high performance computing on graphics processing units: hgpu.org

hgpu.org » Molecular dynamics

Acceleration of the GAMESS-UK electronic structure package on graphical processing units

Karl A. Wilkinson, Paul Sherwood, Martyn F. Guest, Kevin J. Naidoo

Tags: Chemistry, Fortran, Molecular dynamics, Molecular modeling, nVidia

May 21, 2011 by hgpu

Improving numerical reproducibility and stability in large-scale numerical simulations on GPUs

Michela Taufer, Omar Padron, Philip Saponaro, Sandeep Patel

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Tags: Chemistry, CUDA, Floating point error, Molecular dynamics, nVidia, Tesla S1070

April 25, 2011 by hgpu

The development of Mellanox/NVIDIA GPUDirect over InfiniBand-a new model for GPU to GPU communications

Gilad Shainer, Ali Ayoub, Pak Lui, Tong Liu, Michael Kagan, Christian Trott, Greg Scantlen, Paul Crozier

Tags: Computer science, Memory model, Molecular dynamics, Network communications, Networks, nVidia, Tesla

April 15, 2011 by hgpu

GPGPU supported cooperative acceleration in molecular dynamics

Gang Chen, Guobo Li, Songwen Pei, Baifeng Wu

Tags: ATI, Brook, Chemistry, Molecular dynamics

April 5, 2011 by hgpu

GPU Acceleration of High-Speed Collision Molecular Dynamics Simulation

Canqun Yang, Qiang Wu, Juan Chen, Zhen Ge

Tags: Chemistry, CUDA, Molecular dynamics, nVidia, Tesla C870

March 25, 2011 by hgpu

Evaluating force field accuracy with long-time simulations of a beta-hairpin tryptophan zipper peptide

N. R. Hayre, R. R. Singh, D. L. Cox

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Tags: Biophysics, Chemistry, CUDA, Molecular dynamics, nVidia, nVidia GeForce GTX 285

March 22, 2011 by hgpu

Fast heterogeneous computing with CUDA compatible Tesla GPU computing processor (personal supercomputing)

D. Kumar, M. A. Qadeer

Tags: Computer science, CUDA, Heterogeneous systems, Molecular dynamics, nVidia, Tesla

March 8, 2011 by hgpu

General-purpose molecular dynamics simulations on GPU-based clusters

Christian R. Trott, Lars Winterfeld, Paul S. Crozier

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Source codes

Tags: Computational Physics, Condensed matter, CUDA, GPU cluster, Materials Science, Molecular dynamics, MPI, nVidia, nVidia GeForce GTX 280, nVidia GeForce GTX 295, Package, Performance, Physics, Tesla C1060, Tesla S1070

March 8, 2011 by hgpu

Performance of inverse atomistic scale fracture modeling on GPGPU architectures

A.P. Iliopoulos, J.G. Michopoulos, S.G. Lambrakos, N. Bernstein

Tags: Chemistry, Molecular dynamics, Performance

March 1, 2011 by hgpu

Accelerating Molecular Dynamics Simulations with GPUs

John Paul Walters, Vidyananth Balu, Vipin Chaudhary, David Kofke, Andrew Schultz

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

February 28, 2011 by hgpu

A Resource-Efficient Computing Paradigm for Computational Protein Modeling Applications

Yaohang Li, Douglas Wardell, Vincent Freeh

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Tags: Algorithms, Biology, Molecular dynamics

February 24, 2011 by hgpu

Production Floating Point Applications on FPGAs

Martin C. Herbordt, Bharat Sukhwani, Matt Chiu, Md. Ashfaq Khan

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Tags: Chemistry, Computer science, CUDA, FPGA, Molecular dynamics, Molecular modeling, nVidia, Tesla C1060

February 22, 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

Acceleration of the GAMESS-UK electronic structure package on graphical processing units

Improving numerical reproducibility and stability in large-scale numerical simulations on GPUs

The development of Mellanox/NVIDIA GPUDirect over InfiniBand-a new model for GPU to GPU communications

GPGPU supported cooperative acceleration in molecular dynamics

GPU Acceleration of High-Speed Collision Molecular Dynamics Simulation

Evaluating force field accuracy with long-time simulations of a beta-hairpin tryptophan zipper peptide

Fast heterogeneous computing with CUDA compatible Tesla GPU computing processor (personal supercomputing)

General-purpose molecular dynamics simulations on GPU-based clusters

Performance of inverse atomistic scale fracture modeling on GPGPU architectures

Accelerating Molecular Dynamics Simulations with GPUs

A Resource-Efficient Computing Paradigm for Computational Protein Modeling Applications

Production Floating Point Applications on FPGAs

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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