Early performance data on the Blue Matter molecular simulation framework
by R. S. Germain, Y. Zhestkov, M. Eleftheriou, A. Rayshubskiy, F. Suits, T. J. C. Ward, B. G. Fitch
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 results of early performance 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.