high performance computing on graphics processing units: hgpu.org

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Parallel implementation of a spiking neuronal network model of unsupervised olfactory learning on NVidia CUDA

T. Nowotny

Tags: Biology, CUDA, Neural networks, nVidia, Tesla C870

July 8, 2011 by hgpu

An Adaptive Hybrid Multiprocessor technique for bioinformatics sequence alignment

T. Bonny, M.A. Zidan, K.N. Salama

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Tags: Bioinformatics, Biology, CUDA, nVidia, nVidia Quadro FX 4800, Sequence alignment, Smith-Waterman algorithm

July 7, 2011 by hgpu

Striped Smith-Waterman speeds database searches six times over other SIMD implementations

M. Farrar

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Tags: Algorithms, Bioinformatics, Biology, Sequence alignment, Smith-Waterman algorithm

July 6, 2011 by hgpu

Six-fold speed-up of Smith-Waterman sequence database searches using parallel processing on common microprocessors

Torbjorn Rognes, Erling Seeberg

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Tags: Algorithms, Bioinformatics, Biology, Sequence alignment, Smith-Waterman algorithm

July 6, 2011 by hgpu

Graphics processing unit implementations of relative expression analysis algorithms enable dramatic computational speedup

Andrew T. Magis, John C. Earls, Youn-Hee H. Ko, James A. Eddy, Nathan D. Price

Source codes

Tags: Algorithms, Bioinformatics, Biology, CUDA, nVidia, Package

July 1, 2011 by hgpu

CAMPAIGN: An open-source Library of GPU-accelerated Data Clustering Algorithms

Kai J. Kohlhoff, Marc H. Sosnick, William T. Hsu, Vijay S. Pande, Russ B. Altman

Source codes

Tags: Bioinformatics, Biology, Clustering, CUDA, nVidia, Package

July 1, 2011 by hgpu

Accelerating Smith-Waterman Local Sequence Alignment on GPU Cluster

Thuy T. Nguyen, Duc H. Nguyen, Phong H. Pham, Ngoc M. Ta, Tan N. Duong, Hung D. Le

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Tags: Bioinformatics, Biology, CUDA, GPU cluster, MPI, nVidia, nVidia GeForce GTX 295, Sequence alignment, Smith-Waterman algorithm, Tesla C1060

June 27, 2011 by hgpu

Fast cell detection in high-throughput imagery using GPU-accelerated machine learning

David Mayerich, Jaerock Kwon, Aaron Panchal, John Keyser, Yoonsuck Choe

Tags: Biology, Image processing, Machine learning, nVidia

June 24, 2011 by hgpu

Accelerating Smith-Waterman on Heterogeneous CPU-GPU Systems

Jaideep Singh, Ipseeta Aruni

Tags: Bioinformatics, Biology, CUDA, Heterogeneous systems, nVidia, Smith-Waterman algorithm

June 24, 2011 by hgpu

Protein alignment algorithms with an efficient backtracking routine on multiple GPUs

Jacek Blazewicz, Wojciech Frohmberg, Michal Kierzynka, Erwin Pesch, Pawel Wojciechowski

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Tags: Bioinformatics, Biology, CUDA, nVidia, nVidia GeForce GTX 280, nVidia GeForce GTX 480, Package, Sequence alignment, Tesla S1070

June 21, 2011 by hgpu

Accelerating Genome-Wide Association Studies Using CUDA Compatible Graphics Processing Units

Rui Jiang, Feng Zeng, Wangshu Zhang, Xuebing Wu, Zhihong Yu

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Tags: Bioinformatics, Biology, CUDA, Genetics, nVidia, nVidia GeForce GTX 280

June 15, 2011 by hgpu

The accelerating implementation of BLAST with stream processor

Gang Wei, Chao Ma, Songwen Pei, Baifeng Wu

Tags: ATI, ATI Radeon HD 4850, Bioinformatics, Biology, BLAST, Brook, Sequence alignment

June 15, 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

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high performance computing on graphics processing units: hgpu.org

Applications

Parallel implementation of a spiking neuronal network model of unsupervised olfactory learning on NVidia CUDA

An Adaptive Hybrid Multiprocessor technique for bioinformatics sequence alignment

Striped Smith-Waterman speeds database searches six times over other SIMD implementations

Six-fold speed-up of Smith-Waterman sequence database searches using parallel processing on common microprocessors

Graphics processing unit implementations of relative expression analysis algorithms enable dramatic computational speedup

CAMPAIGN: An open-source Library of GPU-accelerated Data Clustering Algorithms

Accelerating Smith-Waterman Local Sequence Alignment on GPU Cluster

Fast cell detection in high-throughput imagery using GPU-accelerated machine learning

Accelerating Smith-Waterman on Heterogeneous CPU-GPU Systems

Protein alignment algorithms with an efficient backtracking routine on multiple GPUs

Accelerating Genome-Wide Association Studies Using CUDA Compatible Graphics Processing Units

The accelerating implementation of BLAST with stream processor

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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