high performance computing on graphics processing units: hgpu.org

Applications

Harnessing the power of idle GPUs for acceleration of biological sequence alignment

Fumihiko Ino, Yuki Kotani, Yuma Munekawa, Kenichi Hagihara

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Tags: Bioinformatics, Biology, CUDA, nVidia, nVidia GeForce 7900 GTX, nVidia GeForce 7950 GX2, nVidia GeForce 8800 GTX, OpenGL, Sequence alignment

July 12, 2011 by hgpu

Graphics processing unit parallel accelerated solution of the discrete ordinates for photon transport in biological tissues

Kuan Peng, Xinbo Gao, Xiaochao Qu, Nunu Ren, Xueli Chen, Xiaowei He, Xiaorei Wang, Jimin Liang, Jie Tian

Tags: Biology, CUDA, Image reconstruction, nVidia, nVidia GeForce GTX 260, Optics, Tomography

July 12, 2011 by hgpu

Parallel implementation of a spiking neuronal network model of unsupervised olfactory learning on NVidia CUDA

T. Nowotny

Tags: Biology, CUDA, Neural networks, nVidia, Tesla C870

July 8, 2011 by hgpu

An Adaptive Hybrid Multiprocessor technique for bioinformatics sequence alignment

T. Bonny, M.A. Zidan, K.N. Salama

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Tags: Bioinformatics, Biology, CUDA, nVidia, nVidia Quadro FX 4800, Sequence alignment, Smith-Waterman algorithm

July 7, 2011 by hgpu

Striped Smith-Waterman speeds database searches six times over other SIMD implementations

M. Farrar

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Tags: Algorithms, Bioinformatics, Biology, Sequence alignment, Smith-Waterman algorithm

July 6, 2011 by hgpu

Six-fold speed-up of Smith-Waterman sequence database searches using parallel processing on common microprocessors

Torbjorn Rognes, Erling Seeberg

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Tags: Algorithms, Bioinformatics, Biology, Sequence alignment, Smith-Waterman algorithm

July 6, 2011 by hgpu

Graphics processing unit implementations of relative expression analysis algorithms enable dramatic computational speedup

Andrew T. Magis, John C. Earls, Youn-Hee H. Ko, James A. Eddy, Nathan D. Price

Source codes

Tags: Algorithms, Bioinformatics, Biology, CUDA, nVidia, Package

July 1, 2011 by hgpu

CAMPAIGN: An open-source Library of GPU-accelerated Data Clustering Algorithms

Kai J. Kohlhoff, Marc H. Sosnick, William T. Hsu, Vijay S. Pande, Russ B. Altman

Source codes

Tags: Bioinformatics, Biology, Clustering, CUDA, nVidia, Package

July 1, 2011 by hgpu

Accelerating Smith-Waterman Local Sequence Alignment on GPU Cluster

Thuy T. Nguyen, Duc H. Nguyen, Phong H. Pham, Ngoc M. Ta, Tan N. Duong, Hung D. Le

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Tags: Bioinformatics, Biology, CUDA, GPU cluster, MPI, nVidia, nVidia GeForce GTX 295, Sequence alignment, Smith-Waterman algorithm, Tesla C1060

June 27, 2011 by hgpu

Fast cell detection in high-throughput imagery using GPU-accelerated machine learning

David Mayerich, Jaerock Kwon, Aaron Panchal, John Keyser, Yoonsuck Choe

Tags: Biology, Image processing, Machine learning, nVidia

June 24, 2011 by hgpu

Accelerating Smith-Waterman on Heterogeneous CPU-GPU Systems

Jaideep Singh, Ipseeta Aruni

Tags: Bioinformatics, Biology, CUDA, Heterogeneous systems, nVidia, Smith-Waterman algorithm

June 24, 2011 by hgpu

Protein alignment algorithms with an efficient backtracking routine on multiple GPUs

Jacek Blazewicz, Wojciech Frohmberg, Michal Kierzynka, Erwin Pesch, Pawel Wojciechowski

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Source codes

Tags: Bioinformatics, Biology, CUDA, nVidia, nVidia GeForce GTX 280, nVidia GeForce GTX 480, Package, Sequence alignment, Tesla S1070

June 21, 2011 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

Applications

Harnessing the power of idle GPUs for acceleration of biological sequence alignment

Graphics processing unit parallel accelerated solution of the discrete ordinates for photon transport in biological tissues

Parallel implementation of a spiking neuronal network model of unsupervised olfactory learning on NVidia CUDA

An Adaptive Hybrid Multiprocessor technique for bioinformatics sequence alignment

Striped Smith-Waterman speeds database searches six times over other SIMD implementations

Six-fold speed-up of Smith-Waterman sequence database searches using parallel processing on common microprocessors

Graphics processing unit implementations of relative expression analysis algorithms enable dramatic computational speedup

CAMPAIGN: An open-source Library of GPU-accelerated Data Clustering Algorithms

Accelerating Smith-Waterman Local Sequence Alignment on GPU Cluster

Fast cell detection in high-throughput imagery using GPU-accelerated machine learning

Accelerating Smith-Waterman on Heterogeneous CPU-GPU Systems

Protein alignment algorithms with an efficient backtracking routine on multiple GPUs

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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