Early experiences scaling VMD molecular visualization and analysis jobs on blue waters

Proceedings - 2013 Extreme Scaling Workshop, XSW 2013

Volumn , Issue , 2013, Pages 43-50

  Stone, John E ^a   Isralewitz, Barry ^a   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

MOLECULAR DYNAMICS; SUPERCOMPUTERS;

EXPERIMENTAL METHODS; MOLECULAR DYNAMICS SIMULATIONS; MOLECULAR VISUALIZATION; NANOSECOND RESOLUTION; SIMULATION OUTPUTS; TRAJECTORY ANALYSIS; VISUALIZATION ALGORITHMS; VISUALIZATION TOOLS;

VISUALIZATION;

EID: 84901007959     PISSN: None     EISSN: None     Source Type: Conference Proceeding    
DOI: 10.1109/XSW.2013.10     Document Type: Conference Paper

References (24)

1. Gongpu Zhao, Juan R. Perilla, Ernest L. Yufenyuy, Xin Meng, Bo Chen,Jiying Ning, Jinwoo Ahn, Angela M. Gronenborn, Klaus Schulten,Christopher Aiken, and Peijun Zhang. Mature HIV-1 capsid structureby cryo-electron microscopy and all-atom molecular dynamics. Nature,497:643-646, 2013. doi:10.1038/nature12162.
2. William Humphrey, Andrew Dalke, and Klaus Schulten. VMD-VisualMolecular Dynamics. J. Mol. Graphics, 14:33-38, 1996.
3. Tiankai Tu, Charles A. Rendleman, David W. Borhani, Ron O. Dror,Justin Gullingsrud, Morten Ø. Jensen, John L. Klepeis, Paul Maragakis,Patrick Miller, Kate A. Stafford, and David E. Shaw. A scalableparallel framework for analyzing terascale molecular dynamics simulationtrajectories. In Proceedings of the 2008 ACM/IEEE conferenceon Supercomputing, SC '08, pages 56:1-56:12, Piscataway, NJ, USA,2008. IEEE Press.
4. John E. Stone, James C. Phillips, Peter L. Freddolino, David J. Hardy,Leonardo G. Trabuco, and Klaus Schulten. Accelerating molecularmodeling applications with graphics processors. J. Comp. Chem.,28:2618-2640, 2007.
5. Ivan S. Ufimtsev and Todd J. Martinez. Quantum chemistry on graphicalprocessing units. 1. Strategies for two-electron integral evaluation.J. Chem. Theor. Comp., 4(2):222-231, 2008.
6. Michael Garland, Scott Le Grand, John Nickolls, Joshua Anderson,Jim Hardwick, Scott Morton, Everett Phillips, Yao Zhang, and VasilyVolkov. Parallel computing experiences with CUDA. IEEE Micro,28(4):13-27, 2008.
7. G. Giupponi, M.J. Harvey, and G. De Fabritiis. The impact ofaccelerator processors for high-throughput molecular modeling andsimulation. Drug Discovery Today, 13(23-24):1052-1058, 2008.
8. Mark S. Friedrichs, Peter Eastman, Vishal Vaidyanathan, Mike Houston,Scott Legrand, Adam L. Beberg, Daniel L. Ensign, Christopher M.Bruns, and Vijay S. Pande. Accelerating molecular dynamic simulationon graphics processing units. J. Comp. Chem., 30(6):864-872, 2009.
9. John E. Stone, David J. Hardy, Ivan S. Ufimtsev, and Klaus Schulten.GPU-accelerated molecular modeling coming of age. J. Mol. Graph.Model., 29:116-125, 2010.
10. Jeremy Enos, Craig Steffen, Joshi Fullop, Michael Showerman,Guochun Shi, Kenneth Esler, Volodymyr Kindratenko, John E. Stone,and James C. Phillips. Quantifying the impact of GPUs on performanceand energy efficiency in HPC clusters. In International Conference onGreen Computing, pages 317-324, 2010.
11. Kalyana Chadalavada and Robert Sisneros. Analysis of the Blue Watersfile system architecture for application I/O performance. In Cray UserGroup Meeting (CUG 2013), May 2013.
12. Mark Swan and Doug Petesch. Blue Waters I/O performance. In CrayUser Group Meeting (CUG 2013), May 2013.
13. Kyle Spafford, Jeremy S. Meredith, and Jeffrey S. Vetter. QuantifyingNUMA and contention effects in multi-GPU systems. In Proceedingsof the Fourth Workshop on General Purpose Processing on GraphicsProcessing Units, GPGPU-4, pages 11:1-11:7, New York, NY, USA,2011. ACM.
14. Jun Shirako, David M. Peixotto, Vivek Sarkar, and William N. Scherer.Phasers: a unified deadlock-free construct for collective and point-topointsynchronization. In Proceedings of the 22nd annual internationalconference on Supercomputing, ICS '08, pages 277-288, New York,NY, USA, 2008. ACM.
15. John E. Stone, Kirby L. Vandivort, and Klaus Schulten. Immersiveout-of-core visualization of large-size and long-timescale moleculardynamics trajectories. Lect. Notes in Comp. Sci., 6939:1-12, 2011.
16. David J. Hardy, John E. Stone, and Klaus Schulten. Multilevelsummation of electrostatic potentials using graphics processing units.J. Paral. Comp., 35:164-177, 2009.
17. John E. Stone, Jan Saam, David J. Hardy, Kirby L. Vandivort, WenmeiW. Hwu, and Klaus Schulten. High performance computation andinteractive display of molecular orbitals on GPUs and multi-core CPUs.In Proceedings of the 2nd Workshop on General-Purpose Processing onGraphics Processing Units, ACM International Conference ProceedingSeries, volume 383, pages 9-18, New York, NY, USA, 2009. ACM.
18. Benjamin G. Levine, John E. Stone, and Axel Kohlmeyer. Fast analysisof molecular dynamics trajectories with graphics processing units- radialdistribution function histogramming. J. Comp. Phys., 230:3556-3569,2011.
19. Michael Krone, John E. Stone, Thomas Ertl, and Klaus Schulten. Fastvisualization of Gaussian density surfaces for molecular dynamics andparticle system trajectories. In EuroVis-Short Papers 2012, pages 67-71, 2012. DOI: 10.2312/PE/EuroVisShort/EuroVisShort2012/067-071.
20. Barry Isralewitz. Timeline: a VMD plugin for trajectory analysis.Tutorial, Theoretical and Computational Biophysics Group, Universityof Illinois at Urbana-Champaign, 2012.
21. Nathan D. Thomsen and James M. Berger. Running in reverse: Thestructural basis for translocation polarity in hexameric helicases. Cell,139(3):523-534, 2009.
22. John E. Stone. An Efficient Library for Parallel Ray Tracing andAnimation. Master's thesis, Computer Science Department, Universityof Missouri-Rolla, April 1998.
23. John Stone and Mark Underwood. Rendering of numerical flowsimulations using MPI. In Second MPI Developer's Conference, pages138-141. IEEE Computer Society Technical Committee on DistributedProcessing, IEEE Computer Society Press, 1996.
24. Steven G. Parker, James Bigler, Andreas Dietrich, Heiko Friedrich,Jared Hoberock, David Luebke, David McAllister, Morgan McGuire,Keith Morley, Austin Robison, and Martin Stich. OptiX: a general purposeray tracing engine. In ACM SIGGRAPH 2010 papers, SIGGRAPH'10, pages 66:1-66:13, New York, NY, USA, 2010. ACM.