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

sycl-bench: SYCL Benchmark Suite

SYCL-Bench: A Versatile Single-Source Benchmark Suite for Heterogeneous Computing

BlaBla: A Python package for clinical linguistic feature extraction in multiple languages

BlaBla: Linguistic Feature Extraction for Clinical Analysis in Multiple Languages

gocudnn: Go Bindings for cudnn and other cuda pacakges

Deep Learning with GO

Task-Based Parallel Strategies for CFD Application in Heterogeneous CPU/GPU Resources

DALI: a library containing both highly optimized building blocks and an execution engine for data pre-processing in deep learning applications

Importance of Data Loading Pipeline in Training Deep Neural Networks

AutoParBench: a benchmark framework to evaluate compilers and tools designed to automatically insert OpenMP directives

AutoParBench: A Unified Test Framework for OpenMP-based Parallelizers

DeePMD-kit: A deep learning package for many-body potential energy representation and molecular dynamics

86 PFLOPS Deep Potential Molecular Dynamics simulation of 100 million atoms with ab initio accuracy

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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

sycl-bench: SYCL Benchmark Suite

BlaBla: A Python package for clinical linguistic feature extraction in multiple languages

gocudnn: Go Bindings for cudnn and other cuda pacakges

Task-Based Parallel Strategies for CFD Application in Heterogeneous CPU/GPU Resources

DALI: a library containing both highly optimized building blocks and an execution engine for data pre-processing in deep learning applications

AutoParBench: a benchmark framework to evaluate compilers and tools designed to automatically insert OpenMP directives

DeePMD-kit: A deep learning package for many-body potential energy representation and molecular dynamics

cuda-kat: The CUDA Kernel Author's Toolkit

HPCC FPGA: A OpenCL-based FPGA benchmark suite for HPC

GEVO: GPU Code Optimization using Evolutionary Computation

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8th International Workshop on OpenCL, including SYCLCon, 2019

7th International Workshop on OpenCL, 2019

Distributed Heterogeneous Programming in C/C++ (DHPCC++), 2019

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

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