high performance computing on graphics processing units: hgpu.org

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Parallel Particle-Based Reaction Diffusion: A GPU Implementation

Lorenzo Dematte

Tags: Algorithms, Biochemistry, Biology, CUDA, nVidia, nVidia GeForce GT 220, nVidia GeForce GTX 260, nVidia Quadro FX 570 M

May 17, 2011 by hgpu

GPU-based triangulation of the van der Waals surface

S. Dias, A. Gomes

Tags: Biology, Chemistry, Molecular modeling, Molecular surface

May 14, 2011 by hgpu

Fast short exact repeats finding on GPU

Weidong Sun, Weiwei Wang, Zongmin Ma

Tags: Algorithms, Biology, CUDA, Genetics, nVidia, Pattern Search

May 13, 2011 by hgpu

Fast network centrality analysis using GPUs

Zhiao Shi, Bing Zhang

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Source codes

Tags: All-Pairs Distance, Bioinformatics, Biology, CUDA, nVidia, Package, Tesla C2050

May 13, 2011 by hgpu

Exact and complete short-read alignment to microbial genomes using Graphics Processing Unit programming

Jochen Blom, Tobias Jakobi, Daniel Doppmeier, Sebastian Jaenicke, Jorn Kalinowski, Jens Stoye, Alexander Goesmann

Source codes

Tags: Algorithms, Bioinformatics, Biology, CUDA, Next-Generation sequencing, nVidia, Package

May 10, 2011 by hgpu

Fast Parallel Tandem Mass Spectral Library Searching Using GPU Hardware Acceleration

Lydia A. Baumgardner, Avinash K. Shanmugam, Henry Lam, Jimmy K. Eng, Daniel B. Martin

Tags: Biology, Chemistry, CUDA, nVidia, Search, Spectrometry

May 10, 2011 by hgpu

Efficient Parallelization of the Stochastic Simulation Algorithm for Chemically Reacting Systems On the Graphics Processing Unit

Hong Li, Linda Petzold

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Tags: Biology, Chemistry, CUDA, nVidia, nVidia GeForce 8800 GTX, Stochastic simulation

May 10, 2011 by hgpu

A GPU-based architecture for real-time data assessment at synchrotron experiments

Suren Chilingaryan, Alessandro Mirone, Andrew Hammersley,Claudio Ferrero, Lukas Helfen, Andreas Kopmann, Tomy dos Santos Rolo

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Tags: Biology, Image reconstruction, Materials Science, Medicine, nVidia, nVidia GeForce GTX 280, nVidia GeForce GTX 295, nVidia GeForce GTX 480, Poster, Tomography

May 8, 2011 by hgpu

GPU Based Parallel Computing on Blast Program

Huang Lican, Hu Ya

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Tags: Bioinformatics, Biology, BLAST, Sequence alignment

May 7, 2011 by hgpu

GPU acceleration for statistical gene classification

Alfredo Benso, Stefano Di Carlo, Gianfranco Politano, Alessandro Savino

Tags: Bioinformatics, Biology, CUDA, Genetics, nVidia

May 5, 2011 by hgpu

Accelerating scientific applications using GPU’s

M. Taher

Tags: Bioinformatics, Biology, Computer science, CUDA, FFT, nVidia, Security, Sequence alignment

May 3, 2011 by hgpu

Accelerating DNA analysis applications on GPU clusters

A. Tumeo, O. Villa

Tags: Bioinformatics, Biology, GPU cluster, MPI, nVidia, Tesla C1060

April 28, 2011 by hgpu

SimSYCL: Synchronous, single-threaded, library-only SYCL implementation for debugging and verification

SimSYCL: A SYCL Implementation Targeting Development, Debugging, Simulation and Conformance

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

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

94% on CIFAR-10 in 3.29 Seconds on a Single GPU

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

See all packages

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high performance computing on graphics processing units: hgpu.org

Parallel Particle-Based Reaction Diffusion: A GPU Implementation

GPU-based triangulation of the van der Waals surface

Fast short exact repeats finding on GPU

Fast network centrality analysis using GPUs

Exact and complete short-read alignment to microbial genomes using Graphics Processing Unit programming

Fast Parallel Tandem Mass Spectral Library Searching Using GPU Hardware Acceleration

Efficient Parallelization of the Stochastic Simulation Algorithm for Chemically Reacting Systems On the Graphics Processing Unit

A GPU-based architecture for real-time data assessment at synchrotron experiments

GPU Based Parallel Computing on Blast Program

GPU acceleration for statistical gene classification

Accelerating scientific applications using GPU’s

Accelerating DNA analysis applications on GPU clusters

Recent source codes

SimSYCL: Synchronous, single-threaded, library-only SYCL implementation for debugging and verification

GPU plugin for PySCF

QArray

Celerity: High-level C++ for Accelerator Clusters

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

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

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

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