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Development and evaluation of a GPU-optimized N-body term for the simulation of biomolecules

Timo Strunk, Moritz Wolf, Wolfgang Wenzel

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Tags: ATI, ATI Radeon HD 5870, Benchmarking, Biology, Biomolecules, Monte Carlo simulation, N-body simulation, nVidia, nVidia GeForce GTX 285, OpenCL, Optimization

October 30, 2011 by hgpu

FPGA acceleration of rigid-molecule docking codes

Bharat Sukhwani, Martin C. Herbordt

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Tags: Biology, Biomolecules, CUDA, FPGA, Molecular modeling, nVidia, Performance, Tesla C1060

August 15, 2011 by hgpu

Molecular Dynamics Simulations Using Graphics Processing Units

John A. Baker, Jonathan D. Hirst

Tags: Biomolecules, Chemistry, Molecular dynamics, Molecular modeling

July 22, 2011 by hgpu

Massively parallelized replica-exchange simulations of polymers on GPUs

Jonathan Gross, Wolfhard Janke, Michael Bachmann

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Tags: Biomolecules, Computational Physics, Condensed matter, CUDA, Monte Carlo simulation, nVidia, nVidia GeForce GTX 285, nVidia GeForce GTX 480, Physics, Polymer Systems, Tesla C1060

July 19, 2011 by hgpu

Towards accelerating molecular modeling via multi-scale approximation on a GPU

M. Daga, Wu-chun Feng, T. Scogland

Tags: Algorithms, Biomolecules, Electrostatic potential, Medicine, Molecular modeling

May 5, 2011 by hgpu

Probing biomolecular machines with graphics processors

James C. Phillips, John E. Stone

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Tags: Biology, Biomolecules, CUDA, GPU cluster, Molecular simulation, nVidia, OpenCL, Review, Tesla S1070

February 23, 2011 by hgpu

Fast Calculation of Electrostatic Potentials on the GPU or the ASIC MD-GRAPE-3

Tetsu Narumi, Kenji Yasuoka, Makoto Taiji, Francesco Zerbetto, Siegfried Hofinger

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Tags: Biomolecules, Biophysics, Chemistry, Molecular simulation, nVidia, nVidia GeForce GTX 280, Poisson Boltzmann

January 25, 2011 by hgpu

Langevin dynamics simulations of biomolecules on graphics processors

A. Zhmurov, R. I. Dima, Y. Kholodov, V. Barsegov

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Tags: Biological Physics, Biomolecules, Condensed matter, CUDA, Molecular dynamics, nVidia, nVidia GeForce GTX 295, Physics, Soft Condensed Matter

November 12, 2010 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

Development and evaluation of a GPU-optimized N-body term for the simulation of biomolecules

FPGA acceleration of rigid-molecule docking codes

Molecular Dynamics Simulations Using Graphics Processing Units

Massively parallelized replica-exchange simulations of polymers on GPUs

Towards accelerating molecular modeling via multi-scale approximation on a GPU

Probing biomolecular machines with graphics processors

Fast Calculation of Electrostatic Potentials on the GPU or the ASIC MD-GRAPE-3

Langevin dynamics simulations of biomolecules on graphics processors

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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