Skip to main content
SpringerLink
Log in
Book cover

International Conference on High-Performance Computing and Networking

HPCN-Europe 1994: High-Performance Computing and Networking pp 189–196Cite as

Object oriented simulation software for drug design

  • Conference paper
  • First Online:

Part of the book series: Lecture Notes in Computer Science ((LNCS,volume 796))

Abstract

In this paper, we report on the design and implementation of a parallel object-oriented implementation of a protein simulation application, which is the heart of a drug design software package, to be exploited at Novo Nordisk Research Labs on a large cluster of workstations.

The application is implemented in C++ on top of the XENOOPS environment, which offers location independent object invocation at the application programming interface. Thus the software is truly objectoriented — as opposed to C++ combined with low level message passing primitives.

We evaluate the productivity of software developers in this application and illustrate the role of the object-oriented environment and methodology. We compare different versions of the simulator, as different decompositions have been realised (resulting in various degrees of concurrency). Our paper reveals many positive experiences as a result of this (still ongoing) R&D effort. The conclusion includes a recommendation to exploit modern software engineering techniques to develop HPCN software.

This is a preview of subscription content, log in via an institution.

Preview

Unable to display preview. Download preview PDF.

Unable to display preview. Download preview PDF.

References

  1. S.W. de Leeuw, J.W. Perram, and E.R. Smith. Simulation of electrostatic systems in periodic boundary conditions. i lattice sums and dielectric constants. Proc. Roy. Soc., 27:A373, 1980.

    Google Scholar 

  2. Wouter Joosen, Stijn Bijnens, and Pierre Verbaeten. Massively Parallel Programming Using Object Parallelism. In Working Conference on Massively Parallel Programming Models. IEEE, September 1993.

    Google Scholar 

  3. Wouter Joosen Stijn Bijnens and Pierre Verbaeten. A Reflective Invocation Scheme to realise Advanced Object Management. In M. Riveill R. Guerraoui, O. Nierstrasz, editor, Object-Based Distributed Programming, volume 791, pages 142–154. Springer Verlag, 1994.

    Google Scholar 

  4. J.W. Perram S.W. de Leeuw and H.G. Petersen. Hamilton's Equations for Constrained Dynamical Systems. J. Stat. Phys., 61:1203–1222, 1990.

    Google Scholar 

Download references

Author information

Authors and Affiliations

  1. Novo Nordisk A/S, Novo Alle, DK-2880, Bagsvaerd, Denmark

    Robert Bywater

  2. Dept. of Comp. Sc., K.U.Leuven, Celestijnenlaan 200A, B-3001, Leuven, Belgium

    Wouter Joosen, Stijn Bijnens & Pierre Verbaeten

  3. LCAM Odense, Forskerparken 10, DK-5230, Odense, Denmark

    Thomas Larsen & John Perram

Authors
  1. Robert Bywater
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Wouter Joosen
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Stijn Bijnens
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Pierre Verbaeten
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Thomas Larsen
    View author publications

    You can also search for this author in PubMed Google Scholar

  6. John Perram
    View author publications

    You can also search for this author in PubMed Google Scholar

Editor information

Wolfgang Gentzsch Uwe Harms

Rights and permissions

Reprints and permissions

Copyright information

© 1994 Springer-Verlag Berlin Heidelberg

About this paper

Cite this paper

Bywater, R., Joosen, W., Bijnens, S., Verbaeten, P., Larsen, T., Perram, J. (1994). Object oriented simulation software for drug design. In: Gentzsch, W., Harms, U. (eds) High-Performance Computing and Networking. HPCN-Europe 1994. Lecture Notes in Computer Science, vol 796. Springer, Berlin, Heidelberg. https://doi.org/10.1007/BFb0020371

Download citation

  • DOI: https://doi.org/10.1007/BFb0020371

  • Published:

  • Publisher Name: Springer, Berlin, Heidelberg

  • Print ISBN: 978-3-540-57980-9

  • Online ISBN: 978-3-540-48406-6

  • eBook Packages: Springer Book Archive

Publish with us

Policies and ethics

Search

Navigation