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I want to play with a friend and wanted to use my 2 monitors to play a game on both with one controller on one instance and the other controller on the second instance. I created 2 instances of desmume but they only accept 1 controller and completely ignore the second one.
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You haven't configured the controls. If you had, you'd see it's possible to configure only one set of controls. I guess you expected desmume 1 to magically know to get input from controller 1 and desmume 2 to magically know to get input from controller 2? You're really confused.
use 2 different desmume directories and configure them independently; also use config > background input
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