high performance computing on graphics processing units: hgpu.org

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Accelerating the Stochastic Simulation Algorithm

David Jenkins, Gregory D. Peterson

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Tags: Biology, CUDA, Monte Carlo simulation, MPI, nVidia, Stochastic simulation, Tesla C870

February 21, 2011 by hgpu

A massively parallel framework using P systems and GPUs

Jose M. Cecilia, Gines D. Guerrero, Jose M. Garcia, Miguel A. Martinez-del-Amor, Ignacio Perez-Hurtado, Mario J. Perez-Jimenez

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Tags: Biology, Computer science, CUDA, nVidia, P systems, Tesla C1060

February 21, 2011 by hgpu

Enhancing the simulation of P systems for the SAT problem on GPUs

J.M. Cecilia, J.M. Garcia, G.D. Guerrero, M.A. Martinez-Amor, M.J. Perez-Jimenez, M. Ujaldon

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Tags: Biology, CUDA, nVidia, P systems, SAT, Tesla C1060

February 16, 2011 by hgpu

Accelerating the Stochastic Simulation Algorithm using Emerging Architectures

David Dewayne Jenkins

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Tags: Biology, CUDA, Monte Carlo simulation, nVidia, nVidia GeForce 8600 M, Stochastic simulation, Tesla C1060, Tesla C870, Thesis

February 16, 2011 by hgpu

GPU Accelerated Stochastic Simulation

David D. Jenkins, Gregory D. Peterson

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Tags: Biology, CUDA, Monte Carlo simulation, nVidia, nVidia GeForce GTX 480, Stochastic simulation, Tesla C1060

February 16, 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

Next-generation acceleration and code optimization for light transport in turbid media using GPUs

Erik Alerstam, William C. Yip Lo, Tianyi D. Han, Jonathan Rose, Stefan Andersson-Engels, Lothar Lilge

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Source codes

Tags: Biology, CUDA, Monte Carlo simulation, nVidia, nVidia GeForce GTX 280, nVidia GeForce GTX 295, nVidia GeForce GTX 480, Optics, Package

February 9, 2011 by hgpu

Two Level Approach to Efficient Visualization of Protein Dynamics

Ove Daae Lampe, Ivan Viola, Nathalie Reuter, Helwig Hauser

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Tags: Biology, Molecular dynamics, nVidia, nVidia GeForce 8800 GTX, OpenGL, Visualization

February 4, 2011 by hgpu

Efficient Bayesian inference in stochastic chemical kinetic models using graphical processing units

Jarad Niemi, Matthew Wheeler

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Tags: Bayesian, Biology, Chemistry, CUDA, nVidia, Stochastic simulation, Tesla T10

January 26, 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

Accelerating the Stochastic Simulation Algorithm

A massively parallel framework using P systems and GPUs

Enhancing the simulation of P systems for the SAT problem on GPUs

Accelerating the Stochastic Simulation Algorithm using Emerging Architectures

GPU Accelerated Stochastic Simulation

GPU-powered tools boost molecular visualization

Next-generation acceleration and code optimization for light transport in turbid media using GPUs

Two Level Approach to Efficient Visualization of Protein Dynamics

Efficient Bayesian inference in stochastic chemical kinetic models using graphical processing units

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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