Adapting a message-driven parallel application to GPU-accelerated clusters

2008 SC - International Conference for High Performance Computing, Networking, Storage and Analysis, SC 2008

Volumn , Issue , 2008, Pages

  Phillips, James C ^a,b   Stone, John E ^a,b   Schulten, Klaus ^b  

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

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

Author keywords

[No Author keywords available]

Indexed keywords

APPLICATION DEVELOPMENT; CPU CORES; GENERAL PURPOSE; GRAPHICS PROCESSING UNITS; PARALLEL APPLICATION; PARALLEL MOLECULAR DYNAMICS SIMULATION; SCIENTIFIC COMPUTATION; SOFTWARE DEVELOPMENT TOOLS; SYSTEM INTEGRATION;

MOLECULAR DYNAMICS; PROGRAM PROCESSORS; SOFTWARE ENGINEERING;

COMPUTER GRAPHICS EQUIPMENT;

EID: 70350754499     PISSN: None     EISSN: None     Source Type: Conference Proceeding    
DOI: 10.1109/SC.2008.5214716     Document Type: Conference Paper

References (35)

1. J. E. Stone, J. C. Phillips, P. L. Freddolino, D. J. Hardy, L. G. Trabuco, and K. Schulten, "Accelerating molecular modeling applications with graphics processors," J. Comp. Chem., vol. 28, pp. 2618-2640, 2007.
2. J. D. Owens, M. Houston, D. Luebke, S. Green, J. E. Stone, and J. C. Phillips, "GPU computing," Proceedings of the IEEE, vol. 96, pp. 879-899, 2008.
3. J. A. Anderson, C. D. Lorenz, and A. Travesset, "General purpose molecular dynamics simulations fully implemented on graphics processing units," J. Chem. Phys., vol. 227, no. 10, pp. 5342-5359, 2008.
4. I. Ufimtsev and T. Martinez, "Quantum chemistry on graphical processing units. 1. strategies for two-electron integral evaluation," Journal of Chemical Theory and Computation, vol. 4, no. 2, pp. 222-231, 2008.
5. C. I. Rodrigues, D. J. Hardy, J. E. Stone, K. Schulten, and W.-M. W. Hwu, "GPU acceleration of cutoff pair potentials for molecular modeling applications," in CF'08: Proceedings of the 2008 conference on Computing frontiers. New York, NY, USA: ACM, 2008, pp. 273-282.
6. I. Buck, T. Foley, D. Horn, J. Sugerman, K. Fatahalian, M. Houston, and P. Hanrahan, "Brook for GPUs: Stream Computing on Graphics Hardware," in SIGGRAPH '04: ACM SIGGRAPH 2004 Papers. New York, NY, USA: ACM Press, 2004, pp. 777-786.
7. M. McCool, S. Du Toit, T. Popa, B. Chan, and K. Moule, "Shader algebra," ACM Transactions on Graphics, vol. 23, no. 3, pp. 787-795, Aug. 2004.
8. M. Charalambous, P. Trancoso, and A. Stamatakis, "Initial experiences porting a bioinformatics application to a graphics processor." in Panhellenic Conference on Informatics, 2005, pp. 415-425.
9. D. R. Horn, M. Houston, and P. Hanrahan, "ClawHMMER: A streaming HMMer-search implementation," in SC '05: Proceedings of the 2005 ACM/IEEE Conference on Supercomputing. Washington, DC, USA: IEEE Computer Society, 2005, p. 11.
10. E. Elsen, V. Vishal, M. Houston, V. Pande, P. Hanrahan, and E. Darve, "N-body simulations on GPUs," Stanford University, Stanford, CA, Tech. Rep., Jun. 2007, http://arxiv.org/abs/0706.3060.
11. "NVIDIA CUDA Compute Unified Device Architecture Programming Guide," NVIDIA, NVIDIA, Santa Clara, CA, USA, 2007.
12. M. McCool, "Data-parallel programming on the Cell BE and the GPU using the RapidMind development platform," in GSPx Multicore Applications Conference, Oct./Nov. 2006.
13. Advanced Micro Devices Inc., "Brook+ SC07 BOF session," in Supercomputing 2007 Conference, Nov. 2007.
14. J. Stratton, S. Stone, and W. mei Hwu, "MCUDA: An efficient implementation of CUDA kernels on multi-cores," University of Illinois at Urbana-Champaign, Tech. Rep. IMPACT-08-01, March 2008. [Online]. Available: http://www.gigascale.org/pubs/1278.html
15. J. Nickolls, I. Buck, M. Garland, and K. Skadron, "Scalable parallel programming with CUDA," ACM Queue, vol. 6, no. 2, pp. 40-53, 2008.
16. Z. Fan, F. Qiu, A. Kaufman, and S. Yoakum-Stover, "GPU cluster for high performance computing," in SC '04: Proceedings of the 2004 ACM/IEEE conference on Supercomputing. Washington, DC, USA: IEEE Computer Society, 2004, p. 47.
17. D. Göddeke, R. Strzodka, J. Mohd-Yusof, P. McCormick, S. H. M. Buijssen, M. Grajewski, and S. Turek, "Exploring weak scalability for FEM calculations on a GPU-enhanced cluster," Parallel Comput., vol. 33, no. 10-11, pp. 685-699, 2007.
18. J. N. Glosli, K. J. Caspersen, J. A. Gunnels, D. F. Richards, R. E. Rudd, and F. H. Streitz, "Extending stability beyond CPU millennium: A micron-scale atomistic simulation of Kelvin-Helmholtz instability," in Proceedings of the 2007 ACM/IEEE Conference on Supercomputing, 2007.
19. J. W. Sheaffer, D. P. Luebke, and K. Skadron, "A hardware redundancy and recovery mechanism for reliable scientific computation on graphics processors," in GH '07: Proceedings of the 22nd ACM SIGGRAPH/ EUROGRAPHICS symposium on graphics hardware. Airela-Ville, Switzerland, Switzerland: Eurographics Association, 2007, pp. 55-64.
20. Q. Gao, W. Yu, W. Huang, and D. K. Panda, "Application-transparent checkpoint/restart for MPI programs over Infiniband," International Conference on Parallel Processing, 2006., pp. 471-478, Aug. 2006.
21. 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," J. Comp. Phys., vol. 151, pp. 283-312, 1999.
22. J. C. Phillips, R. Braun, W. Wang, J. Gumbart, E. Tajkhorshid, E. Villa, C. Chipot, R. D. Skeel, L. Kale, and K. Schulten, "Scalable molecular dynamics with NAMD," J. Comp. Chem., vol. 26, pp. 1781-1802, 2005.
23. M. Nelson, W. Humphrey, A. Gursoy, A. Dalke, L. Kalé, R. Skeel, K. Schulten, and R. Kufrin, "MDScope - A visual computing environment for structural biology," Comput. Phys. Commun., vol. 91, no. 1-3, pp. 111-134, 1995.
24. M. Nelson, W. Humphrey, A. Gursoy, A. Dalke, L. Kalé, R. D. Skeel, and K. Schulten, "NAMD - A parallel, object-oriented molecular dynamics program," Int. J. Supercomp. Appl. High Perform. Comp., vol. 10, pp. 251-268, 1996.
25. J. Phillips, G. Zheng, S. Kumar, and L. Kale, "NAMD: Biomolecular simulation on thousands of processors." in Proceedings of the IEEE/ACM SC2002 Conference, Technical Paper 277. IEEE Press, 2002.
26. P. L. Freddolino, F. Liu, M. Gruebele, and K. Schulten, "Tenmicrosecond MD simulation of a fast-folding WW domain," Biophys. J., vol. 94, pp. L75-L77, 2008.
27. P. L. Freddolino, A. S. Arkhipov, S. B. Larson, A. McPherson, and K. Schulten, "Molecular dynamics simulations of the complete satellite tobacco mosaic virus," Structure, vol. 14, pp. 437-449, 2006.
28. L. V. Kale and S. Krishnan, "Charm++: Parallel Programming with Message-Driven Objects," in Parallel Programming using C++, G. V. Wilson and P. Lu, Eds. MIT Press, 1996, pp. 175-213.
29. L. V. Kale, E. Bohm, C. L. Mendes, T. Wilmarth, and G. Zheng, "Programming Petascale Applications with Charm++ and AMPI," in Petascale Computing: Algorithms and Applications, D. Bader, Ed. Chapman & Hall / CRC Press, 2008, pp. 421-441.
30. A. Gursoy and L. Kalé, "Performance and modularity benefits of messagedriven execution," Journal of Parallel and Distributed Computing, vol. 64, pp. 461-480, 2004.
31. S. Pakin, V. Karamcheti, and A. A. Chien, "Fast messages: Efficient, portable communication for workstation clusters and mpps," IEEE Parallel Distrib. Technol., vol. 5, no. 2, pp. 60-73, 1997.
32. T. von Eicken, D. E. Culler, S. C. Goldstein, and K. E. Schauser, "Active messages: a mechanism for integrated communication and computation," SIGARCH Comput. Archit. News, vol. 20, no. 2, pp. 256-266, 1992.
33. L. V. Kalé, "The virtualization model of parallel programming: Runtime optimizations and the state of art," in LACSI 2002, Albuquerque, October 2002.
34. W. Huang, G. Santhanaraman, H. W. Jin, Q. Gao, and D. K. Panda, "Design of high performance MVAPICH2: MPI2 over InfiniBand," in Sixth IEEE International Symposium on Cluster Computing and the Grid (CCGRID'06). Los Alamitos, CA, USA: IEEE Computer Society, 2006, pp. 43-48.
35. 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, vol. 22, no. 3, February 2006, pp. 347-358.