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I was wondering whether you can choose a pair of gpus to render in a three gpu machine. Maybe a checkbox-like option in which you designate which graphics cards to use. All that Blender is allowing is either using all three cards or just one.

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    $\begingroup$ Strange, I never had a 3 card setup but I have 2 and in user pref. in the system tab I'm able to select which card or combination of the two to use (if you have a multi-cpu card like mine) . Are you sure you don't have them connect in SLI? In that case the system (not blender) see it as one $\endgroup$ – diramazioni Mar 16 '16 at 10:53
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Yes, when you have more than 1 GPU blender options are all the GPUs at once and then each single individual GPU.

This feature is on the dev's todo list for longer than 2 years.

You can check it here: https://developer.blender.org/T37717

Dec 8 2013, Brecht wrote:

It's on my todo list to improve graphics card configuration for 2.70, to allow you to select individual cards and enable/disable them. This is not considered a bug at the moment however.

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