high performance computing on graphics processing units: hgpu.org

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hgpu.org » Applications » Biology

First Experiences Optimizing Smith-Waterman on Intel’s Knights Landing Processor

Enzo Rucci, Carlos Garcia, Guillermo Botella, Armando De Giusti, Marcelo Naiouf, Manuel Prieto-Matias

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Tags: Bioinformatics, Biology, Computer science, Intel Xeon Phi, Sequence alignment, Smith-Waterman algorithm

February 26, 2017 by hgpu

Analysis and implementation of a BLAST-Like algorithm for MIC architectures

Felipe Sulser Larraz

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Tags: Benchmarking, Bioinformatics, Biology, Computer science, Databases, Filtering, Intel Xeon Phi, Sequence alignment, Smith-Waterman algorithm, Thesis

February 2, 2017 by hgpu

Using efficient parallelization in Graphic Processing Units to parameterize stochastic fire propagation models

Monica Denham, Karina Laneri, Juan Manuel Morales

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Tags: Biology, CUDA, Earth and Space Sciences, nVidia, nVidia GeForce GTX 780, nVidia GeForce GTX Titan, Package, Tesla C2070, Tesla K40

January 16, 2017 by hgpu

BioEM: GPU-accelerated computing of Bayesian inference of electron microscopy images

Pilar Cossio, David Rohr, Fabio Baruffa, Markus Rampp, Volker Lindenstruth, Gerhard Hummer

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Tags: Bayesian, Biology, Biomolecules, CUDA, Electron microscopy, Heterogeneous systems, Medicine, Microscopy, MPI, nVidia, nVidia GeForce GTX Titan, OpenMP, Package, Tesla K20, Tomography

October 8, 2016 by hgpu

Parallel Tree Traversal for Nearest Neighbor Query on the GPU

Moohyeon Nam, Jinwoong Kim, Beomseok Nam

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Tags: Algorithms, Biology, Computational biology, Computer science, CUDA, Information Retrieval, Nearest neighbour, nVidia, Tesla K40

September 5, 2016 by hgpu

Drug Drug Interaction Extraction from Biomedical Literature Using Syntax Convolutional Neural Network

Zhehuan Zhao, Zhihao Yang, Ling Luo, Hongfei Lin, Jian Wang

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Tags: Bioinformatics, Biology, CUDA, Deep learning, Neural networks, NLP, nVidia, Package, Python, Tesla K20, Text mining

August 1, 2016 by hgpu

Gerbil: A Fast and Memory-Efficient k-mer Counter with GPU-Support

Marius Erbert, Steffen Rechner, Matthias Muller-Hannemann

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Tags: Bioinformatics, Biology, Computer science, CUDA, nVidia, nVidia GeForce GTX 970, nVidia GeForce GTX Titan, Package

July 26, 2016 by hgpu

Accelerated cryo-EM structure determination with parallelisation using GPUs in relion-2

Dari Kimanius, Bjorn O Forsberg, Sjors HW Scheres, Erik Lindahl

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Tags: Biology, Cryo-EM, CUDA, Image processing, nVidia, nVidia GeForce GTX 1080, nVidia GeForce GTX 980 Ti

July 5, 2016 by hgpu

PROJECTION Algorithm for Motif Finding on GPUs

Jhoirene B. Clemente, Francis George C. Cabarle, Henry N. Adorna

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Tags: Algorithms, Biology, Computational biology, CUDA, nVidia

May 26, 2016 by hgpu

sPEGG: high throughput eco-evolutionary simulations on commodity graphics processors

Kenichi W. Okamoto, Priyanga Amarasekare

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Tags: Biology, CUDA, Genetics, nVidia, nVidia GeForce GTX 690, Package

April 3, 2016 by hgpu

A Massively Parallel Algorithm for Cell Classification Using CUDA

Samuel Schmidt

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Tags: Bioinformatics, Biology, CUDA, Machine learning, nVidia, nVidia GeForce GTX 770, RNA, Thesis

March 20, 2016 by hgpu

Accelerating Wright-Fisher Forward Simulations on the Graphics Processing Unit

David S. Lawrie

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Tags: Algorithms, Biology, CUDA, Genetics, nVidia, nVidia GeForce GTX 780 M, nVidia GeForce GTX 980

March 10, 2016 by hgpu

NVPTX-SPIR-V Translator

Supporting CUDA for an extended RISC-V GPU architecture

Taichi Lattice Boltmann

Data-Oriented Language Implementation of Lattice-Boltzmann Method for Dense and Sparse Geometries

WarpDrive: Extremely Fast End-to-End Deep Multi-Agent Reinforcement Learning on a GPU

MLIR: Multi-Level Intermediate Representation

High Performance GPU Code Generation for Matrix-Matrix Multiplication using MLIR: Some Early Results

SeisSol: High Resolution Simulation os Seismic Wave Propagation in Realistic Media with Complex Geomerty

Performance Portability and Evaluation of Heterogeneous Components of SeisSol Targeted to Upcoming Intel HPC GPUs

perf4sight: A toolflow to model CNN training performance on Edge GPUs

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high performance computing on graphics processing units: hgpu.org

Applications

First Experiences Optimizing Smith-Waterman on Intel’s Knights Landing Processor

Analysis and implementation of a BLAST-Like algorithm for MIC architectures

Using efficient parallelization in Graphic Processing Units to parameterize stochastic fire propagation models

BioEM: GPU-accelerated computing of Bayesian inference of electron microscopy images

Parallel Tree Traversal for Nearest Neighbor Query on the GPU

Drug Drug Interaction Extraction from Biomedical Literature Using Syntax Convolutional Neural Network

Gerbil: A Fast and Memory-Efficient k-mer Counter with GPU-Support

Accelerated cryo-EM structure determination with parallelisation using GPUs in relion-2

PROJECTION Algorithm for Motif Finding on GPUs

sPEGG: high throughput eco-evolutionary simulations on commodity graphics processors

A Massively Parallel Algorithm for Cell Classification Using CUDA

Accelerating Wright-Fisher Forward Simulations on the Graphics Processing Unit

Recent source codes

NVPTX-SPIR-V Translator

Taichi Lattice Boltmann

WarpDrive: Extremely Fast End-to-End Deep Multi-Agent Reinforcement Learning on a GPU

MLIR: Multi-Level Intermediate Representation

SeisSol: High Resolution Simulation os Seismic Wave Propagation in Realistic Media with Complex Geomerty

perf4sight: A toolflow to model CNN training performance on Edge GPUs

Parament: Parallelized Matrix Exponentiation for Numerical Time evolution

ndzip: A High-Throughput Parallel Lossless Compressor for Scientific Data

ScaleHLS Project

POCL: Portable Computing Language

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