Abstract
Molecular dynamics simulations are a common and often repeated task in molecular biology. The need for speeding up this treatment comes from the requirement for large system simulations with many atoms and numerous time steps. In this paper we present a new approach to high performance molecular dynamics simulations on graphics processing units. Using modern graphics processing units for high performance computing is facilitated by their enhanced programmability and motivated by their attractive price/performance ratio and incredible growth in speed. To derive an efficient mapping onto this type of architecture, we have used the Compute Unified Device Architecture (CUDA) to design and implement a new parallel algorithm. This results in an implementation with significant runtime savings on an off-the-shelf computer graphics card.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
Preview
Unable to display preview. Download preview PDF.
References
Krüger, J., Westermann, R.: Linear algebra operators for gpu implementation of numerical algorithms. ACM Trans. Graph. 22, 908–916 (2003)
Xu, F., Müller, K.: Ultra-fast 3d filtered backprojection on commodity graphics hardware. In: IEEE International Symposium on Biomedical Imaging 2004 (2004)
Liu, W., Schmidt, B., Voss, G., Müller-Wittig, W.: Streaming algorithms for biological sequence alignment on gpus. IEEE Transactions on Parallel and Distributed Systems 18(9), 1270–1281 (2007)
Horn, D., Houston, M., Hanrahan, P.: Clawhmmer: a streaming hmmer-search implementation. In: Proceedings of Supercomputing 2005 (2005)
Moreland, K., Angel, E.: The fft on a gpu. In: Proceedings SIGGRAPH/Eurographics Workshop on Graphics Hardware, pp. 112–119 (2003)
Owens, J., Luebke, D., Govindaraju, N., Harris, M., Kruger, J., Lefohn, A., Purcell, T.: A survey of general-purpose computation on graphics hardware. In: Eurographics 2005, pp. 21–51 (2005)
Nvidia: NVIDIA CUDA Homepage, http://developer.nvidia.com/object/cuda.html
Sheng, H., Guerrieri, R., Sangiovanni-Vincentelli, A.L.: Three-dimensional monte carlo device simulation for massively parallel architectures. Technical Report UCB/ERL M95/53, EECS Department, University of California, Berkeley (1995)
Ercolessi, F.: A molecular dynamics primer. Technical report (1997) http://www.fisica.uniud.it/~ercolessi/md/
Allen, M.: Introduction to molecular dynamics simulation. Computational Soft Matter-From Synthetic Polymers to Proteins 23, 1–28 (2004)
Lennard-Jones, J.: Cohesion. In: Proceedings of Physical Society, pp. 461–482 (1931)
Shu, J., Wang, B., Zheng, W.: Cluster-based parallel simulation for large scale molecular dynamics in microscale thermophysics. In: Cao, J., Yang, L.T., Guo, M., Lau, F. (eds.) ISPA 2004. LNCS, vol. 3358, pp. 200–211. Springer, Heidelberg (2004)
Plimpton, S.: Fast parallel algorithms for short-range molecular dynamics. Journal of Computational Physics 117, 1–19 (1995)
Hut, P., Makino, J.: Computational physics – astrophysics on the grape family of special-purpose computers. Science 283, 501–505 (1999)
Bakker, A., Gilmer, G., Grabow, M., Thompson, K.: A special purpose computer for molecular dynamics calculations. Journal of Computational Physics 90, 313–335 (1990)
Fine, R., Dimmler, G., Levinthal, C.: Fastrun: A special purpose, hardwired computer for molecular simulation. Proteins 11, 242–253 (1991)
Narumi, T., Ohno, Y., Okimoto, N., Suenaga, A., Yanai, R., Taiji, M.: A high-speed special-purpose computer for molecular dynamics simulations: Mdgrape-3. In: NIC Workshop 2006, vol. 34, pp. 29–36 (2006)
Mink, A., Bailly, C.: Parallel implementation of a molecular dynamics simulation program. In: Simulation Conference Proceedings, vol. 1, pp. 13–16 (1998)
Nakano, P., Kalia, R.: Parallel multiple-time-step molecular dynamics with three-body interaction. Computer Physics Communications 77, 303–312 (1993)
Tamayo, P., Mesirov, J., Boghosian, B.: Parallel approaches to short-range molecular dynamics simulations. Supercomputing, 462–470 (1991)
Nvidia: NVIDIA CUDA Compute Unified Device Architecture-Programming Guide, (2007) http://developer.download.nvidia.com/compute/cuda
Berendsen, H., Van Der Spoel, D., Van Drunen, R.: Gromacs: A message-passing parallel molecular dynamics implementation. Computer Physics Communications 91, 43–56 (1995)
Morris, G., Goodsell, D., Huey, R., Olson, A.: Distributed automated docking of flexible ligands to proteins: Parallel applications of autodock 2.4. Journal of Computer-Aided Molecular Design 10(2), 293–304 (1996)
Author information
Authors and Affiliations
Editor information
Rights and permissions
Copyright information
© 2007 Springer-Verlag Berlin Heidelberg
About this paper
Cite this paper
Liu, W., Schmidt, B., Voss, G., Müller-Wittig, W. (2007). Molecular Dynamics Simulations on Commodity GPUs with CUDA. In: Aluru, S., Parashar, M., Badrinath, R., Prasanna, V.K. (eds) High Performance Computing – HiPC 2007. HiPC 2007. Lecture Notes in Computer Science, vol 4873. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-540-77220-0_20
Download citation
DOI: https://doi.org/10.1007/978-3-540-77220-0_20
Publisher Name: Springer, Berlin, Heidelberg
Print ISBN: 978-3-540-77219-4
Online ISBN: 978-3-540-77220-0
eBook Packages: Computer ScienceComputer Science (R0)