You can only disable a GPU through the miner options under group config!

Under you can find examples for different miners, and all examples will disable GPU2 (the third GPU) in a 6 GPU rig:

TeamRedMiner

--devices=0,1,3,4,5

lolMiner

--devices 0,1,3,4,5

T-rex

--devices 0,1,3,4,5

PhoenixMiner

-gpus 1,2,4,5,6

Gminer

--devices 0,1,3,4,5

NBMiner

-d 0,1,3,4,5

SRBMiner

--gpu-id 0!1!3!4!5


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