high performance computing on graphics processing units: hgpu.org

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Multifactor dimensionality reduction for graphics processing units enables genome-wide testing of epistasis in sporadic ALS

Casey S. Greene, Nicholas A. Sinnott-Armstrong, Daniel S. Himmelstein, Paul J. Park, Jason H. Moore, Brent T. Harris

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Tags: Bioinformatics, Biology, CUDA, Genetics, nVidia, nVidia GeForce GTX 295, Package

November 7, 2010 by hgpu

Parallel hyperbolic PDE simulation on clusters: Cell versus GPU

Scott Rostrup, Hans De Sterck

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Tags: Cell processor, CUDA, Hyperbolic PDEs, Hyperbolic system, Mathematics, nVidia, Package, Tesla C2050, Tesla T10

November 7, 2010 by hgpu

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

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

SAPPORO: A way to turn your graphics cards into a GRAPE-6

Evghenii Gaburov, Stefan Harfst, Simon P. Zwart

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Tags: Astrophysics, CUDA, Instrumentation and Methods for Astrophysics, nVidia, nVidia GeForce 9800 GX2, Package, Physics

November 6, 2010 by hgpu

GPU’s for event reconstruction in the FairRoot framework

M. {Al-Turany}, F. {Uhlig}, R. {Karabowicz}

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Tags: CUDA, Instrumentation and measurement, Nuclear physics, nVidia, Package, Particle physics and field theory, Physics, Tesla C1060

November 5, 2010 by hgpu

RenderAnts: Interactive REYES Rendering on GPUs

Kun Zhou, Qiming Hou, Zhong Ren, Minmin Gong, Xin Sun, Baining Guo

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Tags: Computer science, Image generation, nVidia, nVidia GeForce GTX 280, Package, Raytracing, Rendering, Shaders

November 5, 2010 by hgpu

The Scalable Heterogeneous Computing (SHOC) benchmark suite

Anthony Danalis,Gabriel Marin,Collin McCurdy,Jeremy S. Meredith,Philip C. Roth,Kyle Spafford,Vinod Tipparaju,Jeffrey S. Vetter

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Tags: ATI, ATI Radeon HD 5770, ATI Radeon HD 5870, ATI Stream, Benchmarking, Computer science, CUDA, Heterogeneous systems, nVidia, nVidia GeForce 8800 GT, nVidia GeForce 8800 GTS, nVidia GeForce 8800 GTX, nVidia GeForce 9400 M, OpenCL, Package, Performance, Tesla C1060

November 5, 2010 by hgpu

CLUEstering: a high-performance density-based clustering library for scientific computing

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high performance computing on graphics processing units: hgpu.org

Packages

Multifactor dimensionality reduction for graphics processing units enables genome-wide testing of epistasis in sporadic ALS

Parallel hyperbolic PDE simulation on clusters: Cell versus GPU

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

StoreGPU: exploiting graphics processing units to accelerate distributed storage systems

Accelerating Dust Temperature Calculations with Graphics Processing Units

SAPPORO: A way to turn your graphics cards into a GRAPE-6

GPU’s for event reconstruction in the FairRoot framework

RenderAnts: Interactive REYES Rendering on GPUs

The Scalable Heterogeneous Computing (SHOC) benchmark suite

Recent source codes

CLUEstering: a high-performance density-based clustering library for scientific computing

PyOMP: OpenMP for Python in Numba

HiRep

GPPerf: Energy-Aware GPU Performance Prediction and Optimization Framework

gpuPairHMM: Ultra-fast GPU-based PairHMM for DNA Variant Calling

Gaia AVU-GSR

Kokkidio: Kokkos+Eigen - write fast, readable multi-platform code

LLaMA-Inference-Bench

MATAR

Over-synchronization in GPU Programs

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