LISP and Symbolic Computation

, Volume 7, Issue 2–3, pp 231–247 | Cite as

Using Multilisp for solving constraint satisfaction problems: An application to nucleic acid 3D structure determination

  • Marc Feeley
  • Marcel Turcotte
  • Guy Lapalme
Article

Abstract

This paper describes and evaluates a parallel program for determining the three-dimensional structure of nucleic acids. A parallel constraint satisfaction algorithm is used to search a discrete space of shapes. Using two realistic data sets, we compare a previous sequential version of the program written in Miranda to the new sequential and parallel versions written in C, Scheme, and Multilisp, and explain how these new versions were designed to attain good absolute performance. Critical issues were the performance of floating-point operations, garbage collection, load balancing, and contention for shared data. We found that speedup was dependent on the data set. For the first data set, nearly linear speedup was observed for up to 64 processors whereas for the second the speedup was limited to a factor of 16.

Keywords

Parallel Computation Symbolic Computation Multilisp Constraint Satisfaction Functional Programming Applications 
This is a preview of subscription content, log in to check access.

Preview

Unable to display preview. Download preview PDF.

Unable to display preview. Download preview PDF.

References

  1. 1.
    BBN Advanced Computers Inc., Cambridge, MA.Inside the GP1000, 1989.Google Scholar
  2. 2.
    R. Bernstein, T. F. Koetzle, G. J. Williams, E. F. Meyer, M. D. Brice, J. R. Rodgers, O. Kennard, T. Shimanouchi, and M. Tasumi. The Protein Data Bank: A computer-based archival file for macromolecular structures.Eur. Biochem., 80:319–324, 1977.Google Scholar
  3. 3.
    C. J. Cheney. A nonrecursive list compacting algorithm.Communications of the ACM, 13(11):677–678, November 1970.Google Scholar
  4. 4.
    P. Dumas, D. Moras, C. Florentz, and R. Giegé. 3-D Graphics Modelling of the tRNA-like 3′-end of Turnip Yellow Mosaic Virus RNA: Structural and Functional Implications.J. Biomol. Str. Dynam., 4:707–728, 1987.Google Scholar
  5. 5.
    M. Feeley.An Efficient and General Implementation of Futures on Large Scale Shared-Memory Multiprocessors. PhD thesis, Brandeis University Department of Computer Science, 1993. Available as publication #869 from département d'informatique et recherche opérationnelle de l'Université de Montréal.Google Scholar
  6. 6.
    M. Feeley. A message passing implementation of lazy task creation. InParallel Symbolic Computing: Languages, Systems, and Applications (US/Japan Workshop Proceedings). Springer-Verlag Lecture Notes in Computer Science 748, November 1993.Google Scholar
  7. 7.
    M. Feeley and J. S. Miller. A parallel virtual machine for efficient Scheme compilation. InProceedings of the 1990 ACM Conference on Lisp and Functional Programming Languages and Computer Architecture, Nice, France, June 1990.Google Scholar
  8. 8.
    K. A. Frenkel. The human genome project and informatics.Communications of the ACM, 34(11):41–51, November 1991.Google Scholar
  9. 9.
    D. Gautheret and R. Cedergren. Modeling the three-dimensional structure of RNA.FASEB Journal, 7:97–105, January 1993.Google Scholar
  10. 10.
    Vipin Kumar. Algorithms for constraint-satisfaction problems: A survey.AI magazine, 13(1):32–44, 1992.Google Scholar
  11. 11.
    F. Leclerc, R. Cedergren, and A. D. Ellington. A three-dimensional model of the Rev Binding Element of HIV-1 derived from analyses of in vitro selected variants (submitted to Nature Structural Biology).Nature Structural Biology. This paper (in press) describes a protocol to apply energy minimization techniques to MC-SYM models.Google Scholar
  12. 12.
    F. Major, G. Lapalme, and R. Cedergren. Domain Generating Functions for Solving Constraint Satisfaction Problems.J. Funct. Prog., 1(2):213–227, 1991.Google Scholar
  13. 13.
    F. Major, M. Turcotte, D. Gautheret, G. Lapalme, E. Fillion, and R. Cedergren. The Combination of Symbolic and Numerical Computation for Three-Dimensional Modeling of RNA.Science, 253:1255–1260, September 1991.Google Scholar
  14. 14.
    Research Software Limited, Canterbury, England.Miranda System Manual, 1989.Google Scholar
  15. 15.
    W. Saenger.Principles of Nucleic Acid Structure. Springer-Verlag, New-York, 1984.Google Scholar
  16. 16.
    J. D. Watson, N. H. Hopkins, J. W. Roberts, J. Steitz Argetsinger, and A. M. Weiner.Molecular Biology of the Gene, Volume I & II. Benjamin Cummings, Menlo-Park, 1987.Google Scholar

Copyright information

© Kluwer Academic Publishers 1994

Authors and Affiliations

  • Marc Feeley
    • 1
  • Marcel Turcotte
    • 1
  • Guy Lapalme
    • 1
  1. 1.Département d'informatique et de recherche opérationnelleUniversité de MontréalMOntréalCanada

Personalised recommendations