Title :
The scaling of molecular dynamics on the KSR1
Author :
Haacke, Robert ; Pettitt, B. Montgomery
Author_Institution :
Dept. of Chem. & Comput. Sci., Houston Univ., TX, USA
Abstract :
Molecular dynamics and many other particle based simulation techniques are often highly parallelizable in principle. In practice many algorithms for concurrency can lead to irreproducible trajectories. We suggest a method for providing reproducible simulations that suffers only a small performance penalty. Results for scaling of the molecular dynamics code ESP to the KSR1 parallel computer are also given and the effects of trying to overlap computation and communication on the KSR are discussed. Algorithms are discussed with particular attention focused on the force summation aspects
Keywords :
digital simulation; molecular dynamics method; parallel algorithms; parallel machines; physics; physics computing; ESP; KSR1 parallel computer; concurrency; highly parallelizable; irreproducible trajectories; molecular dynamics; particle based simulation techniques; performance penalty; reproducible simulations; Application software; Biological system modeling; Central Processing Unit; Chemistry; Computational biology; Computational modeling; Computer science; Computer simulation; Concurrent computing; Parallel programming;
Conference_Titel :
System Sciences, 1995. Proceedings of the Twenty-Eighth Hawaii International Conference on
Conference_Location :
Wailea, HI
Print_ISBN :
0-8186-6930-6
DOI :
10.1109/HICSS.1995.375342