high performance computing on graphics processing units: hgpu.org

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High-throughput sequence alignment using Graphics Processing Units

Michael Schatz, Cole Trapnell, Arthur Delcher, Amitabh Varshney

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Tags: Bioinformatics, Biology, Computational biology, CUDA, nVidia, nVidia GeForce 8800 GTX, Package, Sequence alignment

November 1, 2010 by hgpu

Bio-sequence database scanning on a GPU

Weiguo Liu, B. Schmidt, G. Voss, A. Schroder, W. Muller-Wittig

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Tags: Biology, Computational biology, GLSL, nVidia, nVidia GeForce 6800 GTO, nVidia GeForce 7800 GTX, OpenGL, Smith-Waterman algorithm

October 30, 2010 by hgpu

Graphics Processing Units and High-Dimensional Optimization

Hua Zhou, Kenneth Lange, Marc A. Suchard

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Tags: Block relaxation, CUBLAS, CUDA, EM and MM algorithms, Mathematics, Multidimensional scaling, Nonnegative matrix factorization, nVidia, nVidia GeForce GTX 280, PET scanning, Statistics

October 30, 2010 by hgpu

How GPUs Work

David Luebke, Greg Humphreys

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Tags: Computer science, Review

October 30, 2010 by hgpu

GPUs: A Closer Look

Kayvon Fatahalian, Mike Houston

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Tags: Computer science, Review

October 30, 2010 by hgpu

Quantum Chemistry on Graphical Processing Units. 1. Strategies for Two-Electron Integral Evaluation

Ivan S. Ufimtsev, Todd J. Martinez

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Tags: Chemistry, Computational chemistry, CUDA, Molecular modeling, nVidia, nVidia GeForce 8800 GTX

October 30, 2010 by hgpu

Mapping computational concepts to GPUs

Mark Harris

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Tags: Computer science, Review

October 30, 2010 by hgpu

Accelerating Density Functional Calculations with Graphics Processing Unit

Koji Yasuda

Tags: Chemistry, Computational chemistry, Molecular modeling

October 30, 2010 by hgpu

A Memory Model for Scientific Algorithms on Graphics Processors

Naga K. Govindaraju, Scott Larsen, Jim Gray, Dinesh Manocha

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Tags: Algorithms, Computer science, FFT, Memory model, nVidia, nVidia GeForce 6800 Ultra, nVidia GeForce 7800 GTX, nVidia GeForce 7900 GTX, Sorting

October 30, 2010 by hgpu

A hardware redundancy and recovery mechanism for reliable scientific computation on graphics processors

Jeremy W. Sheaffer, David P. Luebke, Kevin Skadron

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Tags: Computer science, Error recovery

October 30, 2010 by hgpu

Performance enhancement of MAGIC FDTD-PIC plasma-wave simulations using GPU processing

Andrew J. Woods, Lars D. Ludeking

Tags: Physics, Plasma physics

October 30, 2010 by hgpu

Optimizing data intensive GPGPU computations for DNA sequence alignment

Cole Trapnell, Michael C. Schatz

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Tags: Bioinformatics, Biology, Computational biology, CUDA, nVidia, nVidia GeForce 8800 GTX, Package, Sequence alignment, Short read mapping, Suffix trees

October 30, 2010 by hgpu

Over-synchronization in GPU Programs

profile_util: simple C++ library to report memory, timing, thread affinity

Profile Util library: A quick and easy way to get MPI, OpenMP and GPU runtime information

MaC: Mamba CPU performance predictor

MambaCPU: Enhanced Correlation Mining with State Space Models for CPU Performance Prediction

Mixed-precision finite element kernels

Mixed-precision finite element kernels and assembly: Rounding error analysis and hardware acceleration

SHMT: The Simultaneous and Heterogenous Multithreading project

General-Purpose Computing on Tensor Processors

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high performance computing on graphics processing units: hgpu.org

Applications

High-throughput sequence alignment using Graphics Processing Units

Bio-sequence database scanning on a GPU

Graphics Processing Units and High-Dimensional Optimization

How GPUs Work

GPUs: A Closer Look

Quantum Chemistry on Graphical Processing Units. 1. Strategies for Two-Electron Integral Evaluation

Mapping computational concepts to GPUs

Accelerating Density Functional Calculations with Graphics Processing Unit

A Memory Model for Scientific Algorithms on Graphics Processors

A hardware redundancy and recovery mechanism for reliable scientific computation on graphics processors

Performance enhancement of MAGIC FDTD-PIC plasma-wave simulations using GPU processing

Optimizing data intensive GPGPU computations for DNA sequence alignment

Recent source codes

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MATAR

Over-synchronization in GPU Programs

profile_util: simple C++ library to report memory, timing, thread affinity

MaC: Mamba CPU performance predictor

Mixed-precision finite element kernels

SHMT: The Simultaneous and Heterogenous Multithreading project

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