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An Efficient Simulation Environment for Modeling Large-Scale Cortical Processing

Micah Richert, Jayram Moorkanikara Nageswaran, Nikil Dutt, Jeffrey L. Krichmar

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Tags: Biology, CUDA, Neural networks, Neuroscience, nVidia, Package, Tesla C1060

December 19, 2011 by hgpu

A Novel Multi-GPU Neural Simulator

C. M. Thibeault, R. Hoang, F. C. Harris Jr.

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Tags: Biology, Biophysics, CUDA, Neuroscience, nVidia, nVidia GeForce GTX 480

December 14, 2011 by hgpu

Fast extraction of neuron morphologies from large-scale SBFSEM image stacks

Stefan Lang, Panos Drouvelis, Enkelejda Tafaj, Peter Bastian, Bert Sakmann

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Tags: Algorithms, Biology, CUDA, Electron microscopy, Image processing, Microscopy, Neuroscience, nVidia, Tesla C1060

December 8, 2011 by hgpu

GPU-Euler: Sequence Assembly Using GPGPU

Syed F. Mahmood, Huzefa Rangwala

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Tags: Biology, CUDA, Genetics, nVidia, nVidia Quadro FX 5800

December 5, 2011 by hgpu

kNN Query Processing in Metric Spaces Using GPUs

Ricardo J. Barrientos, Jose I. Gomez, Christian Tenllado, Manuel Prieto Matias, Mauricio Marin

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Tags: Algorithms, Biology, Computational biology, CUDA, Databases, Information Retrieval, nVidia, nVidia GeForce GTX 280

December 4, 2011 by hgpu

On the design of architecture-aware algorithms for emerging applications

Seunghwa Kang

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Tags: Algorithms, Benchmarking, Biology, Cell processor, Computational biology, CUDA, Image processing, MapReduce, nVidia, Package, Tesla C1060, Thesis

December 2, 2011 by hgpu

Parallel-META: A high-performance computational pipeline for metagenomic data analysis

Xiaoquan Su, Jian Xu, Kang Ning

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Tags: Biology, Databases, Genetics, nVidia, Optimization, Tesla C2070

December 2, 2011 by hgpu

Parallelized agent-based simulation on CPU and graphics hardware for spatial and stochastic models in biology

Martin Falk, Michael Ott, Thomas Ertl, Michael Klann, Heinz Koeppl

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Tags: Biology, CUDA, nVidia, nVidia GeForce GTX 465, Programming techniques

November 24, 2011 by hgpu

A Parallel Deconvolution Algorithm in Perfusion Imaging

Fan Zhu, David Rodriguez Gonzalez, Trevor Carpenter, Malcolm Atkinson, Joanna Wardlaw

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Tags: Algorithms, Biology, CUDA, Medicine, nVidia, nVidia GeForce GTX 280, Performance, Tesla C1060

November 23, 2011 by hgpu

Accelerating Protein Sequence Search in a Heterogeneous Computing System

Shucai Xiao, Heshan Lin, Wu-chun Feng

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Tags: Algorithms, Bioinformatics, Biology, BLAST, Databases, Heterogeneous systems, nVidia, Optimization, Tesla C1060, Tesla C2050

November 23, 2011 by hgpu

Application of GPGPU for Acceleration of Short DNA Sequence Alignment in Unipro UGENE Project

Konstantin Okonechinkov, German Grekhov, Konstantin Stepanyuk, Mikhail Fursov

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Tags: Algorithms, Bioinformatics, Biology, nVidia, OpenCL, Package, Sequence alignment, Tesla C1060, Tesla C2070

November 22, 2011 by hgpu

Using Graphics Processors for a High Performance Normalization of Gene Expressions

Andres Rodriguez, Oswaldo Trelles, Manuel Ujaldon

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Tags: Bioinformatics, Biology, CUDA, nVidia, nVidia GeForce 9800 GX2

November 22, 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

An Efficient Simulation Environment for Modeling Large-Scale Cortical Processing

A Novel Multi-GPU Neural Simulator

Fast extraction of neuron morphologies from large-scale SBFSEM image stacks

GPU-Euler: Sequence Assembly Using GPGPU

kNN Query Processing in Metric Spaces Using GPUs

On the design of architecture-aware algorithms for emerging applications

Parallel-META: A high-performance computational pipeline for metagenomic data analysis

Parallelized agent-based simulation on CPU and graphics hardware for spatial and stochastic models in biology

A Parallel Deconvolution Algorithm in Perfusion Imaging

Accelerating Protein Sequence Search in a Heterogeneous Computing System

Application of GPGPU for Acceleration of Short DNA Sequence Alignment in Unipro UGENE Project

Using Graphics Processors for a High Performance Normalization of Gene Expressions

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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