Paper Citing NAMD - Abstract
Germain, R.S.; Zhestkov, Y.; Eleftheriou, M.; Rayshubskiy, A.; Suits, F.; Ward, T.J.C.; Fitch, B.G.
Early performance data on the Blue Matter molecular simulation framework
IBM JOURNAL OF RESEARCH AND DEVELOPMENT, 49:447-455, MAR-MAY 2005
Blue Matter is the application framework being developed in conjunction with the scientific portion of the IBM Blue Gene(®) project. We describe the parallel decomposition currently, being used to target the Blue Gene/L machine and discuss the application-based trace tools used to analyze the performance of the application. We also present the resuits of early performace studies, including a comparison of the performance of the Ewald and the particle-particle particle-mesh (P3ME) methods, compare the measured performance of some key collective operations with the limitations imposed by the hardware, and discuss some future directions for research.
