Overcoming scaling challenges in biomolecular simulations across multiple platforms

IPDPS Miami 2008 - Proceedings of the 22nd IEEE International Parallel and Distributed Processing Symposium, Program and CD-ROM

Volumn , Issue , 2008, Pages

  Bhatelé, Abhinav ^a   Kumarz, Sameer ^b   Mei, Chao ^a   Phillips, James C ^c   Zheng, Gengbin ^a   Kalé, Laxmikant V ^a  

^a University of Illinois at Urbana Champaign   (United States)

^b IBM T J WATSON RESEARCH CENTER   (United States)

^c UNIVERSITY OF ILLINOIS AT URBANA CHAMPAIGN   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

BIOMOLECULAR SIMULATIONS; MULTIPLE PLATFORMS; PARALLEL AND DISTRIBUTED PROCESSING; SCALING CHALLENGES;

DISTRIBUTED PARAMETER NETWORKS;

EID: 51049100635     PISSN: None     EISSN: None     Source Type: Conference Proceeding    
DOI: 10.1109/IPDPS.2008.4536317     Document Type: Conference Paper

References (15)

1. A. Bhatele. Application-specific topology-aware mapping and load balancing for three-dimensional torus topologies. Master's thesis, Dept. of Computer Science, University of Illinois, 2007. http://charm.cs.uiuc.edu/papers/ BhateleMSThesis07.shtml.
2. K. J. Bowers, E. Chow, H. Xu, R. O. Dror, M. P. Eastwood, B. A. Gregersen, J. L. Klepeis, I. Kolossvary, M. A. Moraes, F. D. Sacerdoti, J. K. Salmon, Y. Shan, and D. E. Shaw. Scalable algorithms for molecular dynamics simulations on commodity clusters. In SC '06: Proceedings of the 2006 ACM/IEEE conference on Supercomputing, New York, NY, USA, 2006. ACM Press.
3. C. Catlett and et. al. TeraGrid: Analysis of Organization, System Architecture, and Middleware Enabling New Types of Applications. In L. Grandinetti, editor, HPC and Grids in Action, Amsterdam, 2007. IOS Press.
4. T. Darden, D. York, and L. Pedersen. Particle mesh Ewald. An N·log(N) method for Ewald sums in large systems. JCP, 98:10089-10092, 1993.
5. M. Eleftheriou, B. G. Fitch, A. Rayshubskiy, T. J. C. Ward, and R. S. Germain. Scalable framework for 3D FFTs on the Blue Gene/L supercomputer: Implementation and early performance measurements. IBM Journal of Research and Development, 49(2/3), 2005.
6. B. Fitch, R. Germain, M. Mendell, J. Pitera, M. Pitman, A. Rayshubskiy, Y. Sham, F. Suits, W. Swope, T. Ward, Y. Zhestkov, and R. Zhou. Blue Matter, an application framework for molecular simulation on Blue Gene. Journal of Parallel and Distributed Computing, 63:759-773, 2003.
7. B. G. Fitch, A. Rayshubskiy, M. Eleftheriou, T. J. C. Ward, M. Giampapa, and M. C. Pitman. Blue matter: Approaching the limits of concurrency for classical molecular dynamics. In SC '06: Proceedings of the 2006 ACM/IEEE conference on Supercomputing, New York, NY, USA, 2006. ACM Press.
8. L. Greengard and V. I. Rokhlin. A fast algorithm for particle simulations. Journal of Computational Physics, 73, 1987.
9. L. Kalé, R. Skeel, M. Bhandarkar, R. Brunner, A. Gursoy, N. Krawetz, J. Phillips, A. Shinozaki, K. Varadarajan, and K. Schulten. NAMD2: Greater scalability for parallel molecular dynamics. Journal of Computational Physics, 1998.
10. L. V. Kale, G. Zheng, C.W. Lee, and S. Kumar. Scaling Applications to Massively Parallel Machines Using Projections Performance Analysis Tool. In Future Generation Computer Systems Special Issue on: Large-Scale System Performance Modeling and Analysis, volume 22, pages 347-358, February 2006.
11. S. Kumar, C. Huang, G. Almasi, and L. V. Kalé. Achieving strong scaling with NAMD on Blue Gene/L. In Proceedings of IEEE International Parallel and Distributed Processing Symposium 2006, April 2006.
12. S. Kumar, C. Huang, G. Zheng, E. Bohm, A. Bhatele, J. C. Phillips, H. Yu, and L. V. Kalé. Scalable Molecular Dynamics with NAMD on Blue Gene/L. IBM Journal of Research and Development: Applications of Massively Parallel Systems (to appear), 52(1/2), 2007.
13. S. J. Plimpton and B. A. Hendrickson. A new parallel method for molecular-dynamics simulation of macromolecular systems. J Comp Chem, 17:326-337, 1996.
14. K. Schulten, J. C. Phillips, L. V. Kale, and A. Bhatele. Biomolecular modeling in the era of petascale computing. In D. Bader, editor, Petascale Computing: Algorithms and Applications, pages 165-181. Chapman & Hall / CRC Press, 2008.
15. M. Snir. A note on n-body computations with cutoffs. Theory of Computing Systems, 37:295-318, 2004.