high performance computing on graphics processing units: hgpu.org

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hgpu.org » Applications » Biology

Fast Parallel Markov Clustering in Bioinformatics Using Massively Parallel Graphics Processing Unit Computing

Alhadi Bustamam, Kevin Burrage, Nicholas A. Hamilton

Tags: Bioinformatics, Biology, CUDA, MPI, nVidia, Sparse matrix

May 30, 2011 by hgpu

Acceleration of spiking neural networks in emerging multi-core and GPU architectures

Mohammad A. Bhuiyan, Vivek K. Pallipuram, Melissa C. Smith

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

May 28, 2011 by hgpu

GPU implementation of map-MRF for microscopy imagery segmentation

Danny Crookes, Paul Miller, Hugh Gribben, Charles Gillan, Damian McCaughey

Tags: Algorithms, Biology, CUDA, Image processing, Medicine, nVidia, nVidia GeForce 8800 GTX

May 25, 2011 by hgpu

Parallel Particle-Based Reaction Diffusion: A GPU Implementation

Lorenzo Dematte

Tags: Algorithms, Biochemistry, Biology, CUDA, nVidia, nVidia GeForce GT 220, nVidia GeForce GTX 260, nVidia Quadro FX 570 M

May 17, 2011 by hgpu

GPU-based triangulation of the van der Waals surface

S. Dias, A. Gomes

Tags: Biology, Chemistry, Molecular modeling, Molecular surface

May 14, 2011 by hgpu

Fast short exact repeats finding on GPU

Weidong Sun, Weiwei Wang, Zongmin Ma

Tags: Algorithms, Biology, CUDA, Genetics, nVidia, Pattern Search

May 13, 2011 by hgpu

Fast network centrality analysis using GPUs

Zhiao Shi, Bing Zhang

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Tags: All-Pairs Distance, Bioinformatics, Biology, CUDA, nVidia, Package, Tesla C2050

May 13, 2011 by hgpu

Exact and complete short-read alignment to microbial genomes using Graphics Processing Unit programming

Jochen Blom, Tobias Jakobi, Daniel Doppmeier, Sebastian Jaenicke, Jorn Kalinowski, Jens Stoye, Alexander Goesmann

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

May 10, 2011 by hgpu

Fast Parallel Tandem Mass Spectral Library Searching Using GPU Hardware Acceleration

Lydia A. Baumgardner, Avinash K. Shanmugam, Henry Lam, Jimmy K. Eng, Daniel B. Martin

Tags: Biology, Chemistry, CUDA, nVidia, Search, Spectrometry

May 10, 2011 by hgpu

Efficient Parallelization of the Stochastic Simulation Algorithm for Chemically Reacting Systems On the Graphics Processing Unit

Hong Li, Linda Petzold

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Tags: Biology, Chemistry, CUDA, nVidia, nVidia GeForce 8800 GTX, Stochastic simulation

May 10, 2011 by hgpu

A GPU-based architecture for real-time data assessment at synchrotron experiments

Suren Chilingaryan, Alessandro Mirone, Andrew Hammersley,Claudio Ferrero, Lukas Helfen, Andreas Kopmann, Tomy dos Santos Rolo

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Tags: Biology, Image reconstruction, Materials Science, Medicine, nVidia, nVidia GeForce GTX 280, nVidia GeForce GTX 295, nVidia GeForce GTX 480, Poster, Tomography

May 8, 2011 by hgpu

GPU Based Parallel Computing on Blast Program

Huang Lican, Hu Ya

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Tags: Bioinformatics, Biology, BLAST, Sequence alignment

May 7, 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

See all packages

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high performance computing on graphics processing units: hgpu.org

Applications

Fast Parallel Markov Clustering in Bioinformatics Using Massively Parallel Graphics Processing Unit Computing

Acceleration of spiking neural networks in emerging multi-core and GPU architectures

GPU implementation of map-MRF for microscopy imagery segmentation

Parallel Particle-Based Reaction Diffusion: A GPU Implementation

GPU-based triangulation of the van der Waals surface

Fast short exact repeats finding on GPU

Fast network centrality analysis using GPUs

Exact and complete short-read alignment to microbial genomes using Graphics Processing Unit programming

Fast Parallel Tandem Mass Spectral Library Searching Using GPU Hardware Acceleration

Efficient Parallelization of the Stochastic Simulation Algorithm for Chemically Reacting Systems On the Graphics Processing Unit

A GPU-based architecture for real-time data assessment at synchrotron experiments

GPU Based Parallel Computing on Blast Program

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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