high performance computing on graphics processing units: hgpu.org

Applications

hgpu.org » Applications » Chemistry

Evaluating force field accuracy with long-time simulations of a beta-hairpin tryptophan zipper peptide

N. R. Hayre, R. R. Singh, D. L. Cox

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Tags: Biophysics, Chemistry, CUDA, Molecular dynamics, nVidia, nVidia GeForce GTX 285

March 22, 2011 by hgpu

GPU based acceleration of first principles calculation

H. Tomono, M. Aoki, T. Iitaka, K. Tsumuraya

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Tags: Chemistry, CUDA, FFT, Molecular modeling, nVidia, nVidia GeForce GTX 285

March 16, 2011 by hgpu

Automatic Generation of Multicore Chemical Kernels

John C. Linford, John Michalakes, Manish Vachharajani, Adrian Sandu

Tags: Cell processor, Chemistry, Code generation, Computer science, CUDA, nVidia, OpenMP

March 6, 2011 by hgpu

Redesigning combustion modeling algorithms for the Graphics Processing Unit (GPU): Chemical kinetic rate evaluation and ordinary differential equation integration

Yu Shi, William H. Green, Hsi-Wu Wong, Oluwayemisi O. Oluwole

Tags: Chemistry, Computational modelling, CUDA, nVidia, nVidia GeForce GTX 260, Tesla C2050

March 4, 2011 by hgpu

Performance of inverse atomistic scale fracture modeling on GPGPU architectures

A.P. Iliopoulos, J.G. Michopoulos, S.G. Lambrakos, N. Bernstein

Tags: Chemistry, Molecular dynamics, Performance

March 1, 2011 by hgpu

Accelerating Molecular Dynamics Simulations with GPUs

John Paul Walters, Vidyananth Balu, Vipin Chaudhary, David Kofke, Andrew Schultz

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Tags: Chemistry, CUDA, Molecular dynamics, Molecular simulation, nVidia, nVidia GeForce 8800 GTX

February 28, 2011 by hgpu

Accelerating Energy Minimization using Graphics Processors

Bharat Sukhwani, Martin C. Herbordt

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Tags: Chemistry, CUDA, Molecular modeling, nVidia, Tesla C1060

February 22, 2011 by hgpu

Production Floating Point Applications on FPGAs

Martin C. Herbordt, Bharat Sukhwani, Matt Chiu, Md. Ashfaq Khan

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Tags: Chemistry, Computer science, CUDA, FPGA, Molecular dynamics, Molecular modeling, nVidia, Tesla C1060

February 22, 2011 by hgpu

Evaluating one-sided programming models for GPU cluster computations

Jeff R. Hammond and A. Eugene DePrince III

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Tags: Chemistry, Computer science, CUDA, GPU cluster, Matrix multiplication, nVidia, Tesla T10

February 17, 2011 by hgpu

Simulations of Large Membrane Regions using GPU-enabled Computations – Preliminary Results

Narayan Ganesan, Michela Taufer, Sandeep Patel

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Tags: Chemistry, CUDA, Membrane computing, Molecular dynamics, nVidia, Performance

February 17, 2011 by hgpu

Direct Self-Consistent Field Computations on GPU Clusters

Guochun Shi, V. Kindratenko, I. Ufimtsev, T. Martinez

Tags: Chemistry, CUDA, GPU cluster, Molecular modeling, nVidia

February 15, 2011 by hgpu

Generation of Kernels for Calculating Electron Repulsion Integrals of High Angular Momentum Functions on GPUs – Preliminary Results

Alexey V. Titov, Volodymyr V. Kindratenko, Ivan S. Ufimtsev, Todd J. Martinez

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Tags: Chemistry, CUDA, Molecular modeling, nVidia

February 15, 2011 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

Applications

Evaluating force field accuracy with long-time simulations of a beta-hairpin tryptophan zipper peptide

GPU based acceleration of first principles calculation

Automatic Generation of Multicore Chemical Kernels

Redesigning combustion modeling algorithms for the Graphics Processing Unit (GPU): Chemical kinetic rate evaluation and ordinary differential equation integration

Performance of inverse atomistic scale fracture modeling on GPGPU architectures

Accelerating Molecular Dynamics Simulations with GPUs

Accelerating Energy Minimization using Graphics Processors

Production Floating Point Applications on FPGAs

Evaluating one-sided programming models for GPU cluster computations

Simulations of Large Membrane Regions using GPU-enabled Computations – Preliminary Results

Direct Self-Consistent Field Computations on GPU Clusters

Generation of Kernels for Calculating Electron Repulsion Integrals of High Angular Momentum Functions on GPUs – Preliminary Results

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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