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PhoenixMiner
[Miner software]
Info for both supported coins, parameters, and changelog for PhoenixMiner.
 
-gpus
[Miner parameter]
Specify which GPUs you want to use.

If you have a 6 GPU rig, and want to disable GPU2 (the third gpu):

-gpus 1,2,4,5,6

This will make GPU0, GPU1, GPU3, GPU4 and GPU5 be active/mining.