Linux operating system Click to see full answer. Regarding this, which operating system is used in supercomputer? Linux Beside above, do supercomputers run Windows? Only 3 of the world’s most powerful computers run Windows. Even though it still hasn’t found its way onto our desktops, in the world of supercomputers, Linux is king. Even Microsoft can’t touch them there. Case in point: a new study showing that a whopping 94% of supercomputers run Linux. Also to know is, where are supercomputers used? Supercomputers play an important role in the field of computational science, and are used for a wide range of computationally intensive tasks in various fields, including quantum mechanics, weather forecasting, climate research, oil and gas exploration, molecular modeling (computing the structures and properties ofWhy do all supercomputers use Linux?And basically that is why most supercomputers use Linux. They need a operating system that they can modify to an atomic level, so that they can squeeze out every single bit of performance out of their hardware down to the very last CPU cycle.