John E. Stone
- Senior Research Programmer, Theoretical and Computational Biophysics Group and NIH Resource for Macromolecular Modeling and Bioinformatics
- Associate Director, NVIDIA CUDA Center of Excellence at University of Illinois
Contact:Tel: (217) 244-3349johns@ks.uiuc.edu |
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| Comet McNaught
C/2006 P1, Jan 2007 Champaign, Illinois |
Veil Nebula complex in Cygnus (supernova remnant)
SBIG ST-8XE w/ Canon 200mm f/2.8L-II @ f2.8, 112 mins exposure (14x8min) w/ 6nm H-α filter. Illinois Dark Skies Star Party, September 27, 2008 |
Research interests:
VMD:
High performance visualization of biomolecular complexes,
haptic feedback, interactive molecular dynamics simulations,
programmable shading
GPU Computing:
Accelerating scientific applications using graphics processing units
Tachyon:
Multiprocessor ray tracing on shared memory and
distributed memory architectures, molecular visualization,
visualization of large models
FreeVR:
A free multi-platform alternative to the CAVE library.
Research Publications:
Follow this link to the Publications Page where you can read abstractacts as well as download PDF copies of many group publications.- "Probing Biomolecular Machines with Graphics Processors"
- James C. Phillips, John E. Stone
- Communications of the ACM 52(10):34-41, 2009
- Online full text of paper
- Communications of the ACM 52(10):34-41, 2009
- "GPU Clusters for High Performance Computing"
- Volodymyr Kindratenko, Jeremy Enos, Guochun Shi, Michael Showerman,
Galen Arnold, John E. Stone, James Phillips, Wen-mei Hwu
- Workshop on Parallel Programming on Accelerator Clusters (PPAC), IEEE Cluster 2009 (In press)
- Workshop on Parallel Programming on Accelerator Clusters (PPAC), IEEE Cluster 2009 (In press)
- "Visualization of Cyclic and Multi-branched Molecules with VMD"
- Simon Cross, Michelle M. Kuttell, John E. Stone, and James E. Gain.
- Journal of Molecular Graphics and Modelling. 28:131-139, 2009.
- Online full text of paper
- Journal of Molecular Graphics and Modelling. 28:131-139, 2009.
- "Long time-scale simulations of in vivo diffusion using GPU hardware"
- Elijah Roberts, John E. Stone, Leonardo Sepulveda, Wen-mei W. Hwu, and Zaida Luthey-Schulten.
- IPDPS '09: Proceedings of the 2009 IEEE International Symposium on Parallel & Distributed Processing, pp. 1-8, 2009
- HiCOMB Online Proceedings
- IPDPS '09: Proceedings of the 2009 IEEE International Symposium on Parallel & Distributed Processing, pp. 1-8, 2009
- "High Performance Computation and Interactive Display of Molecular Orbitals on GPUs and Multi-core CPUs"
- John E. Stone, Jan Saam, David J. Hardy, Kirby L. Vandivort,
Wen-mei W. Hwu, and Klaus Schulten.
- In Proceedings of the 2nd Workshop on General-Purpose Processing on Graphics Processing Units, ACM International Conference Proceeding Series, volume 383, pp. 9-18, 2009.
- Online full text of paper
- In Proceedings of the 2nd Workshop on General-Purpose Processing on Graphics Processing Units, ACM International Conference Proceeding Series, volume 383, pp. 9-18, 2009.
- "Multilevel Summation of Electrostatic Potentials Using Graphics Processing Units"
- David J. Hardy, John E. Stone, and Klaus Schulten.
- Parallel Computing, 28:164-177, 2009.
- Online full text of paper
- Parallel Computing, 28:164-177, 2009.
- "Adapting a Message-driven Parallel Application to GPU-Accelerated Clusters"
- James C. Phillips, John E. Stone, and Klaus Schulten.
- In SC '08: Proceedings of the 2008 ACM/IEEE Conference on Supercomputing, pp. 1-9, Piscataway, NJ, USA, 2008. IEEE Press.
- Online full text of paper
- In SC '08: Proceedings of the 2008 ACM/IEEE Conference on Supercomputing, pp. 1-9, Piscataway, NJ, USA, 2008. IEEE Press.
- "Using VMD - An Introductory Tutorial"
- Jen Hsin, Anton Arkhipov, Ying Yin, John E. Stone, and Klaus Schulten.
- Current Protocols - Bioinformatics, 5:Unit 5.7, 2008
- Online full text of paper
- Current Protocols - Bioinformatics, 5:Unit 5.7, 2008
- "GPU Acceleration of Cutoff Pair Potentials for Molecular Modeling Applications"
- Christopher I. Rodrigues, David J. Hardy, John E. Stone, Klaus Schulten, Wen-Mei W. Hwu
- In CF'08: Proceedings of the 2008 conference on Computing frontiers, pp. 273-282, New York, NY, USA, 2008. ACM.
- Online full text of paper
- In CF'08: Proceedings of the 2008 conference on Computing frontiers, pp. 273-282, New York, NY, USA, 2008. ACM.
- "GPU Computing"
- John D. Owens, Mike Houston, David Luebke, Simon Green, John E. Stone, James C. Phillips
- Proceedings of the IEEE, 96:879-899, 2008.
- Online full text of paper
- Proceedings of the IEEE, 96:879-899, 2008.
- "Accelerating Molecular Modeling Applications with Graphics Processors"
- John E. Stone, James C. Phillips, Peter L. Freddolino, David J. Hardy, Leonardo G. Trabuco, Klaus Schulten
- Journal of Computational Chemistry, 28:2618-2640, 2007.
- Online full text of paper
- Journal Web Site
- Journal of Computational Chemistry, 28:2618-2640, 2007.
- "A System for Interactive Molecular Dynamics Simulation"
- John E. Stone, Justin Gullingsrud, Klaus Schulten, Paul Grayson
- In 2001 ACM Symposium on Interactive 3D Graphics,
- John F. Hughes and Carlo H. Sequin, editors, pages 191-194, New York, 2001, ACM SIGGRAPH
- ACM Digital Library, citations, online full text, etc
- Online full text of paper
- I3D 2001 Conference Home Page
- In 2001 ACM Symposium on Interactive 3D Graphics,
- "An Efficient Library for Parallel Ray Tracing and Animation"
- John E. Stone
- Master's Thesis, University of Missouri-Rolla, Department of Computer Science, April 1998
- Master's Thesis, University of Missouri-Rolla, Department of Computer Science, April 1998
- "Accelerating Software-based MPEG Encoding Using the VIS Instruction Set"
- John Stone, Ahmad Zandi
- 1997 NAB Interactive Insights: A Multimedia Compendium
- 1997 National Association of Broadcasters Convention
- Las Vegas, Nevada
- 1997 NAB Interactive Insights: A Multimedia Compendium
- "Rendering of Numerical Flow Simulations Using MPI"
- John Stone, Mark Underwood
- 1996 MPI Developers Conference
- University of Notre Dame, IN
- 1996 MPI Developers Conference
- "Numerical Flow Simulation and Rendering Using MPI"
- John Stone, Mark Underwood
- 1996 Intel Supercomputer Users Group Conference
- Oak Ridge National Laboratory, Knoxville TN
- 1996 Intel Supercomputer Users Group Conference
- "An Efficient Library for Parallel Ray Tracing and Animation"
- John Stone
- 1995 Intel Supercomputer Users Group Conference
- Sandia National Laboratory, Albequerque NM
- 1995 Intel Supercomputer Users Group Conference
Short articles:
Presentations, talks, and demonstrations:
- An Introduction to OpenCL,
- IACAT/CCOE GPU Brown Bag Forum, University of Illinois, 10/21/2009
- High Performance Molecular Visualization and Analysis with GPU Computing,
- Beckman Institute Forum for Imaging and Visualization, University of Illinois, 10/20/2009
- GPU Accelerated Visualization and Analysis in VMD and Recent NAMD Developments,
- GPU Technology Conference, San Jose, CA, 10/1/2009
- Case Study - Accelerating Molecular Dynamics Experimentation,
- VSCSE: Many-Core Processors for Science and Engineering Applications, NCSA, 8/13/2008
- Multidisciplinary Panel,
- VSCSE: Many-Core Processors for Science and Engineering Applications, NCSA, 8/10/2008
- Accelerating Molecular Dynamics on a GPU
- Careers in High-Performance Systems Mentoring Workshop, National Center for Supercomputing Applications, 7/25/2009
- GPU Accelerated Visualization and Analysis in VMD
- Center for Molecular Modeling, University of Pennsylvania, 6/9/2009
- Keynote: Accelerating Molecular Modeling Applications with GPU Computing
- Second Sharcnet Symposium on GPU and Cell Computing, University of Waterloo, 5/20/2009
- Experiences with Multi-GPU Acceleration in VMD
- Path to Petascale: Adapting GEO/CHEM/ASTRO Applications for Accelerators and Accelerator Clusters, NCSA, 4/2/2009
- High Performance Computation and Interactive Display of Molecular Orbitals on GPUs and Multi-core CPUs
- Second Workshop on General-Purpose Processing on Graphics Processing Units, Washington D.C., 3/8/2009
- High Performance Computation and Interactive Display of Molecular Orbitals on GPUs and Multi-core CPUs
- IACAT Accelerator Workshop, NCSA, 1/23/2009
- GPU Computing Case Study: Molecular Modeling Applications
- ECE 598SP: Massively Parallel Processors, University of Illinois, 11/11/2008
- GPU Computing,
- Cape Linux Users Group, South Africa, 10/28/2008
- Visualizing Biomolecular Complexes with VMD,
- Centre for High Performance Computing,
CSIR Rosebank Campus, Cape Town, South Africa, 10/27/2008
- An Introduction to Molecular Visualization with VMD,
- Centre for High Performance Computing,
CSIR Rosebank Campus, Cape Town, South Africa, 10/27/2008
- Accelerating Molecular Modeling Applications with Graphics Processors,
- Computer Science Department, University of Cape Town, South Africa, 10/23/2008
- Accelerating Computational Biology by 100x Using CUDA,
- NVISION 08, San Jose Convention Center, San Jose, CA, 8/26/2008
- Case Study - Accelerating Molecular Dynamics Experimentation,
- VSCSE: Accelerators for Science and Engineering Applications: GPUs and Multicore, NCSA, 8/21/2008
- Accelerating Scientific Applications with GPUs,
- Workshop on Programming Massively Parallel Processors, NCSA, 7/10/2008
- Accelerating Molecular Modeling Applications with Graphics Processors
- SIAM conference on Parallel Processing for Scientific Computing, Atlanta, GA 3/12/2008
- Case Study: Molecular Visualization and Analysis
- Supercomputing 2007 Tutorial: High Performance Computing with CUDA, Reno, NV, 11/11/2007
- GPU Acceleration of Scientific Applications Using CUDA
- AstroGPU 2007, Institute for Advanced Study, Princeton University, 11/09/2007
- ECE498AL CUDA Performance Case Studies: Ion Placement Tool, VMD
- University of Illinois at Urbana-Champaign, 10/15/2007
- ECE498AL CUDA Performance Case Studies: Ion Placement Tool, VMD
- University of Illinois at Urbana-Champaign, 3/14/2007
- Visualization of Nano-Scale Structures
- University of Texas Health Science Center at Houston, 4/20/2006
- Universidad Nacional Autónoma de Mexico, DGSCA, 8/11/2006 (Video Conference Presentation)
- Universidad Nacional Autónoma de Mexico, DGSCA, 8/11/2006 (Video Conference Presentation)
- VMD: Algorithms and Methods for Large Scale Biomolecular Visualization
- San Diego Supercomputer Center, 9/12/2005
- Dancing Proteins: 3-D Visualization of Protein Structure and Dynamics on Next-Generation Graphics Hardware
- ITG Forum at University of Illinois at Urbana-Champaign, 2/15/2005
- CS Colloqium at University of Missouri-Rolla, 2/22/2005
- Purdue University Envision Center, 2/25/2005
- CS Colloqium at University of Missouri-Rolla, 2/22/2005
- VMD: Biomolecular Visualization and Analysis
- The Scripps Research Institute, La Jolla CA,
July 31, 2003
- Designing a Cluster for a Small Research Group
- Summer School on Theoretical Biophysics, Beckman Institute UIUC,
June 11, 2003
- Biomolecular Visualization in the CAVE with VMD
- Center for Parallel Computing, Swedish Royal Institute of Technology, Stockholm Sweden,
October 3, 2001
- Cluster-based visualization with VMD on a tiled display wall
- NCSA Terascale Clusters Dedication, September 5, 2001
- Biomolecular Visualization, Interactive Molecular Dynamics
- Siggraph 2001, Sun Microsystems Booth, August 14-16, 2001
- "Low-Cost Linux Clusters for Biomolecular Simulations Using NAMD"
- Beckman Institute UIUC, June 26, 2001
- Software Development Tutorial for Biomedical Research Scientists
- Beckman Institute UIUC, April 3, 2001
- "Linux Clusters"
- Beckman Institute UIUC, November 11, 1999
Service:
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Book reviews:
- GPU Gems 3 (chapter reviewer, published 2007)
- Geometric Tools for Computer Graphics (reviewer, published 2002)
- Real-Time Rendering (reviewer, first edition, published 1999)
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Program Committee and Editorial Board Memberships:
- Member, Guest Editorial Board, IEEE TPDS Special Issue on High Performance Computing with Accelerators
- Ninth IEEE International Workshop on High Performance Computational Biology (HiCOMB 2010)
- 2010 Workshop on Language, Compiler, and Architecture support for GPGPU
- 2009 Symposium on Application Accelerators in High Performance Computing (SAAHPC'09)
- Eighth IEEE International Workshop on High Performance Computational Biology (HiCOMB 2009)
- NCSA/IACAT Workshop on Programming Massively Parallel Processors (PMPP 2008)
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Manuscript reviews:
- Supercomputing 2009
- PPAM 2009 Eighth International Conference on Parallel Processing and Applied Mathematics (2009)
- Computing in Science and Engineering (2009)
- BMC Structural Biology (2008, 2009)
- Journal of Computational Chemistry (2008)
- Computer Graphics Forum (2008, 2009)
- Journal of Parallel Computing (2008)
- Siggraph 2008
- IEEE VIS 2007
- 2006 IEEE Symposium on Interactive Ray Tracing
- ACM Computing Surveys (2006)
- Virtual Reality, Volume 9 number 1 (2005)
- International Journal of Parallel and Distributed Systems and Networks (2002)
- 2000 IEEE International Parallel & Distributed Processing Symposium
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Advisory Board Memberships:
- Computer Science Advisory Board (2008, 2009), Missouri University of Science and Technology
- Computer Science Advisory Board (2007), University of Missouri-Rolla
Press articles and interviews:
- TG Daily: NVIDIA teams up with Microsoft for HPC",
by Andrew Thomas, September 28, 2009 - Wired: "Personal Supercomputers Promise Teraflops on Your Desk",
by Priya Ganapati, August 3, 2009 - NVIDIA: "NVIDIA Appoints First CUDA Center of Excellence",
Andrew Humber, June 30, 2008 - Bio-IT World: "Life Scientists Get Their Game Faces On",
by Mike May, April 1, 2008 - Genome Technology: "Not Just for Kids Anymore",
by Matthew Dublin, September, 2007 - BeHardware: "NVIDIA CUDA: practical uses" (English),
by Damien Triolet, August 17, 2007 - Hardware.fr: "NVIDIA CUDA: plus en pratique" (French),
by Damien Triolet, August 9, 2007 - TG Daily: "NCSA: A look inside one of the world's most capable supercomputer facilities",
by Rick C. Hodgin, July 2, 2007 - Beyond3D: "NVIDIA Tesla: GPU computing gets its own brand",
by Tim Murray, June 20, 2007 - TG Daily: "NVIDIA unveils Tesla, moves into supercomputing",
by Wolfgang Gruener, June 20, 2007
Education:
- Master of Science in Computer Science
- Master's Program Advisor: Dr. Fikret Ercal
- University of Missouri-Rolla
- University of Missouri-Rolla
- Bachelor of Science in Computer Science
- University of Missouri-Rolla
Other Accomplishments:
-
I developed a sophisticated software module for
synchronized 3-D stereoscopic display of asynchronously parallel-decoded
video streams that formed the basis for the
RushPlay 3D digital dailies system
used in producing the Lionsgate 3-D movie
My Bloody Valentine 3-D,
released in January 2009.
- I was previously a Senior Programmer/Analyst at Heuris/Pulitzer, and later Heuris Logic, developing commercial video encoding and transcoding software used in service bureaus, the standalone commercial MPEG Power Professional software, and plug-ins for the leading non-linear video editing systems. My work in this era was noteworthy mainly for my early use of parallel processing and SIMD instruction set extensions for acceleration of the routines for color space conversions, image filtering and de-noising, and motion estimation within the video encoder subsystem.
- I served as the vice president of the Champaign-Urbana Astronomical Society (CUAS) for 2008 and 2009.
- I was one of the founding members of the University of Missouri-Rolla Solar Car Team
- 17th Place in 21st Annual ACM International Collegiate Programming Contest,
- 1996 World Finals, Philadelphia PA
- 1st Place in 1996 ACM Mid-Central Regional Programming Contest
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