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Flexible neuronal network simulation framework using code generation for NVidia CUDA

Thomas Nowotny

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Tags: Bioinformatics, Biology, CUDA, Neural networks, Neuroscience, nVidia, nVidia Quadro FX 5800, Poster

October 26, 2011 by hgpu

BEAGLE: an Application Programming Interface and High-Performance Computing Library for Statistical Phylogenetics

Daniel L. Ayres, Aaron Darling, Derrick J. Zwickl, Peter Beerli, Mark T. Holder, Paul O. Lewis, John P. Huelsenbeck, Fredrik Ronquist, David L. Swofford, Michael P. Cummings, Andrew Rambaut, Marc A. Suchard

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Tags: Bayesian, Bioinformatics, Biology, CUDA, Genetics, nVidia, nVidia GeForce GTX 580

October 25, 2011 by hgpu

An Evolutionary Optimization Strategy Using Graphics Processing Units to Efficiently Investigate Gene-Gene Interactions in Genetic Association Studies

Joel B. Fontanarosa, Yang Dai

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Tags: Algorithms, Biology, CUDA, Evolutionary Computations, Genetics, nVidia, nVidia GeForce GTX 470, Optimization

October 25, 2011 by hgpu

Computational Biology and Applied Bioinformatics

Heitor Silverio Lopes, Leonardo Magalhaes Cruz

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Tags: Bioinformatics, Biology, Book, Computational biology, CUDA, nVidia, Review, Sequence alignment, Spectrometry

October 23, 2011 by hgpu

Accelerating molecular docking and binding site mapping using FPGAs and GPUs

Bharat Sukhwani

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Tags: Algorithms, Biology, Biomechanics, CUDA, FPGA, Molecular modeling, nVidia, Tesla C1060, Thesis

October 22, 2011 by hgpu

DOPA: GPU-based protein alignment using database and memory access optimizations

Laiq Hasan, Marijn Kentie, Zaid Al-Ars

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Tags: Algorithms, Bioinformatics, Biology, Computational Complexity, CUDA, Databases, nVidia, nVidia GeForce GTX 275, Optimization, Package, Sequence alignment, Smith-Waterman algorithm

October 21, 2011 by hgpu

Heterogeneous Accelerated Bioinformatics-Perspectives for Cancer Research

Eric A. Stahlberg, T. Steinke, M. C. Smith, S. Chandrasekaran, B. Chapman

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Tags: Bioinformatics, Biology, CUDA, FPGA, Heterogeneous systems, Medicine, nVidia, OpenCL, Review

October 19, 2011 by hgpu

PlinkGPU: A Framework for GPU Acceleration of Whole Genome Data Analysis

Jeffrey Poznanovic

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Tags: Bioinformatics, Biology, CUDA, Genetics, nVidia, OpenCL, Tesla S1070

October 13, 2011 by hgpu

Performance improvements for iterative electron tomography reconstruction using graphics processing units (GPUs)

W.J. Palenstijna, K.J. Batenburga, J. Sijbersa

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Tags: Biology, Image reconstruction, Medicine, nVidia GeForce GTX 280, nVidia GeForce GTX 480, Tomography

October 8, 2011 by hgpu

GPGPU-assisted prediction of ion binding sites in proteins

Leonid Uroshlev, Sergei Rahmanov, Ivan Kulakovskiy, Vsevolod Makeev

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Tags: Biology, Biophysics, CUDA, Molecular modeling, nVidia

October 7, 2011 by hgpu

Democratic Population Decisions Result in Robust Policy-Gradient Learning: A Parametric Study with GPU Simulations

Paul Richmond, Lars Buesing, Michele Giugliano, Eleni Vasilaki

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Tags: Biology, CUDA, Neuroscience, nVidia, nVidia GeForce GTX 480, Package, Python

October 5, 2011 by hgpu

GPU-Accelerated DNA Distance Matrix Computation

Zhi Ying, Xinhua Lin, Simon Chong-Wee See, Minglu Li

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Tags: ATI, ATI Radeon HD 5850, Bioinformatics, Biology, Genetics, nVidia, OpenCL, Performance, Tesla C2050

October 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

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

Flexible neuronal network simulation framework using code generation for NVidia CUDA

BEAGLE: an Application Programming Interface and High-Performance Computing Library for Statistical Phylogenetics

An Evolutionary Optimization Strategy Using Graphics Processing Units to Efficiently Investigate Gene-Gene Interactions in Genetic Association Studies

Computational Biology and Applied Bioinformatics

Accelerating molecular docking and binding site mapping using FPGAs and GPUs

DOPA: GPU-based protein alignment using database and memory access optimizations

Heterogeneous Accelerated Bioinformatics-Perspectives for Cancer Research

PlinkGPU: A Framework for GPU Acceleration of Whole Genome Data Analysis

Performance improvements for iterative electron tomography reconstruction using graphics processing units (GPUs)

GPGPU-assisted prediction of ion binding sites in proteins

Democratic Population Decisions Result in Robust Policy-Gradient Learning: A Parametric Study with GPU Simulations

GPU-Accelerated DNA Distance Matrix Computation

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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