high performance computing on graphics processing units: hgpu.org

Performance of a GPU-based Direct Summation Algorithm for Computation of Small Angle Scattering Profile

Konstantin Berlin, Nail A. Gumerov, Ramani Duraiswami, David Fushman

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Tags: Algorithms, Biology, Biomolecules, Fast multipole method, Macromolecule, nVidia, nVidia GeForce GT 330 M, nVidia GeForce GTX 295, OpenCL, RNA

June 12, 2013 by hgpu

GPU Multiple Sequence Alignment Fourier-Space Cross-Correlation Alignment

Matthias Alexander Lee

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Tags: Bioinformatics, Biology, Computational Complexity, CUDA, nVidia, Package, Python, RNA, Sequence alignment, Signal processing

May 31, 2013 by hgpu

Improved Performance of CaFE and IRIS Model Fitting Using CUDA

Dylan Jackson

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Tags: Biology, Biomolecules, CUDA, nVidia, nVidia GeForce GTX 680, Sensing, Thesis

May 31, 2013 by hgpu

Rapid Computation of Sodium Bioscales Using GPU-Accelerated Image Reconstruction

Ian C. Atkinson, Geng Liu, Nady Obeid, Keith R. Thulborn, Wen-mei Hwu

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Tags: Algorithms, Biology, CUDA, FFT, Image reconstruction, Magnetic resonance imaging, MRI, nVidia, Tesla C2050

May 27, 2013 by hgpu

GPU-accelerated protein family identification for metagenomics

Changjun Wu, Ananth Kalyanaraman

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Tags: Biology, Clustering, CUDA, Graph theory, nVidia, Tesla K20

May 25, 2013 by hgpu

A Distributed CPU-GPU Framework for Pairwise Alignments on Large-Scale Sequence Datasets

Da Li, Kittisak Sajjapongse, Huan Truong, Gavin Conant, Michela Becchi

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Tags: Bioinformatics, Biology, Computational biology, CUDA, GPU cluster, Heterogeneous systems, MPI, nVidia, nVidia Quadro FX 2000, Sequence alignment, Tesla K20

May 11, 2013 by hgpu

The GPU-based High-performance Pattern-matching Algorithm for Intrusion Detection

Dongliang Xu, Hongli Zhang, Yujian Fan

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Tags: Biology, Computer science, CUDA, Information Retrieval, nVidia, nVidia GeForce 9800 GTS, nVidia GeForce GTX 570, Security, String matching

May 11, 2013 by hgpu

Simulation of Biological Tissue using Mass-Spring-Damper Models

Emil Eriksson

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Tags: ATI, ATI Radeon HD 7970, Biology, OpenCL, Surgical simulation, Thesis, Visualization

May 6, 2013 by hgpu

GPU-based Steady-State Solution of the Chemical Master Equation

Marco Maggioni, Tanya Berger-Wolf, Jie Liang

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Tags: Biology, CUDA, Macromolecule, nVidia, nVidia GeForce GTX 580, Probability, Sparse matrix

May 1, 2013 by hgpu

SW# – GPU enabled exact alignments on genome scale

Matija Korpar, Mile Sikic

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Tags: Bioinformatics, Biology, Computer science, CUDA, nVidia, nVidia GeForce GTX 560, nVidia GeForce GTX 570, nVidia GeForce GTX 690, Package, Sequence alignment, Smith-Waterman algorithm

April 23, 2013 by hgpu

GPU-SD and DPD Parallelization for Gromacs tools for molecular dynamics simulations

Nicolae Goga, Siewert Marrink, Ruxandra Cioromela, Florica Moldoveanu

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Tags: Algorithms, Bioinformatics, Biology, Chemistry, CUDA, Molecular dynamics, nVidia, nVidia GeForce 9600 GT

April 21, 2013 by hgpu

CUDASW++ 3.0: accelerating Smith-Waterman protein database search by coupling CPU and GPU SIMD instructions

Yongchao Liu, Adrianto Wirawan, Bertil Schmidt

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Tags: Bioinformatics, Biology, CUDA, nVidia, nVidia GeForce GTX 680, nVidia GeForce GTX 690, Package, PTX, Sequence alignment, Smith-Waterman algorithm

April 10, 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

Performance of a GPU-based Direct Summation Algorithm for Computation of Small Angle Scattering Profile

GPU Multiple Sequence Alignment Fourier-Space Cross-Correlation Alignment

Improved Performance of CaFE and IRIS Model Fitting Using CUDA

Rapid Computation of Sodium Bioscales Using GPU-Accelerated Image Reconstruction

GPU-accelerated protein family identification for metagenomics

A Distributed CPU-GPU Framework for Pairwise Alignments on Large-Scale Sequence Datasets

The GPU-based High-performance Pattern-matching Algorithm for Intrusion Detection

Simulation of Biological Tissue using Mass-Spring-Damper Models

GPU-based Steady-State Solution of the Chemical Master Equation

SW# – GPU enabled exact alignments on genome scale

GPU-SD and DPD Parallelization for Gromacs tools for molecular dynamics simulations

CUDASW++ 3.0: accelerating Smith-Waterman protein database search by coupling CPU and GPU SIMD instructions

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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