high performance computing on graphics processing units: hgpu.org

Trevor Bekolay, James Bergstra, Eric Hunsberger, Travis DeWolf, Terrence C. Stewart, Daniel Rasmussen, Xuan Choo, Aaron Russell Voelker, Chris Eliasmith

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Tags: ATI, ATI Radeon HD 7970, Biology, Neuroscience, nVidia, nVidia GeForce GTX 280, OpenCL, Package, PyOpenCL, Python

January 9, 2014 by hgpu

Multicore Computing: Algorithms, Architectures, and Applications

Sanguthevar Rajasekaran, Lance Fiondella, Mohamed Ahmed, Reda A. Ammar

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Tags: Algorithms, Biology, Book, Computer science, CUDA, Linear Algebra, nVidia, String matching, Tesla

January 6, 2014 by hgpu

HUGO: Hierarchical mUlti-reference Genome cOmpression for aligned reads

Pinghao Li, Xiaoqian Jiang, Shuang Wang, Jihoon Kim, Hongkai Xiong, Lucila Ohno-Machado

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Tags: Algorithms, Bioinformatics, Biology, Clustering, Compression, CUDA, nVidia, Package, Sequence alignment, Tesla M2090

December 27, 2013 by hgpu

Accelerating Pairwise DNA Sequence Alignment using the CUDA Compatible GPU

H. Khaled, R. El Gohary, N. L. Badr, H. M. Faheem

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Tags: Algorithms, Bioinformatics, Biology, CUDA, nVidia, nVidia GeForce GT 540 M, Sequence alignment, Smith-Waterman algorithm

December 22, 2013 by hgpu

Efficient Multi-GPU Computation of All-Pairs Shortest Paths

Hristo Djidjev, Sunil Thulasidasan, Guillaume Chapuis, Rumen Andonov, Dominique Lavenier

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Tags: Algorithms, Bioinformatics, Biology, CUDA, GPU cluster, nVidia, Tesla C2090

December 18, 2013 by hgpu

Exploiting parallel features of modern computer architectures in bioinformatics

Guillaume Chapuis

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Tags: Algorithms, Bioinformatics, Biology, CUDA, Genetics, nVidia, Path problems, Tesla C2050, Tesla C2090, Thesis

December 16, 2013 by hgpu

Neurokernel: An Open Scalable Software Framework for Emulation and Validation of Drosophila Brain Models on Multiple GPUs

Lev E. Givon, Aurel A. Lazar

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Tags: Biology, CUDA, Neuroscience, nVidia, Package, Python

November 18, 2013 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

Applications

Parallel implementation of 3D protein structure similarity searches using a GPU and the CUDA

GPU-Accelerated BWT Construction for Large Collection of Short Reads

Accelerating a Bayesian Phylogenetic Inference Application with OpenACC

Optimal Alignment of Three Sequences On A GPU

A tool for mapping Single Nucleotide Polymorphisms using Graphics Processing Units

Nengo: a Python tool for building large-scale functional brain models

Multicore Computing: Algorithms, Architectures, and Applications

HUGO: Hierarchical mUlti-reference Genome cOmpression for aligned reads

Accelerating Pairwise DNA Sequence Alignment using the CUDA Compatible GPU

Efficient Multi-GPU Computation of All-Pairs Shortest Paths

Exploiting parallel features of modern computer architectures in bioinformatics

Neurokernel: An Open Scalable Software Framework for Emulation and Validation of Drosophila Brain Models on Multiple GPUs

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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