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Towards Large-Scale Molecular Dynamics Simulations on Graphics Processors

Joseph E. Davis, Adnan Ozsoy, Sandeep Patel, Michela Taufer

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Tags: Biology, Chemistry, CUDA, Molecular dynamics, nVidia, nVidia GeForce 9800 GX2, nVidia GeForce GTX 280, nVidia Quadro FX 5600

January 3, 2011 by hgpu

Analysis of a Computational Biology Simulation Technique on Emerging Processing Architectures

Jeremy S. Meredith, Sadaf R. Alam, Jeffrey S. Vetter

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Tags: Biology, Cell processor, Cg, Computational biology, Molecular dynamics, nVidia, nVidia GeForce 7900 GTX

January 2, 2011 by hgpu

Population Parallel GP on the G80 GPU

Denis Robilliard, Virginie Marion-Poty, Cyril Fonlupt

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Tags: Bioinformatics, Biology, CUDA, Genetics, nVidia, nVidia GeForce 8800 GTX, Package

December 29, 2010 by hgpu

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

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

A New Parallel Method of Smith-Waterman Algorithm on a Heterogeneous Platform

Bo Chen, Yun Xu, Jiaoyun Yang, Haitao Jiang

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Tags: Biology, CUDA, nVidia, nVidia GeForce 9800 GT, Sequence alignment, Smith-Waterman algorithm

December 17, 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

Integrative multicellular biological modeling: a case study of 3D epidermal development using GPU algorithms

Scott Christley, Briana Lee, Xing Dai, Qing Nie

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Tags: Biology, CUDA, nVidia, nVidia GeForce GTX 285

December 15, 2010 by hgpu

Scalable and Interactive Segmentation and Visualization of Neural Processes in EM Datasets

Won-ki Jeong, Johanna Beyer, Student Member, Markus Hadwiger, Amelio Vazquez, Student Member, Hanspeter Pfister, Senior Member, Ross T. Whitaker

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Tags: Biology, Electron microscopy, Neuroscience, nVidia, nVidia Quadro FX 5800, Rendering, Tesla C1060

December 15, 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

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

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high performance computing on graphics processing units: hgpu.org

Towards Large-Scale Molecular Dynamics Simulations on Graphics Processors

Analysis of a Computational Biology Simulation Technique on Emerging Processing Architectures

Population Parallel GP on the G80 GPU

A SIMD Interpreter for Genetic Programming on GPU Graphics Cards

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

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

A New Parallel Method of Smith-Waterman Algorithm on a Heterogeneous Platform

GPU Accelerated RNA Folding Algorithm

Integrative multicellular biological modeling: a case study of 3D epidermal development using GPU algorithms

Scalable and Interactive Segmentation and Visualization of Neural Processes in EM Datasets

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

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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