high performance computing on graphics processing units: hgpu.org

Parallel Implementation of Dynamic Programming Algorithm Using Graphics Processing Unit

M. Khurram Rehman, M. Umer Sarwar, M. Ramzan Talib, M. Salman Mansoor, M. Bilal Sarwar

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Tags: Algorithms, Bioinformatics, Biology, Computer science, CUDA, Matrix multiplication, nVidia, nVidia GeForce GT 525 M, nVidia GeForce GT 610 M, Sequence alignment

April 6, 2013 by hgpu

CMCpy: Genetic Code-Message Coevolution Models in Python

Peter J. Becich, Brian P. Stark, Harish S. Bhat, David H. Ardell

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Tags: Bioinformatics, Biology, CUDA, nVidia, nVidia GeForce GTX 460, Package, Python

March 31, 2013 by hgpu

GPU-Based Cloud Service for Smith-Waterman algorithm Using Frequency Distance Filtration Scheme

Sheng-Ta Lee, Chun-Yuan Lin, Che Lun Hung

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Tags: Bioinformatics, Biology, Cloud, CUDA, nVidia, Sequence alignment, Smith-Waterman algorithm, Tesla C2050

March 18, 2013 by hgpu

GPU based Eulerian Assembly of Genomes

Syed Faraz Mahmood

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Tags: Bioinformatics, Biology, CUDA, Genetics, nVidia, nVidia Quadro FX 5800, Thesis

March 7, 2013 by hgpu

On continuous maximum flow image segmentation algorithm

Laszlo Marak

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Tags: Algorithms, Biology, Materials Science, nVidia, nVidia GeForce GTX 470, OpenCL, Tesla C2050, Thesis, Tomography

March 2, 2013 by hgpu

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

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

Streaming Data from HDD to GPUs for Sustained Peak Performance

Lucas Beyer, Paolo Bientinesi

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Tags: Biology, Computational biology, CUDA, nVidia, nVidia Quadro FX 6000, Tesla S2050

February 20, 2013 by hgpu

ClusCo: clustering and comparison of protein models

Jamroz Michal, Kolinski Andrzej

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Tags: Biology, Biomolecules, Clustering, Computational Engineering, CUDA, Finance, nVidia, nVidia GeForce GTX 470, Package

February 20, 2013 by hgpu

Extending the Computational Application of Reaction-Diffusion Chemistry by Modelling Artificial Neural Networks

James Stovold

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Tags: Biology, Chemistry, CUDA, Neural networks, nVidia, nVidia GeForce 9600 M GT

February 12, 2013 by hgpu

Binary Interval Search: a scalable algorithm for counting interval intersections

Ryan M. Layer, Kevin Skadron, Gabriel Robins, Ira M. Hall, Aaron R. Quinlan

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Tags: Algorithms, Bioinformatics, Biology, Computer science, CUDA, Monte Carlo simulation, nVidia, Package, Sequence alignment

February 6, 2013 by hgpu

Hardware Accelerated Molecular Docking: A Survey

Imre Pechan, Bela Feher

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Tags: Bioinformatics, Biology, CUDA, FPGA, Molecular simulation, nVidia, Tesla C1060

February 6, 2013 by hgpu

GPU-Accelerated High-Accuracy Molecular Docking using Guided Differential Evolution

Martin Simonsen, Mikael H. Christensen, Rene Thomsen, Christian N. S. Pedersen

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Tags: Biology, CUDA, Differential evolution, Medicine, nVidia, nVidia GeForce 8800 GT, Pharmaceuticals

February 5, 2013 by hgpu

MSCCL++: A GPU-driven communication stack for scalable AI applications

MSCCL++: Rethinking GPU Communication Abstractions for Cutting-edge AI Applications

Benchmark compute shader of Unity against InteropUnityCUDA

InteropUnityCUDA: A Tool for Interoperability Between Unity and CUDA

Data-efficient LLM Fine-tuning for Code Generation

DeepSpeed is a deep learning optimization library that makes distributed training and inference easy, efficient, and effective.

DeepCompile: A Compiler-Driven Approach to Optimizing Distributed Deep Learning Training

Large Language Model Powered C-to-CUDA Code Translation: A Novel Auto-Parallelization Framework

GigaAPI: a user-space API that simplifies multi-GPU programming, bridging the gap between the capabilities of parallel GPU systems and the ability of developers to harness their full potential

GigaAPI for GPU Parallelization

Coccinelle: a C code transformation engine using SmPL for matches, refactorings, and bug fixing

Advances in Semantic Patching for HPC-oriented Refactorings with Coccinelle

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high performance computing on graphics processing units: hgpu.org

Applications

Parallel Implementation of Dynamic Programming Algorithm Using Graphics Processing Unit

CMCpy: Genetic Code-Message Coevolution Models in Python

GPU based Eulerian Assembly of Genomes

On continuous maximum flow image segmentation algorithm

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

Streaming Data from HDD to GPUs for Sustained Peak Performance

ClusCo: clustering and comparison of protein models

Extending the Computational Application of Reaction-Diffusion Chemistry by Modelling Artificial Neural Networks

Binary Interval Search: a scalable algorithm for counting interval intersections

Hardware Accelerated Molecular Docking: A Survey

GPU-Accelerated High-Accuracy Molecular Docking using Guided Differential Evolution

Recent source codes

MSCCL++: A GPU-driven communication stack for scalable AI applications

Benchmark compute shader of Unity against InteropUnityCUDA

Data-efficient LLM Fine-tuning for Code Generation

DeepSpeed is a deep learning optimization library that makes distributed training and inference easy, efficient, and effective.

Large Language Model Powered C-to-CUDA Code Translation: A Novel Auto-Parallelization Framework

GigaAPI: a user-space API that simplifies multi-GPU programming, bridging the gap between the capabilities of parallel GPU systems and the ability of developers to harness their full potential

Coccinelle: a C code transformation engine using SmPL for matches, refactorings, and bug fixing

DuoReduce: MLIR's benchmark

Shamrock: Multi-GPU hydrodynamics for astrophysics

LLMPerf: GPU Performance Modeling meets Large Language Models

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