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I noticed pictures of some mining rigs that appeared to show GPUs hooked up to cables going to a mother board and not using pci slots. What are these cables called and how can I use them to increase the number of cards I have on one board?

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They may have been using an adaptor cable which allows use of different slots, such as the one pictured here: https://bitcointalk.org/index.php?topic=66070.0

During mining the data going to and from the graphics card isn't nearly as much as when the card is used for gaming, so there's no substantial deterioration in mining output.

However, I do remember reading about at least one case where circuitry was overloaded doing this (ie it burnt out), possibly due to a faulty cable, but also possibly because graphics cards aren't designed to work that way.

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