Unfortunately I am having no luck with this. I also tried black listing the GPU on the 16X slot based on guides I found online (eg:
http://www.se7ensins.com/forums/thre...-vfio.1371980/) but also had no luck.
I have an AMD r9 390 on the 16x slot and a Nvidia 610 on the 4x slot. I have a dual input monitor where the AMD card is connected to the HDMI input of the monitor and the Nvidia card connected to the VGA input of the monitor. I wanted to have the 390 used as the pci passthrough on KVM to a windows guest while the nvidia 610 would be used for the linux host.
I have been attempting this on both KDE mint 17.3 and Kubuntu 16.04. Currently using Kubuntu for this and given the current issues with AMD drivers and the latest Ubuntu version, I have about 10s to hit clt+alt+F1 before the display crashes. This is the only way I can make any changes to the system.
Once Kubuntu boots I can switch between the 2 inputs, the main desktop on the 390(DVI) and the extended on the 610(VGA) for a short while before the display crashes. No matter what I try, the DVI(R9 390)remains active. At one point running "dmesg | grep pci-stubs" show the 390 being claimed but the HDMI(390) display still worked when this happened????
I guess what I can try as a test is to probably try to pass the Nvida 610 on to a guest and see if that works. If I am successful with that, I am guessing that i have to use the device on the 4x slot to perform a pci pass through, well at least for a GPU ayway.