Advertisement

Massive Parallelism: The Hardware for Computational Chemistry?

  • M. F. Guest
  • P. Sherwood
  • J. A. Nichols

Abstract

Computational chemistry covers a wide spectrum of activities ranging from quantum mechanical calculations of the electronic structure of molecules, to classical mechanical simulations of the dynamical properties of many-atom systems, to the mapping of both structure-activity relationships and reaction synthesis steps. Although chemical theory and insight play important roles in this work, the prediction of physical observables is almost invariably bounded by the available computer capacity.

Keywords

Density Functional Theory Self Consistent Field Pacific Northwest National Laboratory Global Array Environmental Molecular Science Laboratory 
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.
    Additional information on the EMSL is available via Worldwide Web URLhttp://www.pnl.gov:2080.Google Scholar
  2. 2.
    I.T. Foster, J.Jl Tilson, A.F. Wagner, R. Shepard, D.E. Bernholdt, R.J. Harrison, R.A. Kendall, R.J. Littlefield and A.T. Wong, Toward high-performance computational chemistry: I. Scalable Fock matrix construction algorithms, J. Comp. Chem.17:109–123(1996).CrossRefGoogle Scholar
  3. 3.
    R.J. Harrison, M.F. Guest, R.A. Kendall, D.E. Bernholdt, A.T. Wong, M. Stave, J.L. An-chell, A.C. Hess, R.J. Littlefield, G.I. Fann, J. Nieplocha, G.S. Thomas, D. Elwood, J. Tilson, R.L. Shepard, A.F. Wagner, I.T. Foster, E. Lusk and R. Stevens, Toward high-performance computational chemistry: II. A scalable self-consistent field program, J. Comp. Chem. 17:124–132 (1996).CrossRefGoogle Scholar
  4. 4.
    M.F. Guest, E. Apra, D.E. Bernholdt, H.A. Fruechtl, R.J, Harrison, R.A. Kendall, R.A. Kutteh, X. Long, J.B. Nicholas, J.A. Nichols, H.L. Taylor, A.T. Wong, G.I. Fann, R.J. Littlefield and J. Nieplocha, Future Generation Computer Systems 12:273–289 (1996).CrossRefGoogle Scholar
  5. 5.
    A.T. Wong, R.J. Harrison and A.P. Rendell, Parallel Direct Four Index Transformations, Theor. Chim. Acta 93:317–31 (1996).CrossRefGoogle Scholar
  6. 6.
    D.E. Bernholdt and R.J. Harrison, Large-Scale Correlated Electronic Structure Calculations: the RI-MP2 Method on Parallel Computers, Chem: Phys. Lett. 250:477–84 (1996).Google Scholar
  7. 7.
    D.E. Bernholdt and R.J. Harrison, Orbital invariant second-order many-body perturbation theory on parallel computers. An approach for large molecules, J. Chem. Phys. 102:9582–89 (1995).CrossRefGoogle Scholar
  8. 8.
    G. Booch, Object-Oriented Analysis and Design, 2nd edition, Benjamin/Cummings Publishing Co, Inc. (1994).Google Scholar
  9. 9.
    B. Stroustrup, The C++ Programming Language, 2nd edition, Addison-Wesley Publishing Company (1991).Google Scholar
  10. 10.
    The MPI Forum, MPI: A Message-Passing Interface Standard, University of Tennessee (1994).Google Scholar
  11. 11.
    R.A. Kendall, R.J. Harrison, R.J. Littlefield and M.F. Guest, in: Reviews in Computational Chemistry, K.B. Lipkowitz and D.B. Boyd eds., VCH Publishers, Inc., New York (1994).Google Scholar
  12. 12.
    The MPI Forum, A message passing interface, in: Supercomputing’ 93, pp878–83, IEEE Computer Society Press, Los Alamitos, California, Portland, OR (1993).Google Scholar
  13. 13.
    M.E. Colvin, C.L. Janssen, R.A. Whiteside and C.H. Tong, Theoretica Chimica Acta 84:301–14 (1993).CrossRefGoogle Scholar
  14. 14.
    T.R. Furlani and H.F. King, J. Comp. Chem.(1995).Google Scholar
  15. 15.
    J. Nieplocha, R.J. Harrison and R.J. Littlefield, Global arrays; A portable shared memory programming model for distributed memory computers, in: Supercomputing’ 94, IEEE Computer Society Press, Washington, D.C. (1994).Google Scholar
  16. 16.
    M. Arango, D. Berndt, N. Carriero, D. Gelernter and D. Gilmore, Supercomputer Review 3(10) (1990).Google Scholar
  17. 17.
    M. Schuler, T. Kovar, H. Lischka, R. Shepard and R.J. Harrison, Theoretica Chimica Acta 84:489–509 (1993).CrossRefGoogle Scholar
  18. 18.
    A.P. Rendell, M.F. Guest and R.A. Kendall, J. Comp. Chem. 14:1429–39 (1993).CrossRefGoogle Scholar
  19. 19.
    J. Choi, J.J. Dongarra, L.S. Ostrouchov, A.P. Petitet, R.C. Whaley, J. Demmel, I. Dhillon and K. Stanley, LAPACK Working Note: Installation Guide for ScaLAPACK, Department of Computer Science, University of Tennessee, Knoxville, TN, (1995). Available from anonymous@ftp:ftp.netlib.org.Google Scholar
  20. 20.
    S.S. Lo, B. Phillipps and A. Sameh, SIAM J. Sci. Stat. Comput. 8(2) (1987).Google Scholar
  21. 21.
    G. Fann and R.J. Littlefield, Parallel inverse iteration with reorthogonalization, in: Sixth SIAM Conference on Parallel Processing for Scientific Computing (SIAM), pp409–13 (1993).Google Scholar
  22. 22.
    E. Anderson, Z. Bai, C. Bischof, J. Demmel, J.J. Dongarra, J. Du Croz, A. Greenbaum, S. Hammerling, A. McKenney, S. Ostrouchov and D. Sorensen, LAPACK User’s Guide, SIAM (1992).Google Scholar
  23. 23.
    R.D. Amos, I.L. Alberts, J.S. Andrews, S.M. Colwell, N.C. Handy, D. Jayatilaka, P.J. Knowles, R. Kobayashi, N. Koga, K.E. Laidig, P.E. Maslen, C.W. Murray, J.E. Rice, J. Sanz, E.D. Simandiras, A.J. Stone and M.-D. Su, CADPAC, Issue 6, University of Cambridge, (1995).Google Scholar
  24. 24.
    M.W. Schmidt, et al., QCPE Bulletin 7:115 (1987).Google Scholar
  25. 25.
    MOLPRO is a package of ab initio programs written by H.-J. Werner and P.J. Knowles, with contributions from R.D. Amos, A. Berning, D.L. Cooper, M.J.O. Deegan, A.J. Dobbyn, F. Eckert, C. Hampel, T. Leininger, R. Lindh, A.W. Lloyd, W. Meyer, M.E. Mura, A. Nicklass, P. Palmieri, K. Peterson, R. Pitzer, P. Pulay, G. Rauhut, M. Schütz, H. Stoll, A.J, Stone and T. Thorsteinsson.Google Scholar
  26. 26.
    R. Ahlrichs, M. Br, M. Hser, H. Horn and C. Klmel, Electronic structure calculations on workstation computers: The program system TURBOMOLE, Chem. Phys. Letters 162:165 (1989); R. Ahlrichs and M.v. Arnim, TURBOMOLE, parallel implementation of SCF, density functional, and chemical shift modules, in; Methods and Techniques in Computational Chemistry: METECC-95, E. Clementi and G. Corongiu, eds.Google Scholar
  27. 27.
    M. Dupuis, J.D. Watts, H.O. Villar and G.J.B. Hurst, The general atomic and molecular electronic structure system HONDO: version 7.0., Comput Phys. Commun. 52:415 (1989); M. Dupuis, A. Farazdel, S.P. Karma and S.A. Maluendes, HONDO: A general atomic and molecular electronic structure system, in: MOTECC, E. Clementi ed., ESCOM, Leiden (1990).Google Scholar
  28. 28.
    GAMESS-UK is a package of ab initio programs written by M.F. Guest, J.H. van Lenthe, J. Kendrick, K. Schoffel and P. Sherwood, with contributions from R.D. Amos, R.J. Buenker, M. Dupuis, N.C. Handy, I.H. Hillier, P.J. Knowles, V. Bonacic-Koutecky, W. von Niessen, R.J. Harrison, A.P. Rendell, V.R. Saunders, and A.J. Stone. The package is derived from the original GAMESS code due to M. Dupuis, D. Spangler and J. Wendoloski, NRCC Software Catalog, Vol. 1, Program No. QG01 (GAMESS), 1980; M.F. Guest, R.J. Harrison, J.H. van Lenthe and L.C.H. van Corler, Theo. Chim. Acta 71:117 (1987); M.F. Guest et al., Computing for Science Ltd., CCLRC Daresbury Laboratory, Daresbury, Warrington WA4 4AD, UK.Google Scholar
  29. 29.
    M. Frisch et al., Gaussian, Inc., 4415 Fifth Avenue, Pittsburgh, PA 15213, USA (1992).Google Scholar
  30. 30.
    M. Feyereisen, G. Fitzgerald, A. Komornicki, Chem. Phys. Lett. 208:359–63 (1993).CrossRefGoogle Scholar
  31. 31.
    O. Vahtras, J. Almlof and M. Feyereisen, Chem. Phys. Lett. 213:514 (1993).CrossRefGoogle Scholar
  32. 32.
    P. Hohenberg and W. Kohn, Phys. Rev. B.136:864–71 (1964); W. Kohn and L.J. Sham, Phys. Rev. A. 140:1133-38 (1965).CrossRefGoogle Scholar
  33. 33.
    E. Wimmer, Density Functional Methods in Chemistry, J.K. Labanowski and J.W. Andzelm, eds. pp7–31 Springer-Verlag, Berlin (1991).CrossRefGoogle Scholar
  34. 34.
    B.I. Dunlap, J.W.D. Connolly and J.R. Sabin, J. Chem. Phys. 71:3396, 4993 (1979).CrossRefGoogle Scholar
  35. 35.
    G.B. Bacskay, Chem. Phys. 61:385 (1982).CrossRefGoogle Scholar
  36. 36.
    P. Pulay, Chem. Phys. Lett. 100:151–4 (1983).CrossRefGoogle Scholar
  37. 37.
    P. Pulay and S. Saebo, Theor. Chim. Acta 69:357–68 (1986); S. Saebo and P. Pulay, Annu. Rev. Phys. Chem. 44:213-236 (1993).Google Scholar
  38. 38.
    H.A. Fruechtl and R.A. Kendall, A Scalable Implementation of the RI-SCF Algorithm, Int. J. Quant Chem. 64:63–69 (1997).CrossRefGoogle Scholar
  39. 39.
    G.D. Fletcher, A.P. Rendell and P. Sherwood, A parallel second-order Moller-Plesset gradient, Molec. Phys. 91:431–38 (1997).CrossRefGoogle Scholar

Copyright information

© Springer Science+Business Media New York 1999

Authors and Affiliations

  • M. F. Guest
    • 1
  • P. Sherwood
    • 1
  • J. A. Nichols
    • 2
  1. 1.Department for Computation and InformationCCLRC Daresbury LaboratoryDaresburyCheshireUK
  2. 2.High Performance Computational Chemistry GroupEnvironmental Molecular Sciences Laboratory, Pacific Northwest National LaboratoryRichlandUSA

Personalised recommendations