Before Linux made its move, Unix was supercomputing's dominant operating system. Since 2003, the top operating system by performance share on the Top500 List underwent a complete flip from 96 percent Unix to 96 percent Linux. By 2004, Linux had taken over the lead for good.
According to The Linux Foundation, "Linux [became] the driving force behind the breakthroughs in computing power that have fueled research and technological innovation. In other words, Linux is dominant in supercomputing, at least in part, because it is what is helping researchers push the limits on computing power."
The Foundation believes that this has happened because of two reasons. First, since most of the world’s top supercomputers are superscalar research machines built for specialized tasks, each supercomputer is a standalone project with unique characteristics and optimization requirements. Thus, it's not affordable for anyone to develop a custom operating system for each system. With Linux, however, research teams can easily modify and optimize Linux to the one-off, groundbreaking designs that characterize the modern generation of supercomputers.
And, just as importantly, "The licensing cost of a custom, self-supported Linux distribution is the same, whether you’re using 20 nodes or 20-million nodes." Thus, "by tapping into the vast open-source Linux community, projects had access to free support and developer resources to help keep developer costs on par with, or below other operating systems."
The result of this has been supercomputers that are going faster than ever. By total RMax, a supercomputer's maximum achieved performance on the Linpack benchmark, supercomputer performance has outpaced Moore’s Law (The number of transistors incorporated in a chip will approximately double every 24 months.) by doubling roughly every 14 months. At the top end, supercomputing is progressing at even more rapid rate. The RMax of the fastest supercomputer on the Top500 list has increased by a factor of three to reach the Tianhe-2’s 33.86 petaflop/second in 2013 from the CM-5’s 59.7 gigaflop/s in 1993."
Therefore, The Linux Foundation concluded, "By isolating RMax by operating system using the past 20 years of Top500 data, it’s clear that Linux is not only responsible for supporting the majority of supercomputers today, but is a driving force behind the disproportionate growth in supercomputing capacity over the past decade. In continuing to drive progress and innovation in computing, Linux is also helping to explore the mysteries of the universe and solve our toughest problems."