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If I have two GPU-intensive processes running, is there a way to "prefer" the load from one over the other, as "nice" does in the *nix kernel scheduler?

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You might have luck using cgroups (Linux documentation, Wikipedia article).

It's mostly used for linux containers and such but you can allow or deny the usage of devices to processes of your choice.

This Gentoo forum thread has some samples of how to restrict GPU usage (by denying /dev/nvidia0 to certain processes for example)

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