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A Domain Specific Language for Performance Portable Molecular Dynamics Algorithms

William R. Saunders, James Grant, Eike H. Muller

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Tags: Algorithms, Biology, Chemistry, Code generation, Computer science, CUDA, Differential equations, DSL, Molecular dynamics, nVidia, Package, Partial differential equations, PDEs, Physics, Python, Tesla K20

April 15, 2017 by hgpu

Exploiting Multi-level Parallelism on a Many-core System for the Application of Hyperheuristics to a Molecular Docking Problem

Jose M. Cecilia, Jose-Matias, Cutillas-Lozano, Domingo Gimenez, Baldomero Imbernon

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Tags: Bioinformatics, Biology, Chemistry, Intel Xeon Phi, Metaheuristics, molecular docking

March 20, 2017 by hgpu

First Experiences Optimizing Smith-Waterman on Intel’s Knights Landing Processor

Enzo Rucci, Carlos Garcia, Guillermo Botella, Armando De Giusti, Marcelo Naiouf, Manuel Prieto-Matias

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Tags: Bioinformatics, Biology, Computer science, Intel Xeon Phi, Sequence alignment, Smith-Waterman algorithm

February 26, 2017 by hgpu

Analysis and implementation of a BLAST-Like algorithm for MIC architectures

Felipe Sulser Larraz

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Tags: Benchmarking, Bioinformatics, Biology, Computer science, Databases, Filtering, Intel Xeon Phi, Sequence alignment, Smith-Waterman algorithm, Thesis

February 2, 2017 by hgpu

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

Parallel Tree Traversal for Nearest Neighbor Query on the GPU

Moohyeon Nam, Jinwoong Kim, Beomseok Nam

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Tags: Algorithms, Biology, Computational biology, Computer science, CUDA, Information Retrieval, Nearest neighbour, nVidia, Tesla K40

September 5, 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

Accelerated cryo-EM structure determination with parallelisation using GPUs in relion-2

Dari Kimanius, Bjorn O Forsberg, Sjors HW Scheres, Erik Lindahl

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Tags: Biology, Cryo-EM, CUDA, Image processing, nVidia, nVidia GeForce GTX 1080, nVidia GeForce GTX 980 Ti

July 5, 2016 by hgpu

PROJECTION Algorithm for Motif Finding on GPUs

Jhoirene B. Clemente, Francis George C. Cabarle, Henry N. Adorna

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Tags: Algorithms, Biology, Computational biology, CUDA, nVidia

May 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

CATO: automatic source transformation to apply HPC frameworks with minimal user interaction

Compiler-assisted distribution of OpenMP code for improved scalability

ADIOS2.jl: a Julia interface to ADIOS2

Julia as a unifying end-to-end workflow language on the Frontier exascale system

Code generated HPC Kernels Using Llama-2-70b

Comparing Llama-2 and GPT-3 LLMs for HPC kernels generation

Scope is all you need: Transforming LLMs for HPC Code

pocl - Portable Computing Language

PoCL-R: An Open Standard Based Offloading Layer for Heterogeneous Multi-Access Edge Computing with Server Side Scalability

HPAC-Offload: Accelerating HPC Applications with Portable Approximate Computing on the GPU

openCLDispatcher

Novel insights on atomic synchronization for sort-based group-by on GPUs

CEED Benchmarks

Performant low-order matrix-free finite element kernels on GPU architectures

Sieve: Stratified GPU-Compute Workload Sampling

EngineCL: Usability and Performance in Heterogeneous Computing

Mashing load balancing algorithm to boost hybrid kernels in molecular dynamics simulations

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high performance computing on graphics processing units: hgpu.org

Applications

A Domain Specific Language for Performance Portable Molecular Dynamics Algorithms

Exploiting Multi-level Parallelism on a Many-core System for the Application of Hyperheuristics to a Molecular Docking Problem

First Experiences Optimizing Smith-Waterman on Intel’s Knights Landing Processor

Analysis and implementation of a BLAST-Like algorithm for MIC architectures

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

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

Parallel Tree Traversal for Nearest Neighbor Query on the GPU

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

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

Accelerated cryo-EM structure determination with parallelisation using GPUs in relion-2

PROJECTION Algorithm for Motif Finding on GPUs

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

Recent source codes

CATO: automatic source transformation to apply HPC frameworks with minimal user interaction

ADIOS2.jl: a Julia interface to ADIOS2

Code generated HPC Kernels Using Llama-2-70b

Scope is all you need: Transforming LLMs for HPC Code

pocl - Portable Computing Language

HPAC-Offload: Accelerating HPC Applications with Portable Approximate Computing on the GPU

openCLDispatcher

CEED Benchmarks

Sieve: Stratified GPU-Compute Workload Sampling

EngineCL: Usability and Performance in Heterogeneous Computing

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