high performance computing on graphics processing units: hgpu.org

hgpu.org » Molecular dynamics

Exploring SIMD for Molecular Dynamics, Using Intel Xeon Processors and Intel Xeon Phi Coprocessors

S. J. Pennycook, C. J. Hughes, M. Smelyanskiy, S. A. Jarvis

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Tags: Algorithms, Benchmarking, Computer science, Intel, Intel Phi, Molecular dynamics

February 14, 2013 by hgpu

Bouncing Behavior of Microscopic Dust Aggregates

Alexander Seizinger, Wilhelm Kley

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Tags: Astrophysics, Earth and Planetary Astrophysics, Molecular dynamics, nVidia, nVidia GeForce GTX 460, nVidia GeForce GTX 570, Tesla C2070

January 17, 2013 by hgpu

GPU-Optimized Coarse-Grained MD Simulations of Protein and RNA Folding and Assembly

Andrew J. Proctor, Tyson J. Lipscomb, Anqi Zou, Joshua A. Anderson, Samuel S. Cho

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Tags: Bioinformatics, Biology, CUDA, Macromolecule, Molecular dynamics, nVidia, RNA, Tesla C2070

January 8, 2013 by hgpu

Long Timestep Molecular Dynamics on the Graphical Processing Unit

James C. Sweet, Ronald J. Nowling, Trevor Cickovski, Christopher R. Sweet, Vijay S. Pande, Jesus A. Izaguirre

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Source codes

Tags: Biology, Chemistry, CUDA, Molecular dynamics, nVidia, nVidia GeForce GTX 580, OpenCL, Package

January 4, 2013 by hgpu

Molecular dynamics simulations with many-body potentials on multiple GPUs – the implementation, package and performance

Qing Hou, Min Li, Yulu Zhou, Jiechao Cui, Zhenguo Cui, Jun Wang

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Tags: Computational Physics, CUDA, GPU cluster, Materials Science, Molecular dynamics, nVidia, Physics, Tesla C2050

January 2, 2013 by hgpu

Molecular dynamics for long-range interacting systems on Graphic Processing Units

Tarcisio M. Rocha Filho

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Tags: Algorithms, Computational Physics, CUDA, Molecular dynamics, nVidia, nVidia GeForce GTX 690, Physics, Statistical Mechanics

December 4, 2012 by hgpu

Accelerated molecular dynamics force evaluation on graphics processing units for thermal conductivity calculations

Zheyong Fan, Topi Siro, Ari Harju

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Tags: Computational Physics, Condensed matter, CUDA, Materials Science, Molecular dynamics, nVidia, Physics, Tesla M2070

November 19, 2012 by hgpu

Parallel execution of a parameter sweep for molecular dynamics simulations in a hybrid GPU/CPU environment

Emmanuel N. Millan, Carlos Garcia Garino, Eduardo M. Bringa

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Source codes

Tags: Chemistry, CUDA, Molecular dynamics, nVidia, OpenMPI, Package, Ruby, Tesla C2050

November 10, 2012 by hgpu

Computational Physics on Graphics Processing Units

Ari Harju, Topi Siro, Filippo Federici-Canova, Samuli Hakala, Teemu Rantalaiho

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Tags: Computational Physics, High Energy Physics - Lattice, Molecular dynamics, Physics, Review

October 31, 2012 by hgpu

Performance Analysis Cluster and GPU Computing Environment on Molecular Dynamic Simulation of BRV-1 and REM2 with GROMACS

Heru Suhartanto, Arry Yanuar, Ari Wibisono

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Tags: Cluster computing, Computer science, CUDA, GPU cluster, Molecular dynamics, nVidia, nVidia GeForce GTS 250, nVidia GeForce GTX 465, nVidia GeForce GTX 470, nVidia Quadro FX 4000

October 17, 2012 by hgpu

Kinetics of liquid-solid phase transition in large nickel clusters

Alexander V. Yakubovich, Gennady Sushko, Stefan Schramm, Andrey V. Solov'yov

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Tags: ATI, ATI Radeon HD 5870, Computational Physics, Mesoscale and Nanoscale Physics, Molecular dynamics, OpenCL, Phase transition, Physics, Solidification

October 15, 2012 by hgpu

Towards accelerating Smoothed Particle Hydrodynamics simulations for free-surface flows on multi-GPU clusters

Daniel Valdez-Balderas, Jose M. Dominguez, Benedict D. Rogers, Alejandro J.C. Crespo

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Tags: Algorithms, Computational Physics, Condensed matter, CUDA, Fluid dynamics, GPU cluster, Instrumentation and Methods for Astrophysics, Molecular dynamics, MPI, nVidia, nVidia GeForce GTX 480, Physics, Sorting, Tesla M2050

October 4, 2012 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

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high performance computing on graphics processing units: hgpu.org

Exploring SIMD for Molecular Dynamics, Using Intel Xeon Processors and Intel Xeon Phi Coprocessors

Bouncing Behavior of Microscopic Dust Aggregates

GPU-Optimized Coarse-Grained MD Simulations of Protein and RNA Folding and Assembly

Long Timestep Molecular Dynamics on the Graphical Processing Unit

Molecular dynamics simulations with many-body potentials on multiple GPUs – the implementation, package and performance

Molecular dynamics for long-range interacting systems on Graphic Processing Units

Accelerated molecular dynamics force evaluation on graphics processing units for thermal conductivity calculations

Parallel execution of a parameter sweep for molecular dynamics simulations in a hybrid GPU/CPU environment

Computational Physics on Graphics Processing Units

Performance Analysis Cluster and GPU Computing Environment on Molecular Dynamic Simulation of BRV-1 and REM2 with GROMACS

Kinetics of liquid-solid phase transition in large nickel clusters

Towards accelerating Smoothed Particle Hydrodynamics simulations for free-surface flows on multi-GPU clusters

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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