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Dynamic Parallelism in GPU Optimized Barnes Hut Trees for Molecular Dynamics Simulations

Melisa Carranza Zuniga

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Tags: Algorithms, Biology, Biomolecules, Biophysics, Chemistry, CUDA, Molecular dynamics, nVidia, nVidia GeForce GTX 480, Physics, Thesis

August 26, 2017 by hgpu

OpenCL-Based Implementation of an FPGA Accelerator for Molecular Dynamics Simulation

Hasitha Muthumala Waidyasooriya, Masanori Hariyama, Kota Kasahara

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Tags: Chemistry, FPGA, Heterogeneous systems, Molecular dynamics, OpenCL

July 5, 2017 by hgpu

A Domain Specific Language for Performance Portable Molecular Dynamics Algorithms

William R. Saunders, James Grant, Eike H. Muller

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Tags: Algorithms, Biology, Chemistry, Code generation, Computer science, CUDA, Differential equations, DSL, Molecular dynamics, nVidia, Package, Partial differential equations, PDEs, Physics, Python, Tesla K20

April 15, 2017 by hgpu

Architectural Principles and Experimentation of Distributed High Performance Virtual Clusters

Andrew J. Younge

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Tags: Cloud, Computer science, CUDA, Distributed computing, Molecular dynamics, nVidia, OpenCL, Tesla C2075, Tesla K20, Thesis, Virtualization

March 9, 2017 by hgpu

LAMMPS’ PPPM Long-Range Solver for the Second Generation Xeon Phi

William McDoniel, Markus Hohnerbach, Rodrigo Canales, Ahmed E. Ismail, Paolo Bientinesi

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Tags: Chemistry, Computer science, Intel Xeon Phi, Molecular dynamics, Performance

February 18, 2017 by hgpu

An FPGA Accelerator for Molecular Dynamics Simulation Using OpenCL

Hasitha Muthumala Waidyasooriya, Masanori Hariyama, Kota Kasahara

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Tags: Chemistry, FPGA, Heterogeneous systems, Molecular dynamics, OpenCL, Performance, Physics

January 10, 2017 by hgpu

A hybrid algorithm for parallel molecular dynamics simulations

Chris M. Mangiardi, Ralf Meyer

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Tags: Condensed matter, Intel Xeon Phi, Materials Science, Molecular dynamics

November 3, 2016 by hgpu

Efficient molecular dynamics simulations with many-body potentials on graphics processing units

Zheyong Fan, Wei Chen, Ville Vierimaa, Ari Harju

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Tags: Computational Physics, CUDA, Materials Science, Molecular dynamics, nVidia, Physics, Tesla K40

October 15, 2016 by hgpu

GeauxDock: Accelerating Structure-Based Virtual Screening with Heterogeneous Computing

Ye Fang, Yun Ding, Wei P. Feinstein, David M. Koppelman, Juana Moreno, Mark Jarrell, J. Ramanujam, Michal Brylinski

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Tags: Algorithms, Chemistry, CUDA, Heterogeneous systems, Intel Xeon Phi, Medicine, Molecular dynamics, nVidia, nVidia GeForce GTX 980, OpenMP, Package

July 16, 2016 by hgpu

GPU Accelerated Discrete Element Method (DEM) Molecular Dynamics for Conservative, Faceted Particle Simulations

Matthew Spellings, Ryan L. Marson, Joshua A. Anderson, Sharon C. Glotzer

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Tags: Computational Physics, CUDA, Molecular dynamics, nVidia, nVidia Quadro M 6000, Package, Particle simulation, Physics

July 13, 2016 by hgpu

The Vectorization of the Tersoff Multi-Body Potential: An Exercise in Performance Portability

Markus Hohnerbach, Ahmed E. Ismail, Paolo Bientinesi

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Tags: Chemistry, Computational chemistry, Computer science, CUDA, Intel Xeon Phi, Materials Science, Molecular dynamics, MPI, nVidia, Package, performance portability, Tesla K20, Tesla K40

July 13, 2016 by hgpu

Optimization of Molecular Dynamics Simulation Code and Applications to Biomolecular Systems

David M. Bowman

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Tags: Biochemistry, Biomolecules, Chemistry, CUDA, Molecular dynamics, MPI, nVidia, OpenCL, OpenMP, Thesis

March 1, 2016 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

Dynamic Parallelism in GPU Optimized Barnes Hut Trees for Molecular Dynamics Simulations

OpenCL-Based Implementation of an FPGA Accelerator for Molecular Dynamics Simulation

A Domain Specific Language for Performance Portable Molecular Dynamics Algorithms

LAMMPS’ PPPM Long-Range Solver for the Second Generation Xeon Phi

An FPGA Accelerator for Molecular Dynamics Simulation Using OpenCL

A hybrid algorithm for parallel molecular dynamics simulations

Efficient molecular dynamics simulations with many-body potentials on graphics processing units

GeauxDock: Accelerating Structure-Based Virtual Screening with Heterogeneous Computing

GPU Accelerated Discrete Element Method (DEM) Molecular Dynamics for Conservative, Faceted Particle Simulations

The Vectorization of the Tersoff Multi-Body Potential: An Exercise in Performance Portability

Optimization of Molecular Dynamics Simulation Code and Applications to Biomolecular Systems

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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