It's not really my area, but I'd be surprised if some subsystems on something big and complex like the ISS didn't use Linux. I'm not suggesting for a minute they should be used for the avionics, which are obviously going to use systems with a proven track record in that arena. As I said, they're extremely conservative and will just work with whatever they're familiar with. Even things like IP comms are still considered a bit new-fangled in industrial control, which is comical really.
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