822
OS market share in Top 500 supercomputers
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That's certainly a big part of it. When one needs to buy a metric crap load of CPUs, one tends to shop outside the popular defaults.
Another big reason, historically, is that Supercomputers didn't typically have any kind of non-command-line way to interact with them, and Windows needed it.
Until PowerShell and Windows 8, there were still substantial configuration options in Windows that were 100% managed by graphical packages. They could be changed by direct file edits and registry editing, but it added a lot of risk. All of the "did I make a mistake" tools were graphical and so unavailable from command line.
So any version of Windows stripped down enough to run on any super-computer cluster was going to be missing a lot of features, until around 2006.
Since Linux and Unix started as command line operating systems, both already had plenty fully featured options for Supercomputing.