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Development of biological and chemical applications on a 64-node PC cluster

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4 Author(s)
Akiyama, Y. ; Real World Computing Partnership, Japan ; Onizuka, K. ; Noguchi, T. ; Ando, M.

We describe the development of two parallel applications running on our PC cluster which consists of 64 Pentium Pro 200MHz microprocessors. One is an integrated parallel calculation system, called the PAPIA system, dedicated to protein information analysis. The PAPIA system enables very fast protein database searches (3-0 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 RWCR We have starteda WWWsewice (http://www. rwcp.oKjp/papid) so any biologist can easily submit jobs to the PAPIA system through a WWW browse,: The service has been accessed from 55 countries in the world. The other application is parallel molecular dynamics simulation. We have eficiently ported the AMBER program to the PC cluster; and then appended an optional functionality of the Barnes-Hut tree code for quick and accurate calculation of Coulomb potentials without a cut-off approximation (PPPC method). The RWC PC Cluster shows good scalability in these two real parallel applications.

Published in:

Innovative Architecture for Future Generation High-Performance Processors and Systems, 1998

Date of Conference:

24-24 Oct. 1998