high performance computing on graphics processing units: hgpu.org

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Two-Level Approach to Efficient Visualization of Protein Dynamics

Ove Daae Lampe, I. Viola, N. Reuter, H. Hauser

Tags: Bioinformatics, Biology, Molecular dynamics, Rendering, Visualization

August 31, 2011 by hgpu

Fine-grain Parallelism using Multi-core, Cell/BE, and GPU Systems

Frederico Pratas, Pedro Trancoso, Leonel Sousa, Alexandros Stamatakis, Guochun Shi, Volodymyr Kindratenko

Tags: Bioinformatics, Biology, Cell processor, CUDA, Molecular dynamics, nVidia

August 25, 2011 by hgpu

Efficient Calculation of Pairwise Nonbonded Forces

Matt Chiu, Md. Ashfaquzzaman Khan, Martin C. Herbordt

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Tags: Chemistry, Electrostatics, FPGA, Molecular dynamics, Optimization, Performance

August 15, 2011 by hgpu

The distributed diagonal force decomposition method for parallelizing molecular dynamics simulations

Urban Borstnik, Benjamin T. Miller, Bernard R. Brooks, Dusanka Janezic

Tags: Algorithms, Chemistry, Computational chemistry, Molecular dynamics, Performance

August 8, 2011 by hgpu

Structural, dynamic, and electrostatic properties of fully hydrated DMPC bilayers from molecular dynamics simulations accelerated with graphical processing units (GPUs)

Narayan Ganesan, Brad A. Bauer, Timothy R. Lucas, Sandeep Patel, Michela Taufer

Tags: Algorithms, Chemistry, Computational chemistry, Electrostatic potential, Electrostatics, Molecular dynamics

August 8, 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

Molecular Dynamics Simulations Using Graphics Processing Units

John A. Baker, Jonathan D. Hirst

Tags: Biomolecules, Chemistry, Molecular dynamics, Molecular modeling

July 22, 2011 by hgpu

Coming Soon: Research in a Cloud

Pam Frost Gorder

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Source codes

Tags: Chemistry, Cloud, CUDA, Molecular dynamics, nVidia, nVidia GeForce GTX 280, Package

June 18, 2011 by hgpu

Interactive Visualization of Molecular Surface Dynamics

Michael Krone, Katrin Bidmon, Thomas Ertl

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Tags: Chemistry, GLSL, Molecular dynamics, Molecular surface, nVidia, nVidia GeForce GTX 280, OpenGL, Rendering, Visualization

June 18, 2011 by hgpu

Brownian dynamics simulations on CPU and GPU with BD_BOX

Maciej Dlugosz, Pawel Zielinski, Joanna Trylska

Source codes

Tags: Chemistry, CUDA, Molecular dynamics, MPI, nVidia, OpenMP, Package

June 16, 2011 by hgpu

Loose capacity-constrained representatives for the qualitative visual analysis in molecular dynamics

Steffen Frey, Thomas Schlomer, Sebastian Grottel, Carsten Dachsbacher, Oliver Deussen, Thomas Ertl

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Tags: Computer science, CUDA, Molecular dynamics, nVidia, nVidia GeForce GTX 480, Visualization, Voronoi diagram

June 15, 2011 by hgpu

Accelerating All-Atom Normal Mode Analysis with Graphics Processing Unit

Li Liu, Xiaofeng Liu, Jiayu Gong, Hualiang Jiang, Honglin Li

Tags: Biology, Chemistry, CUDA, Macromolecule, Molecular dynamics, nVidia, Pharmaceuticals

June 2, 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

Two-Level Approach to Efficient Visualization of Protein Dynamics

Fine-grain Parallelism using Multi-core, Cell/BE, and GPU Systems

Efficient Calculation of Pairwise Nonbonded Forces

The distributed diagonal force decomposition method for parallelizing molecular dynamics simulations

Structural, dynamic, and electrostatic properties of fully hydrated DMPC bilayers from molecular dynamics simulations accelerated with graphical processing units (GPUs)

Hardware accelerators for biocomputing: A survey

Molecular Dynamics Simulations Using Graphics Processing Units

Interactive Visualization of Molecular Surface Dynamics

Brownian dynamics simulations on CPU and GPU with BD_BOX

Loose capacity-constrained representatives for the qualitative visual analysis in molecular dynamics

Accelerating All-Atom Normal Mode Analysis with Graphics Processing Unit

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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