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A Highly Extensible Framework for Molecule Dynamic Simulation on GPUs

Xiao Zhang, Wan Guo, Xiao Qin, Xiaonan Zhao

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Tags: Chemistry, CUDA, Molecular dynamics, nVidia, Package, Tesla C2070, Tesla M2070, Tesla S1070

December 8, 2013 by hgpu

PG-PuReMD: A Parallel-GPU Reactive Molecular Dynamics Package

Sudhir B Kylasa, Hasan Metin Aktulga, Ananth Grama

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Tags: Algorithms, Chemistry, CUDA, Molecular dynamics, nVidia, Tesla C2050

November 26, 2013 by hgpu

Probing the Statistical Validity of the Ductile-to-Brittle Transition in Metallic Nanowires Using GPU Computing

William R. French, Amulya K. Pervaje, Andrew P. Santos, Christopher R. Iacovella, Peter T. Cummings

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Tags: Condensed matter, CUDA, Mesoscale and Nanoscale Physics, Molecular dynamics, nVidia, nVidia GeForce GTX 680, OpenMPI, Physics, Tesla M2090

November 18, 2013 by hgpu

Computational kinetics of a large scale biological process on GPU workstations: DNA bending

Arnold Peter Ruymgaart

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Tags: Biology, CUDA, Molecular dynamics, nVidia, nVidia GeForce GTX 480, Thesis

November 8, 2013 by hgpu

Molecular Simulations using CUDA

Gerhard Burger

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Tags: CUDA, Molecular dynamics, Molecular simulation, Monte Carlo simulation, nVidia, nVidia GeForce GT 520, nVidia GeForce GTX 480, nVidia GeForce GTX 580, Physics, Tesla C2075, Thesis

October 29, 2013 by hgpu

Scaling Soft Matter Physics to Thousands of GPUs in Parallel

Alan Gray, Alistair Hart, Oliver Henrich, Kevin Stratford

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Tags: CUDA, Fluid dynamics, Lattice Boltzmann model, Molecular dynamics, nVidia, Physics, Tesla K20

October 15, 2013 by hgpu

Measurements of performance of hardware and general purpose classical molecular dynamics simulation software

Jose O. Sotero-Esteva

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Tags: CUDA, Molecular dynamics, nVidia, Physics, Tesla C2075

October 5, 2013 by hgpu

Kokkos: Enabling performance portability across manycore architectures

H. Carter Edwards, Christian R. Trott

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Tags: Code generation, Computer science, CUDA, Intel Phi, Molecular dynamics, nVidia, Package, Tesla K20

September 17, 2013 by hgpu

On the Use of Graphics Processing Units (GPUs) for Molecular Dynamics Simulation of Spherical Particles

R.C. Hidalgo, T. Kanzaki, F. Alonso-Marroquin, S. Luding

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Tags: CUDA, Molecular dynamics, nVidia, nVidia GeForce GT 430, Physics

August 28, 2013 by hgpu

The development and expansion of HOOMD-blue through six years of GPU proliferation

Joshua A. Anderson, Sharon C. Glotzer

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Tags: Computational Physics, CUDA, Molecular dynamics, nVidia, nVidia GeForce 9800 GTX, nVidia GeForce GTX 580, nVidia GeForce GTX Titan, Package, Physics, Python, Software Engineering, Tesla S1070

August 27, 2013 by hgpu

Tight Binding Molecular Dynamics on CPU and GPU clusters

Dimitar Pashov

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Tags: Algorithms, CUDA, Electrostatics, Fortran, GPU cluster, Linear Algebra, Molecular dynamics, MPI, nVidia, Physics, Tesla K20

August 23, 2013 by hgpu

Implementing Molecular Dynamics on Hybrid High Performance Computers – Three-Body Potentials

W. Michael Brown, Masako Yamada

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Tags: Algorithms, Chemistry, CUDA, Molecular dynamics, nVidia, Package, Physics, Tesla K20

August 20, 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 Highly Extensible Framework for Molecule Dynamic Simulation on GPUs

PG-PuReMD: A Parallel-GPU Reactive Molecular Dynamics Package

Probing the Statistical Validity of the Ductile-to-Brittle Transition in Metallic Nanowires Using GPU Computing

Computational kinetics of a large scale biological process on GPU workstations: DNA bending

Molecular Simulations using CUDA

Scaling Soft Matter Physics to Thousands of GPUs in Parallel

Measurements of performance of hardware and general purpose classical molecular dynamics simulation software

Kokkos: Enabling performance portability across manycore architectures

On the Use of Graphics Processing Units (GPUs) for Molecular Dynamics Simulation of Spherical Particles

The development and expansion of HOOMD-blue through six years of GPU proliferation

Tight Binding Molecular Dynamics on CPU and GPU clusters

Implementing Molecular Dynamics on Hybrid High Performance Computers – Three-Body Potentials

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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