Performance Evaluation of a Scalable Molecular Dynamics Simulation Framework on a Massively-Parallel System

Author

Alam, Sadaf R. ; Agarwal, Pratul K. ; Kuehn, Jeffery A.

Author_Institution

Oak Ridge Nat. Lab., Oak Ridge

fYear

2007

fDate

14-17 Oct. 2007

Firstpage

1459

Lastpage

1466

Abstract

The successors of distributed-memory, massively-parallel processing (MPP) systems that are based on multi-core processor technologies and high-bandwidth communication networks are expected to deliver Petascale computing power for scientific communities in near future. This report presents preliminary performance evaluation and benchmarking results of a scalable biomolecular simulation framework on the Cray XT4 MPP system that contains multi-core Opteron processors. We identify not only the performance enhancing features but also the bottlenecks for biomolecular simulation test cases on this system using a combination of application and vendor specific performance tools. Our results show that unprecedented performance has been achieved for large-scale test cases on the system; however, the critical challenges remain for longer time scale simulations on MPP systems.

Keywords

biology computing; distributed memory systems; molecular biophysics; molecular dynamics method; multiprocessing programs; parallel programming; software performance evaluation; Cray XT4 MPP system; Opteron processors; Petascale computing; biomolecular simulation; distributed memory systems; high-bandwidth communication networks; massively parallel system; multicore processor technologies; scalable molecular dynamics simulation framework; Analytical models; Atomic measurements; Computational modeling; Instruments; Large-scale systems; Multicore processing; Performance analysis; Performance evaluation; System testing; Timing; Petascale computing; biomolecular simulations; massively parallel systems; performanceevaluation and analysis; scalability;

fLanguage

English

Publisher

ieee

Conference_Titel

Bioinformatics and Bioengineering, 2007. BIBE 2007. Proceedings of the 7th IEEE International Conference on

Conference_Location

Boston, MA

Print_ISBN

978-1-4244-1509-0

Type

conf

DOI

10.1109/BIBE.2007.4375777

Filename

4375777