On the Parallelization of CHARMM on the CM-5/5E

  • Jill P. Mesirov
  • Pablo Tamayo
  • Robert J. Nagle
Part of the The IMA Volumes in Mathematics and its Applications book series (IMA, volume 82)

Abstract

We describe a new port of CHARMM to the CM-5 supercomputer. This port is based on the original B-H parallelization of CHARMM[2] for MIMD machines but it has an improved communications library.

Keywords

Load Imbalance Active Message Communication Library Vector Global Innermost Loop 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.

Preview

Unable to display preview. Download preview PDF.

Unable to display preview. Download preview PDF.

References

  1. [1]
    B. R. Brooks, R. E. Bruccoleri, B. D. Olafson, D. J. States, S. Swaminathan and M. Karplus, J. Comp. Chem. 4, 187 (1983).CrossRefGoogle Scholar
  2. [2]
    B. R. Brooks and M. Hodošček, Chemical Design Automation News 7, 16 (1992).Google Scholar
  3. [3]
    G. C. Fox, M. A. Johnson, G. A. Lyszerga, S. W. Otto, J. K. Salmon and D. W. Walker, Solving Problems on Concurrent Processors, Vol. 1, Prentice Hall, Englewod Cliffs, NJ (1988).Google Scholar
  4. [4]
    R. A. van de Geijn, Technical Report CS-91-138 University of Tennessee.Google Scholar
  5. [5]
    T. von Eicken, D. E. Culler, S. C. Glodstein and K. E. Schauser, in Procs. of the 19th International Symposium on Computer Architecture. ACM Press, Australia, May 1992.Google Scholar
  6. [6]
    L. W. Tucker and A. Mainwaring, Parallel Computing, 20, No 4, March 31, 1994.Google Scholar
  7. [7]
    The apogee apf77 compiler (version 2.3) is a commercial product provided by Apogee Software Inc.Google Scholar

Copyright information

© Springer-Verlag New York, Inc. 1996

Authors and Affiliations

  • Jill P. Mesirov
    • 1
  • Pablo Tamayo
    • 2
  • Robert J. Nagle
    • 3
  1. 1.Computer Science DepartmentBoston UniversityBostonUSA
  2. 2.Thinking Machines Corp.CambridgeUSA
  3. 3.Chemistry DepartmentHarvard UniversityCambridgeUSA

Personalised recommendations