the top 20 supercomputers manufacturers (IBM, Cray, and SGI) have preferred Linux with respect to other operating systems. Why that happened? IBM has been using Linux since 2002, when a former top level supercomputer (BlueGene) was developed. According to IBM, Linux has been choosen because it is open and it can be extended to run a BlueGene (or Roadrunner) class machine. Moreover, Linux has behind a huge community working all over the world and they can provide valuable support, feedbacks and suggestions.
http://dev.emcelettronica.com/supercomputers-love-linux