high performance computing on graphics processing units: hgpu.org

Applications

A combined MPI-CUDA parallel solution of linear and nonlinear Poisson-Boltzmann equation

Jose Colmenares, Antonella Galizia, Jesus Ortiz, Andrea Clematis, Walter Rocchia

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Tags: Algorithms, Biology, Boltzmann equation, CUDA, Electrostatic potential, Electrostatics, Heterogeneous systems, Macromolecule, MPI, nVidia, nVidia GeForce GTX 580, Poisson Boltzmann, Tesla C2075

May 21, 2014 by hgpu

Entropy-based High Performance Computation of Boolean SNP-SNP Interactions Using GPUs

Carlos Riveros, Manuel Ujaldon, Moscato Pablo

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Tags: Bioinformatics, Biology, CUDA, nVidia, nVidia GeForce GTX 480, Tesla C1060, Tesla C2050

May 12, 2014 by hgpu

Accelerating the scoring module of mass spectrometry-based peptide identification using GPUs

You Li, Hao Chi, Leihao Xia, Xiaowen Chu

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Tags: Bioinformatics, Biology, CUDA, GPU cluster, nVidia, nVidia GeForce GTX 580, Spectrometry

May 12, 2014 by hgpu

GAMUT: GPU accelerated microRNA analysis to uncover target genes through CUDA-miRanda

Shuang Wang, Jihoon Kim, Xiaoqian Jiang, Stefan F Brunner, Lucila Ohno-Machado

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Tags: Bioinformatics, Biology, CUDA, nVidia, Package, RNA, Smith-Waterman algorithm, Tesla M2090

May 10, 2014 by hgpu

Understanding Protein Dynamics with L1-Regularized Reversible Hidden Markov Models

Robert T. McGibbon, Bharath Ramsundar, Mohammad M. Sultan, Gert Kiss, Vijay S. Pande

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Tags: Algorithms, Biology, Biophysics, CUDA, Distributed computing, Machine learning, Molecular dynamics, nVidia, nVidia GeForce GTX Titan

May 9, 2014 by hgpu

Exercising high-level parallel programming on streams: a systems biology use case

Marco Aldinucci, Maurizio Drocco, Guilherme Peretti Pezzi, Claudia Misale, Fabio Tordini, Massimo Torquati

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Tags: Bioinformatics, Biology, Cloud, CUDA, Monte Carlo simulation, nVidia, Tesla K40

April 30, 2014 by hgpu

Neural Decoding using a Parallel Sequential Monte Carlo method on Point Processes with Ensemble Effect

Kai Xu, Yiwen Wang, Fang Wang, Yuxi Liao, Qiaosheng Zhang, Hongbao Li, Xiaoxiang Zheng

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Tags: Algorithms, Biology, CUDA, nVidia, nVidia GeForce GT 730 M

April 25, 2014 by hgpu

Local Alignment Tool Based on Hadoop Framework and GPU Architecture

Che-Lun Hun, Guan-Jie Hua

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Tags: Biology, Cloud, CUDA, Hadoop, MapReduce, nVidia, nVidia GeForce GTS 480, Sequence alignment

April 19, 2014 by hgpu

Bayesian Neural Networks for Genetic Association Studies of Complex Disease

Andrew L. Beam, Alison Motsinger-Reif, Jon Doyle

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Tags: Bayesian, Biology, CUDA, Machine learning, Neural networks, nVidia, Package, Python

April 17, 2014 by hgpu

New Efficient Method To Solve Longest Overlap Region Problem For Noncoding DNA Sequence

Yukun Zhong, ZhiWei He, XianHong Wang, Liao Gang

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Tags: Algorithms, Bioinformatics, Biology, CUDA, nVidia, nVidia GeForce GT 610 M

April 16, 2014 by hgpu

A Way For Accelerating The DNA Sequence Reconstruction Problem By CUDA

Yukun Zhong, ZhiWei He, XianHong Wang, XiongBin Cao

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Tags: Algorithms, Bioinformatics, Biology, CUDA, nVidia, nVidia GeForce GT 610 M, Sorting

April 16, 2014 by hgpu

An efficient GPU acceptance-rejection algorithm for the selection of the next reaction to occur for Stochastic Simulation Algorithms

Neri Mickael, Denis Mestivier

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Tags: Algorithms, Biology, Computer science, CUDA, nVidia, Optimization, Stochastic simulation, Tesla K10, Tesla K20, Tesla M2075, Tesla M2090

April 4, 2014 by hgpu

Awesome LLM-Driven Kernel Generation

Towards Automated Kernel Generation in the Era of LLMs

PhysProver: Advancing Automatic Theorem Proving for Physics

ParaCodex: A Profiling-Guided Autonomous Coding Agent for Reliable Parallel Code Generation and Translation

SeedFold: Scaling Biomolecular Structure Prediction

Tilus: A Tile-Level GPU Kernel Programming Language

Tilus: A Tile-Level GPGPU Programming Language for Low-Precision Computation

Memory-Efficient Acceleration of Block Low-Rank Foundation Models on Resource Constrained GPUs

BoltzGen:Toward Universal Binder Design

CUDA-L2: Surpassing cuBLAS Performance for Matrix Multiplication through Reinforcement Learning

cuPilot: A Strategy-Coordinated Multi-agent Framework for CUDA Kernel Evolution

MATLAB Tensor Core models

Accurate Models of NVIDIA Tensor Cores

See all packages

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high performance computing on graphics processing units: hgpu.org

Applications

A combined MPI-CUDA parallel solution of linear and nonlinear Poisson-Boltzmann equation

Entropy-based High Performance Computation of Boolean SNP-SNP Interactions Using GPUs

Accelerating the scoring module of mass spectrometry-based peptide identification using GPUs

GAMUT: GPU accelerated microRNA analysis to uncover target genes through CUDA-miRanda

Understanding Protein Dynamics with L1-Regularized Reversible Hidden Markov Models

Neural Decoding using a Parallel Sequential Monte Carlo method on Point Processes with Ensemble Effect

Bayesian Neural Networks for Genetic Association Studies of Complex Disease

New Efficient Method To Solve Longest Overlap Region Problem For Noncoding DNA Sequence

A Way For Accelerating The DNA Sequence Reconstruction Problem By CUDA

An efficient GPU acceptance-rejection algorithm for the selection of the next reaction to occur for Stochastic Simulation Algorithms

Recent source codes

Awesome LLM-Driven Kernel Generation

PhysProver: Advancing Automatic Theorem Proving for Physics

ParaCodex: A Profiling-Guided Autonomous Coding Agent for Reliable Parallel Code Generation and Translation

SeedFold: Scaling Biomolecular Structure Prediction

Tilus: A Tile-Level GPU Kernel Programming Language

Memory-Efficient Acceleration of Block Low-Rank Foundation Models on Resource Constrained GPUs

BoltzGen:Toward Universal Binder Design

CUDA-L2: Surpassing cuBLAS Performance for Matrix Multiplication through Reinforcement Learning

cuPilot: A Strategy-Coordinated Multi-agent Framework for CUDA Kernel Evolution

MATLAB Tensor Core models

Most viewed papers (last 30 days)