high performance computing on graphics processing units: hgpu.org

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FPGA-based acceleration of CHARMM-potential minimization

Bharat Sukhwani, Martin C. Herbordt

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Tags: Chemistry, FPGA, Molecular modeling, nVidia, Performance, Tesla C1060

January 3, 2011 by hgpu

Efficiency of the energy transfer in the Fenna-Matthews-Olson complex using hierarchical equations on graphics processing units

Christoph Kreisbeck, Tobias Kramer, Mirta Rodriguez, Birgit Hein

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Tags: CUDA, Molecular modeling, nVidia, Physics, Tesla C2050

December 21, 2010 by hgpu

Accelerating Correlated Quantum Chemistry Calculations Using Graphical Processing Units

Mark Watson, Roberto Olivares-Amaya, Richard G. Edgar, Alan Aspuru-Guzik

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Tags: Chemistry, Computational chemistry, Molecular modeling, nVidia, Tesla C1060

December 17, 2010 by hgpu

OpenMM: A Hardware-Independent Framework for Molecular Simulations

Peter Eastman, Vijay Pande

Source codes

Tags: Chemistry, Computational chemistry, Molecular modeling, Package

December 16, 2010 by hgpu

A massively multicore parallelization of the Kohn-Sham energy gradients

Philip Brown, Christopher J. Woods, Simon McIntosh-Smith, Frederick R. Manby

Tags: Chemistry, Computational chemistry, Molecular modeling

December 16, 2010 by hgpu

Two-electron integral evaluation on the graphics processor unit

Koji Yasuda

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Tags: Chemistry, Computational chemistry, CUDA, Molecular modeling, nVidia, nVidia GeForce 8800 GTX

December 12, 2010 by hgpu

The impact of accelerator processors for high-throughput molecular modeling and simulation

G. Giupponi, M. Harvey, G. Defabritiis

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Tags: Bioinformatics, Cell processor, Chemistry, Medicine, Molecular modeling, nVidia, Review

December 11, 2010 by hgpu

Graphical Processing Units for Quantum Chemistry

I. S. Ufimtsev, T. J. Martinez

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Tags: Chemistry, Computational chemistry, CUDA, Molecular modeling, nVidia, nVidia GeForce 8800 GTX

December 10, 2010 by hgpu

Molecular structural mechanics approach to carbon nanotubes on graphics processing units

Xia Jian-ming, Wei De-min

Tags: Matrix multiplication, Molecular modeling, Physics

November 25, 2010 by hgpu

Density functional theory calculation on many-cores hybrid central processing unit-graphic processing unit architectures

Luigi Genovese, Matthieu Ospici, Thierry Deutsch, Jean F. Méhaut, Alexey Neelov, Stefan Goedecker

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Tags: Chemistry, CUDA, Density-functional theory, Molecular modeling, nVidia, Physics, Tesla S1070

November 25, 2010 by hgpu

Quantum Chemistry on Graphical Processing Units. 3. Analytical Energy Gradients, Geometry Optimization, and First Principles Molecular Dynamics

Ivan S. Ufimtsev, Todd J. Martinez

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Tags: Chemistry, Computational chemistry, CUDA, Molecular dynamics, Molecular modeling, nVidia, nVidia GeForce GTX 295

November 25, 2010 by hgpu

GPU-accelerated molecular modeling coming of age

John E. Stone, David J. Hardy, Ivan S. Ufimtsev, Klaus Schulten

Tags: Chemistry, Molecular dynamics, Molecular modeling

November 22, 2010 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

FPGA-based acceleration of CHARMM-potential minimization

Efficiency of the energy transfer in the Fenna-Matthews-Olson complex using hierarchical equations on graphics processing units

Accelerating Correlated Quantum Chemistry Calculations Using Graphical Processing Units

OpenMM: A Hardware-Independent Framework for Molecular Simulations

A massively multicore parallelization of the Kohn-Sham energy gradients

Two-electron integral evaluation on the graphics processor unit

The impact of accelerator processors for high-throughput molecular modeling and simulation

Graphical Processing Units for Quantum Chemistry

Molecular structural mechanics approach to carbon nanotubes on graphics processing units

Density functional theory calculation on many-cores hybrid central processing unit-graphic processing unit architectures

Quantum Chemistry on Graphical Processing Units. 3. Analytical Energy Gradients, Geometry Optimization, and First Principles Molecular Dynamics

GPU-accelerated molecular modeling coming of age

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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