Probing biomolecular machines with graphics processors

Abstract

GPU acceleration and other computer performance increases will offer critical benefits to biomedical science.

References

1. Anderson, J.A., Lorenz, C.D., and Travesset, A. General-purpose molecular dynamics simulations fully implemented on graphics processing units. Journal of Chemical Physics 227, 10 (2008), 5342--5359.
2. Buck, I., Foley, T., Horn, D., Sugerman, J., Fatahalian, K., Houston, M., and Hanrahan, P. Brook for GPUs: Stream computing on graphics hardware. In Proceedings of 2004 ACM SIGGRAPH. ACM, NY, 777--786
3. Davis, D., Lucas, R., Wagenbreth, G., Tran, J., and Moore, J. A GPU-enhanced cluster for accelerated FMS. In Proceedings of the 2007 DoD High-performance Computing Modernization Program Users Group Conference. IEEE Computer Society, 305--309.
4. Dynerman, D., Butzlaff, E., and Mitchell, J.C. CUSA and CUDE: GPU-accelerated methods for estimating solvent accessible surface area and desolvation. Journal of Computational Biology 16, 4 (2009), 523--537.
5. Elsen, E., Vishal, V., Houston, M., Pande, V., Hanrahan, P., and Darve, E. N-body simulations on GPUs. Technical Report, Stanford University (June 2007); http://arxiv.org/abs/0706.3060.
6. Fan, Z., Qiu, F., Kaufman, A., and Yoakum-Stover, S. GPU cluster for high-performance computing. In Proceedings of the 2004 ACM/IEEE Conference on Supercomputing. IEEE Computer Society, 47.
7. Friedrichs, M.S., Eastman, P., Vaidyanathan, V., Houston, M., Legrand, S., Beberg, A.L., Ensign, D.L., Bruns, C.M., and Pande, V.S. Accelerating molecular dynamic simulation on graphics processing units. Journal of Computational Chemistry 30, 6 (2009), 864--872.
8. Göddeke, D., Strzodka, R., Mohd-Yusof, J., McCormick, P., Buijssen, S.H.M., Grajewski, M., and Turek, S. Exploring weak scalability for FEM calculations on a GPU-enhanced cluster. Parallel Computing 33, 10--11 (2007), 685--699.
9. Hardy, D.J., Stone, J.E., and Schulten, K. Multilevel summation of electrostatic potentials using graphics processing units. Parallel Computing 35 (2009), 164--177.
10. Humphrey, W., Dalke, A., and Schulten, K. VMD: Visual molecular dynamics. Journal of Molecular Graphics 14 (1996), 33--38.
11. Lindholm, E., Nickolls, J., Oberman, S., and Montrym, J. Nvidia Tesla: A unified graphics and computing architecture. IEEE Micro 28, 2 (2008), 39--55.
12. McCool, M. Data-parallel programming on the Cell BE and the GPU using the RapidMind development platform. In Proceedings of GSPx Multicore Applications Conference (Oct.--Nov. 2006).
13. McCool, M., Du Toit, S., Popa, T., Chan, B., and Moule, K. Shader algebra. ACM Transactions on Graphics 23, 3 (2004), 787--795.
14. Munshi, A. OpenCL specification version 1.0 (2008); http://www.khronos.org/registry/cl/.
15. Nickolls, J., Buck, I., Garland, M., and Skadron, K. Scalable parallel programming with CUDA. ACM Queue 6, 2 (2008): 40--53.
16. Nvidia CUDA (Compute Unified Device Architecture) Programming Guide. Nvidia, Santa Clara, CA 2007.
17. Owens, J.D., Houston, M., Luebke, D., Green, S., Stone, J.E., and Phillips, J.C. GPU computing. In Proceedings of IEEE 96 (2008), 879--899.
18. Phillips, J.C., Braun, R., Wang, W., Gumbart, J., Tajkhorshid, E., Villa, E., Chipot, C., Skeel, R.D., Kale, L., and Schulten, K. Scalable molecular dynamics with NAMD. Journal of Computational Chemistry 26 (2005), 1781--1802.
19. Phillips, J.C., Stone, J.E., and Schulten, K. Adapting a message-driven parallel application to GPU-accelerated clusters. In Proceedings of the 2008 ACM/IEEE Conference on Supercomputing. IEEE Press, 2008.
20. Rodrigues, C.I., Hardy, D.J., Stone, J.E., Schulten, K., and Hwu, W.W. GPU acceleration of cutoff pair potentials for molecular modeling applications. In Proceedings of the 2008 ACM Conference on Computing Frontiers (2008), 273--282.
21. Showerman, M., Enos, J., Pant, A., Kindratenko, V., Steffen, C., Pennington, R., and Hwu, W. QP: A heterogeneous multi-accelerator cluster. In Proceedings of the 10th LCI International Conference on High-performance Clustered Computing (Mar. 2009).
22. Stone, J.E., Phillips, J.C., Freddolino, P.L., Hardy, D.J., Trabuco, L.G., and Schulten, K. Accelerating molecular modeling applications with graphics processors. Journal of Computational Chemistry 28 (2007), 2618--2640.
23. Stone, J. E., Saam, J., Hardy, D. J., Vandivort, K. L., Hwu, W. W., and Schulten, K. High-performance computation and interactive display of molecular orbitals on GPUs and multicore CPUs. In Proceedings of the 2nd Workshop on General-purpose Processing on Graphics Processing Units. ACM International Conference Proceeding Series 383 (2009), 9--18.
24. Takizawa, H. and Kobayashi, H. Hierarchical parallel processing of large-scale data clustering on a PC cluster with GPU coprocessing. Journal of Supercomputing 36, 3 (2006), 219--234.
25. Ufimtsev, I.S. and Martinez, T.J. Quantum chemistry on graphical processing units. Strategies for two-electron integral evaluation. Journal of Chemical Theory and Computation 4, 2 (2008), 222--231.

Index Terms

• Applied computing

  • Life and medical sciences

• Computer systems organization

  • Architectures

    • Parallel architectures

  • Dependable and fault-tolerant systems and networks

• Computing methodologies

  • Modeling and simulation

    • Simulation types and techniques

• General and reference

  • Cross-computing tools and techniques

    • Performance

• Networks

  • Network performance evaluation