high performance computing on graphics processing units: hgpu.org

hgpu.org » Molecular dynamics

A GPU implementation for improved granular simulations with LAMMPS

Emmanuel N. Millan, Christian Ringl, Carlos S. Bederian, Maria Fabiana Piccoli, Carlos Garcia Garino, Herbert M. Urbassek, Eduardo M. Bringa

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Tags: CUDA, Molecular dynamics, nVidia, Performance, Physics, Tesla C2050, Tesla C2075, Tesla M2090

August 18, 2013 by hgpu

Molecular Dynamics Simulation of Multi-Scale Flows on GPUs

S. Mulla, S. Ivekovic, J.M. Reese

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Tags: Biology, Chemistry, CUDA, Molecular dynamics, nVidia, OpenCL, Tesla M2075

August 12, 2013 by hgpu

Hybrid Acceleration of a Molecular Dynamics Simulation Using Short-Ranged Potentials

Julian Hornich

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Tags: Algorithms, Chemistry, CUDA, Molecular dynamics, nVidia, Tesla M2090, Thesis

July 5, 2013 by hgpu

GPU-Optimized Hybrid Neighbor/Cell List Algorithm for Coarse-Grained Molecular Dynamics Simulations

Andrew J. Proctor

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Tags: Algorithms, Biomolecules, Computer science, Molecular dynamics, nVidia, nVidia GeForce GTX 480, Tesla C2070, Thesis

June 16, 2013 by hgpu

A flexible algorithm for calculating pair interactions on SIMD architectures

Szilard Pall, Berk Hess

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Tags: Algorithms, Computational Physics, CUDA, Molecular dynamics, nVidia, Physics

June 10, 2013 by hgpu

Implementing Continuous Integration Software in an Established Computational Chemistry Software Package

Robin M. Betz, Ross C. Walker

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Tags: Benchmarking, Chemistry, Computational chemistry, CUDA, Molecular dynamics, nVidia, Software Engineering, Tesla M2090

May 21, 2013 by hgpu

Programming for scientific computing on peta-scale heterogeneous parallel systems

Yang Can-qun, Wu Qiang, Tang Tao, Wang Feng, Xue Jing-ling

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Tags: Computer science, CUDA, Heterogeneous systems, Molecular dynamics, nVidia, Tesla M2050

May 13, 2013 by hgpu

GPU-SD and DPD Parallelization for Gromacs tools for molecular dynamics simulations

Nicolae Goga, Siewert Marrink, Ruxandra Cioromela, Florica Moldoveanu

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Tags: Algorithms, Bioinformatics, Biology, Chemistry, CUDA, Molecular dynamics, nVidia, nVidia GeForce 9600 GT

April 21, 2013 by hgpu

Simulation of a flowing snow avalanche using molecular dynamics

Denizhan Gucer, Halil Bulent Ozguc

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Tags: Algorithms, Collision detection, Computer science, CUDA, Molecular dynamics, nVidia, nVidia GeForce 8800 GT, Rendering

March 14, 2013 by hgpu

Large-scale ferrofluid simulations on graphics processing units

A.Yu. Polyakov, T.V. Lyutyy, S. Denisov, V.V. Reva, P. Hanggi

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Tags: CUDA, Fluid simulation, Molecular dynamics, Numerical simulation, nVidia, Physics, Tesla M2050

March 2, 2013 by hgpu

Acceleration of Coarse Grain Molecular Dynamics on GPU Architectures

Ardita Shkurti, Mario Orsi, Enrico Macii, Elisa Ficarra, Andrea Acquaviva

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Tags: Algorithms, Chemistry, CUDA, Molecular dynamics, nVidia, nVidia GeForce GTX 480

March 2, 2013 by hgpu

Developing Performance-Portable Molecular Dynamics Kernels in OpenCL

S. J. Pennycook, S. A. Jarvis

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Source codes

Tags: ATI, ATI FirePro V7800, ATI Radeon HD 6550, Benchmarking, Computer science, Molecular dynamics, nVidia, nVidia GeForce GTX 680, OpenCL, Package, Performance, Tesla C1060, Tesla C2050

February 14, 2013 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

A GPU implementation for improved granular simulations with LAMMPS

Molecular Dynamics Simulation of Multi-Scale Flows on GPUs

Hybrid Acceleration of a Molecular Dynamics Simulation Using Short-Ranged Potentials

GPU-Optimized Hybrid Neighbor/Cell List Algorithm for Coarse-Grained Molecular Dynamics Simulations

A flexible algorithm for calculating pair interactions on SIMD architectures

Implementing Continuous Integration Software in an Established Computational Chemistry Software Package

Programming for scientific computing on peta-scale heterogeneous parallel systems

GPU-SD and DPD Parallelization for Gromacs tools for molecular dynamics simulations

Simulation of a flowing snow avalanche using molecular dynamics

Large-scale ferrofluid simulations on graphics processing units

Acceleration of Coarse Grain Molecular Dynamics on GPU Architectures

Developing Performance-Portable Molecular Dynamics Kernels in OpenCL

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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