Wen-mei W. Hwu. SECTION 1 SCIENTIFIC SIMULATION. Robert M. Farber.
CHAPTER 1. GPU-Accelerated Computation and Interactive Display of Molecular
.
Computing
GPU
Gems
Emerald Edition
Wen-mei W. Hwu
AMSTERDAM
•
NEW YORK
BOSTON •
SAN FRANCISCO
ELSEVIER
Morgan
•
OXFORD •
HEIDELBERG •
PARIS
•
•
SINGAPORE • SYDNEY
Kaufmann Publishers is
an
LONDON
SAN DIEGO •
TOKYO
imprint of Elsevier
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 Imran S. Haque,
CHAPTER 3
Vijay
on
GPUs
19
S. Pande
Dynamical Quadrature Grids: Applications in Density Functional Calculations Nathan Luehr, Ivan
CHAPTER 4
35 Ufimtsev, Todd Martinez
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 trie, Keiji Morokuma
CHAPTER 6
An Efficient CUDA
Implementation of the Tree-Based Barnes Hut n-Body 75
Algorithm Martin Burtscher, Keshav Pingali
CHAPTER 7
Leveraging the Untapped Computation Power of GPUs: Synthesis Using Texture Interpolation
Fast
Spectral 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
JV-Body Simulation with CUDA
113
Rio Yokota, Lorena A. Barba
V
vi
Contents
CHAPTER 10 Wavelet-Based Density Functional Theory Calculation Parallel Hybrid Architectures
on
Massively 133
Luigi Genovese, Matthieu Ospici, Brice Videau, Thierry Deutsch, Jean-Frangois Mehaut
SECTION 2
LIFE SCIENCES Bertil Schmidt
CHAPTER 11
Accurate
Scanning of Sequence Databases with the Smith-Waterman 155
Algorithm tukasz
Ligowski,
Witold R, Rudnicki,
CHAPTER 12 Massive Parallel Computing Ben Weiss, Mike
Yongchao Liu,
to Accelerate
Bertil Schmidt
Genome-Matching
Bailey
CHAPTER 13 GPU-Supercomputer Acceleration of Pattern Matching Ali
Khajeh-Saeed,
185
J. Blair Perot
CHAPTER 14 GPU Accelerated RNA Folding Algorithm Guillaume
199
Rizk, Dominique Lavenier, Sanjay Rajopadhye
CHAPTER 15 Temporal Data Mining for Neuroscience Wu-chun Feng, Yong Cao,
SECTION 3
173
211
Debprakash Patnaik, Naren Ramakrishnan
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
Laszld Szirmay-Kalos, Balazs Toth, Milan Magdics
CHAPTER 18 High-Performance Iterated Function Systems Christoph Schied, Johannes Hanika, Holger Dammertz, Hendrik
263 P. A. Lensch
SECTION 4 EMERGING DATA-INTENSIVE APPLICATIONS Volodymyr
Kindratenko
CHAPTER 19 Large-scale Machine Learning Jerod J. Weinman, Augustus Lidaka, Shitanshu Aggarwal
277
CHAPTER 20 Multiclass Support Vector Machine
293
Sergio Herrero-Lopez
CHAPTER 21 Template-Driven Agent-Based Modeling and Simulation with CUDA Paul
CHAPTER 22
Richmond,
313
Daniela Romano
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
Carsten Dachsbacher
Jan Novak, Vlastimil Havran,
CHAPTER 27
From
Sparse Mocap
Bernd
CHAPTER 28
Manuel
Bickel,
to
Highly
Programmable Graphics Pipeline in Transparency A
413
CUDA for
Order-Independent 427
Xuehui Liu, Enhua Wu
COMPUTER VISION James
CHAPTER 29
Detailed Facial Animation
Lang
Mengcheng Huang, Fang Liu,
SECTION 7
401
for Random Walks
Fast P.J,
Fung
Graph
Cuts for
Narayanan,
Computer Vision
CHAPTER 30 Visual Saliency Model Anis Rahman,
439
Vibhav Vineet, Timo Stich
on
Multi-GPU
Dominique Houzet,
Denis Pellerin
451
viii
Contents
CHAPTER 31 Real-Time Stereo
on
GPGPU Using Progressive Multiresolution
Adaptive 473
Windows Yong Zhao, Gabriel Taubin
CHAPTER 32 Real-Time Speed-Limit-Sign
Using
a
Recognition
on an Embedded
System 497
GPU
Pinar Muyan-Ozgelik, 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 Ttmo 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
Ondfej Stava, Bedfich Benes
CHAPTER 36 Image De-Mosaicing Joe
SECTION 9
583
Stam, James Fung
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 Gabriel
619
Decoding
Falcao, Vitor Silva, Leonel Sousa
CHAPTER 39 Large-Scale
Fast Fourier Transform
629
Yifeng Chen, Xiang Cui, Hong Me/
SECTION 10 MEDICAL IMAGING Lawrence Tarbox
CHAPTER 40 GPU Acceleration Dana Schaa,
of
Iterative Digital
Breast
Tomosynthesis
Benjamin Brown, Byunghyun Jang, Perhaad Mistry, Rodrigo Dominguez,
David Kaeli, Richard Moore, Daniel B.
Kopans
647
CHAPTER 41 Parallelization of Katsevich CT image Reconstruction Algorithm on
Generic Multi-Core Processors and GPGPU
Abderrahim
CHAPTER 42
3-D
Benquassmi, Eric Fontaine, Hsien-Hsin S.
659 Lee
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 Wu, Justin P. Haldar, Thibault
Marin, Wen-mei
W.
Hwu,
Zhi-Pei Liang, Bradley P. Sutton
CHAPTER 45 11 Minimization in 11-SPIRiT Compressed Sensing Mark Murphy, Miki Lustig
MRI Reconstruction
723
CHAPTER 46 Medical Image Processing Using GPU-Accelerated
ITK
737
Image Filters
Won-Ki Jeong, Hanspeter Pfister, Massimiliano Fatica
CHAPTER 47 Deformable Volumetric Registration Using B-Splines
751
James Shackelford, Nagarajan Kandasamy, Gregory Sharp
CHAPTER 48 Multiscale Unbiased Diffeomorphic Atlas Construction
on
Multi-GPUs
771
Linh Ha, Jens KrQger, Sarang Joshi, Claudio T. Silva
CHAPTER 49 GPU-Accelerated Brain Connectivity Reconstruction Visualization in
Large-Scale
Electron
and
Micrographs
793
Won-Ki Jeong, Hanspeter Pfister, Johanna Beyer, Markus Hadwiger
CHAPTER 50 Fast Simulation of Radiographic Images Using
Transport Algorithm Implemented
in CUDA
a
Monte Carlo
X-Ray 813
Andreu Badal, Aldo Badano
Index
831
