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Efficient parallel algorithms for maximum-density segment problem

Xue Wang, Fasheng Qiu, S.K. Prasad, Guantao Chen

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Tags: Bioinformatics, Biology, CUDA, nVidia, nVidia GeForce GTX 280, Presentation, Sequence alignment

March 7, 2011 by hgpu

STOCHSIMGPU: Parallel stochastic simulation for the Systems Biology Toolbox 2 for MATLAB

Guido Klingbeil, Radek Erban, Mike Giles, Philip K. Maini

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Tags: Bioinformatics, Biology, CUDA, nVidia, nVidia GeForce 8800, Package, Stochastic simulation

February 28, 2011 by hgpu

CUDAlign: using GPU to accelerate the comparison of megabase genomic sequences

Edans Flavius O. Sandes, Alba Cristina M.A. de Melo

Tags: Bioinformatics, Biology, CUDA, nVidia, nVidia GeForce GTX 280, Sequence alignment, Smith-Waterman algorithm

February 27, 2011 by hgpu

Size Matters: Space/Time Tradeoffs to Improve GPGPU Applications Performance

Abdullah Gharaibeh, Matei Ripeanu

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Tags: Bioinformatics, Biology, Computational biology, CUDA, nVidia, nVidia GeForce 8800 GTX, Package, Sequence alignment, Short read mapping, Suffix trees

February 27, 2011 by hgpu

HexServer: an FFT-based protein docking server powered by graphics processors

Gary Macindoe, Lazaros Mavridis, Vishwesh Venkatraman, Marie-Dominique Devignes, David W. Ritchie

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

February 25, 2011 by hgpu

Graphics Processing Units and Genetic Programming: An overview

W. B. Langdon

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Tags: Bioinformatics, Computer science, CUDA, Genetic programming, nVidia, Review

February 15, 2011 by hgpu

GPU-powered tools boost molecular visualization

Matthieu Chavent, Bruno Levy, Michael Krone, Katrin Bidmon, Jean-Philippe P. Nomine, Thomas Ertl, Marc Baaden

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Tags: Bioinformatics, Biology, Molecular modeling, nVidia, Review, Visualization

February 12, 2011 by hgpu

Supercomputing with toys: harnessing the power of NVIDIA 8800GTX and playstation 3 for bioinformatics problem

Justin Wilson, Manhong Dai, Elvis Jakupovic, Stanley Watson, Fan Meng

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Tags: Bioinformatics, Cell processor, CUDA, nVidia, nVidia GeForce 8800 GTX, Performance, Playstation, RapidMind

January 26, 2011 by hgpu

Evolving GeneChip correlation predictors on parallel graphics hardware

William B. Langdon

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Tags: Bioinformatics, Computer science, Genetic programming, nVidia, nVidia GeForce 8800 GTX, OpenGL, Package, RapidMind

January 21, 2011 by hgpu

Energy efficient biomolecular simulations with FPGA-based reconfigurable computing

Ananth Nallamuthu, Melissa C. Smith, Scott Hampton, Pratul K. Agarwal, Sadaf R. Alam

Tags: Bioinformatics, Biology, FPGA, Molecular dynamics

January 19, 2011 by hgpu

Towards microsecond biological molecular dynamics simulations on hybrid processors

Scott Hampton, Pratul K. Agarwal, Sadaf R. Alam, Paul S. Crozier

Tags: Bioinformatics, Biology, CUDA, Molecular dynamics, nVidia, Tesla C1060, Tesla C2050

January 19, 2011 by hgpu

Optimal Utilization of Heterogeneous Resources for Biomolecular Simulations

Scott S. Hampton, Sadaf R. Alam, Paul S. Crozier, Pratul K. Agarwal

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Tags: Bioinformatics, Biology, CUDA, Molecular dynamics, nVidia, Tesla C1060, Tesla C2050

January 19, 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

Efficient parallel algorithms for maximum-density segment problem

STOCHSIMGPU: Parallel stochastic simulation for the Systems Biology Toolbox 2 for MATLAB

CUDAlign: using GPU to accelerate the comparison of megabase genomic sequences

Size Matters: Space/Time Tradeoffs to Improve GPGPU Applications Performance

HexServer: an FFT-based protein docking server powered by graphics processors

Graphics Processing Units and Genetic Programming: An overview

GPU-powered tools boost molecular visualization

Supercomputing with toys: harnessing the power of NVIDIA 8800GTX and playstation 3 for bioinformatics problem

Evolving GeneChip correlation predictors on parallel graphics hardware

Energy efficient biomolecular simulations with FPGA-based reconfigurable computing

Towards microsecond biological molecular dynamics simulations on hybrid processors

Optimal Utilization of Heterogeneous Resources for Biomolecular Simulations

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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