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Using efficient parallelization in Graphic Processing Units to parameterize stochastic fire propagation models

Monica Denham, Karina Laneri, Juan Manuel Morales

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Tags: Biology, CUDA, Earth and Space Sciences, nVidia, nVidia GeForce GTX 780, nVidia GeForce GTX Titan, Package, Tesla C2070, Tesla K40

January 16, 2017 by hgpu

BioEM: GPU-accelerated computing of Bayesian inference of electron microscopy images

Pilar Cossio, David Rohr, Fabio Baruffa, Markus Rampp, Volker Lindenstruth, Gerhard Hummer

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Tags: Bayesian, Biology, Biomolecules, CUDA, Electron microscopy, Heterogeneous systems, Medicine, Microscopy, MPI, nVidia, nVidia GeForce GTX Titan, OpenMP, Package, Tesla K20, Tomography

October 8, 2016 by hgpu

Drug Drug Interaction Extraction from Biomedical Literature Using Syntax Convolutional Neural Network

Zhehuan Zhao, Zhihao Yang, Ling Luo, Hongfei Lin, Jian Wang

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Tags: Bioinformatics, Biology, CUDA, Deep learning, Neural networks, NLP, nVidia, Package, Python, Tesla K20, Text mining

August 1, 2016 by hgpu

Gerbil: A Fast and Memory-Efficient k-mer Counter with GPU-Support

Marius Erbert, Steffen Rechner, Matthias Muller-Hannemann

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Tags: Bioinformatics, Biology, Computer science, CUDA, nVidia, nVidia GeForce GTX 970, nVidia GeForce GTX Titan, Package

July 26, 2016 by hgpu

sPEGG: high throughput eco-evolutionary simulations on commodity graphics processors

Kenichi W. Okamoto, Priyanga Amarasekare

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Tags: Biology, CUDA, Genetics, nVidia, nVidia GeForce GTX 690, Package

April 3, 2016 by hgpu

GeNN: a code generation framework for accelerated brain simulations

Esin Yavuz, James Turner, Thomas Nowotny

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Tags: Biology, Code generation, CUDA, Neural networks, Neuroscience, Numerical simulation, nVidia, nVidia Quadro K 2000 M, Package, Tesla C2070, Tesla K40

January 29, 2016 by hgpu

Genetically Improved BarraCUDA

W. B. Langdon, Brian Yee Hong Lam

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Tags: Algorithms, Benchmarking, Biology, CUDA, Genomics, nVidia, nVidia GeForce GT 730, Package, Tesla K20, Tesla K40, Tesla K80

June 1, 2015 by hgpu

Flexible, Fast and Accurate Sequence Alignment Profiling on GPGPU with PaSWAS

Sven Warris, Feyruz Yalcin, Katherine J. L. Jackson, Jan Peter Nap

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Tags: Bioinformatics, Biology, CUDA, nVidia, nVidia GeForce GTX 285, nVidia GeForce GTX 295, Package, Sequence alignment, Smith-Waterman algorithm, Tesla C1060

April 7, 2015 by hgpu

Real-time multi-view deconvolution

Benjamin Schmid, Jan Huisken

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Tags: Biology, CUDA, Microscopy, nVidia, nVidia GeForce GTX Titan, Package

March 30, 2015 by hgpu

Arioc: high-throughput read alignment with GPU-accelerated exploration of the seed-and-extend search space

Richard Wilton, Tamas Budavari, Ben Langmead, Sarah J. Wheelan, Steven L. Salzberg, Alexander S. Szalay

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Tags: Bioinformatics, Biology, CUDA, nVidia, Package, Sequence alignment, Tesla K20

March 28, 2015 by hgpu

Parallelization, Scalability, and Reproducibility in Next-Generation Sequencing Analysis

Johannes Koster

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Tags: Algorithms, Bayesian, Bioinformatics, Biology, Filtering, Next-Generation sequencing, nVidia, nVidia GeForce GTX 580, nVidia GeForce GTX 780, OpenCL, Package, Thesis

March 23, 2015 by hgpu

Implementation of Smith-Waterman algorithm in OpenCL for GPUs

Dzmitry Razmyslovich, Guillermo Marcus, Markus Gipp, Marc Zapatka, Andreas Szillus

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Tags: Bioinformatics, Biology, nVidia, nVidia GeForce GTX 480, OpenCL, Package, Sequence alignment, Smith-Waterman algorithm

February 27, 2015 by azhar ali

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

Packages

Using efficient parallelization in Graphic Processing Units to parameterize stochastic fire propagation models

BioEM: GPU-accelerated computing of Bayesian inference of electron microscopy images

Drug Drug Interaction Extraction from Biomedical Literature Using Syntax Convolutional Neural Network

Gerbil: A Fast and Memory-Efficient k-mer Counter with GPU-Support

sPEGG: high throughput eco-evolutionary simulations on commodity graphics processors

GeNN: a code generation framework for accelerated brain simulations

Genetically Improved BarraCUDA

Flexible, Fast and Accurate Sequence Alignment Profiling on GPGPU with PaSWAS

Real-time multi-view deconvolution

Arioc: high-throughput read alignment with GPU-accelerated exploration of the seed-and-extend search space

Parallelization, Scalability, and Reproducibility in Next-Generation Sequencing Analysis

Implementation of Smith-Waterman algorithm in OpenCL for GPUs

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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