high performance computing on graphics processing units: hgpu.org

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hgpu.org » Applications » Chemistry

SCELib3.0: The new revision of SCELib, the parallel computational library of molecular properties in the Single Center Approach

N. Sanna, I. Baccarelli, G. Morelli

Tags: Biology, Chemistry, CUDA, Molecular modeling, nVidia

January 11, 2011 by hgpu

Molecular Dynamics Simulations on Commodity GPUs with CUDA

Weiguo Liu, Bertil Schmidt, Gerrit Voss, Wolfgang Muller-Wittig

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Tags: Chemistry, CUDA, Molecular dynamics, nVidia, nVidia GeForce 8800 GTX

January 10, 2011 by hgpu

Towards Large-Scale Molecular Dynamics Simulations on Graphics Processors

Joseph E. Davis, Adnan Ozsoy, Sandeep Patel, Michela Taufer

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Tags: Biology, Chemistry, CUDA, Molecular dynamics, nVidia, nVidia GeForce 9800 GX2, nVidia GeForce GTX 280, nVidia Quadro FX 5600

January 3, 2011 by hgpu

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

Accelerating S3D: A GPGPU Case Study

Kyle Spafford, Jeremy Meredith, Jeffrey Vetter, Jacqueline Chen, Ray Grout and Ramanan Sankaran

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Tags: Chemistry, Computational chemistry, CUDA, nVidia, nVidia GeForce 8800 GTX, Tesla C1060

December 18, 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

A GPU solvent-solvent interaction calculation accelerator for biomolecular simulations using the GROMOS software

Nathan Schmid, Mathias Botschi, Wilfred F. Van Gunsteren

Tags: Chemistry, Computational chemistry, CUDA, Molecular dynamics, nVidia, nVidia Quadro FX 5800, Solvent effects

December 17, 2010 by hgpu

Molecular Dynamics on a Grand Scale

Matthew James Mawson Breeze

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Tags: ATI, ATI Radeon X1600, Chemistry, GLSL, Molecular dynamics, nVidia, nVidia GeForce 6200, nVidia GeForce 8800 GTS, OpenGL, Thesis

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

Accelerating molecular dynamics simulations using Graphics Processing Units with CUDA

W. Liu, B. Schmidt, G. Voss, W. Mullerwittig

Tags: Chemistry, CUDA, Molecular dynamics, nVidia

December 11, 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

SCELib3.0: The new revision of SCELib, the parallel computational library of molecular properties in the Single Center Approach

Molecular Dynamics Simulations on Commodity GPUs with CUDA

Towards Large-Scale Molecular Dynamics Simulations on Graphics Processors

FPGA-based acceleration of CHARMM-potential minimization

Accelerating S3D: A GPGPU Case Study

Accelerating Correlated Quantum Chemistry Calculations Using Graphical Processing Units

A GPU solvent-solvent interaction calculation accelerator for biomolecular simulations using the GROMOS software

Molecular Dynamics on a Grand Scale

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

Accelerating molecular dynamics simulations using Graphics Processing Units with CUDA

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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