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Rapid Computation of Sodium Bioscales Using GPU-Accelerated Image Reconstruction

Ian C. Atkinson, Geng Liu, Nady Obeid, Keith R. Thulborn, Wen-mei Hwu

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Tags: Algorithms, Biology, CUDA, FFT, Image reconstruction, Magnetic resonance imaging, MRI, nVidia, Tesla C2050

May 27, 2013 by hgpu

GPU-accelerated protein family identification for metagenomics

Changjun Wu, Ananth Kalyanaraman

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Tags: Biology, Clustering, CUDA, Graph theory, nVidia, Tesla K20

May 25, 2013 by hgpu

A Distributed CPU-GPU Framework for Pairwise Alignments on Large-Scale Sequence Datasets

Da Li, Kittisak Sajjapongse, Huan Truong, Gavin Conant, Michela Becchi

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Tags: Bioinformatics, Biology, Computational biology, CUDA, GPU cluster, Heterogeneous systems, MPI, nVidia, nVidia Quadro FX 2000, Sequence alignment, Tesla K20

May 11, 2013 by hgpu

The GPU-based High-performance Pattern-matching Algorithm for Intrusion Detection

Dongliang Xu, Hongli Zhang, Yujian Fan

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Tags: Biology, Computer science, CUDA, Information Retrieval, nVidia, nVidia GeForce 9800 GTS, nVidia GeForce GTX 570, Security, String matching

May 11, 2013 by hgpu

Simulation of Biological Tissue using Mass-Spring-Damper Models

Emil Eriksson

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Tags: ATI, ATI Radeon HD 7970, Biology, OpenCL, Surgical simulation, Thesis, Visualization

May 6, 2013 by hgpu

GPU-based Steady-State Solution of the Chemical Master Equation

Marco Maggioni, Tanya Berger-Wolf, Jie Liang

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Tags: Biology, CUDA, Macromolecule, nVidia, nVidia GeForce GTX 580, Probability, Sparse matrix

May 1, 2013 by hgpu

SW# – GPU enabled exact alignments on genome scale

Matija Korpar, Mile Sikic

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Tags: Bioinformatics, Biology, Computer science, CUDA, nVidia, nVidia GeForce GTX 560, nVidia GeForce GTX 570, nVidia GeForce GTX 690, Package, Sequence alignment, Smith-Waterman algorithm

April 23, 2013 by hgpu

GPU-SD and DPD Parallelization for Gromacs tools for molecular dynamics simulations

Nicolae Goga, Siewert Marrink, Ruxandra Cioromela, Florica Moldoveanu

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Tags: Algorithms, Bioinformatics, Biology, Chemistry, CUDA, Molecular dynamics, nVidia, nVidia GeForce 9600 GT

April 21, 2013 by hgpu

CUDASW++ 3.0: accelerating Smith-Waterman protein database search by coupling CPU and GPU SIMD instructions

Yongchao Liu, Adrianto Wirawan, Bertil Schmidt

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Tags: Bioinformatics, Biology, CUDA, nVidia, nVidia GeForce GTX 680, nVidia GeForce GTX 690, Package, PTX, Sequence alignment, Smith-Waterman algorithm

April 10, 2013 by hgpu

Parallel Implementation of Dynamic Programming Algorithm Using Graphics Processing Unit

M. Khurram Rehman, M. Umer Sarwar, M. Ramzan Talib, M. Salman Mansoor, M. Bilal Sarwar

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Tags: Algorithms, Bioinformatics, Biology, Computer science, CUDA, Matrix multiplication, nVidia, nVidia GeForce GT 525 M, nVidia GeForce GT 610 M, Sequence alignment

April 6, 2013 by hgpu

CMCpy: Genetic Code-Message Coevolution Models in Python

Peter J. Becich, Brian P. Stark, Harish S. Bhat, David H. Ardell

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Tags: Bioinformatics, Biology, CUDA, nVidia, nVidia GeForce GTX 460, Package, Python

March 31, 2013 by hgpu

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

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

Rapid Computation of Sodium Bioscales Using GPU-Accelerated Image Reconstruction

GPU-accelerated protein family identification for metagenomics

A Distributed CPU-GPU Framework for Pairwise Alignments on Large-Scale Sequence Datasets

The GPU-based High-performance Pattern-matching Algorithm for Intrusion Detection

Simulation of Biological Tissue using Mass-Spring-Damper Models

GPU-based Steady-State Solution of the Chemical Master Equation

SW# – GPU enabled exact alignments on genome scale

GPU-SD and DPD Parallelization for Gromacs tools for molecular dynamics simulations

CUDASW++ 3.0: accelerating Smith-Waterman protein database search by coupling CPU and GPU SIMD instructions

Parallel Implementation of Dynamic Programming Algorithm Using Graphics Processing Unit

CMCpy: Genetic Code-Message Coevolution Models in Python

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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