if you use risers and the dual-psu. However you're paying for risers and Add2PSU adapter that will be worthless when you end mining
You don't need Add2PSU. Just use paper clip to short green and black wires in 24 pin ATX connector. Plug both PSUs to the same power bar/surge protector and flip the switch to turn both of them at the time. That adapter is useless.
You are right about that 3 cards per motherboard simplifies things. No support racks to hold the GPUs. One PSU per rig.
But if you are building 10+ rigs, space is a factor so you want to run more than 3 cards per motherboard. Ideally, 5-6 cards per system.
Whatever you can squeeze on the same 15A@120V circuit.
Shorting pins is a point of failure? I highly doubt that, not if you do it right. Exceptionally easy with a single strand of cat6 solid. In most cases it is not even necessary, and the riser cables I use have a 1x presence pin jump built in anyway. Besides, I think the jump is just for BIOS initiation, after that point you could probably remove it till you restart.
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Running 3 in one mobo directly is a great way to melt the cards down and obliterate the fans in well under 6 months. I know from experience, no amount of external fan velocity or volume will keep three cards stacked that close in any decent running temps.
Did you undervolt the cards? That said, running cards directly on the motherboard isn't even my main point, but it is rather to not connect more cards than the available PCI-e 16x slots. It doesn't matter if the cards are undervolted or not, they will overheat directly on the motherboard. The reference cooler designs are better, but there are no blower style 280/270 cards that I know of and the 290's run so hot you'd be nuts to try. It would likely limit your hashrate, and the costs of risers might be made up by the extra hashpower over the life of the machine. All that heat will play hell on the motherboard too, especially if it's not supported properly. That's a lot of weight, and a lot of heat...
Why exactly is that you recommend staying to x16 slots only? Is it just some wild hunch or something? Doesn't really make sense, since you advocate the use of riser cables now apparently? The x16 risers are horribly designed and more prone to failure with the extra 15 lanes of unnecessary connections on a crummy ribbon cable, and they are a serious airflow restriction for absolutely no reason! If you use x1 risers, what difference does the slot make? You'd then probably need to jump the x1 presence pin at that point, too.
I have several rigs with multiple power supplies running 6 cards per board, and they do just fine. I would have spent double on supporting hardware if I stayed with 3 cards/rig, for no reason.
@OP: With time improve your design and efficiency. Now, start SIMPLE and SAFER.
