high performance computing on graphics processing units: hgpu.org

hgpu.org » Biology

A parameterisable and scalable Smith-Waterman algorithm implementation on CUDA-compatible GPUs

Cheng Ling, Khaled Benkrid, Tsuyoshi Hamada

View

Tags: Bioinformatics, Biology, Computational biology, CUDA, nVidia, nVidia GeForce 8800 GTX, Sequence alignment, Smith-Waterman algorithm

January 4, 2011 by hgpu

Speeding up subset seed algorithm for intensive protein sequence comparison

Van Hoa Nguyen, Dominique Lavenier

View

Download (PDF)

Tags: Bioinformatics, Biology, CUDA, nVidia, nVidia GeForce 8800 GTX, Sequence alignment

January 4, 2011 by hgpu

Towards Large-Scale Molecular Dynamics Simulations on Graphics Processors

Joseph E. Davis, Adnan Ozsoy, Sandeep Patel, Michela Taufer

View

Download (PDF)

Tags: Biology, Chemistry, CUDA, Molecular dynamics, nVidia, nVidia GeForce 9800 GX2, nVidia GeForce GTX 280, nVidia Quadro FX 5600

January 3, 2011 by hgpu

Analysis of a Computational Biology Simulation Technique on Emerging Processing Architectures

Jeremy S. Meredith, Sadaf R. Alam, Jeffrey S. Vetter

View

Download (PDF)

Tags: Biology, Cell processor, Cg, Computational biology, Molecular dynamics, nVidia, nVidia GeForce 7900 GTX

January 2, 2011 by hgpu

Population Parallel GP on the G80 GPU

Denis Robilliard, Virginie Marion-Poty, Cyril Fonlupt

View

Download (PDF)

Source codes

Tags: Bioinformatics, Biology, CUDA, Genetics, nVidia, nVidia GeForce 8800 GTX, Package

December 29, 2010 by hgpu

A SIMD Interpreter for Genetic Programming on GPU Graphics Cards

William B. Langdon, Wolfgang Banzhaf

View

Download (PDF)

Tags: Bioinformatics, Biology, DirectX, Genetics, nVidia, nVidia GeForce 8800 GTX, OpenGL

December 29, 2010 by hgpu

Design and implementation of the Smith-Waterman algorithm on the CUDA-compatible GPU

Yuma Munekawa, Fumihiko Ino, Kenichi Hagihara

View

Download (PDF)

Tags: Bioinformatics, Biology, CUDA, nVidia, nVidia GeForce 8800 GTX, Smith-Waterman algorithm

December 22, 2010 by hgpu

Long time-scale simulations of in vivo diffusion using GPU hardware

Elijah Roberts, John E. Stone, Leonardo Sepulveda, Wen-Mei W. Hwu, Zaida Luthey-Schulten

View

Download (PDF)

Tags: Bioinformatics, Biology, CUDA, Distributed computing, nVidia, nVidia GeForce GTX 280, nVidia Quadro FX 5600

December 18, 2010 by hgpu

A New Parallel Method of Smith-Waterman Algorithm on a Heterogeneous Platform

Bo Chen, Yun Xu, Jiaoyun Yang, Haitao Jiang

View

Download (PDF)

Tags: Biology, CUDA, nVidia, nVidia GeForce 9800 GT, Sequence alignment, Smith-Waterman algorithm

December 17, 2010 by hgpu

GPU Accelerated RNA Folding Algorithm

Guillaume Rizk, Dominique Lavenier

View

Download (PDF)

Tags: Algorithms, Bioinformatics, Biology, CUDA, nVidia, nVidia GeForce GTX 280, Tesla C870

December 17, 2010 by hgpu

Integrative multicellular biological modeling: a case study of 3D epidermal development using GPU algorithms

Scott Christley, Briana Lee, Xing Dai, Qing Nie

View

Download (PDF)

Tags: Biology, CUDA, nVidia, nVidia GeForce GTX 285

December 15, 2010 by hgpu

Scalable and Interactive Segmentation and Visualization of Neural Processes in EM Datasets

Won-ki Jeong, Johanna Beyer, Student Member, Markus Hadwiger, Amelio Vazquez, Student Member, Hanspeter Pfister, Senior Member, Ross T. Whitaker

View

Download (PDF)

Tags: Biology, Electron microscopy, Neuroscience, nVidia, nVidia Quadro FX 5800, Rendering, Tesla C1060

December 15, 2010 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

* * *

high performance computing on graphics processing units: hgpu.org

A parameterisable and scalable Smith-Waterman algorithm implementation on CUDA-compatible GPUs

Speeding up subset seed algorithm for intensive protein sequence comparison

Towards Large-Scale Molecular Dynamics Simulations on Graphics Processors

Analysis of a Computational Biology Simulation Technique on Emerging Processing Architectures

Population Parallel GP on the G80 GPU

A SIMD Interpreter for Genetic Programming on GPU Graphics Cards

Design and implementation of the Smith-Waterman algorithm on the CUDA-compatible GPU

Long time-scale simulations of in vivo diffusion using GPU hardware

A New Parallel Method of Smith-Waterman Algorithm on a Heterogeneous Platform

GPU Accelerated RNA Folding Algorithm

Integrative multicellular biological modeling: a case study of 3D epidermal development using GPU algorithms

Scalable and Interactive Segmentation and Visualization of Neural Processes in EM Datasets

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

Most viewed papers (last 30 days)