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operated by the College of
Staten Island
and funded, in part, by
grants from the City of
New York, State of New
York, CUNY Research
Foundation, and National
Science Foundation
Grants CNS-0958379,
CNS-0855217 and
ACI 1126113

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Workshop on:


5-6 June 2012
College of Staten Island
City University of New York

A two-day workshop on: the use of "accelerators" such as GPUs, FPGAs, and Intel MIC is a transformational force in high performance computing enabling scientists, engineers, and researchers in industry and academia to accelerate research and mission critical applications.

Topics to be covered include trends in the development of accelerator hardware and programming models and presentations on state-of-the-art applications in the following domains:

- Biosciences
- Computational Chemistry
- Finance
- Mathematical and Physical Sciences
- Multimedia

Keynote speaker:
Dr. Steven Scott, Chief Technology Officer, Tesla-NVIDIA


There is a attendance fee for meals of: $15 for CUNY students, $25 for CUNY faculty/staff/alumni, $50 Non-CUNY attendees. (Valid ID required for CUNY discount) A continental breakfast and a lunch will be provided.

Checks must be made payable to "CSI Auxiliary Services" and sent to: HPC Center 1M-206, College of Staten Island, 2800 Victory Blvd, Staten Island, NY 10314.

*Advance registration is required. To register, please visit:
If you have any questions, please email us at:


Bios and Abstracts



Steven Scott, Chief Technology Officer, Tesla-NVIDIA, “Why the Future of HPC Will Be Green”

Richard Lethin, Directing Engineer, Reservoir Labs, “Automatic Software Optimization and Generation for Programming Accelerated Computers”

John Michalakes, Scientist, Scientific Computing Group, National Renewable Energy Laboratory, "Extreme Scale Computing and Atmospheric Modeling"


Finance -Session 1- Richard Holowczak, Baruch College/CUNY, Moderator

John Melonakos, Chief Executive Officer, AccelerEyes, Inc., “Productive Performance with GPUs in Finance”

Gerald Hanweck, Hanweck Associates, LLC, “Use of GPUs in Financial Engineering”

Stephen P. Weston, Managing Director, JP Morgan Chase, “Use of FPGAs to Speed the Computation of Complex Credit Derivatives”

David Taylor, Vice President of Product Architecture, Exegy, Inc., “FPGAs for Market Data Processing”


Multimedia -Session 2- Robin Bargar, Columbia College/Chicago, Moderator

Stefan Bilbao, Senior Lecturer, University of Edinburgh, “Large-scale Audio Rendering Using GPUs”

Yong Cao, Assistant Professor, Computer Science Director, Animation and Gaming Research Laboratory, Virginia Polytechnic Institute and State University, “Data Intensive Computing and Visualization on Many-Core Architecture”

James Perry, Edinburgh Parallel Computing Centre, University of Edinburgh, “Next Generation Sound Synthesis”

Lynn Lewis, Principle Member Technical Staff, AMD, “Multimedia application opportunities on an APU or Hybrid System Architecture”


Biosciences -Session 3- Dan McCloskey, College of Staten Island, Moderator

Jason Bakos, Assistant Professor, Computer Science and Electronics, University of South Carolina, “High-Performance Heterogeneous Computing for Genomics Applications”

Aurel Lazar, Professor of Electrical Engineering, Columbia University, “Massively Parallel Neural Encoding and Decoding of Visual Stimuli using GPUs”

Colin Torney, Postdoctoral Research Associate, Collective Animal Behaviour Laboratory, Department of Ecology and Evolutionary Biology, Princeton University, “Structure, Function and Evolution in Social Animal Groups: Insights from GPU Accelerated Simulations of Collective Behavior”

Glen Edwards, Director of Design Productivity, Convey Computer Corporation,“Using Hybrid-Core Computing to Solve Bioinformatics Problems"”


Computational Chemistry -Session 4- Arben Jusfi, College of Staten Island/CUNY, Moderator

James Phillips, Senior Research Programmer, Beckman Institute, University of Illinois, “Scalable Molecular Dynamics with NAMD”

Martin Herbordt, Associate Professor, Department of Electrical and Computer Engineering, Boston University, “Molecular Dynamics on Scalable FPGA-Centric Clusters”

Ross Walker, Assistant Professor, San Diego Supercomputer Center and Department of Chemistry & Biochemistry, University of California San Diego, Transforming Research in Molecular Biology through Extreme Acceleration of AMBER Molecular Dynamics Simulations: Sampling for the 99%”

Carlos Sosa, Cray Inc., “Parallel Paradigms and Performance Tools in the Biological Sciences and Computational Chemistry”


Mathematical and Physical Sciences -Session 5- Robert Haralick, The Graduate Center/CUNY, Moderator

Mark Arend, Professor, Electrical Engineering, The City College/CUNY, “Field Programmable Gate Array for Accelerating Coherent Wind Lidar Signal Processing”

Cliff Woolley, CUDA Developer Technology Engineer, Tesla-NVIDIA, “Fundamental Performance Optimizations for GPUs”

German Kolmakov, Assistant Professor, Physics, CityTech/CUNY, “Non-linear Dynamics of Exciton Bose-Einstein Condensate: Numerical Simulations with Graphics Processing Units”

Paula Whitlock, Professor, Computer and Information Sciences, Brooklyn College/CUNY, “Using Multiple GPU's on Multiple Hosts in Simulations of Multi-Dimensional Hypersphere Systems”