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Classical science is based on theory, observation and physical experimentation. Contemporary science is characterized by theory, observation, experimentation and numerical simulation. With the use of hardware and software we can simulate lots of phenomenon. This saves time, money and physical resources. Simulation of a certain phenomenon requires lots of computing power. Answer to these computational power needs is high performance computer. High performance computers consist of numerous processors working on same task in parallel. In the past, high performance computers were very expensive and affordable by few institutions. After Message Passing Interface library is ported to PC platform, commodity clusters can be built of inexpensive PCs and afforded by any researcher. Lots of performance analyses have been conducted on high-end supercomputers. None has been done on commodity clusters. In this thesis, experiments for six major MPI communication functions were performed on eight different configurations of clusters. Performance analyses were then conducted on the results. Based on the results, methods for optimal utilization of inter-process communications on commodity clusters were proposed.