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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Tezuka, H., Hori, A., Ishikawa, Y., Sato. M.: PM: An Operating System Coordinated High Perforamnce Communication Library, High-Performance Computing and Networking '97, Lecture Notes in Computer Science, Vol. 1225. Springer-Verlag (1997) 708–717.
Hori, A., Tezuka H., Ishikawa, Y.: Highly Efficient Gang Scheduling Implementation, Proceedings of SC98 (1998)
Bersntein, F., Koetzle, T., Williams, G., Meyer, E., Brice, M., Rodgers, M.J., Kennard, O., Shimanouchi, T., Tasumi, M.: The Protein Data Bank: A Computer-based Archival File for Macromolecular Structures, J. Mol. Biol., 112 (1977) 535–542
Akiyama, Y., Onizuka, K., Noguchi, T., Ando, M.: Parallel Protein Information Analysis (PAPIA) system running on a 64-node PC Cluster, Proceedings of the 9th Genome Informatics Workshop (GIW'98), Universal Academy Press (1998) 131–140.
Onizuka, K., Noguchi, T., Akiyama, Y.: Parallel PDB Data Retriever ‘PDB Diving Booster', High Performance Computing, Lecture Notes in Computer Science, Vol. 1336. Springer-Verlag (1997) 389–396
Totoki, Y., Akiyama, Y., Onizuka, K., Noguchi, T., Saito, M., Ando, M.: Multiple Protein Sequence Alignment using Parallel Iterative Algorithm and A* Algorithm, Transactions on IPSJ, 40, No. SIG (MPS2) (1999) (in Japanese)
Hirosawa, M., Totoki, Y., Hoshida, M., Ishikawa, M.: Comprehensive Study on Iterative Algorithms of Multiple Sequence Alignment Comput. Applic. Biosci., 11 (1995) 13–18
Pearlman, D.A., Case, D.A., Caldwell, J.W., Ross, W.S., Cheatham III, T.E., Ferguson, D.M., Seibel, G.L., Singh, U.C., Weiner, P.K., Kollman, P.A.: AMBER 4.1, University of California San Francisco (1995)
Duan, Y., Kollman, P.A.: Pathways to a Protein Folding Intermediate Observed in a 1-Microsecond Simulation in Aqueous Solution, Science, 282 (1998) 740–744
Akiyama, Y., Onizuka, K., Noguchi, T. Ando, M.: Development of Chemical and Parallel Applications running on a 64-node PC Cluster, presentation at International Workshop on Innovative Architecture for Future Generation High-Performance Processors and Systems (IWIA'98), MHPCC Maui (1998)
Barnes, J., Hut, P.: A hierarchical O (N log N) force-calculation algorithm, Nature, 324 (1986) 446–449.
Saito, M.: Molecular dynamics simulations of proteins in water without the truncation of long-range Coulomb interactions, Molecular Simulation, 8 (1992) 321–333
Saito, M.: Molecular dynamics simulations of proteins in solution: Artifacts caused by the cutoff approximation, J. Chem. Phys., 101 (1994) 4055–4061
Saito, M., Misoo, K., Shizawa, Y., Marukawa, K., Akiyama, Y., Noguchi, T., Onizuka, K.: Parallelization and Performance Evaluation of MD Program AMBER and Barnes-Hut Tree Code, Proceedings of the 1998 Joint Symposium on Parallel Processing (JSPP'98) (1998) 231–238 (in Japanese)
Misoo, K., Shizawa, Y., Akiyama, Y., Saito, M.: Development of Molecular Dynamics Programs for Proteins with Parallelized Barnes-Hut Tree Code, Proceedings of the 1999 Joint Symposium on Parallel Processing (JSPP'99) (1999) (in Japanese)
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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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