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Implementation of ECEPP-based programs on the IBM SP2 and the SGI Power Challenge computers

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High-Performance Computing and Networking (HPCN-Europe 1996)

Part of the book series: Lecture Notes in Computer Science ((LNCS,volume 1067))

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Abstract

In this paper, we describe the design and implementation of a message-passing algorithm which enables the Empirical Conformational Energy Program for Peptides (ECEPP/3) and related programs to run efficiently on the IBM RISC System/6000 POWERparallel System (SP2). Either the Message Passing Library (MPL) or the Message Passing Interface (MPI) can be used on the SP2; the MPI version also runs on the SGI Power Challenge computer. Some performance data are presented.

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References

  1. Momany, F. A., McGuire, R. F., Burgess, A. W., & Scheraga, H. A., J. Phys. Chem. 79 (1975) 2361–2381

    Google Scholar 

  2. Némethy, G., Pottle, M. S. & Scheraga, H. A., J. Phys. Chem. 87 (1983) 1883–1887

    Google Scholar 

  3. Sippl, M. J., Némethy, G. & Scheraga, H. A., J. Phys. Chem. 88 (1984) 6231–6233

    Google Scholar 

  4. Nemethy, G., Gibson, K. D., Palmer, K. A., Yoon, C. N., Paterlini, G., Zagari, A., Rumsey, S., and Scheraga, H. A., J. Phys. Chem. 96 (1992) 6472–6484

    Google Scholar 

  5. Li, Z. & Scheraga, H. A., Proc. Natl. Acad. Sci. 84 (1987) 6611–6616; Li, Z. & Scheraga, H. A., J. Mol. Struct. (Theochem) 179 (1988) 333–352

    Google Scholar 

  6. Ripoll, D. & Scheraga, H. A., Biopolymers 27 (1988) 1283–1303

    Google Scholar 

  7. Ripoll, D. R., Pottle, M. S., Gibson, K. D., Liwo, A. & Scheraga, H. A., J. Comp. Chem. 16 (1995) 1153–1163

    Google Scholar 

  8. Scheraga, H. A., Adv. Phys. Org. Chem. 6 (1968) 103–184

    Google Scholar 

  9. Vásquez, M., Némethy, G. & Scheraga, H. A., Chem Rev. 94 (1994) 2183–2239

    Google Scholar 

  10. Anfinsen, C. B., Science 181 (1973) 223–230

    PubMed  Google Scholar 

  11. Metropolis, N., Rosenbluth, A. W., Rosenbluth, M. N., Teller, A. H. & Teller, E. J., Chem. Phys. 21 (1953) 1087–1092

    Google Scholar 

  12. Applied Parallel Research. FORGE Explorer Version 2.0 User's Guide. 580 Main Street, Suite I, Placerville, CA 95667. January (1995)

    Google Scholar 

  13. IBM AIX Parallel Environment: Parallel Programming Subroutine Reference, Release 2.0. IBM Corporation, Kingston, New York. June, (1994)

    Google Scholar 

  14. Message Passing Interface Forum. MPI: A Message-Passing Interface Standard, Version 1.1. University of Tennessee, Knoxville, Tennessee. June, (1995)

    Google Scholar 

  15. MPICH is a portable implementation of MPI which resulted from a joint-effort project between Argonne National Laboratory (W. Gropp and E. Lusk) and Mississippi State University (A. Skjellum and N. Doss); mpich.tar.Z is available by anonymous ftp from info.mcs.anl.gov.

    Google Scholar 

  16. Deisenhofer, J. & Steigeman, W. Acta Crystallogr. Sect. B 31 (1975) 238–250

    Google Scholar 

  17. Ripoll, D., Piela, L., Vásquez, M., and Scheraga, H., Proteins, Struc., Func. and Gen. 10 (1991) 188–198

    Google Scholar 

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Authors and Affiliations

  1. Cornell Theory Center, Cornell University, 14853, Ithaca, NY, USA

    Timothy J. O'Donnell, Steven G. Hotovy, Marcia S. Pottle & Daniel R. Ripoll

  2. Baker Laboratory of Chemistry, Cornell University, 14853, Ithaca, NY, USA

    Harold A. Scheraga

Authors
  1. Timothy J. O'Donnell
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  2. Steven G. Hotovy
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  3. Marcia S. Pottle
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  4. Daniel R. Ripoll
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  5. Harold A. Scheraga
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Editor information

Heather Liddell Adrian Colbrook Bob Hertzberger Peter Sloot

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© 1996 Springer-Verlag Berlin Heidelberg

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O'Donnell, T.J., Hotovy, S.G., Pottle, M.S., Ripoll, D.R., Scheraga, H.A. (1996). Implementation of ECEPP-based programs on the IBM SP2 and the SGI Power Challenge computers. In: Liddell, H., Colbrook, A., Hertzberger, B., Sloot, P. (eds) High-Performance Computing and Networking. HPCN-Europe 1996. Lecture Notes in Computer Science, vol 1067. Springer, Berlin, Heidelberg. https://doi.org/10.1007/3-540-61142-8_571

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  • DOI: https://doi.org/10.1007/3-540-61142-8_571

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  • Publisher Name: Springer, Berlin, Heidelberg

  • Print ISBN: 978-3-540-61142-4

  • Online ISBN: 978-3-540-49955-8

  • eBook Packages: Springer Book Archive

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