high performance computing on graphics processing units: hgpu.org

Ruibang Luo, Thomas Wong, Jianqiao Zhu, Chi-Man Liu, Edward Wu, Lap-Kei Lee, Haoxiang Lin, Wenjuan Zhu, David W. Cheung, Hing-Fung Ting, Siu-Ming Yiu, Chang Yu, Yingrui Li, Ruiqiang Li, Tak-Wah Lam

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Tags: Algorithms, Bioinformatics, Biology, CUDA, Next-Generation sequencing, nVidia, Package, Tesla C2070, Tesla M2050

February 25, 2013 by hgpu

G-SNPM – A GPU-based SNP mapping tool

Alessandro Orro, Andrea Manconi, Emanuele Manca, Giuliano Armano, Luciano Milanesi

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Tags: Algorithms, Bioinformatics, Biology, CUDA, Next-Generation sequencing, nVidia, nVidia GeForce GTX 480, Package, Python, Smith-Waterman algorithm

November 14, 2012 by hgpu

GHOSTM: A GPU-Accelerated Homology Search Tool for Metagenomics

Shuji Suzuki, Takashi Ishida, Ken Kurokawa, Yutaka Akiyama

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Tags: Algorithms, Biology, CUDA, Databases, Next-Generation sequencing, nVidia, Package, Tesla S1070

May 10, 2012 by hgpu

Exact and complete short-read alignment to microbial genomes using Graphics Processing Unit programming

Jochen Blom, Tobias Jakobi, Daniel Doppmeier, Sebastian Jaenicke, Jorn Kalinowski, Jens Stoye, Alexander Goesmann

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Tags: Algorithms, Bioinformatics, Biology, CUDA, Next-Generation sequencing, nVidia, Package

May 10, 2011 by hgpu

Exact and complete short read alignment to microbial genomes using GPU programming

Jochen Blom, Tobias Jakobi, Daniel Doppmeier, Sebastian Jaenicke, Jorn Kalinowski, Jens Stoye, Alexander Goesmann

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Tags: Bioinformatics, Biology, CUDA, Next-Generation sequencing, nVidia, nVidia GeForce GTX 280, Package

April 11, 2011 by hgpu

DecGPU: distributed error correction on massively parallel graphics processing units using CUDA and MPI

Yongchao Liu, Bertil Schmidt, Douglas Maskell

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Tags: Bioinformatics, Biology, CUDA, MPI, Next-Generation sequencing, nVidia, OpenMP, Package, Tesla S1070

April 11, 2011 by hgpu

GPU-RMAP: Accelerating Short-Read Mapping on Graphics Processors

Ashwin M. Aji, Liqing Zhang, Wu C. Feng

Tags: Bioinformatics, Biology, Next-Generation sequencing, nVidia

March 9, 2011 by hgpu

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?

hpx: The C++ Standard Library for Parallelism and Concurrency

Integration of CUDA Processing within the C++ library for parallelism and concurrency (HPX)

OpenDwarfs: a benchmark suite consisting of different computation/communication idioms, i.e., dwarfs, for state-of-art multicore CPUs, GPUs, Intel MICs and Altera FPGAs

OpenCL Performance Prediction using Architecture-Independent Features

Rodinia Benchmark Suite ported for OpenCL-capable Intel FPGAs

High Performance Computing with FPGAs and OpenCL

The Ocean Tensor Package

Tornado

Using Compiler Snippets to Exploit Parallelism on Heterogeneous Hardware: A Java Reduction Case Study

pocl: Portable Computing Language

Exploiting Task Parallelism with OpenCL: A Case Study

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high performance computing on graphics processing units: hgpu.org

eccCL: parallelized GPU implementation of Ensemble Classifier Chains

Parallelization, Scalability, and Reproducibility in Next-Generation Sequencing Analysis

SW#db: GPU-accelerated exact sequence similarity database search

GPU-accelerated Computation for Statistical Analysis of the Next-Generation Sequencing Data

cuBLASTP: Fine-Grained Parallelization of Protein Sequence Search on a GPU

SOAP3-dp: Fast, Accurate and Sensitive GPU-based Short Read Aligner

G-SNPM – A GPU-based SNP mapping tool

GHOSTM: A GPU-Accelerated Homology Search Tool for Metagenomics

Exact and complete short-read alignment to microbial genomes using Graphics Processing Unit programming

Exact and complete short read alignment to microbial genomes using GPU programming

DecGPU: distributed error correction on massively parallel graphics processing units using CUDA and MPI

GPU-RMAP: Accelerating Short-Read Mapping on Graphics Processors

Recent source codes

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

hpx: The C++ Standard Library for Parallelism and Concurrency

OpenDwarfs: a benchmark suite consisting of different computation/communication idioms, i.e., dwarfs, for state-of-art multicore CPUs, GPUs, Intel MICs and Altera FPGAs

Rodinia Benchmark Suite ported for OpenCL-capable Intel FPGAs

The Ocean Tensor Package

Tornado

pocl: Portable Computing Language

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International Conference on Image, Video and Signal Processing (IVSP), 2019

International Joint Conference on Signals, Systems and Computers (CSSC), 2018

International Joint Conference on Robotics, Automation and Mechatronics (JCRAM), 2018

International Joint Conference on Robotics and Artificial Intelligence (JCRAI), 2018

International Joint Conference on Computer Vision and Pattern Recognition (CCVPR), 2018