high performance computing on graphics processing units: hgpu.org

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

Accelerating Genomics Research with OpenCL and FPGAs

Chris Rauer, George S. Powley, Mir Ahsan, Nicholas Finamore

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Tags: Algorithms, Biology, Computer science, FPGA, Genomics, OpenCL

October 15, 2017 by hgpu

Dynamic Parallelism in GPU Optimized Barnes Hut Trees for Molecular Dynamics Simulations

Melisa Carranza Zuniga

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Tags: Algorithms, Biology, Biomolecules, Biophysics, Chemistry, CUDA, Molecular dynamics, nVidia, nVidia GeForce GTX 480, Physics, Thesis

August 26, 2017 by hgpu

eccCL: parallelized GPU implementation of Ensemble Classifier Chains

Mona Riemenschneider, Alexander Herbst, Ari Rasch, Sergei Gorlatch, Dominik Heider

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Source codes

Tags: Biology, Computer science, Java, Next-Generation sequencing, nVidia, OpenCL, Package, R, Tesla K20

August 26, 2017 by hgpu

SuperNeurons: FFT-based Gradient Sparsification in the Distributed Training of Deep Neural Networks

CLort: High Throughput and Low Energy Network Intrusion Detection on IoT Devices with Embedded GPUs

SWIFOLD: Smith-Waterman implementation on FPGA with OpenCL for long DNA sequences

Spatter: Benchmark for measuring the performance of sparse and irregular memory access

Spatter: A Benchmark Suite for Evaluating Sparse Access Patterns

StePS: Stereographically Projected Cosmological Simulations

StePS: A Multi-GPU Cosmological N-body Code for Compactified Simulations

AMGCL:C++ library for solving large sparse linear systems with algebraic multigrid method

AMGCL: an Efficient, Flexible, and Extensible Algebraic Multigrid Implementation

PAstudy

Double-precision FPUs in High-Performance Computing: an Embarrassment of Riches?

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2019

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Rome, Italy

International Conference on Frontiers of Neural Networks (ICFNN), 2019

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Miami, Florida, USA

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26-28

Vancouver, Canada

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high performance computing on graphics processing units: hgpu.org

Applications

ASW: Accelerating Smith-Waterman Algorithm on Coupled CPU-GPU Architecture

SWIFOLD: Smith-Waterman implementation on FPGA with OpenCL for long DNA sequences

Interactive GPU active contours for segmenting inhomogeneous objects

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

Accelerating Genomics Research with OpenCL and FPGAs

Dynamic Parallelism in GPU Optimized Barnes Hut Trees for Molecular Dynamics Simulations

eccCL: parallelized GPU implementation of Ensemble Classifier Chains

Recent source codes

schnaps: a finite element solver

GPU-benchmarks

Truchas: 3D Multiphysics Simulation of Metal Casting and Processing

SuperNeurons: FFT-based Gradient Sparsification in the Distributed Training of Deep Neural Networks

CLort: High Throughput and Low Energy Network Intrusion Detection on IoT Devices with Embedded GPUs

SWIFOLD: Smith-Waterman implementation on FPGA with OpenCL for long DNA sequences

Spatter: Benchmark for measuring the performance of sparse and irregular memory access

StePS: Stereographically Projected Cosmological Simulations

AMGCL:C++ library for solving large sparse linear systems with algebraic multigrid method

PAstudy

Most viewed papers (last 30 days)

Featured events

3rd International Workshop on Theoretical Approaches to Performance Evaluation, Modeling and Simulation (TAPEMS), 2019

International Conference on Frontiers of Neural Networks (ICFNN), 2019

International Conference on Frontiers of Artificial Intelligence and Machine Learning (FAIML), 2019

3rd World Conference on Clinical Research and Biomarkers, 2019

3rd International Conference on Vision, Image and Signal Processing (ICVISP), 2019