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Optimized Parallel Implementation of Gillespie’s First Reaction Method on Graphics Processing Units

Cristian Dittamo, Davide Cangelos

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Tags: Algorithms, Biochemistry, Biology, nVidia, nVidia GeForce 8600 M GS, Stochastic simulation

August 12, 2011 by hgpu

Hardware accelerators for biocomputing: A survey

Souradip Sarkar, Turbo Majumder, Ananth Kalyanaraman, Partha Pratim Pande

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Tags: Biology, Cell processor, CUDA, FPGA, Molecular dynamics, nVidia, nVidia GeForce 7800 GTX, Performance, Review, Sequence alignment

August 7, 2011 by hgpu

Accelerated simulation of spiking neural networks using GPUs

Andreas K. Fidjeland, Murray P. Shanahan

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Tags: Biology, CUDA, Neural networks, nVidia, Tesla C1060

August 6, 2011 by hgpu

Unifying stream based and reconfigurable computing to design application accelerators

Bruno Francisco, Frederico Pratas, Leonel Sousa

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Tags: Bioinformatics, Biology, Computer science, Data parallelism, FPGA, nVidia, nVidia GeForce GTX 285

August 2, 2011 by hgpu

Near-real-time simulations of biolelectric activity in small mammalian hearts using graphical processing units

E.J. Vigmond, P.M. Boyle, L.J. Leon, G. Plank

Tags: Biology, Heart, Medicine, ODEs, Ordinary differential equations, Partial differential equations, PDEs

July 27, 2011 by hgpu

High-Throughput Sequence Translation Using CUDA

Sun Wei-dong, Ma Zong-min

Tags: Bioinformatics, Biology, CUDA, nVidia, Sequence matching

July 25, 2011 by hgpu

A Coarse Grain Reconfigurable Architecture for sequence alignment problems in bio-informatics

Pei Liu, A. Hemani

Tags: Algorithms, Bioinformatics, Biology, FPGA, Sequence alignment, Smith-Waterman algorithm

July 25, 2011 by hgpu

On the Robust Mapping of Dynamic Programming onto a Graphics Processing Unit

Shucai Xiao, A.M. Aji, Wu-chun Feng

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Tags: Algorithms, Bioinformatics, Biology, Cell processor, CUDA, Data parallelism, nVidia, nVidia GeForce GTX 280, Sequence alignment, Smith-Waterman algorithm

July 23, 2011 by hgpu

Parallelizing the Cellular Potts Model on graphics processing units

Jose J. Tapia, Roshan M. D'Souza

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Tags: Biology, Computational biology, CUDA, nVidia, Tesla C1060

July 22, 2011 by hgpu

Accelerating Partitional Algorithms for Flow Cytometry on GPUs

Jeremy Espenshade, Andrew Pangborn, Gregor von Laszewski, Douglas Roberts, James S. Cavenaugh

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Tags: Algorithms, Biology, Clustering, CUDA, nVidia, Tesla C870

July 18, 2011 by hgpu

Accelerating the Nussinov RNA folding algorithm with CUDA/GPU

Dar-Jen Chang, C. Kimmer, Ming Ouyang

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Tags: Biology, CUDA, Macromolecule, nVidia, Tesla C1060, Tesla C2050, Tesla C870

July 12, 2011 by hgpu

Harnessing the power of idle GPUs for acceleration of biological sequence alignment

Fumihiko Ino, Yuki Kotani, Yuma Munekawa, Kenichi Hagihara

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Tags: Bioinformatics, Biology, CUDA, nVidia, nVidia GeForce 7900 GTX, nVidia GeForce 7950 GX2, nVidia GeForce 8800 GTX, OpenGL, Sequence alignment

July 12, 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

Optimized Parallel Implementation of Gillespie’s First Reaction Method on Graphics Processing Units

Hardware accelerators for biocomputing: A survey

Accelerated simulation of spiking neural networks using GPUs

Unifying stream based and reconfigurable computing to design application accelerators

Near-real-time simulations of biolelectric activity in small mammalian hearts using graphical processing units

High-Throughput Sequence Translation Using CUDA

A Coarse Grain Reconfigurable Architecture for sequence alignment problems in bio-informatics

On the Robust Mapping of Dynamic Programming onto a Graphics Processing Unit

Parallelizing the Cellular Potts Model on graphics processing units

Accelerating Partitional Algorithms for Flow Cytometry on GPUs

Accelerating the Nussinov RNA folding algorithm with CUDA/GPU

Harnessing the power of idle GPUs for acceleration of biological sequence alignment

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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