Early performance data on the Blue Matter molecular simulation framework

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. © Copyright 2005 by International Business Machines Corporation.