high performance computing on graphics processing units: hgpu.org

Applications

Graphic Processing Unit Simulation of Axon Growth and Guidance through Cue Diffusion on Massively Parallel Processors

Ana M. Mihut, Graham Morgan, Marcus Kaiser

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Tags: Biology, CUDA, GLSL, Neuroscience, nVidia, nVidia GeForce GTX 460, nVidia Quadro 600, OpenGL, Programming techniques, Tesla K20

May 24, 2014 by hgpu

cuBLASTP: Fine-Grained Parallelization of Protein Sequence Search on a GPU

Jing Zhang, Hao Wang, Heshan Lin, Wu-chun Feng

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Tags: Bioinformatics, Biology, CUDA, Next-Generation sequencing, nVidia, Sequence alignment, Tesla K20

May 23, 2014 by hgpu

A performance/cost evaluation for a GPU-based drug discovery application on volunteer computing

Gines David Guerrero Hernandez, Baldomero Imbernon, Horacio Perez-Sanchez, Francisco Sanz, Jose M. Garcia, Jose M. Cecilia

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Tags: Bioinformatics, Biology, CUDA, Medicine, nVidia, nVidia GeForce 7300 GT, nVidia GeForce GTX 465, nVidia GeForce GTX 480, nVidia GeForce GTX 590, Tesla C2070, Tesla K20

May 21, 2014 by hgpu

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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Source codes

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

gpu_tracker: Context manager and CLI that tracks the computational-resource-usage of a code block or shell command, particularly the GPU usage

gpu_tracker: Python package for tracking and profiling GPU utilization in both desktop and high-performance computing environments

LOOPer: a polyhedral compiler for expressing fast and portable data parallel algorithms

LOOPer: A Learned Automatic Code Optimizer For Polyhedral Compilers

OpenMC Monte Carlo Code

Performance Portable Monte Carlo Particle Transport on Intel, NVIDIA, and AMD GPUs

Polygeist: C/C++ frontend for MLIR

Retargeting and Respecializing GPU Workloads for Performance Portability

Parallel Gaussian process with kernel approximation in CUDA

Optical flow algorithms for SYCL

SYCL in the edge: performance and energy evaluation for heterogeneous acceleration

OpenMP5-Offload-OpenMC-Intel-PVC

Distributed OpenMP Offloading of OpenMC on Intel GPU MAX Accelerators

See all packages

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high performance computing on graphics processing units: hgpu.org

Applications

Graphic Processing Unit Simulation of Axon Growth and Guidance through Cue Diffusion on Massively Parallel Processors

cuBLASTP: Fine-Grained Parallelization of Protein Sequence Search on a GPU

A performance/cost evaluation for a GPU-based drug discovery application on volunteer computing

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

Recent source codes

QArray

Celerity: High-level C++ for Accelerator Clusters

CIFAR-10 Airbench: 94% on CIFAR-10 in 3.29 second

gpu_tracker: Context manager and CLI that tracks the computational-resource-usage of a code block or shell command, particularly the GPU usage

LOOPer: a polyhedral compiler for expressing fast and portable data parallel algorithms

OpenMC Monte Carlo Code

Polygeist: C/C++ frontend for MLIR

Parallel Gaussian process with kernel approximation in CUDA

Optical flow algorithms for SYCL

OpenMP5-Offload-OpenMC-Intel-PVC

Most viewed papers (last 30 days)