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A SIMD Interpreter for Genetic Programming on GPU Graphics Cards

William B. Langdon, Wolfgang Banzhaf

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Tags: Bioinformatics, Biology, DirectX, Genetics, nVidia, nVidia GeForce 8800 GTX, OpenGL

December 29, 2010 by hgpu

The GPU on biomedical image processing for color and phenotype analysis

Antonio Ruiz, Manuel Ujaldon, Jose Antonio Andrade

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Tags: Bioinformatics, Image processing, Medicine, nVidia, nVidia GeForce 6800 Ultra, nVidia GeForce 7800 GTX, OpenGL

December 24, 2010 by hgpu

Design and implementation of the Smith-Waterman algorithm on the CUDA-compatible GPU

Yuma Munekawa, Fumihiko Ino, Kenichi Hagihara

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Tags: Bioinformatics, Biology, CUDA, nVidia, nVidia GeForce 8800 GTX, Smith-Waterman algorithm

December 22, 2010 by hgpu

Long time-scale simulations of in vivo diffusion using GPU hardware

Elijah Roberts, John E. Stone, Leonardo Sepulveda, Wen-Mei W. Hwu, Zaida Luthey-Schulten

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Tags: Bioinformatics, Biology, CUDA, Distributed computing, nVidia, nVidia GeForce GTX 280, nVidia Quadro FX 5600

December 18, 2010 by hgpu

GPU Accelerated RNA Folding Algorithm

Guillaume Rizk, Dominique Lavenier

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Tags: Algorithms, Bioinformatics, Biology, CUDA, nVidia, nVidia GeForce GTX 280, Tesla C870

December 17, 2010 by hgpu

Scalable and highly parallel implementation of Smith-Waterman on graphics processing unit using CUDA

Ali Akoglu, Gregory Striemer

Tags: Bioinformatics, Biology, CUDA, nVidia, Sequence alignment, Smith-Waterman algorithm, Tesla C870

December 15, 2010 by hgpu

Real-world comparison of CPU and GPU implementations of SNPrank: a network analysis tool for GWAS

Nicholas A. Davis, Ahwan Pandey, B. A. McKinney

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Tags: Bioinformatics, Biology, CUDA, Genetics, Medicine, nVidia, Package, Tesla M1060

December 13, 2010 by hgpu

The impact of accelerator processors for high-throughput molecular modeling and simulation

G. Giupponi, M. Harvey, G. Defabritiis

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Tags: Bioinformatics, Cell processor, Chemistry, Medicine, Molecular modeling, nVidia, Review

December 11, 2010 by hgpu

Initial Experiences Porting a Bioinformatics Application to a Graphics Processor

Maria Charalambous, Pedro Trancoso, Alexandros Stamatakis

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Tags: Bioinformatics, Biology, Brook, nVidia, nVidia GeForce FX 5700

December 10, 2010 by hgpu

GPU-MEME: Using Graphics Hardware to Accelerate Motif Finding in DNA Sequences

Chen Chen, Bertil Schmidt, Liu Weiguo, Wolfgang Muller-Wittig

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Tags: Bioinformatics, Biology, GLSL, nVidia, nVidia GeForce 8800 GTX, OpenGL, Package, Pattern recognition

December 6, 2010 by hgpu

Locality and parallelism optimization for dynamic programming algorithm in bioinformatics

Guangming Tan, Shengzhong Feng, Ninghui Sun

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Tags: Algorithms, Bioinformatics, Biology, Programming techniques

December 2, 2010 by hgpu

ClawHMMER: A Streaming HMMer-Search Implementation

Daniel R. Horn, Mike Houston, Pat Hanrahan

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Tags: ATI, ATI Radeon X800, Bioinformatics, Biology, Brook, nVidia, nVidia GeForce 6800 Ultra, nVidia GeForce 7800 GTX, Pattern Search

November 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

Superpipeline: A Universal Approach for Reducing GPU Memory Usage in Large Models

EnergyUCB-Bandit

Online Energy Optimization in GPUs: A Multi-Armed Bandit Approach

See all packages

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high performance computing on graphics processing units: hgpu.org

A SIMD Interpreter for Genetic Programming on GPU Graphics Cards

The GPU on biomedical image processing for color and phenotype analysis

Design and implementation of the Smith-Waterman algorithm on the CUDA-compatible GPU

Long time-scale simulations of in vivo diffusion using GPU hardware

GPU Accelerated RNA Folding Algorithm

Scalable and highly parallel implementation of Smith-Waterman on graphics processing unit using CUDA

Real-world comparison of CPU and GPU implementations of SNPrank: a network analysis tool for GWAS

The impact of accelerator processors for high-throughput molecular modeling and simulation

Initial Experiences Porting a Bioinformatics Application to a Graphics Processor

GPU-MEME: Using Graphics Hardware to Accelerate Motif Finding in DNA Sequences

Locality and parallelism optimization for dynamic programming algorithm in bioinformatics

ClawHMMER: A Streaming HMMer-Search Implementation

Recent source codes

Kokkidio: Kokkos+Eigen - write fast, readable multi-platform code

LLaMA-Inference-Bench

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

Superpipeline: A Universal Approach for Reducing GPU Memory Usage in Large Models

EnergyUCB-Bandit

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