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Study of low density nuclear matter with quantum molecular dynamics: the role of the symmetry energy

Rana Nandi, Stefan Schramm

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Tags: AMD FirePro S10000, ATI, Molecular dynamics, Nuclear Theory, OpenCL, Physics

January 12, 2016 by hgpu

Experimentation Procedure for Offloaded Mini-Apps Executed on Cluster Architectures with Xeon Phi Accelerators

Gary Lawson, Vaibhav Sundriyal, Masha Sosonkina, Yuzhong Shen

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Tags: Computer science, Heterogeneous systems, Intel Xeon Phi, Molecular dynamics

September 9, 2015 by hgpu

A parallel algorithm for implicit depletant simulations

Jens Glaser, Andrew S. Karas, Sharon C. Glotzer

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Source codes

Tags: Condensed matter, CUDA, Molecular dynamics, nVidia, Package, Physics, Soft Condensed Matter, Tesla K20, Tesla K80

August 31, 2015 by hgpu

Best bang for your buck: GPU nodes for GROMACS biomolecular simulations

Carsten Kutzner, Szilard Pall, Martin Fechner, Ansgar Esztermann, Bert L. de Groot, Helmut Grubmuller

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Tags: Benchmarking, Biological Physics, Biomolecules, Computational Physics, Computer science, Molecular dynamics, Molecular simulation, MPI, nVidia, Package, Performance, Tesla K20, Tesla K40

July 6, 2015 by hgpu

RUMD: A general purpose molecular dynamics package optimized to utilize GPU hardware down to a few thousand particles

Nicholas P. Bailey, Trond S. Ingebrigtsen, Jesper Schmidt Hansen, Arno A. Veldhorst, Lasse Bohling, Claire A. Lemarchand, Andreas E. Olsen, Andreas K. Bacher, Heine Larsen, Jeppe C. Dyre, Thomas B. Schroder

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Tags: Computational Physics, CUDA, Molecular dynamics, nVidia, nVidia GeForce GTX 780 Ti, Package, Physics, Python

June 17, 2015 by hgpu

Tackling Exascale Software Challenges in Molecular Dynamics Simulations with GROMACS

Pall Szilard, Mark James Abraham, Carsten Kutzner, Berk Hess, Erik Lindahl

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Tags: Algorithms, Biomolecules, Computer science, CUDA, Heterogeneous systems, Molecular dynamics, Molecular simulation, MPI, nVidia, Tesla C2070, Tesla K20

June 5, 2015 by hgpu

Towards Modeling Energy Consumption of Xeon Phi

Gary Lawson, Masha Sosonkina, Yuzhong Shen

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Tags: Computer science, Energy-efficient computing, Intel Xeon Phi, Molecular dynamics

May 28, 2015 by hgpu

Scaling behavior of topologically constrained polymer rings in a melt

Benjamin Trefz, Peter Virnau

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Tags: Condensed matter, CUDA, Molecular dynamics, nVidia, nVidia GeForce GTX 480, Soft Condensed Matter

December 16, 2014 by hgpu

Strong scaling of general-purpose molecular dynamics simulations on GPUs

Jens Glaser, Trung Dac Nguyen, Joshua A. Anderson, Pak Lui, Filippo Spiga, Jaime A. Millan, David C. Morse, Sharon C. Glotzer

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Tags: Computational Physics, CUDA, Molecular dynamics, MPI, nVidia, Physics, Tesla K20

December 12, 2014 by hgpu

On the Efficiency of CPU and Hybrid CPU-GPU Systems in Computational Biology Tasks

Nikolay Pydiura, Pavel Karpov, Yaroslav Blume

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Tags: AMD Radeon R9 280, ATI, Biology, Computational biology, CUDA, Molecular dynamics, nVidia, nVidia GeForce GTX 480, OpenCL

October 25, 2014 by hgpu

Scalable Multi-GPU Simulation of Long-Range Molecular Dynamics

Marcos Novalbos, Jaime Gonzalez, Miguel A. Otaduy, Roberto Martinez Benito, Alberto Sanchez

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Tags: Algorithms, Biomolecules, Chemistry, CUDA, Electrostatic potential, Electrostatics, FFT, Molecular dynamics, Multilevel summation, N-body simulation, nVidia, nVidia GeForce GTX 580, nVidia GeForce GTX Titan

September 15, 2014 by hgpu

An Efficient Cell List Implementation for Monte Carlo Simulation on GPUs

Loren Schwiebert, Eyad Hailat, Kamel Rushaidat, Jason Mick, Jeffrey Potoff

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Tags: Algorithms, Computational Physics, CUDA, Molecular dynamics, Molecular simulation, Monte Carlo simulation, nVidia, nVidia GeForce GTX 480, nVidia GeForce GTX 550 Ti, Physics, Tesla K40

August 19, 2014 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

Study of low density nuclear matter with quantum molecular dynamics: the role of the symmetry energy

Experimentation Procedure for Offloaded Mini-Apps Executed on Cluster Architectures with Xeon Phi Accelerators

A parallel algorithm for implicit depletant simulations

Best bang for your buck: GPU nodes for GROMACS biomolecular simulations

RUMD: A general purpose molecular dynamics package optimized to utilize GPU hardware down to a few thousand particles

Tackling Exascale Software Challenges in Molecular Dynamics Simulations with GROMACS

Towards Modeling Energy Consumption of Xeon Phi

Scaling behavior of topologically constrained polymer rings in a melt

Strong scaling of general-purpose molecular dynamics simulations on GPUs

On the Efficiency of CPU and Hybrid CPU-GPU Systems in Computational Biology Tasks

Scalable Multi-GPU Simulation of Long-Range Molecular Dynamics

An Efficient Cell List Implementation for Monte Carlo Simulation on GPUs

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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