high performance computing on graphics processing units: hgpu.org

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Local Alignment Tool Based on Hadoop Framework and GPU Architecture

Che-Lun Hun, Guan-Jie Hua

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Tags: Biology, Cloud, CUDA, Hadoop, MapReduce, nVidia, nVidia GeForce GTS 480, Sequence alignment

April 19, 2014 by hgpu

Bayesian Neural Networks for Genetic Association Studies of Complex Disease

Andrew L. Beam, Alison Motsinger-Reif, Jon Doyle

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Tags: Bayesian, Biology, CUDA, Machine learning, Neural networks, nVidia, Package, Python

April 17, 2014 by hgpu

New Efficient Method To Solve Longest Overlap Region Problem For Noncoding DNA Sequence

Yukun Zhong, ZhiWei He, XianHong Wang, Liao Gang

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Tags: Algorithms, Bioinformatics, Biology, CUDA, nVidia, nVidia GeForce GT 610 M

April 16, 2014 by hgpu

A Way For Accelerating The DNA Sequence Reconstruction Problem By CUDA

Yukun Zhong, ZhiWei He, XianHong Wang, XiongBin Cao

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Tags: Algorithms, Bioinformatics, Biology, CUDA, nVidia, nVidia GeForce GT 610 M, Sorting

April 16, 2014 by hgpu

An efficient GPU acceptance-rejection algorithm for the selection of the next reaction to occur for Stochastic Simulation Algorithms

Neri Mickael, Denis Mestivier

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Tags: Algorithms, Biology, Computer science, CUDA, nVidia, Optimization, Stochastic simulation, Tesla K10, Tesla K20, Tesla M2075, Tesla M2090

April 4, 2014 by hgpu

Multicore and GPU Algorithms for Nussinov RNA Folding

J. Li, S. Ranka, S. Sahni

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Tags: Biology, CUDA, nVidia, nVidia Tesla C2050, RNA

April 3, 2014 by hgpu

Competing computational approaches to reaction-diffusion equations in clusters of cells

S. Stella, R. Chignola, E. Milotti

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Tags: Biology, CUDA, Diffusion equation, Medicine, nVidia, nVidia Quadro 4000, Partial differential equations, PDEs

March 19, 2014 by hgpu

MaxSSmap: A GPU program for short read mapping with the maximum scoring subsequence

Usman Roshan

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Tags: Bioinformatics, Biology, CUDA, nVidia, Short read mapping, Smith-Waterman algorithm, Tesla M2050

March 12, 2014 by hgpu

Parallelization of DNA alignment algorithms using GPUs

Gustavo Encarnacao

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Tags: Algorithms, Bioinformatics, Biology, CUDA, nVidia, nVidia GeForce GTX 580, Sequence matching, Suffix trees

March 7, 2014 by hgpu

Hybrid Framework for pairwise DNA Sequence Alignment Using the CUDA compatible GPU

H. Khaled, R. El Gohary, N.L. Badr, H. M. Faheem

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Tags: Bioinformatics, Biology, CUDA, nVidia, nVidia GeForce GT 540 M, Sequence alignment, Smith-Waterman algorithm

March 6, 2014 by hgpu

QuickProbs – A Fast Multiple Sequence Alignment Algorithm Designed for Graphics Processors

Adam Gudys, Sebastian Deorowicz

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Tags: ATI, ATI Radeon HD 7970, Bioinformatics, Biology, nVidia, nVidia GeForce GTX 480, nVidia GeForce GTX 580, nVidia GeForce GTX 680, OpenCL, Package, Sequence alignment

March 4, 2014 by hgpu

A Multi GPU Read Alignment Algorithm with Model-based Performance Optimization

Aleksandr Drozd, Naoya Maruyama, Satoshi Matsuoka

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Tags: Algorithms, Bioinformatics, Biology, CUDA, nVidia, Tesla C2050

March 1, 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

Bayesian Neural Networks for Genetic Association Studies of Complex Disease

New Efficient Method To Solve Longest Overlap Region Problem For Noncoding DNA Sequence

A Way For Accelerating The DNA Sequence Reconstruction Problem By CUDA

An efficient GPU acceptance-rejection algorithm for the selection of the next reaction to occur for Stochastic Simulation Algorithms

Multicore and GPU Algorithms for Nussinov RNA Folding

Competing computational approaches to reaction-diffusion equations in clusters of cells

MaxSSmap: A GPU program for short read mapping with the maximum scoring subsequence

Parallelization of DNA alignment algorithms using GPUs

Hybrid Framework for pairwise DNA Sequence Alignment Using the CUDA compatible GPU

QuickProbs – A Fast Multiple Sequence Alignment Algorithm Designed for Graphics Processors

A Multi GPU Read Alignment Algorithm with Model-based Performance Optimization

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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