high performance computing on graphics processing units: hgpu.org

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Implementation of Smith-Waterman algorithm in OpenCL for GPUs

Dzmitry Razmyslovich, Guillermo Marcus, Markus Gipp, Marc Zapatka, Andreas Szillus

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Tags: Bioinformatics, Biology, nVidia, nVidia GeForce GTX 480, OpenCL, Package, Sequence alignment, Smith-Waterman algorithm

February 27, 2015 by azhar ali

NMF-mGPU: non-negative matrix factorization on multi-GPU systems

Edgardo Mejia-Roa, Daniel Tabas-Madrid, Javier Setoain, Carlos Garcia, Francisco Tirado, Alberto Pascual-Montano

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Tags: Algorithms, Bioinformatics, Biology, CUDA, Factorization, GPU cluster, MPI, Nonnegative matrix factorization, nVidia, Package, Tesla C1060

February 19, 2015 by hgpu

CAVE-CL: An OpenCL version of the package for detection and quantitative analysis of internal cavities in a system of overlapping balls: application to proteins

Jan Busa Jr., Jan Busa, Shura Hayryan, Chin-Kun Hu, Ming-Chya Wu

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Tags: Algorithms, Biology, Computer physics, Fortran, nVidia, nVidia GeForce GTX 470, OpenCL, Physics, Tesla C1060

February 10, 2015 by hgpu

Nucleation Studies on Graphics Processing Units

Benjamin J. Block

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Tags: Anisotropy, ATI, ATI Radeon HD 6970, Biology, Chemistry, Differential equations, Ising model, nVidia, nVidia GeForce GTX 480, nVidia GeForce GTX 580, nVidia GeForce GTX 690, nVidia GeForce GTX Titan, OpenCL, Physics, Tesla K20, Thesis

February 6, 2015 by hgpu

On Longest Repeat Queries Using GPU

Yun Tian, Bojian Xu

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Tags: Biology, Computational biology, Computer science, CUDA, nVidia, nVidia GeForce GTX 660 Ti

January 28, 2015 by hgpu

SW#db: GPU-accelerated exact sequence similarity database search

Matija Korpar, Martin Sosic, Dino Blazeka, Mile Sikic

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Tags: Algorithms, Biology, CUDA, Databases, Next-Generation sequencing, nVidia, nVidia GeForce GTX 690, nVidia GeForce GTX 780, Package, Smith-Waterman algorithm

January 16, 2015 by hgpu

Bayesian neural networks for detecting epistasis in genetic association studies

Andrew L Beam, Alison Motsinger-Reif, Jon Doyle

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Tags: Bayesian, Biology, CUDA, CULA, Neural networks, nVidia, Package, Python

December 15, 2014 by hgpu

Hybrid CPU-GPU Pipeline Framework

Fahad Khalid, Frank Feinbube, Andreas Polze

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Tags: Biology, Computational biology, CUDA, Heterogeneous systems, nVidia, nVidia GeForce GTX 680

November 18, 2014 by hgpu

High-accuracy Optimization by Parallel Iterative Discrete Approximation and Multi-GPU Computing

Di Zhao

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Tags: Biology, Computational biology, Computational finance, CUDA, Finance, nVidia, nVidia GeForce GTX 660, Thesis

November 13, 2014 by hgpu

Finding Longest Common Subsequences by GPU-Based Parallel Ant Colony Optimization

David Markvica

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Tags: Algorithms, Biology, Computational biology, Computer science, Heterogeneous systems, Metaheuristics, nVidia, nVidia GeForce GTX 560 Ti, OpenCL, Optimization, Pattern recognition, Thesis

October 27, 2014 by hgpu

On the Efficiency of CPU and Hybrid CPU-GPU Systems in Computational Biology Tasks

Nikolay Pydiura, Pavel Karpov, Yaroslav Blume

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Tags: AMD Radeon R9 280, ATI, Biology, Computational biology, CUDA, Molecular dynamics, nVidia, nVidia GeForce GTX 480, OpenCL

October 25, 2014 by hgpu

Massively parallel read mapping on GPUs with the q-group index and PEANUT

Johannes Koster, Sven Rahmann

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Tags: Algorithms, Bioinformatics, Biology, nVidia, nVidia GeForce GTX 780, OpenCL

October 20, 2014 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

Implementation of Smith-Waterman algorithm in OpenCL for GPUs

NMF-mGPU: non-negative matrix factorization on multi-GPU systems

CAVE-CL: An OpenCL version of the package for detection and quantitative analysis of internal cavities in a system of overlapping balls: application to proteins

Nucleation Studies on Graphics Processing Units

On Longest Repeat Queries Using GPU

SW#db: GPU-accelerated exact sequence similarity database search

Bayesian neural networks for detecting epistasis in genetic association studies

Hybrid CPU-GPU Pipeline Framework

High-accuracy Optimization by Parallel Iterative Discrete Approximation and Multi-GPU Computing

Finding Longest Common Subsequences by GPU-Based Parallel Ant Colony Optimization

On the Efficiency of CPU and Hybrid CPU-GPU Systems in Computational Biology Tasks

Massively parallel read mapping on GPUs with the q-group index and PEANUT

Recent source codes

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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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