high performance computing on graphics processing units: hgpu.org

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hgpu.org » Applications » Chemistry

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

Simulation of Coarse-Grained Protein-Protein Interactions with Graphics Processing Units

Ian Tunbridge, Robert B. Best, James Gain, Michelle M. Kuttel

Tags: Chemistry, Molecular dynamics

December 7, 2010 by hgpu

Efficient Parallelization of Stochastic Simulation Algorithm for Chemically Reacting Systems on the Graphics Processing Unit

Linda Petzold, Hong Li

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Tags: Chemistry, Stochastic simulation

November 27, 2010 by hgpu

Molecular dynamics simulation of complex multiphase flow on a computer cluster with GPUs

Feiguo Chen, Wei Ge, Jinghai Li

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Tags: Chemistry, CUDA, GPU cluster, Molecular dynamics, MPI, nVidia, Tesla C870

November 27, 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

Accelerating electrostatic surface potential calculation with multi-scale approximation on graphics processing units

Ramu Anandakrishnan, Tom R. W. Scogland, Andrew T. Fenley, John C. Gordon, Wu-chun Feng, Alexey V. Onufriev

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Tags: ATI, ATI CAL, ATI Radeon HD 4870, Brook, Chemistry, Molecular modeling, Solvent effects

November 22, 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

Quantum Chemistry on Graphical Processing Units. 2. Direct Self-Consistent-Field Implementation

Ivan S. Ufimtsev, Todd J. Martinez

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Tags: Chemistry, Computational chemistry, CUDA, Molecular modeling, nVidia, nVidia GeForce 8800 GTX, nVidia GeForce GTX 280

November 21, 2010 by hgpu

Using Graphics Processors to Facilitate Explicit Digital Electrochemical Simulation: Theory of Elliptical Disc Electrodes

Ian Cutress, Richard Compton

Tags: Chemistry, Electrochemistry

November 19, 2010 by hgpu

Direct numerical simulation of sub-grid structures in gas-solid flow — GPU implementation of macro-scale pseudo-particle modeling

Qingang Xiong, Bo Li, Feiguo Chen, Jingsen Ma, Wei Ge, Jinghai Li

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Tags: Chemistry, Fluid dynamics, Navier-Stokes equations, NSEs, nVidia

November 17, 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

Applications

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

Graphical Processing Units for Quantum Chemistry

Simulation of Coarse-Grained Protein-Protein Interactions with Graphics Processing Units

Efficient Parallelization of Stochastic Simulation Algorithm for Chemically Reacting Systems on the Graphics Processing Unit

Molecular dynamics simulation of complex multiphase flow on a computer cluster with GPUs

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

Accelerating electrostatic surface potential calculation with multi-scale approximation on graphics processing units

GPU-accelerated molecular modeling coming of age

Quantum Chemistry on Graphical Processing Units. 2. Direct Self-Consistent-Field Implementation

Using Graphics Processors to Facilitate Explicit Digital Electrochemical Simulation: Theory of Elliptical Disc Electrodes

Direct numerical simulation of sub-grid structures in gas-solid flow — GPU implementation of macro-scale pseudo-particle modeling

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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