Eecient Molecular Dynamics on a Network of Personal Computers
نویسندگان
چکیده
The Genoa Active Message Machine (GAMMA) is a high-performance Active Messages-like communication layer implemented at kernel level as an extension of the Linux Operating System, and made available to user applications through a programming library. On low-cost clusters of Personal Computers (PCs) connected by Fast Ethernet, GAMMA achieves much better communication performance compared to public domain implementations of MPI and PVM. We have considered an existing PVM Molecular Dynamics (MD) parallel application, designed to be portable across various MPP as well as NOW platforms. The goal of our work is to show how much migrating such a complex application from PVM to GAMMA is convenient in terms of absolute performance improvement as well as price/performance ratio in the perspective of running MD on a low-cost cluster of PCs. The \mi-gration" approach is then compared to other two alternatives, namely: running the PVM version of MD \as is" on a cluster of PCs and trying tuning the PVM version of MD to match the underlying cluster architecture. It is shown that neither of such two alternatives lead to satisfactory performance.
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