GPU Computing Gems

Emerald Edition

Wen-mei W. Hwu

EISEVIER
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Morgan Kaufmann Publishers is an imprint of Elsevier 1311
Contents

Editors, Reviewers, and Authors ................................................................................................ xi

Introduction ................................................................................................................................ xix
Wen-mei W Hwu

SECTION 1 SCIENTIFIC SIMULATION

Robert M. Farber

CHAPTER 1 GPU-Accelerated Computation and Interactive Display of Molecular

Orbitals .......5
John E. Stone, David J. Hardy, Jan Saam, Kirby L. Vandivort, Klaus Schulten

CHAPTER 2 Large-Scale Chemical Informatics on GPUs ........................................................... 19

Imran S. Haque, Vijay S. Pande

CHAPTER 3 Dynamical Quadrature Grids: Applications in Density Functional

Calculations ............................................................................................................... 35
Nathan Luehr, Ivan Ufimtsev, Todd Martinez

CHAPTER 4 Fast Molecular Electrostatics Algorithms on GPUs ................................................ 43

David J. Hardy, John E. Stone, Kirby L. Vandivort, David Gohara, Christopher Rodrigues,
Klaus Schulten

CHAPTER 5 Quantum Chemistry: Propagation of Electronic Structure on a GPU .................... 59

Jacek Jakowski, Stephan Irle, Keiji Morokuma

CHAPTER 6 An Efficient CUDA Implementation of the Tree-Based Barnes Hut n-Body

Algorithm .................................................................................................................... 75
Martin Burtscher, Keshav Pingali

CHAPTER 7 Leveraging the Untapped Computation Power of GPUs: Fast Spectral

Synthesis Using Texture Interpolation ..................................................................... 93
Richard Townsend, Karthikeyan Sankaralingam, Matthew D. Sinclair

CHAPTER 8 Black Hole Simulations with CUDA .......................................................................... 103

Frank Herrmann, John Silberholz, Manuel Tiglio

CHAPTER 9 Treecode and Fast Multipole Method for N-Body Simulation with CUDA ............ 113
Rio Yokota, Lorena A. Barba
vi Contents

CHAPTER 10 Wavelet-Based Density Functional Theory Calculation on Massively

Parallel Hybrid Architectures .......................................................................... 133
Luigi Genovese, Matthieu Ospici, Brice Videau, Thierry Deutsch, Jean-Fran9ois Mähaut

SECTION 2 LIFE SCIENCES

Bertil Schmidt

CHAPTER 11 Accurate Scanning of Sequence Databases with the Smith-Waterman

Algorithm ......................................................................................................... 155
tukasz Ligowski, Witold R. Rudnicki, Yongchao Liu, Bertil Schmidt

CHAPTER 12 Massive Parallel Computing to Accelerate Genome-Matching ......................... 173

Ben Weiss, Mike Bailey

CHAPTER 13 GPU-Supercomputer Acceleration of Pattern Matching ................................... 185

Ali Khajeh-Saeed, J. Blair Perot

CHAPTER 14 GPU Accelerated RNA Folding Algorithm ......................................................... 199

Guillaume Rizk, Dominique Lavenier, Sanjay Rajopadhye

CHAPTER 15 Temporal Data Mining for Neuroscience ......................................................... 211

Wu-chun Feng, Yong Cao, Debprakash Patnaik, Naren Ramakrishnan

SECTION 3 STATISTICAL MODELING

Mike Giles

CHAPTER 16 Parallelization Techniques for Random Number Generators ............................ 231

Thomas Bradley, Jacques du Toit, Robert Tong, Mike Giles, Paul Woodhams

CHAPTER 17 Monte Carlo Photon Transport on the GPU ...................................................... 247

Läszlö Szirmay-Kalos, Baläzs Töth, Milän Magdics

CHAPTER 18 High-Performance Iterated Function Systems .................................................. 263

Christoph Schied, Johannes Hanika, Holger Dammertz, Hendrik P. A. Lensch

SECTION 4 EMERGING DATA-INTENSIVE APPLICATIONS

Volodymyr Kindratenko

CHAPTER 19 Large-Scale Machine Learning ........................................................................ 277

Jerod J. Weinman, Augustus Lidaka, Shitanshu Aggarwal
 Contents vii

CHAPTER 20 Multiclass Support Vector Machine ........................................................................ 293

Sergio Herrero-Lopez

CHAPTER 21 Template-Driven Agent-Based Modeling and Simulation with CUDA .................. 313
Paul Richmond, Daniela Romano

CHAPTER 22 GPU-Accelerated Ant Colony Optimization ............................................................. 325

Robin M. Weiss

SECTION 5 ELECTRONIC DESIGN AUTOMATION

Sunil P. Khatri

CHAPTER 23 High-Performance Gate-Level Simulation with GP-GPUs ...................................... 343

Debapriya Chatterjee, Andrew DeOrio, Valeria Bertacco

CHAPTER 24 GPU-Based Parallel Computing for Fast Circuit Optimization .............................. 365
Yifang Liu, Jiang Hu

SECTION 6 RAY TRACING AND RENDERING

Austin Robison

CHAPTER 25 Lattice Boltzmann Lighting Models .......................................................................... 381

Robert Geist, James Westall

CHAPTER 26 Path Regeneration for Random Walks ..................................................................... 401

Jan Noväk, Vlastimil Havran, Carsten Dachsbacher

CHAPTER 27 From Sparse Mocap to Highly Detailed Facial Animation .................................... 413
Bernd Bickel, Manuel Lang

CHAPTER 28 A Programmable Graphics Pipeline in CUDA for Order-Independent

Transparency .............................................................................................................. 427
Mengcheng Huang, Fang Liu, Xuehui Liu, Enhua Wu

SECTION 7 COMPUTER VISION

James Fung

CHAPTER 29 Fast Graph Cuts for Computer Vision ....................................................................... 439

P.J. Narayanan, Vibhav Vineet, Timo Stich

CHAPTER 30 Visual Saliency Model on Multi-GPU ....................................................................... 451

Anis Rahman, Dominique Houzet, Denis Pellerin
viii Contents

CHAPTER 31 Real-Time Stereo on GPGPU Using Progressive Multiresolution Adaptive

Windows ..................................................................................................................... 473
Yong Zhao, Gabriel Taubin

CHAPTER 32 Real-Time Speed-Limit-Sign Recognition on an Embedded System

Using a GPU ................................................................................................................ 497
Pinar Muyan-Öz9elik, Vladimir Glavtchev, Jeffrey M. Ota, John D. Owens

CHAPTER 33 Haar Classifiers for Object Detection with CUDA ................................................... 517
Anton Obukhov

SECTION 8 VIDEO AND IMAGE PROCESSING

Timo Stich

CHAPTER 34 Experiences on Image and Video Processing with CUDA and OpenCL ............... 547
Alptekin Temizel, Tugba Halici, Berker Logoglu, Tugba Taskaya Temizel,
Fatih Omruuzun, Ersin Karaman

CHAPTER 35 Connected Component Labeling in CUDA 569

Ondrej Bedfich Beneg

CHAPTER 36 Image De-Mosaicing 583

Joe Stam, James Fung

SECTION 9 SIGNAL AND AUDIO PROCESSING

John Roberts

CHAPTER 37 Efficient Automatic Speech Recognition on the GPU ............................................. 601

Jike Chong, Ekaterina Gonina, Kurt Keutzer

CHAPTER 38 Parallel LDPC Decoding ............................................................................................ 619

Gabriel Falcao, Vitor Silva, Leonel Sousa

CHAPTER 39 Large-Scale Fast Fourier Transform ........................................................................ 629

Yifeng Chen, Xiang Cui, Hong Mei

SECTION 10 MEDICAL IMAGING

Lawrence Tarbox

CHAPTER 40 GPU Acceleration of Iterative Digital Breast Tomosynthesis ................................ 647

Dana Schaa, Benjamin Brown, Byunghyun Jang, Perhaad Mistry, Rodrigo Dominguez,
David Kaeli, Richard Moore, Daniel B. Kopans
 Contents ix

CHAPTER 41 Parallelization of Katsevich CT Image Reconstruction Algorithm

on Generic Multi-Core Processors and GPGPU ...................................................... 659
Abderrahim Benquassmi, Eric Fontaine, Hsien-Hsin S. Lee

CHAPTER 42 3-D Tomographic Image Reconstruction from Randomly Ordered Lines

with CUDA ................................................................................................................... 679
Guillem Pratx, Jing-Yu Cui, Sven Prevrhal, Craig S. Levin

CHAPTER 43 Using GPUs to Learn Effective Parameter Settings for GPU-Accelerated

Iterative CT Reconstruction Algorithms .................................................................. 693
Wei Xu, Klaus Mueller

CHAPTER 44 Using GPUs to Accelerate Advanced MRI Reconstruction with Field

Inhomogeneity Compensation .................................................................................. 709
Yue Zhuo, Xiao-Long Wo, Justin P Ha/dar, Thibault Marin, Wen-mei W Hwu,
Zhi-Pei Liang, Bradley P. Sutton

CHAPTER 45 £1 Minimization in £1-SP1RiT Compressed Sensing MRI Reconstruction .......... 723

Mark Murphy, Miki Lustig

CHAPTER 46 Medical Image Processing Using GPU-Accelerated ITK Image Filters ............... 737
Won-Ki Jeong, Hanspeter Pfister, Massimiliano Fatica

CHAPTER 47 Deformable Volumetric Registration Using B-Splines ........................................... 751

James Shackelford, Nagarajan Kandasamy, Gregoty Sharp

CHAPTER 48 Multiscale Unbiased Diffeomorphic Atlas Construction on Multi-GPUs ............. 771

Linh Ha, Jens Krüger, Sarang Joshi, Cläudio T. Silva

CHAPTER 49 GPU-Accelerated Brain Connectivity Reconstruction and ......................................

Visualization in Large-Scale Electron Micrographs 793
Won-Ki Jeong, Hanspeter Pfister, Johanna Beyer, Markus Hadwiger

CHAPTER 50 Fast Simulation of Radiographic Images Using a Monte Carlo X-Ray

Transport Algorithm Implemented in CUDA ............................................................. 813
Andreu Badal, Aldo Badano

Index .......................................................................................................................................................................... 831