Early performance data on the blue matter molecular simulation framework

Authors:
R. S. Germain;Y. Zhestkov;M. Eleftheriou;A. Rayshubskiy;F. Suits;T. J. C. Ward;B. G. Fitch
Affiliations:
IBM Research Division, Thomas J. Watson Research Center, Yorktown Heights, New York;IBM Research Division, Thomas J. Watson Research Center, Yorktown Heights, New York;IBM Research Division, Thomas J. Watson Research Center, Yorktown Heights, New York;IBM Research Division, Thomas J. Watson Research Center, Yorktown Heights, New York;IBM Research Division, Thomas J. Watson Research Center, Yorktown Heights, New York;IBM United Kingdom Limited, Winchester, England;IBM Research Division, Thomas J. Watson Research Center, Yorktown Heights, New York
Venue:
IBM Journal of Research and Development
Year:
2005

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Abstract

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.