Abstract
We describe the development of biological and chemical parallel applications running on a PC cluster. Our parallel cluster consists of 64 Pentium Pro 200MHz microprocessors. We describe one biological parallel application on our integrated parallel cluster system, called PAPIA. This system is dedicated to protein information analysis. The PAPIA system enables very fast protein database searches (3-D structure matching and sequence, homology search) by fully utilizing the power of the 64 local hard-disks, as well as fast parallel calculations supported by the high-bandwidth and low-latency communication driver developed by RWCP. We also present a web service (http://www.rwcp.or.jp/papia/) so any biologist can easily submit jobs to the PAPIA system through a web browser. This service has been accessed from 58 countries in the world to date.
We also present our work on chemical applications with our parallel molecular dynamics simulation. We have ported the AMBER program to the PC cluster, and appended additional functionality of the Barnes-Hut tree code for quick and accurate calculation of Coulomb potentials without a cut-off approximation (PPPC method). Our RWC PC Cluster shows good scalability in these two real parallel applications.
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Akiyama, Y., Onizuka, K., Noguchi, T., Ando, M. (1999). Biological- and chemical-parallel applications on a PC cluster. In: Polychronopoulos, C., Fukuda, K.J.A., Tomita, S. (eds) High Performance Computing. ISHPC 1999. Lecture Notes in Computer Science, vol 1615. Springer, Berlin, Heidelberg. https://doi.org/10.1007/BFb0094924
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DOI: https://doi.org/10.1007/BFb0094924
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