Dynamic topology aware load balancing algorithms for molecular dynamics applications

Proceedings of the International Conference on Supercomputing

Volumn , Issue , 2009, Pages 110-116

  Bhatelé, Abhinav ^a   Kalé, Laxmikant V ^a   Kumar, Sameer ^b  

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

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

Author keywords

Load balancing; Mapping; Mesh; Topology; Torus

Indexed keywords

3D MESHES; BIO-MOLECULAR; BIOLOGICAL PHENOMENA; DYNAMIC TOPOLOGIES; LOAD BALANCER; LOAD BALANCING; LOAD BALANCING ALGORITHMS; MD SIMULATION; MESH TOPOLOGIES; PARALLEL MACHINE; PARALLELIZATIONS; PERFORMANCE BENEFITS; TIME-SCALES; TOPOLOGY AWARE;

ATOMS; INTELLIGENT CONTROL; MAPPING; MOLECULAR DYNAMICS;

TOPOLOGY;

EID: 70449713898     PISSN: None     EISSN: None     Source Type: Conference Proceeding    
DOI: 10.1145/1542275.1542295     Document Type: Conference Paper

References (18)

1. Laxmikant Kalé, Robert Skeel, Milind Bhandarkar, Robert Brunner, Attila Gursoy, Neal Krawetz, James Phillips, Aritomo Shinozaki, Krishnan Varadarajan, and Klaus Schulten. NAMD2: Greater scalability for parallel molecular dynamics. Journal of Computational Physics, 151:283-312, 1999.
2. Kevin J. Bowers, Edmond Chow, Huafeng Xu, Ron O. Dror, Michael P. Eastwood, Brent A. Gregersen, John L. Klepeis, Istvan Kolossvary, Mark A. Moraes, Federico D. Sacerdoti, John K. Salmon, Yibing Shan, and David 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. Blake G. Fitch, Aleksandr Rayshubskiy, Maria Eleftheriou, T. J. Christopher Ward, Mark Giampapa, and Michael 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.
4. 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.
5. James C. Phillips, Gengbin Zheng, Sameer Kumar, and Laxmikant V. Kalé. NAMD: Biomolecular simulation on thousands of processors. In Proceedings of the 2002 ACM/IEEE conference on Supercomputing, pages 1-18, Baltimore, MD, September 2002.
6. Abhinav Bhatele, Sameer Kumar, Chao Mei, James C. Phillips, Gengbin Zheng, and Laxmikant V. Kale. Overcoming Scaling Challenges in Biomolecular Simulations across Multiple Platforms. In Proceedings of IEEE International Parallel and Distributed Processing Symposium 2008, April 2008.
7. L.V. Kalé and S. Krishnan. CHARM++: A Portable Concurrent Object Oriented System Based on C++. In A. Paepcke, editor, Proceedings of OOPSLA'93, pages 91-108. ACM Press, September 1993.
8. L. V. Kalé, Milind Bhandarkar, and Robert Brunner. Load balancing in parallel molecular dynamics. In Fifth International Symposium on Solving Irregularly Structured Problems in Parallel, volume 1457 of Lecture Notes in Computer Science, pages 251-261, 1998.
9. T. P. Straatsma and J. A. McCammon. Load balancing of molecular dynamics simulation with NWChem. IBM Syst. J., 40(2):328-341, 2001.
10. Shahid H. Bokhari. On the mapping problem. IEEE Trans. Computers, 30(3):207-214, 1981.
11. P. Sadayappan and F. Ercal. Nearest-neighbor mapping of finite element graphs onto processor meshes. IEEE Trans. Computers, 36(12):1408-1424, 1987.
12. Francois Gygi, Erik W. Draeger, Martin Schulz, Bronis R. De Supinski, John A. Gunnels, Vernon Austel, James C. Sexton, Franz Franchetti, Stefan Kral, Christoph Ueberhuber, and Juergen Lorenz. Large-Scale Electronic Structure Calculations of High-Z Metals on the Blue Gene/L Platform. In Proceedings of the International Conference in Supercomputing. ACM Press, 2006.
13. Hideaki Kikuchi, Bijaya B. Karki, and Subhash Saini. Topology-aware parallel molecular dynamics simulation algorithm. In PDPTA, pages 1083-1088, 2006.
14. Abhinav Bhatelé and Laxmikant V. Kalé. Benefits of Topology Aware Mapping for Mesh Interconnects. Parallel Processing Letters (Special issue on Large-Scale Parallel Processing), 18(4):549-566, 2008.
15. Peter L. Freddolino, Anton S. Arkhipov, Steven B. Larson, Alexander McPherson, and Klaus Schulten. Molecular dynamics simulations of the complete satellite tobacco mosaic virus. 14:437-449, 2006.
16. Abhinav Bhatele and Laxmikant V. Kale. An Evaluation of the Effect of Interconnect Topologies on Message Latencies in Large Supercomputers. In Proceedings of Workshop on Large-Scale Parallel Processing (IPDPS '09), May 2009.
17. Sameer Kumar, Chao Huang, Gengbin Zheng, Eric Bohm, Abhinav Bhatele, James C. Phillips, Hao Yu, and Laxmikant V. Kalé. Scalable Molecular Dynamics with NAMD on Blue Gene/L. IBM Journal of Research and Development: Applications of Massively Parallel Systems, 52(1/2):177-187, 2008.
18. Gengbin Zheng. Achieving High Performance on Extremely Large Parallel Machines: Performance Prediction and Load Balancing. PhD thesis, Department of Computer Science, University of Illinois at Urbana-Champaign, 2005.