high performance computing on graphics processing units: hgpu.org

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CuHMMer: A load-balanced CPU-GPU cooperative bioinformatics application

Ping Yao, Hong An, Mu Xu, Gu Liu, Xiaoqiang Li, Yaobin Wang, Wenting Han

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Tags: Bioinformatics, Biology, CUDA, nVidia, nVidia GeForce 8800 GTX, Pattern Search

March 29, 2011 by hgpu

A GPU Implementation of Fast Parallel Markov Clustering in Bioinformatics Using EllPACK-R Sparse Data Format

A. Bustamam, K. Burrage, N.A. Hamilton

Tags: Bioinformatics, Biology, CUDA, nVidia

March 25, 2011 by hgpu

GPU implemention of fast Gabor filters

Xin Xin Wang, E. Shi Bertram

Tags: Biology, Filtering, Image processing, nVidia, nVidia GeForce 9800 GTX

March 21, 2011 by hgpu

MrBayes on a Graphics Processing Unit

Jianfu Zhou, Xiaoguang Liu, Douglas S. Stones, Qiang Xie, Gang Wang

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Tags: Bayesian, Bioinformatics, Biology, CUDA, nVidia, nVidia GeForce GTX 480, Package

March 18, 2011 by hgpu

GBOOST : A GPU-based tool for detecting gene-gene interactions in genome-wide case control studies

Ling Sing S. Yung, Can Yang, Xiang Wan, Weichuan Yu

Source codes

Tags: Bioinformatics, Biology, Genetics, nVidia, nVidia GeForce GTX 285, Package

March 12, 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

Application-guided tool development for architecturally diverse computation

Roger D. Chamberlain, Jeremy Buhler, Mark A. Franklin, James H. Buckley

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Tags: Algorithms, Astrophysics, Biology, Computer science, CUDA, Finance, FPGA, Heterogeneous systems, Monte Carlo simulation, nVidia, nVidia GeForce GTX 260, Search, Security

March 7, 2011 by hgpu

A tile-based parallel Viterbi algorithm for biological sequence alignment on GPU with CUDA

Zhihui Du, Zhaoming Yin, David A. Bader

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Tags: Bioinformatics, Biology, CUDA, nVidia, nVidia GeForce 9800 GTX, Sequence alignment

March 7, 2011 by hgpu

Efficient parallel algorithms for maximum-density segment problem

Xue Wang, Fasheng Qiu, S.K. Prasad, Guantao Chen

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Tags: Bioinformatics, Biology, CUDA, nVidia, nVidia GeForce GTX 280, Presentation, Sequence alignment

March 7, 2011 by hgpu

FluoroSim: A Visual Problem-Solving Environment for Fluorescence Microscopy

Cory W. Quammen, Alvin C. Richardson, Julian Haase, Benjamin D. Harrison, Russell M. Taylor, Kerry S. Bloom

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Tags: Algorithms, Biology, CUDA, Image generation, Microscopy, nVidia, nVidia GeForce 8800 GTX, OpenGL, Package

March 2, 2011 by hgpu

STOCHSIMGPU: Parallel stochastic simulation for the Systems Biology Toolbox 2 for MATLAB

Guido Klingbeil, Radek Erban, Mike Giles, Philip K. Maini

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Tags: Bioinformatics, Biology, CUDA, nVidia, nVidia GeForce 8800, Package, Stochastic simulation

February 28, 2011 by hgpu

CUDAlign: using GPU to accelerate the comparison of megabase genomic sequences

Edans Flavius O. Sandes, Alba Cristina M.A. de Melo

Tags: Bioinformatics, Biology, CUDA, nVidia, nVidia GeForce GTX 280, Sequence alignment, Smith-Waterman algorithm

February 27, 2011 by hgpu

Efficient GPU Implementation of Multi-Precision Integer Division

ParEval: A Parallel Code Evaluation Benchmark

ParEval-Repo: A Benchmark Suite for Evaluating LLMs with Repository-level HPC Translation Tasks

FlashSparse: Minimizing Computation Redundancy for Fast Sparse Matrix Multiplications on Tensor Cores

Libra: Synergizing CUDA and Tensor Cores for High-Performance Sparse Matrix Multiplication

exa-AMD: Exascale Accelerated Materials Discovery

Accelerated discovery and design of Fe-Co-Zr magnets with tunable magnetic anisotropy through machine learning and parallel computing

WiLLM: An Open Wireless LLM Communication System

Vcc: the Vulkan Clang Compiler

No More Shading Languages: Compiling C++ to Vulkan Shaders

hpcbench: A set of benchmarking utilities for biomolecular simulation tools

Engineering Supercomputing Platforms for Biomolecular Applications

HPCTransCompile: An AI Compiler Generated Dataset for High-Performance CUDA Transpilation and LLM Preliminary Exploration

chemtrain: Training Molecular Dynamics Potentials in JAX

chemtrain-deploy: A parallel and scalable framework for machine learning potentials in million-atom MD simulations

microSYCL: SYCL micro-benchmarks repository

Exploring SYCL as a Portability Layer for High-Performance Computing on CPUs

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high performance computing on graphics processing units: hgpu.org

Applications

CuHMMer: A load-balanced CPU-GPU cooperative bioinformatics application

A GPU Implementation of Fast Parallel Markov Clustering in Bioinformatics Using EllPACK-R Sparse Data Format

GPU implemention of fast Gabor filters

MrBayes on a Graphics Processing Unit

GBOOST : A GPU-based tool for detecting gene-gene interactions in genome-wide case control studies

GPU-RMAP: Accelerating Short-Read Mapping on Graphics Processors

Application-guided tool development for architecturally diverse computation

A tile-based parallel Viterbi algorithm for biological sequence alignment on GPU with CUDA

Efficient parallel algorithms for maximum-density segment problem

FluoroSim: A Visual Problem-Solving Environment for Fluorescence Microscopy

STOCHSIMGPU: Parallel stochastic simulation for the Systems Biology Toolbox 2 for MATLAB

CUDAlign: using GPU to accelerate the comparison of megabase genomic sequences

Recent source codes

Efficient GPU Implementation of Multi-Precision Integer Division

ParEval: A Parallel Code Evaluation Benchmark

FlashSparse: Minimizing Computation Redundancy for Fast Sparse Matrix Multiplications on Tensor Cores

exa-AMD: Exascale Accelerated Materials Discovery

WiLLM: An Open Wireless LLM Communication System

Vcc: the Vulkan Clang Compiler

hpcbench: A set of benchmarking utilities for biomolecular simulation tools

HPCTransCompile: An AI Compiler Generated Dataset for High-Performance CUDA Transpilation and LLM Preliminary Exploration

chemtrain: Training Molecular Dynamics Potentials in JAX

microSYCL: SYCL micro-benchmarks repository

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