high performance computing on graphics processing units: hgpu.org

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

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

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

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high performance computing on graphics processing units: hgpu.org

High performance transcription factor-DNA docking with GPU computing

Algorithms for the mapping of genome sequences in GPGPU

GPUmotif: An Ultra-Fast and Energy-Efficient Motif Analysis Program Using Graphics Processing Units

Design of high-performance parallelized gene predictors in MATLAB

MetaBinG: Using GPUs to Accelerate Metagenomic Sequence Classification

GPU Accelerated PK-means Algorithm for Gene Clustering

GPU-Euler: Sequence Assembly Using GPGPU

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

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

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

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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