high performance computing on graphics processing units: hgpu.org

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hgpu.org » Applications » Biology

GPU-Based Cloud Service for Smith-Waterman algorithm Using Frequency Distance Filtration Scheme

Sheng-Ta Lee, Chun-Yuan Lin, Che Lun Hung

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Tags: Bioinformatics, Biology, Cloud, CUDA, nVidia, Sequence alignment, Smith-Waterman algorithm, Tesla C2050

March 18, 2013 by hgpu

GPU based Eulerian Assembly of Genomes

Syed Faraz Mahmood

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Tags: Bioinformatics, Biology, CUDA, Genetics, nVidia, nVidia Quadro FX 5800, Thesis

March 7, 2013 by hgpu

On continuous maximum flow image segmentation algorithm

Laszlo Marak

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Tags: Algorithms, Biology, Materials Science, nVidia, nVidia GeForce GTX 470, OpenCL, Tesla C2050, Thesis, Tomography

March 2, 2013 by hgpu

SOAP3-dp: Fast, Accurate and Sensitive GPU-based Short Read Aligner

Ruibang Luo, Thomas Wong, Jianqiao Zhu, Chi-Man Liu, Edward Wu, Lap-Kei Lee, Haoxiang Lin, Wenjuan Zhu, David W. Cheung, Hing-Fung Ting, Siu-Ming Yiu, Chang Yu, Yingrui Li, Ruiqiang Li, Tak-Wah Lam

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Tags: Algorithms, Bioinformatics, Biology, CUDA, Next-Generation sequencing, nVidia, Package, Tesla C2070, Tesla M2050

February 25, 2013 by hgpu

Streaming Data from HDD to GPUs for Sustained Peak Performance

Lucas Beyer, Paolo Bientinesi

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Tags: Biology, Computational biology, CUDA, nVidia, nVidia Quadro FX 6000, Tesla S2050

February 20, 2013 by hgpu

ClusCo: clustering and comparison of protein models

Jamroz Michal, Kolinski Andrzej

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Tags: Biology, Biomolecules, Clustering, Computational Engineering, CUDA, Finance, nVidia, nVidia GeForce GTX 470, Package

February 20, 2013 by hgpu

Extending the Computational Application of Reaction-Diffusion Chemistry by Modelling Artificial Neural Networks

James Stovold

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Tags: Biology, Chemistry, CUDA, Neural networks, nVidia, nVidia GeForce 9600 M GT

February 12, 2013 by hgpu

Binary Interval Search: a scalable algorithm for counting interval intersections

Ryan M. Layer, Kevin Skadron, Gabriel Robins, Ira M. Hall, Aaron R. Quinlan

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Tags: Algorithms, Bioinformatics, Biology, Computer science, CUDA, Monte Carlo simulation, nVidia, Package, Sequence alignment

February 6, 2013 by hgpu

Hardware Accelerated Molecular Docking: A Survey

Imre Pechan, Bela Feher

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Tags: Bioinformatics, Biology, CUDA, FPGA, Molecular simulation, nVidia, Tesla C1060

February 6, 2013 by hgpu

GPU-Accelerated High-Accuracy Molecular Docking using Guided Differential Evolution

Martin Simonsen, Mikael H. Christensen, Rene Thomsen, Christian N. S. Pedersen

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Tags: Biology, CUDA, Differential evolution, Medicine, nVidia, nVidia GeForce 8800 GT, Pharmaceuticals

February 5, 2013 by hgpu

A Comparison of CPU and OpenCL Parallelization Methods for Correlation and Graph Layout Algorithms used in the Network Analysis of High Dimensional Data

Athanasios Theocharidis, Gibran Hemani, Michael Kargas, Tom C. Freeman

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Tags: ATI, ATI Radeon HD 5870, ATI Radeon HD 6970, Biology, Graph layout, nVidia, nVidia GeForce GTX 285, nVidia GeForce GTX 580, OpenCL, OpenGL, Package, Visualization

February 5, 2013 by hgpu

Real-Time Phase Masks for Interactive Stimulation of Optogenetic Neurons

Stephan C. Kramer, Johannes Hagemann, D. Russell Luke

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Tags: Biology, CUDA, Mathematics, Neurons and Cognition, nVidia, Optimization, Tesla C2070

February 5, 2013 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

GPU based Eulerian Assembly of Genomes

On continuous maximum flow image segmentation algorithm

SOAP3-dp: Fast, Accurate and Sensitive GPU-based Short Read Aligner

Streaming Data from HDD to GPUs for Sustained Peak Performance

ClusCo: clustering and comparison of protein models

Extending the Computational Application of Reaction-Diffusion Chemistry by Modelling Artificial Neural Networks

Binary Interval Search: a scalable algorithm for counting interval intersections

Hardware Accelerated Molecular Docking: A Survey

GPU-Accelerated High-Accuracy Molecular Docking using Guided Differential Evolution

A Comparison of CPU and OpenCL Parallelization Methods for Correlation and Graph Layout Algorithms used in the Network Analysis of High Dimensional Data

Real-Time Phase Masks for Interactive Stimulation of Optogenetic Neurons

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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