A scalable parallel framework for analyzing terascale molecular dynamics simulation trajectories

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

Volumn , Issue , 2008, Pages

  Tu, Tiankai ^a   Rendleman, Charles A ^a   Borhani, David W ^a   Dror, Ron O ^a   Gullingsrud, Justin ^a   Jensen, Morten O ^a   Klepeis, John L ^a   Maragakis, Paul ^a   Miller, Patrick ^a   Stafford, Kate A ^a   Shaw, David E ^a,b  

^a D E SHAW RESEARCH   (United States)

^b Och Spine at New York Presbyterian Hospitals   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

LINUX CLUSTERS; MOLECULAR DYNAMICS SIMULATIONS; NOVEL METHODS; PARALLEL ALGORITHMS AND ARCHITECTURES; PARALLEL ANALYSIS; PARALLEL EXECUTIONS; PARALLEL FRAMEWORK; PARALLEL PROCESSING; PERFORMANCE EVALUATION; PROGRAMMING INTERFACE; SEQUENTIAL ANALYSIS; SIMULATION DATA; TERASCALE; TRAJECTORY ANALYSIS; TRAJECTORY DATA;

COMPUTER OPERATING SYSTEMS; COMPUTER SCIENCE; MOLECULAR DYNAMICS; SIMULATORS; TRAJECTORIES;

PARALLEL ALGORITHMS;

EID: 70350786551     PISSN: None     EISSN: None     Source Type: Conference Proceeding    
DOI: 10.1109/SC.2008.5214715     Document Type: Conference Paper

References (22)

1. Y.-S. Hwang, R. Das, J. H. Saltz, M. Hodoscek, B. R. Brooks, "Parallelizing Molecular Dynamics Programs for Distributed-Memory Machines," IEEE Computational Science and Engineering, vol. 02, no. 2, pp. 18-29, 1995.
2. J. C. Phillips, R. Braun, W. Wang, J. Gumbart, E. Tajkhorshid, E. Villa, C. Chipot, R. D. Skeel, L. Kalé, and K. Schulten, "Scalable molecular dynamics with NAMD," J. Comp. Chem., vol. 26, no. 16, pp. 1781-1802, 2005.
3. D. A. Case, T. E. Cheatham III, T. Darden, H. Gohlke, R. Luo, K. M. Merz Jr., A. Onufriev, C. Simmerling, B. Wang, and R. J. Woods, "The Amber biomolecular simulation programs," J. Comp. Chem., vol. 26, no. 16, pp. 1668-1688, 2005.
4. M. Christen, P. H. Hünenberger, D. Bakowies, R. Baron, R. Bürgi, D. P. Geerke, T. N. Heinz, M. A. Kastenholz, V. Kräutler, C. Oostenbrink, C. Peter, D. Trzesniak, and W. F. van Gunsteren, "The GROMOS software for biomolecular simulation: GROMOS05," J. Comp. Chem., vol. 26, no. 16, pp. 1719-1751, 2005.
5. K. J. Bowers, E. Chow, H. Xu, R. O. Dror, M. P. Eastwood, B. A. Gregersen, J. L. Klepeis, I. Kolossváry, M. A. Moraes, F. D. Sacerdoti, J. K. Salmon, Y. Shan, and D. E. Shaw, "Scalable algorithms for molecular dynamics simulations on commodity clusters," in Proc. 2006 ACM/IEEE Conf. on Supercomputing (SC06), Tampa, FL, November 2006.
6. B. Hess, C. Kutzner, D. van der Spoel, and E. Lindahl, "GROMACS 4: Algorithms for highly efficient, load-balanced, and scalable molecular simulation," J. Chem. Theory and Comp., vol. 4, no. 3, pp. 435-447, 2008.
7. B. G. Fitch, A. Rayshubskiy, M. Eleftheriou, T. J. C. Ward, M. E. Giampapa, M. C. Pitman, J. W. Pitera, W. C. Swope, and R. S. Germain, "Blue Matter: Scaling of N-body simulations to one atom per node," IBM J. Research and Develop., vol. 52, no. 1/2, pp. 145-158, 2008.
8. R. Fine, G. Dimmler, and C. Levinthal, "FASTRUN: A special purpose, hardwired computer for molecular simulation," Proteins, vol. 11, no. 4, pp. 242-253, 1991, (erratum: 14(3): 421-422, 1992).
9. S. Toyoda, H. Miyagawa, K. Kitamura, T. Amisaki, E. Hashimoto, H. Ikeda, A. Kusumi, and N. Miyakawa, "Development of MD Engine: High-speed accelerator with parallel processor design for molecular dynamics simulations," J. Comp. Chem., vol. 20, no. 2, pp. 185-199, 1999.
10. M. Taiji, T. Narumi, Y. Ohno, N. Futatsugi, A. Suenaga, N. Takada, and A. Konagaya, "Protein Explorer: A petaflops special-purpose computer system for molecular dynamics simulations," in Proc. 2003 ACM/IEEE Conf. on Supercomputing (SC03), Phoenix, AZ, November 2003.
11. D. E. Shaw, M. M. Deneroff, R. O. Dror, J. S. Kuskin, R. H. Larson, J. K. Salmon, C. Young, B. Batson, K. J. Bowers, J. C. Chao, M. P. Eastwood, J. Gagliardo, J. P. Grossman, R. C. Ho, D. J. Ierardi, I. Kolossváry, J. L. Klepeis, T. Layman, C. McLeavey, M. A. Moraes, R. Mueller, E. C. Priest, Y. Shan, J. Spengler, M. Theobald, B. Towles, and S. C. Wang, "Anton, a special-purpose machine for molecular dynamics simulation," in Proc. 34th Ann. Intl. Symp. on Computer Architecture, San Diego, June 2007, pp. 1-12.
12. K. Barker, K. Davis, A. Hoisie, D. Kerbyson, M. Lang, S. Pakin, and J. C. Sancho, "Entering the petaflop era: The architecture and performance of roadrunner," in Proc. 2008 ACM/IEEE Conf. on Supercomputing (SC08), Austin, TX, November 2008.
13. J. Dean and S. Ghemawat, "MapReduce: Simplified data processing on large clusters," in Proc. 6th Symp. on Operating System Design and Implementation (OSDI04), San Francisco, CA, December 2004.
14. --, "MapReduce: Simplified data processing on large clusters," Comm. ACM, vol. 51, no. 1, pp. 107-113, 2008.
15. W. Humphrey, A. Dalke, and K. Schulten, "VMD-Visual Molecular Dynamics," J. Mol. Graphics, vol. 14, no. 1, pp. 33-38, 1996.
16. PDB File Format, http://www.rcsb.org/pdb/home/home.do.
17. J. S. Vitter, "External memory algorithms and data structures: Dealing with massive data," ACM Computing Surveys, vol. 33, no. 2, pp. 209-271, 2001.
18. Hadoop, http://hadoop.apache.org/core/.
19. S. Ghemawat, H. Gobioff, and S.-T. Leung, "The Google file system," in Proc. 19th ACM Symp. Operating Systems Principles, Bolton Landing, NY, October 2003.
20. pyMPI, http://pympi.sourceforge.net/.
21. P. H. Carns, W. B. Ligon III, R. B. Ross, and R. Thakur, "PVFS: A parallel file system for Linux clusters," in Proc. 4th Ann. Linux Showcase and Conf., Atlanta, GA, October 2000.
22. PVFS, http://www.pvfs.org/.