high performance computing on graphics processing units: hgpu.org

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Many-body quantum chemistry on graphics processing units

A. Eugene DePrince III, Jeff R. Hammond, Stephen K. Gray

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Tags: Algorithms, Chemistry, Computational chemistry, CUDA, Heterogeneous systems, Matrix multiplication, Molecular modeling, nVidia, Tesla C2050

November 11, 2011 by hgpu

Accelerating the Smoldyn Spatial Stochastic Biochemical Reaction Network Simulator Using GPUs

Denis V. Gladkov, Samuel Alberts, Roshan M. D'Souza, Steven Andrews

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Tags: Algorithms, Biochemistry, Computational Complexity, Computer science, CUDA, nVidia, Tesla C2050

November 11, 2011 by hgpu

Run, Stencil, Run! – A Comparison of Modern Parallel Programming Paradigms

Helmar Burkhart, Matthias Christen, Max Rietmann, Madan Sathe, Olaf Schenk

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Tags: Benchmarking, Computer science, CUDA, MPI, nVidia, OpenMP, Tesla C2050

November 10, 2011 by hgpu

PATUS: A Code Generation and Auto-Tuning Framework For Parallel Stencil Computations

Matthias Christen, Olaf Schenk, Helmar Burkhart

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Source codes

Tags: Code generation, Computer science, CUDA, nVidia, Optimization, Package, Tesla C2050

November 8, 2011 by hgpu

Performance analysis of a hybrid MPI/CUDA implementation of the NASLU benchmark

S.J. Pennycook, S.D. Hammond, S.A. Jarvis, G.R. Mudalige

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Tags: Benchmarking, Computer science, CUDA, MPI, nVidia, nVidia GeForce 8400 GS, nVidia GeForce 9400 GT, Operating systems, Performance, Tesla C1060, Tesla C2050, Tesla T10

November 8, 2011 by hgpu

High performance massively parallel direct N-body simulations on large GPU clusters

Peter Berczik, Keigo Nitadori, Shiyan Zhong, Rainer Spurzem, Tsuyoshi Hamada, Xiaowei Wang, Ingo Berentzen, Alexander Veles, Wei Ge

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Tags: Astrophysics, CUDA, GPU cluster, MPI, N-body simulation, nVidia, Tesla C1060, Tesla C2050

November 8, 2011 by hgpu

GPUinspiral – a low-latency, high-performance implementation of the matched-filter gravitational wave search algorithm

G. Debreczeni, B. Somhegyi

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Source codes

Tags: Algorithms, Astrophysics, ATI, ATI Radeon HD 5970, Filtering, Gravitation, nVidia, nVidia GeForce GTX 295, OpenCL, Package, Tesla C2050

November 7, 2011 by hgpu

Acceleration of physics simulation engine through OpenCL

Jorge Miguel Raposeira Lagarto

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Tags: Algorithms, Collision detection, nVidia, nVidia Quadro FX 3800, OpenCL, Physics-based simulation, Tesla C2050

November 7, 2011 by hgpu

Transformation of Scientific Algorithms to Parallel Computing Code: Single GPU and MPI multi GPU Backends with Subdomain Support

Bjorn Meyer, Christian Plessl, Jens Forstner

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Tags: Algorithms, Code generation, CUDA, FPGA, GPU cluster, MPI, nVidia, nVidia GeForce GTX 480, Tesla C2050

November 5, 2011 by hgpu

Improving CUDASW++, a Parallelization of Smith-Waterman for CUDA Enabled Devices

Doug Hains, Zach Cashero, Mark Ottenberg, Wim Bohm, Sanjay Rajopadhye

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Tags: Algorithms, Bioinformatics, Biology, CUDA, nVidia, Sequence alignment, Smith-Waterman algorithm, Tesla C1060, Tesla C2050

November 5, 2011 by hgpu

VASP on a GPU: application to exact-exchange calculations of the stability of elemental boron

Maxwell Hutchinson, Michael Widom

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Tags: Computational chemistry, Computational Physics, Condensed matter, CUDA, nVidia, Physics, Tesla C2050, Tesla C2075

November 4, 2011 by hgpu

Performance Portability of a GPU Enabled Factorization with the DAGuE Framework

George Bosilca, Aurelien Bouteiller, Thomas Herault, Pierre Lemarinier, Narapat Ohm Saengpatsa, Stanimire Tomov, Jack J. Dongarra

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Tags: Computer science, Factorization, GPU cluster, Heterogeneous systems, Linear Algebra, nVidia, Performance, Tesla C1060, Tesla C2050, Tesla S1070

November 3, 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

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high performance computing on graphics processing units: hgpu.org

Many-body quantum chemistry on graphics processing units

Accelerating the Smoldyn Spatial Stochastic Biochemical Reaction Network Simulator Using GPUs

Run, Stencil, Run! – A Comparison of Modern Parallel Programming Paradigms

PATUS: A Code Generation and Auto-Tuning Framework For Parallel Stencil Computations

Performance analysis of a hybrid MPI/CUDA implementation of the NASLU benchmark

High performance massively parallel direct N-body simulations on large GPU clusters

GPUinspiral – a low-latency, high-performance implementation of the matched-filter gravitational wave search algorithm

Acceleration of physics simulation engine through OpenCL

Transformation of Scientific Algorithms to Parallel Computing Code: Single GPU and MPI multi GPU Backends with Subdomain Support

Improving CUDASW++, a Parallelization of Smith-Waterman for CUDA Enabled Devices

VASP on a GPU: application to exact-exchange calculations of the stability of elemental boron

Performance Portability of a GPU Enabled Factorization with the DAGuE Framework

Recent source codes

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

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

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