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Accelerating the Nussinov RNA folding algorithm with CUDA/GPU

Dar-Jen Chang, C. Kimmer, Ming Ouyang

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Tags: Biology, CUDA, Macromolecule, nVidia, Tesla C1060, Tesla C2050, Tesla C870

July 12, 2011 by hgpu

Harnessing the power of idle GPUs for acceleration of biological sequence alignment

Fumihiko Ino, Yuki Kotani, Yuma Munekawa, Kenichi Hagihara

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Tags: Bioinformatics, Biology, CUDA, nVidia, nVidia GeForce 7900 GTX, nVidia GeForce 7950 GX2, nVidia GeForce 8800 GTX, OpenGL, Sequence alignment

July 12, 2011 by hgpu

Graphics processing unit parallel accelerated solution of the discrete ordinates for photon transport in biological tissues

Kuan Peng, Xinbo Gao, Xiaochao Qu, Nunu Ren, Xueli Chen, Xiaowei He, Xiaorei Wang, Jimin Liang, Jie Tian

Tags: Biology, CUDA, Image reconstruction, nVidia, nVidia GeForce GTX 260, Optics, Tomography

July 12, 2011 by hgpu

Parallel implementation of a spiking neuronal network model of unsupervised olfactory learning on NVidia CUDA

T. Nowotny

Tags: Biology, CUDA, Neural networks, nVidia, Tesla C870

July 8, 2011 by hgpu

An Adaptive Hybrid Multiprocessor technique for bioinformatics sequence alignment

T. Bonny, M.A. Zidan, K.N. Salama

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Tags: Bioinformatics, Biology, CUDA, nVidia, nVidia Quadro FX 4800, Sequence alignment, Smith-Waterman algorithm

July 7, 2011 by hgpu

Striped Smith-Waterman speeds database searches six times over other SIMD implementations

M. Farrar

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Tags: Algorithms, Bioinformatics, Biology, Sequence alignment, Smith-Waterman algorithm

July 6, 2011 by hgpu

Six-fold speed-up of Smith-Waterman sequence database searches using parallel processing on common microprocessors

Torbjorn Rognes, Erling Seeberg

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Tags: Algorithms, Bioinformatics, Biology, Sequence alignment, Smith-Waterman algorithm

July 6, 2011 by hgpu

Graphics processing unit implementations of relative expression analysis algorithms enable dramatic computational speedup

Andrew T. Magis, John C. Earls, Youn-Hee H. Ko, James A. Eddy, Nathan D. Price

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Tags: Algorithms, Bioinformatics, Biology, CUDA, nVidia, Package

July 1, 2011 by hgpu

CAMPAIGN: An open-source Library of GPU-accelerated Data Clustering Algorithms

Kai J. Kohlhoff, Marc H. Sosnick, William T. Hsu, Vijay S. Pande, Russ B. Altman

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Tags: Bioinformatics, Biology, Clustering, CUDA, nVidia, Package

July 1, 2011 by hgpu

Accelerating Smith-Waterman Local Sequence Alignment on GPU Cluster

Thuy T. Nguyen, Duc H. Nguyen, Phong H. Pham, Ngoc M. Ta, Tan N. Duong, Hung D. Le

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Tags: Bioinformatics, Biology, CUDA, GPU cluster, MPI, nVidia, nVidia GeForce GTX 295, Sequence alignment, Smith-Waterman algorithm, Tesla C1060

June 27, 2011 by hgpu

Fast cell detection in high-throughput imagery using GPU-accelerated machine learning

David Mayerich, Jaerock Kwon, Aaron Panchal, John Keyser, Yoonsuck Choe

Tags: Biology, Image processing, Machine learning, nVidia

June 24, 2011 by hgpu

Accelerating Smith-Waterman on Heterogeneous CPU-GPU Systems

Jaideep Singh, Ipseeta Aruni

Tags: Bioinformatics, Biology, CUDA, Heterogeneous systems, nVidia, Smith-Waterman algorithm

June 24, 2011 by hgpu

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

DuoReduce: MLIR's benchmark

Hardware-Assisted Software Testing and Debugging for Heterogeneous Computing

Shamrock: Multi-GPU hydrodynamics for astrophysics

The Shamrock code: I- Smoothed Particle Hydrodynamics on GPUs

LLMPerf: GPU Performance Modeling meets Large Language Models

Hercules: A Compiler for Productive Programming of Heterogeneous Systems

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high performance computing on graphics processing units: hgpu.org

Accelerating the Nussinov RNA folding algorithm with CUDA/GPU

Harnessing the power of idle GPUs for acceleration of biological sequence alignment

Graphics processing unit parallel accelerated solution of the discrete ordinates for photon transport in biological tissues

Parallel implementation of a spiking neuronal network model of unsupervised olfactory learning on NVidia CUDA

An Adaptive Hybrid Multiprocessor technique for bioinformatics sequence alignment

Striped Smith-Waterman speeds database searches six times over other SIMD implementations

Six-fold speed-up of Smith-Waterman sequence database searches using parallel processing on common microprocessors

Graphics processing unit implementations of relative expression analysis algorithms enable dramatic computational speedup

CAMPAIGN: An open-source Library of GPU-accelerated Data Clustering Algorithms

Accelerating Smith-Waterman Local Sequence Alignment on GPU Cluster

Fast cell detection in high-throughput imagery using GPU-accelerated machine learning

Accelerating Smith-Waterman on Heterogeneous CPU-GPU Systems

Recent source codes

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

Hercules: A Compiler for Productive Programming of Heterogeneous Systems

Celerity Runtime: High-level C++ for Accelerator Clusters

wgpy: WebGL accelerated numpy-compatible array library for web browser

Microbenchmarking OpenMP target offload with Catch2

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