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In this paper, we compare running the Linux operating system on the compute nodes of ASCI Red hardware to running a specialized, highly-optimized lightweight kernel (LWK) operating system. We have ported Linux to the compute and service nodes of the ASCI Red supercomputer, and have run several benchmarks. We present performance and scalability results for Linux compared with the LWK environment. To our knowledge, this is the first direct comparison on identical hardware of Linux and an operating system designed specifically for large-scale supercomputers. In addition to presenting these results, we discuss the limitations of both operating systems, in terms of the empirical evidence as well as other important factors.