high performance computing on graphics processing units: hgpu.org

Programming

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Biomolecular electrostatics simulation with a parallel FMM-based BEM, using up to 512 GPUs

Rio Yokota, Jaydeep P. Bardhan, Matthew G. Knepley, L. A. Barba, Tsuyoshi Hamada

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Tags: Chemistry, CUDA, GPU cluster, Molecular modeling, nVidia, nVidia GeForce GTX 295, Package

November 7, 2010 by hgpu

MDLab: A molecular dynamics simulation prototyping environment

Trevor Cickovski, Santanu Chatterjee, Jacob Wenger, Christopher R. Sweet, Jesus A. Izaguirre

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Tags: Chemistry, Computational chemistry, CUDA, Molecular dynamics, nVidia, Package, Python

November 6, 2010 by hgpu

CUDASW++ 2.0: enhanced Smith-Waterman protein database search on CUDA-enabled GPUs based on SIMT and virtualized SIMD abstractions

Yongchao Liu, Bertil Schmidt, Douglas Maskell

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Tags: Bioinformatics, Biology, Computational biology, CUDA, nVidia, nVidia GeForce GTX 280, nVidia GeForce GTX 295, Package, Smith-Waterman algorithm

November 6, 2010 by hgpu

Automatic fitting of spiking neuron models to electrophysiological recordings

Cyrille Rossant, Dan F. Goodman, Jonathan Platkiewicz, Romain Brette

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Tags: Adaptive threshold, Biology, CUDA, Distributed computing, Neuroscience, nVidia, nVidia GeForce GTX 295, Optimization, Package

November 6, 2010 by hgpu

Exploring the multiple-GPU design space

Dana Schaa, David Kaeli

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Tags: Computer science, CUDA, GPU cluster, nVidia, nVidia GeForce 8800 GTX

November 6, 2010 by hgpu

GPU Computing for Atmospheric Modeling

Rory Kelly

Tags: CUDA, Earth and Space Sciences, nVidia

November 6, 2010 by hgpu

A Practical Quicksort Algorithm for Graphics Processors

Daniel Cederman, Philippas Tsigas

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Tags: Algorithms, Computer science, CUDA, nVidia, nVidia GeForce 8600 GTS, nVidia GeForce 8800 GTX, Sorting

November 6, 2010 by hgpu

StoreGPU: exploiting graphics processing units to accelerate distributed storage systems

Samer Al-Kiswany, Abdullah Gharaibeh, Elizeu Santos-Neto, George Yuan, Matei Ripeanu

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Tags: Computer science, CUDA, Hashing, nVidia, nVidia GeForce 8600 GTS, nVidia GeForce 9800 GTX, Package, Storage system

November 6, 2010 by hgpu

Accelerating Dust Temperature Calculations with Graphics Processing Units

Patrik Jonsson, Joel Primack

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Tags: Astrophysics, CUDA, Instrumentation and Methods for Astrophysics, nVidia, Package, Physics, Tesla C1060

November 6, 2010 by hgpu

Fast scale invariant feature detection and matching on programmable graphics hardware

Nico Cornelis, Luc Van Gool

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Tags: Computer science, Computer vision, CUDA, nVidia, nVidia GeForce 8800 GTX

November 6, 2010 by hgpu

Efficient simulation of large-scale spiking neural networks using CUDA graphics processors

Jayram M. Nageswaran, Nikil Dutt, Jeffrey L. Krichmar, Alex Nicolau, Alex Veidenbaum

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Tags: Biology, Computer science, CUDA, Neural networks, nVidia, nVidia GeForce GTX 280, STDP

November 6, 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

Programming

Biomolecular electrostatics simulation with a parallel FMM-based BEM, using up to 512 GPUs

MDLab: A molecular dynamics simulation prototyping environment

CUDASW++ 2.0: enhanced Smith-Waterman protein database search on CUDA-enabled GPUs based on SIMT and virtualized SIMD abstractions

Automatic fitting of spiking neuron models to electrophysiological recordings

Exploring the multiple-GPU design space

GPU Computing for Atmospheric Modeling

A Practical Quicksort Algorithm for Graphics Processors

StoreGPU: exploiting graphics processing units to accelerate distributed storage systems

Accelerating Dust Temperature Calculations with Graphics Processing Units

Fast scale invariant feature detection and matching on programmable graphics hardware

Efficient simulation of large-scale spiking neural networks using CUDA 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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