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I was looking around the net and came across the Maximus VI extreme motherboard. While reading the specs, I saw it had 5 PCI-E 16x slots running off a Z87 chipset. Is there any point to this, because haswell only has 16 PCIE lanes, making the slots run in 4x4x4x2x2x if fully utilized, and there's not even enough space for 5 two slot GPUs (not that you can do 5 way sli/crossfire anyway).

Does anyone know why they did it?

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The 4 red slots probably run off a PCI-E 3.0 controller. If you look at the specs, it makes sense. Scroll down to expansion slots.

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From your link: 

 

- 5 x PCI Express 3.0*/2.0 x16 slots (Single at native x16, dual at native x8/x8**, triple at x8/x16/x8, quad at x8/x16/x8/x8)

 

 

I think they add LSI PCIe chips that increase the number of lanes available. That is also why they gave the huge heatsinks, the LCI chips tend to run pretty hot.  

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They're not useful though. You can't actually fit more that 4 GPUs on the board, and Xfire and sli only go up to 4. While you could use other cards (eg raid, sound), the way it's laid out isn't very practical.

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You do have a lot more freedom to chose where you place your cards, how many sockets your cards take up etc. I can't imagine the idea is that you should utilise them all for graphics

Edit: for instance, you can run three way sli with cards that occupy more than the usual two slots

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