high performance computing on graphics processing units: hgpu.org

Applications

hgpu.org » Applications » Biology

Enabling Energy-Efficient Analysis of Massive Neural Signals Using GPGPU

Dan Chen, Lizhe Wang, Shuaiting Wang, Muzhou Xiong, Gregor von Laszewski, Xiaoli Li

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Tags: Biology, CUDA, Medicine, Neuroscience, nVidia, nVidia GeForce GTX 295, Signal processing

April 5, 2011 by hgpu

GPGPU-Aided Ensemble Empirical-Mode Decomposition for EEG Analysis During Anesthesia

Dan Chen, Duan Li, Muzhou Xiong, Hong Bao, Xiaoli Li

Tags: Biology, Medicine, Signal processing

April 5, 2011 by hgpu

Neuromorphic models on a GPGPU cluster

Bing Han, T.M. Taha

Tags: Biology, GPU cluster, MPI, Neuroscience, nVidia, Tesla S1070

April 5, 2011 by hgpu

GPGPU implementation of a synaptically optimized, anatomically accurate spiking network simulator

Ruggero Scorcioni

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Tags: Biology, CUDA, Neuroscience, nVidia

April 4, 2011 by hgpu

The optimization of parallel Smith-Waterman sequence alignment using on-chip memory of GPGPU

Qian Zhang, Hong An, Gu Liu, Wenting Han, Ping Yao, Mu Xu, Xiaoqiang Li

Tags: Bioinformatics, Biology, CUDA, nVidia, Sequence alignment, Smith-Waterman algorithm

April 4, 2011 by hgpu

Poster: GPU-accelerated rigid body fitting of atomic structures into electron density maps

Edward W. Lowe Jr., Nils Woetzel, Jens Meiler

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Source codes

Tags: ATI, ATI Radeon HD 5970, Biology, Cryo-EM, Molecular modeling, nVidia, nVidia GeForce GTX 470, OpenCL, Package, Poster, Tesla C1060, Tesla C2050

April 1, 2011 by hgpu

Poster: GPU-accelerated artificial neural network for QSAR modeling

Edward W. Lowe Jr., Nils Woetzel, Jens Meiler

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Tags: ATI, ATI Radeon HD 5970, Biology, Neural networks, nVidia, nVidia GeForce GTX 470, OpenCL, Poster, Tesla C1060, Tesla C2050

April 1, 2011 by hgpu

Optimizing Smith-Waterman algorithm on Graphics Processing Unit

A. Khalafallah, H.F. Elbabb, O. Mahmoud, A. Elshamy

Tags: Bioinformatics, Biology, OpenCL, Sequence alignment, Smith-Waterman algorithm

April 1, 2011 by hgpu

Implementation of Smith-Waterman Algorithm in OpenCL for GPUs

Dzmitry Razmyslovich, Guillermo Marcus, Markus Gipp, Marc Zapatka, Andreas Szillus

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Tags: Bioinformatics, Biology, CUDA, nVidia, nVidia GeForce GTX 260, nVidia GeForce GTX 480, OpenCL, Poster, Sequence alignment, Smith-Waterman algorithm

March 31, 2011 by hgpu

CuHMMer: A load-balanced CPU-GPU cooperative bioinformatics application

Ping Yao, Hong An, Mu Xu, Gu Liu, Xiaoqiang Li, Yaobin Wang, Wenting Han

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Tags: Bioinformatics, Biology, CUDA, nVidia, nVidia GeForce 8800 GTX, Pattern Search

March 29, 2011 by hgpu

A GPU Implementation of Fast Parallel Markov Clustering in Bioinformatics Using EllPACK-R Sparse Data Format

A. Bustamam, K. Burrage, N.A. Hamilton

Tags: Bioinformatics, Biology, CUDA, nVidia

March 25, 2011 by hgpu

GPU implemention of fast Gabor filters

Xin Xin Wang, E. Shi Bertram

Tags: Biology, Filtering, Image processing, nVidia, nVidia GeForce 9800 GTX

March 21, 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

Enabling Energy-Efficient Analysis of Massive Neural Signals Using GPGPU

GPGPU-Aided Ensemble Empirical-Mode Decomposition for EEG Analysis During Anesthesia

Neuromorphic models on a GPGPU cluster

GPGPU implementation of a synaptically optimized, anatomically accurate spiking network simulator

The optimization of parallel Smith-Waterman sequence alignment using on-chip memory of GPGPU

Poster: GPU-accelerated rigid body fitting of atomic structures into electron density maps

Poster: GPU-accelerated artificial neural network for QSAR modeling

Optimizing Smith-Waterman algorithm on Graphics Processing Unit

Implementation of Smith-Waterman Algorithm in OpenCL for GPUs

CuHMMer: A load-balanced CPU-GPU cooperative bioinformatics application

A GPU Implementation of Fast Parallel Markov Clustering in Bioinformatics Using EllPACK-R Sparse Data Format

GPU implemention of fast Gabor filters

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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