high performance computing on graphics processing units: hgpu.org

Mark S. Friedrichs, Peter Eastman, Vishal Vaidyanathan, Mike Houston, Scott Legrand, Adam L. Beberg, Daniel L. Ensign, Christopher M. Bruns, Vijay S. Pande

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Source codes

Tags: ATI, ATI Radeon HD 4870, ATI Stream, Biology, Brook, Chemistry, Computational chemistry, Molecular dynamics, nVidia, nVidia GeForce GTX 280, Package, Solvent effects

October 30, 2010 by hgpu

CUSA and CUDE: GPU-accelerated methods for estimating solvent accessible surface area and desolvation

David Dynerman, Erick Butzlaff, Julie C. Mitchell

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Tags: Bioinformatics, Biology, Biophysics, Chemistry, Computational biology, CUDA, Molecular dynamics, nVidia, nVidia GeForce GTX 280, Solvent effects

October 29, 2010 by hgpu

Current performance gains from utilizing the GPU or the ASIC MDGRAPE-3 within an enhanced Poisson Boltzmann approach

Tetsu Narumi, Kenji Yasuoka, Makoto Taiji, Siegfried Hofinger

Tags: ASIC, Chemistry, Computational chemistry, MDGRAPE, Poisson Boltzmann, Solvent effects

October 29, 2010 by hgpu

GPU acceleration of cutoff pair potentials for molecular modeling applications

Christopher I. Rodrigues, David J. Hardy, John E. Stone, Klaus Schulten, Wen Mei

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Tags: Algorithms, Biology, Chemistry, CUDA, Medicine, Molecular dynamics, nVidia, Tesla C870

October 28, 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

Applications

Parallel, stochastic measurement of molecular surface area

PAPER – Accelerating parallel evaluations of ROCS

Accelerating Resolution-of-the-Identity Second-Order Moller-Plesset Quantum Chemistry Calculations with Graphical Processing Units

Multilevel summation of electrostatic potentials using graphics processing units

General purpose molecular dynamics simulations fully implemented on graphics processing units

Quantum Chemistry on Graphical Processing Units. 1. Strategies for Two-Electron Integral Evaluation

Accelerating Density Functional Calculations with Graphics Processing Unit

Accelerating molecular modeling applications with graphics processors

Accelerating molecular dynamic simulation on graphics processing units

CUSA and CUDE: GPU-accelerated methods for estimating solvent accessible surface area and desolvation

Current performance gains from utilizing the GPU or the ASIC MDGRAPE-3 within an enhanced Poisson Boltzmann approach

GPU acceleration of cutoff pair potentials for molecular modeling applications

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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