high performance computing on graphics processing units: hgpu.org

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Fast and Flexible GPU Accelerated Binding Free Energy Calculations within the AMBER Molecular Dynamics Package

Daniel J. Mermelstein, Charles Lin, Gard Nelson, Rachael Kretsch, J. Andrew McCammon, Ross C. Walker

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Tags: Algorithms, Bioinformatics, Biology, CUDA, Molecular dynamics, nVidia, nVidia GeForce GTX 1080 Ti, nVidia GeForce GTX Titan X

January 20, 2018 by hgpu

pyPaSWAS: Python-based multi-core CPU and GPU sequence alignment

Sven Warris, N. Roshan N. Timal, Marcel Kempenaar, Arne M. Poortinga, Henri van de Geest, Ana L. Varbanescu, Jan-Peter Nap

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Tags: Bioinformatics, Biology, CUDA, nVidia, nVidia GeForce GTX 1070, OpenCL, Package, Python, Sequence alignment, Smith-Waterman algorithm

January 13, 2018 by hgpu

Molecular dynamics recipes for genome research

Tommaso Biagini, Giovanni Chillemi, Gianluigi Mazzoccoli, Alessandro Grottesi, Caterina Fusilli, Daniele Capocefalo, Stefano Castellana, Angelo Luigi Vescovi, Tommaso Mazza

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Tags: Benchmarking, Bioinformatics, Biology, Chemistry, CUDA, Genomics, Molecular dynamics, nVidia, OpenCL, Physics, Tesla C2070

December 19, 2017 by hgpu

HCudaBLAST: an implementation of BLAST on Hadoop and Cuda

Nilay Khare, Alind Khare and Farhan Khan

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Tags: Algorithms, Bioinformatics, Biology, BLAST, CUDA, Hadoop, nVidia, nVidia Quadro 2000, nVidia Quadro 600, Tesla C2075

December 3, 2017 by hgpu

A Hybrid-parallel Architecture for Applications in Bioinformatics

Jan Christian Kassens

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Tags: Algorithms, Bioinformatics, Biology, Computer science, CUDA, FPGA, nVidia, nVidia GeForce GTX 780 Ti, Thesis

December 3, 2017 by hgpu

High Performance Streaming Smith-Waterman Implementation with Implicit Synchronization on Intel FPGA using OpenCL

Ernst Joachim Houtgast, Vlad-Mihai Sima, Zaid Al-Ars

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Tags: Algorithms, Bioinformatics, Biology, FPGA, OpenCL, Smith-Waterman algorithm

November 26, 2017 by hgpu

A Study of Time and Energy Efficient Algorithms for Parallel and Heterogeneous Computing

Jude-Thaddeus Ojiaku

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Tags: ATI, ATI Radeon HD 7750, ATI Radeon HD 7970, Bioinformatics, Computer science, Graph layout, Heterogeneous systems, nVidia, nVidia GefForce GTX 650, nVidia GefForce GTX 680, OpenCL, Thesis

October 29, 2017 by hgpu

Smith-Waterman Acceleration in Multi-GPUs: A Performance per Watt Analysis

Jesus Perez Serrano, Edans Flavius De Oliveira Sandes, Alba Cristina Magalhaes Alves de Melo, Manuel Ujaldon

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Tags: Bioinformatics, Biology, CUDA, Energy-efficient computing, nVidia, nVidia GeForce GTX 980, Performance, Smith-Waterman algorithm

June 10, 2017 by hgpu

Exploiting Multi-level Parallelism on a Many-core System for the Application of Hyperheuristics to a Molecular Docking Problem

Jose M. Cecilia, Jose-Matias, Cutillas-Lozano, Domingo Gimenez, Baldomero Imbernon

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Tags: Bioinformatics, Biology, Chemistry, Intel Xeon Phi, Metaheuristics, molecular docking

March 20, 2017 by hgpu

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

Molecular Activity Prediction using Deep Learning Software Library

Yoshiki Kato, Shinji Hamada, Hitoshi Goto

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Tags: Bioinformatics, Chemistry, Computer science, CUDA, Deep learning, nVidia, Package, Python, Tesla K20

November 5, 2016 by hgpu

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OpenCLIPER: an OpenCL-based C++ Framework for Overhead-Reduced Medical Image processing and Reconstruction on heterogeneous Devices

OpenCLIPER: an OpenCL-based C++ Framework for Overhead-Reduced Medical Image Processing and Reconstruction on Heterogeneous Devices

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2018

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Guangzhou, China

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02-04

Academic Exchange Center in Ocean University of China, Qingdao, China

The 4th International Conference on Communication and Information Processing (ICCIP), 2018

2018

November

27-30

Hida Takayama, Japan

The Third International Workshop on GPU Computing and AI (GCA), 2018

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19-21

Nagoya University, Japan

The 5th International Conference on Power and Energy Systems Engineering (CPESE), 2018

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22-24

MediaCityUK, Salford Quays, Greater Manchester, England

The 10th International Conference on Information Management and Engineering (ICIME), 2018

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high performance computing on graphics processing units: hgpu.org

Fast and Flexible GPU Accelerated Binding Free Energy Calculations within the AMBER Molecular Dynamics Package

pyPaSWAS: Python-based multi-core CPU and GPU sequence alignment

Molecular dynamics recipes for genome research

HCudaBLAST: an implementation of BLAST on Hadoop and Cuda

A Hybrid-parallel Architecture for Applications in Bioinformatics

High Performance Streaming Smith-Waterman Implementation with Implicit Synchronization on Intel FPGA using OpenCL

A Study of Time and Energy Efficient Algorithms for Parallel and Heterogeneous Computing

Smith-Waterman Acceleration in Multi-GPUs: A Performance per Watt Analysis

Exploiting Multi-level Parallelism on a Many-core System for the Application of Hyperheuristics to a Molecular Docking Problem

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

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

Molecular Activity Prediction using Deep Learning Software Library

Recent source codes

OCLADock - OpenCL Accelerated Molecular Docking

sentiment-discovery: Unsupervised Language Modeling at scale for robust sentiment classification

Parallax: A Tool for Automatic Parallelization of Deep Learning Training in Distributed Multi-GPU Environments

OpenCLIPER: an OpenCL-based C++ Framework for Overhead-Reduced Medical Image processing and Reconstruction on heterogeneous Devices

Spatial: Specify Parameterized Accelerators Through Inordinately Abstract Language

cuPentBatch: A batched pentadiagonal solver for NVIDIA GPUs

LeFlow: Enabling Flexible FPGA High-Level Synthesis of Tensorflow Deep Neural Networks

CloudCL: Single-Paradigm Distributed Heterogeneous Computing for Cloud Infrastructures

Calamari: OCR Engine based on OCRopy and Kraken

FluidFFT: efficient and easy Fast Fourier Transform for Python

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Featured events

The 3rd International Conference on Computer Systems and Communication Technology (ICCSCT), 2018

The 4th International Conference on Communication and Information Processing (ICCIP), 2018

The Third International Workshop on GPU Computing and AI (GCA), 2018

The 5th International Conference on Power and Energy Systems Engineering (CPESE), 2018

The 10th International Conference on Information Management and Engineering (ICIME), 2018