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

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

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

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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