In the latest Top 500 Supercomputer list list, which was released on June 20th, Linux accounts for 91.00 % of the top supercomputers. Linux is followed by Unix with 4.6%; and Windows with 1.2%. When it comes to super-fast computers like supercomputers or IBM Jeopardy winning Watson, Linux rules.
Of the fastest of the fast, the top ten supercomputers all run Linux. The top ten, lead by the K Computer at the RIKEN Advanced Institute for Computational Science (AICS) in Kobe Japan, are all capable of performing more than 8 quadrillion calculations per second (petaflop/s) This ranking is determined by how fast the computers can run Linpack, "a benchmark application developed to solve a dense system of linear equations." The highest ranking pure Windows supercomputer, the Magic Cube at China's Shanghai Supercomputer Center, comes in at 40th.
It's not just supercomputers and expert systems like Watson that run Linux though. The world's stock exchanges are all moving to Linux. They're doing it because in today's stock markets, microseconds can spell the difference between profit and loss. Only Linux is fast and stable enough to keep up the modern markets' high-frequency traders.