The object-oriented development of a parallel application in protein dynamics

Why we need software tools for HPCN applications

Lars Bækdal, Wouter Joosen, Thomas Larsen, Jiri Kolafa, Jens H. Ovesen, John W. Perram, Henrik G. Petersen, Robert Bywater, Mark A Ratner

Research output: Contribution to journalArticle

4 Citations (Scopus)

Abstract

We analyse the concurrency and performance of the various types of force calculations involved in the molecular dynamics simulation of large protein or polyelectrolyte molecules. Although this analysis can in principle be used to write a meta-program to optimize load-balancing of this application on an MPP system, we argue that it is an enormous undertaking not appropriate for the computational scientist. Instead we argue that it is better to exploit research in parallel execution environments which provide automatic load-balancing for concurrent Object-Oriented applications. We also argue that use of Object-Oriented technology in the design of simulation software encapsulates the natural concurrency of the system. We illustrate this point with a discussion of the constraint force calculation for a polymeric molecule.

Original languageEnglish
Pages (from-to)124-135
Number of pages12
JournalComputer Physics Communications
Volume97
Issue number1-2
Publication statusPublished - Aug 2 1996

Fingerprint

software development tools
Resource allocation
massively parallel processors
proteins
Proteins
Molecules
Polyelectrolytes
Molecular dynamics
molecules
simulation
molecular dynamics
computer programs
Computer simulation

ASJC Scopus subject areas

  • Computer Science Applications
  • Physics and Astronomy(all)

Cite this

The object-oriented development of a parallel application in protein dynamics : Why we need software tools for HPCN applications. / Bækdal, Lars; Joosen, Wouter; Larsen, Thomas; Kolafa, Jiri; Ovesen, Jens H.; Perram, John W.; Petersen, Henrik G.; Bywater, Robert; Ratner, Mark A.

In: Computer Physics Communications, Vol. 97, No. 1-2, 02.08.1996, p. 124-135.

Research output: Contribution to journalArticle

Bækdal, L, Joosen, W, Larsen, T, Kolafa, J, Ovesen, JH, Perram, JW, Petersen, HG, Bywater, R & Ratner, MA 1996, 'The object-oriented development of a parallel application in protein dynamics: Why we need software tools for HPCN applications', Computer Physics Communications, vol. 97, no. 1-2, pp. 124-135.
Bækdal, Lars ; Joosen, Wouter ; Larsen, Thomas ; Kolafa, Jiri ; Ovesen, Jens H. ; Perram, John W. ; Petersen, Henrik G. ; Bywater, Robert ; Ratner, Mark A. / The object-oriented development of a parallel application in protein dynamics : Why we need software tools for HPCN applications. In: Computer Physics Communications. 1996 ; Vol. 97, No. 1-2. pp. 124-135.
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