Performance potential of molecular dynamics simulations on high performance reconfigurable computing systems

Proceedings - 2nd International Workshop on High-Performance Reconfigurable Computing Technology and Applications, HPRCTA 2008 - Held in Conjunction with SC08

Volumn , Issue , 2008, Pages

  Chiu, Matt ^a   Herbordt, Martin C ^a   Langhammer, Martin ^b  

^a Boston University   (United States)

^b Altera UK Ltd   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

ARITHMETIC ALGORITHMS; CURRENT TECHNOLOGIES; DESIGN SPACES; END USERS; FLOATING POINTS; HIGH PERFORMANCE RECONFIGURABLE COMPUTING; MOLECULAR-DYNAMICS SIMULATIONS; MULTI CORES; PARTICLE PAIRS; PERFORMANCE LIMITS; PERFORMANCE POTENTIALS; SIMULATION QUALITIES; SINGLE PRECISION; TRADE OFFS;

MOLECULAR DYNAMICS; PIPELINES;

DYNAMICS;

EID: 62949153055     PISSN: None     EISSN: None     Source Type: Conference Proceeding    
DOI: 10.1109/HPRCTA.2008.4745685     Document Type: Conference Paper

References (31)

1. Alam, S., Agarwal, P., Smith, M., Vetter, J., and Caliga, D. Using FPGA devices to accelerate biomolecular simulations. Computer 40, 3 (2007), 66-73.
2. Amisaki, T., Fujiwara, T., Kusumi, A., Miyagawa, H., and Kitamura, K. Error evaluation in the design of a special-purpose processor that calculates nonbonded forces in molecular dynamics simulations. Journal of Computational Chemistry 16, 9 (1995), 1120-1130.
3. Azizi, N., Kuon, 1., Egier, A., Darabiha, A., and Chow, P. Reconfigurable molecular dynamics simulator. In Proceedings of the IEEE Symposium on Field Programmable Custom Computing Machines (2004), pp. 197-206.
4. Bowers, K.J., et al. Scalable algorithms for molecular dynamics simulations on commodity clusters. In Proceedings of Supercomputing (2006).
5. Darden, T., York, D., and Pedersen, L. Particle Mesh Ewald: an Nlog(N) method for Ewald sums in large systems. J. Chemical Physics 98 (1993), 10089-10092.
6. Fitch, B.G, et al. Blue Matter: Approaching the limits of concurrency for classical molecular dynamics. In Proceedigs of Supercomputing (2006).
7. Gu, Y., and Herbordt, M. High performance molecular dynamics simulations with FPGA coprocessors. In Proceedings of the Reconfigurable Systems Summer Institute (2007).
8. Gu, Y., VanCourt, T., and Herbordt, M. Accelerating molecular dynamics simulations with configurable circuits. lEE Proceedings on Computers and Digital Technology 153, 3 (2006), 189-195.
9. Gu, Y., VanCourt, T., and Herbordt, M. Improved interpolation and system integration for FPGA-based molecular dynamics simulations. In Proceedings of the IEEE Conference on Field Programmable Logic and Applications (2006), pp. 21-28.
10. Gu, Y., VanCourt, T., and Herbordt, M. Explicit design of FPGA-based coprocessors for short-range force computation in molecular dynamics simulations. Parallel Computing 34, 4-5 (2008), 261-27l.
11. Hamada, T., and Nakasato, N. Massively parallel processors generator for reconfigurable system. Proceedings of the IEEE Symposium on Field Programmable Custom Computing Machines (2005).
12. Izaguirre, J., Hampton, S., and Matthey, T. Parallel multigrid summation for the n-body problem. Journal of Parallel and Distributed Computing 65 (2005), 949962.
13. Kindratenko, V., and Pointer, D. A case study in porting a production scientific supercomputing application to a reconfigurable computer. In Proceedings of the IEEE Symposium on Field Programmable Custom Computing Machines (2006), pp. 13-22.
14. Koeher, S., Curreri, J., and George, A. Performance analysis challenges and framework for high performance reconfigurable computing. Parallel Computing 34 4-5 (2008), 217-230.
15. Komeiji, Y., Uebayasi, M., Takata, R., Shimizu, A., Itsukashi, and Taiji, M. Fast and accurate molecular dynamics simulation of a protein using a specialpurpose computer. Journal of Computational Chemistry 18, 12 (1997), 1546-1563.
16. Langhammer, M. Floating point datapath synthesis for FPGAs. In Proceedings of the IEEE Conference on Field Programmable Logic and Applications (2008), pp. 355-360.
17. Matthey, T. ProtoMol, an object-oriented framework for prototyping novel algorithms for molecular dynamics. ACM Trans. Mathematical Software 30, 3 (2004), 237-265.
18. Phillips, J., Zheng, G., and Kale, L. NAMD: biomolecular simulation on thousands of processors. In Supercomputing (2002).
19. Rapaport, D. The Art of Molecular Dynamics Simulation. Cambridge University Press, 2004.
20. Rodrigues, C., Hardy, D., Stone, J., Schulten, K and Hwu, W.-M. GPU acceleration of cutoff pair potentialsfor molecular modeling applications. In Proc. ACM Int. Conf. on Computing Frontiers (2008).
21. Scrofano, R., and Prasanna, V. Preliminary investigation of advanced electrostatics in molecular dynamics on reconfigurable computers. In Supercomputing (2006).
22. Shan, Y., Klepeis, J., Eastwood, M., Dror, R., and Shaw, D. Gaussian split Ewald: A fast Ewald mesh method for molecular simulation. Journal of Chemical Physics 122, 4 (2005).
23. Shaw, D.E., et al. Anton, a special-purpose machine for molecular dynamics simulation. In Proceedings of the International Symposium on Computer Architecture (2007), pp. 1-12.
24. Shi, G., and Kindratenko, V. Implementation of NAMD molecular dynamics non-bonded force-field on the Cell Broadband Engine processor. In Proc. 9th Int. IEEE Workshop on Parallel and Distributed Scientific and Engineering Computing (2008).
25. Skeel, R., Tezcan, I., and Hardy, D. Multiple grid methods for classical molecular dynamics. Journal of Computational Chemistry 23 (2002), 673-684.
26. Stone, J., Phillips, J., Freddolino, P., Hardy, D., Trabuco, L., and Schulten, K. Accelerating molecular modeling applications with graphics processors. Journal of Computational Chemistry 28 (2007), 2618-2640.
27. Taiji, M., Narumi, T., Ohno, Y., Futatsugi, N., Suenaga, A., Takada, N., and Konagaya, A. Protein Explorer: A petaflops special-purpose computer system for molecular dynamics simulations. In Supercomputing (2003).
28. van der Spoel, D. Gromacs exercises. CSC Course, Espo, Finland, February 2004.
29. van der Spoel, D., Lindahl, E., Hess, B., Groenhof, G., Mark, A., and Berendsen, H. GROMACS: fast, flexible, and free. Journal of Computational Chemistry 26 (2005), 1701-1718.
30. Villareal, J., Cortes, J., and Najjar, W. Compiled code acceleration of NAMD on FPGAs. In Proceedings of the Reconfigurable Systems Summer Institute (2007).
31. Wolff, D., and Rudd, W. Tabulated potentials in molecular dynamics simulations. Computer Physics Communications 120 (1999), 20-32.