• 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) 244-3349
johns@ks.uiuc.edu

Office Schedule

Linked-In Profile

Personal web site

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

"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)

"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

"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

"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

"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

"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

"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

"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

"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

"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

"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

"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

"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

"Rendering of Numerical Flow Simulations Using MPI"
John Stone, Mark Underwood
1996 MPI Developers Conference
University of Notre Dame, IN

"Numerical Flow Simulation and Rendering Using MPI"
John Stone, Mark Underwood
1996 Intel Supercomputer Users Group Conference
Oak Ridge National Laboratory, Knoxville TN

"An Efficient Library for Parallel Ray Tracing and Animation"
John Stone
1995 Intel Supercomputer Users Group Conference
Sandia National Laboratory, Albequerque NM

Short articles:

"Random Numbers, Efficiency, and Other Things"
John Stone
Ray Tracing News, Volume 20, Number 1, May 19, 2007

"Real-Time GPU Spheres"
John Stone
Ray Tracing News, Volume 18, Number 1, December 12, 2005

"Workstation Clusters for Parallel Computing"
John Stone, Fikret Ercal
IEEE Potentials pages 31-33, April/May 2001
IEEE Home page

"The Ups and Downs of Multithreaded Ray Tracing and Optimization"
John Stone
Ray Tracing News, Volume 12, Number 2, December 21, 1999

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)

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

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:


Press articles and interviews:


Education:

Master of Science in Computer Science
Master's Program Advisor: Dr. Fikret Ercal
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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