high performance computing on graphics processing units: hgpu.org

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Development and evaluation of a GPU-optimized N-body term for the simulation of biomolecules

Timo Strunk, Moritz Wolf, Wolfgang Wenzel

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Tags: ATI, ATI Radeon HD 5870, Benchmarking, Biology, Biomolecules, Monte Carlo simulation, N-body simulation, nVidia, nVidia GeForce GTX 285, OpenCL, Optimization

October 30, 2011 by hgpu

Parallel Computing the Longest Common Subsequence (LCS) on GPUs: Efficiency and Language Suitability

Amine Dhraief, Raik Issaoui, Abdelfettah Belghith

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Tags: Algorithms, Bioinformatics, Biology, CUDA, nVidia, nVidia GeForce GT 430, OpenCL, Sequence alignment

October 28, 2011 by hgpu

Flexible neuronal network simulation framework using code generation for NVidia CUDA

Thomas Nowotny

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Tags: Bioinformatics, Biology, CUDA, Neural networks, Neuroscience, nVidia, nVidia Quadro FX 5800, Poster

October 26, 2011 by hgpu

BEAGLE: an Application Programming Interface and High-Performance Computing Library for Statistical Phylogenetics

Daniel L. Ayres, Aaron Darling, Derrick J. Zwickl, Peter Beerli, Mark T. Holder, Paul O. Lewis, John P. Huelsenbeck, Fredrik Ronquist, David L. Swofford, Michael P. Cummings, Andrew Rambaut, Marc A. Suchard

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Tags: Bayesian, Bioinformatics, Biology, CUDA, Genetics, nVidia, nVidia GeForce GTX 580

October 25, 2011 by hgpu

An Evolutionary Optimization Strategy Using Graphics Processing Units to Efficiently Investigate Gene-Gene Interactions in Genetic Association Studies

Joel B. Fontanarosa, Yang Dai

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Tags: Algorithms, Biology, CUDA, Evolutionary Computations, Genetics, nVidia, nVidia GeForce GTX 470, Optimization

October 25, 2011 by hgpu

Computational Biology and Applied Bioinformatics

Heitor Silverio Lopes, Leonardo Magalhaes Cruz

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Tags: Bioinformatics, Biology, Book, Computational biology, CUDA, nVidia, Review, Sequence alignment, Spectrometry

October 23, 2011 by hgpu

Accelerating molecular docking and binding site mapping using FPGAs and GPUs

Bharat Sukhwani

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Tags: Algorithms, Biology, Biomechanics, CUDA, FPGA, Molecular modeling, nVidia, Tesla C1060, Thesis

October 22, 2011 by hgpu

DOPA: GPU-based protein alignment using database and memory access optimizations

Laiq Hasan, Marijn Kentie, Zaid Al-Ars

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Tags: Algorithms, Bioinformatics, Biology, Computational Complexity, CUDA, Databases, nVidia, nVidia GeForce GTX 275, Optimization, Package, Sequence alignment, Smith-Waterman algorithm

October 21, 2011 by hgpu

Heterogeneous Accelerated Bioinformatics-Perspectives for Cancer Research

Eric A. Stahlberg, T. Steinke, M. C. Smith, S. Chandrasekaran, B. Chapman

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Tags: Bioinformatics, Biology, CUDA, FPGA, Heterogeneous systems, Medicine, nVidia, OpenCL, Review

October 19, 2011 by hgpu

PlinkGPU: A Framework for GPU Acceleration of Whole Genome Data Analysis

Jeffrey Poznanovic

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Tags: Bioinformatics, Biology, CUDA, Genetics, nVidia, OpenCL, Tesla S1070

October 13, 2011 by hgpu

Performance improvements for iterative electron tomography reconstruction using graphics processing units (GPUs)

W.J. Palenstijna, K.J. Batenburga, J. Sijbersa

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Tags: Biology, Image reconstruction, Medicine, nVidia GeForce GTX 280, nVidia GeForce GTX 480, Tomography

October 8, 2011 by hgpu

GPGPU-assisted prediction of ion binding sites in proteins

Leonid Uroshlev, Sergei Rahmanov, Ivan Kulakovskiy, Vsevolod Makeev

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Tags: Biology, Biophysics, CUDA, Molecular modeling, nVidia

October 7, 2011 by hgpu

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

Efficient Graph Embedding at Scale: Optimizing CPU-GPU-SSD Integration

Can Large Language Models Predict Parallel Code Performance?

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high performance computing on graphics processing units: hgpu.org

Development and evaluation of a GPU-optimized N-body term for the simulation of biomolecules

Parallel Computing the Longest Common Subsequence (LCS) on GPUs: Efficiency and Language Suitability

Flexible neuronal network simulation framework using code generation for NVidia CUDA

BEAGLE: an Application Programming Interface and High-Performance Computing Library for Statistical Phylogenetics

An Evolutionary Optimization Strategy Using Graphics Processing Units to Efficiently Investigate Gene-Gene Interactions in Genetic Association Studies

Computational Biology and Applied Bioinformatics

Accelerating molecular docking and binding site mapping using FPGAs and GPUs

DOPA: GPU-based protein alignment using database and memory access optimizations

Heterogeneous Accelerated Bioinformatics-Perspectives for Cancer Research

PlinkGPU: A Framework for GPU Acceleration of Whole Genome Data Analysis

Performance improvements for iterative electron tomography reconstruction using graphics processing units (GPUs)

GPGPU-assisted prediction of ion binding sites in proteins

Recent source codes

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

XaaS containers

SYCL Container

CASS: Cuda-Amd aSSembly

Cluser of smartphones for edge computing application using TensorFlow

CFAL-bench

Efficient Graph Embedding at Scale: Optimizing CPU-GPU-SSD Integration

Can Large Language Models Predict Parallel Code Performance?

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