIOS there is an option to prioritize off-board VGA (i.e. a graphics card in a PCIe slot). Via the IPMI network connection you should be able to get into the BIOS settings to set things right.

apparently this can be managed within the IPMI interface.

Ok, there you have it then. Even in theory H12 should not support a Zen1 CPU. It would have been a handy backwards compatibility option indeed. But who knows, maybe someone can still demonstrate that it actually does work, and Zen1 CPU lets all the PCIe slots in the H12 board operate as PCIe...

I do not believe zen1 will work in a H12SSL or H12DSL board until someone actually demonstrates it. And no funky adapted BIOS. Just a normal bios from the supermicro site. Too many people just shout: "it should work". Yes, in theory maybe. But does it actually work? Also, H12 boards have pcie...