Referring to this BBC Article: Supercomputing superpowers
Almost all the supercomputers are using Linux as operating system. Why is Linux so popular?
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Scalability, for one. Also, the fact that it is open source is important, since super computers exist almost solely for research and researchers love the flexibility of open-source software. They can hack and slash the OS to be ultra-tuned to fit their very specific need at the small cost of the source code and some bandwidth for anyone that's curious about what they did.