I've look around some, but it is not completely clear whether agp support is needed for PCIE. I would think not, they are two completely different interfaces with no real relation to one another. Also, I have a nvidia PCIE card and I recently built a kernel with AGP support completely taken out. There was no change in performance. So, I think it's not necessary, but I have to tell you that it's quite difficult to disable it, you have to disable lots of other stuff to be able to turn it off.
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