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How will thunderbolt 3 on motherboards work for video?

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I would like the ability to support thunderbolt 3 5K monitors when they are released in the next few months. How important is it to purchase a motherboard that has a thunderbolt 3 port on it or do you anticipate that the nvidia 1070 cards will have thunderbolt 3 ports once the monitors are in broader circulation? I really want to get a smaller ATX board but none of those seem to have the thunderbolt 3. I know that the new nvidia cards are not currently supported, but I am curious if I can get away with using the integrated graphics using a bad monitor and then upgrade to a 5K monitor and a new nvidia card once they finally get supported.

As an aside, how do the thunderbolt 3 ports even work when they are on the motherboard? Would you just buy a supported video card and plug it into the motherboard instead of the video card and then set that up in the bios?

Thanks!
 
Thunderbolt ports on the motherboard will use the iGPU, no matter if you've installed an additional PCIE graphics card. For TB2, there are solutions like the Asus ThunderboltEX II to multiplex the video signal of a discrete GPU into a Thunderbolt screen. I don't know if something similar exists for TB3, but TB3 isn't supported by OS X anyway.

By the way, Thunderbolt 3 isn't needed for high-resolution displays, DisplayPort can do that as well (it's actually part of Thunderbolt). I don't expect anyone but Apple to release a Thunderbolt only display, since Thunderbolt's additionally data transfer features are not necessary for a simple display, unless you want to implement docking features over the same cable.
 
That's really helpful, thanks! I didn't realize that displayport 1.3 isn't in the thunderbolt 3 form factor. Do you anticipate that there will eventually be a cheap converter from displayport 1.3 to thunderbolt to allow future macs to use these non-apple 5K+ monitors or will the converters be the $100+ heavy duty kind?
 
Thunderbolt 3 contains up to two streams of DisplayPort 1.2, so it's capable of driving a 5K display through a single cable in MST mode (I don't know if such a display already exists). Current 5K displays use two distinct DP 1.2 cables. It shouldn't require more than a simple passive adapter to connect a DP 1.2 display to a Thunderbolt 3 port.

It's not possible to adapt in the other direction though, so you can't attach a Thunderbolt display (e.g. Apple's discontinued Cinema Display) to a non-Thunderbolt computer, no matter what you do. But as I said, I doubt this will ever occur on a non-Apple display.
 
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