They still probably need a ton of customization and tuning at the driver level and beyond, which open source allows for.

I am sure there is plenty of existing “super computer”-grade software in the wild already, but a majority of it probably needs quite a bit of hacking to get running smoothly on newer hardware configurations.

As a matter of speculation, the engineers and scientists that build these things are probably hyper-picky about how some processes execute and need extreme flexibility.

So, I would say it’s a combination of factors that make Linux a good choice.