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 language | English |
|---|---|
| Pages (from-to) | 124-135 |
| Number of pages | 12 |
| Journal | Computer Physics Communications |
| Volume | 97 |
| Issue number | 1-2 |
| Publication status | Published - Aug 2 1996 |
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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 journal › Article
}
TY - JOUR
T1 - The object-oriented development of a parallel application in protein dynamics
T2 - Why we need software tools for HPCN applications
AU - Bækdal, Lars
AU - Joosen, Wouter
AU - Larsen, Thomas
AU - Kolafa, Jiri
AU - Ovesen, Jens H.
AU - Perram, John W.
AU - Petersen, Henrik G.
AU - Bywater, Robert
AU - Ratner, Mark A
PY - 1996/8/2
Y1 - 1996/8/2
N2 - 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.
AB - 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.
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UR - http://www.scopus.com/inward/citedby.url?scp=0030564732&partnerID=8YFLogxK
M3 - Article
VL - 97
SP - 124
EP - 135
JO - Computer Physics Communications
JF - Computer Physics Communications
SN - 0010-4655
IS - 1-2
ER -