high performance computing on graphics processing units: hgpu.org

Applications

High performance computation and interactive display of molecular orbitals on GPUs and multi-core CPUs

John E. Stone, Jan Saam, David J. Hardy, Kirby L. Vandivort, Wen-mei W. Hwu, Klaus Schulten

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Tags: Algorithms, Chemistry, CUDA, nVidia, nVidia GeForce 8800 GTX, nVidia GeForce GTX 280, Performance, Programming techniques, Rendering, Visualization

September 7, 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

GPU-accelerated atom and dynamic bond visualization using hyperballs: A unified algorithm for balls, sticks, and hyperboloids

Matthieu Chavent, Antoine Vanel, Alex Tek, Bruno Levy, Sophie Robert, Bruno Raffin, Marc Baaden

Tags: Algorithms, Chemistry, Macromolecule, Molecular modeling, Visualization

July 23, 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

Fat vs. Thin Threading Approach on GPUs: Application to Stochastic Simulation of Chemical Reactions

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

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Tags: Chemistry, CUDA, nVidia, nVidia GeForce GTX 260, Programming techniques, Stochastic simulation

July 14, 2011 by hgpu

GPU Accelerated Chemical Similarity Calculation for Compound Library Comparison

Chao Ma, Lirong Wang, Xiang-Qun Xie

Tags: Algorithms, Chemistry, CUDA, Nearest neighbour, nVidia

July 6, 2011 by hgpu

Neural network modeling on evolution of hydration reaction for Portland cement

Lin Wang, Bo Yang, Yuehui Chen, Xiuyang Zhao, Jun Chang, Haiyang Wang

Tags: Chemistry, Materials Science, Neural networks, Physics

June 20, 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

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

High performance computation and interactive display of molecular orbitals on GPUs and multi-core CPUs

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)

GPU-accelerated atom and dynamic bond visualization using hyperballs: A unified algorithm for balls, sticks, and hyperboloids

Molecular Dynamics Simulations Using Graphics Processing Units

Fat vs. Thin Threading Approach on GPUs: Application to Stochastic Simulation of Chemical Reactions

GPU Accelerated Chemical Similarity Calculation for Compound Library Comparison

Neural network modeling on evolution of hydration reaction for Portland cement

Interactive Visualization of Molecular Surface Dynamics

Brownian dynamics simulations on CPU and GPU with BD_BOX

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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