high performance computing on graphics processing units: hgpu.org

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hgpu.org » Applications

High-throughput sequence alignment using Graphics Processing Units

Michael Schatz, Cole Trapnell, Arthur Delcher, Amitabh Varshney

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Tags: Bioinformatics, Biology, Computational biology, CUDA, nVidia, nVidia GeForce 8800 GTX, Package, Sequence alignment

November 1, 2010 by hgpu

Optimizing data intensive GPGPU computations for DNA sequence alignment

Cole Trapnell, Michael C. Schatz

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Tags: Bioinformatics, Biology, Computational biology, CUDA, nVidia, nVidia GeForce 8800 GTX, Package, Sequence alignment, Short read mapping, Suffix trees

October 30, 2010 by hgpu

Mars: a MapReduce framework on graphics processors

Bingsheng He, Wenbin Fang, Qiong Luo, Naga K. Govindaraju, Tuyong Wang

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Tags: Computer science, CUDA, Data parallelism, MapReduce, nVidia, nVidia GeForce 8800 GTX, Package, Programming techniques, Web Analysis

October 30, 2010 by hgpu

Exploiting graphics processing units for computational biology and bioinformatics

Joshua L. Payne, Nicholas A. Sinnott-Armstrong, Jason H. Moore

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Tags: All-Pairs Distance, Bioinformatics, Biology, Computational biology, CUDA, nVidia, nVidia GeForce 9600 M, Package

October 30, 2010 by hgpu

Accelerating molecular dynamic simulation on graphics processing units

Mark S. Friedrichs, Peter Eastman, Vishal Vaidyanathan, Mike Houston, Scott Legrand, Adam L. Beberg, Daniel L. Ensign, Christopher M. Bruns, Vijay S. Pande

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Tags: ATI, ATI Radeon HD 4870, ATI Stream, Biology, Brook, Chemistry, Computational chemistry, Molecular dynamics, nVidia, nVidia GeForce GTX 280, Package, Solvent effects

October 30, 2010 by hgpu

A performance study of general-purpose applications on graphics processors using CUDA

S. Che, M. Boyer, J. Meng, D. Tarjan, J. Sheaffer, K. Skadron

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Tags: Computer science, CUDA, nVidia, nVidia GeForce GTX 260, OpenMP, Package, Performance

October 30, 2010 by hgpu

GPU-based Video Feature Tracking and Matching

Sudipta N. Sinha, Jan-michael Frahm, Marc Pollefeys, Yakup Genc

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Tags: Computer science, Image processing, nVidia, nVidia GeForce 7900 GTX, OpenGL, Package, SIFT

October 29, 2010 by hgpu

The Heisenberg spin glass model on GPU: myths and actual facts

M. Bernaschi, G. Parisi, L. Parisi

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Tags: Condensed matter, CUDA, Disordered Systems and Neural Networks, nVidia, nVidia GeForce GTX 480, Package, Physics, Spin Systems, Tesla C1060, Tesla C2050

October 28, 2010 by hgpu

CUDA compatible GPU cards as efficient hardware accelerators for Smith-Waterman sequence alignment

Svetlin Manavski, Giorgio Valle

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Tags: Bioinformatics, Biology, Computational biology, Computer science, CUDA, nVidia, nVidia GeForce 8800 GTX, Package, Sequence alignment, Smith-Waterman algorithm

October 28, 2010 by hgpu

GpuCV: A GPU-Accelerated Framework for Image Processing and Computer Vision

Yannick Allusse, Patrick Horain, Ankit Agarwal, Cindula Saipriyadarshan

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Tags: Computer science, Computer vision, CUDA, GLSL, Image processing, nVidia, nVidia GeForce GTX 280, OpenGL, Package

October 28, 2010 by hgpu

The gputools package enables GPU computing in R

Joshua Buckner, Justin Wilson, Mark Seligman, Brian Athey, Stanley Watson, Fan Meng

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Tags: Computer science, CUBLAS, CUDA, nVidia, Package

October 28, 2010 by hgpu

High performance cellular level agent-based simulation with FLAME for the GPU

Paul Richmond, Dawn Walker, Simon Coakley, Daniela Romano

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Tags: Bioinformatics, Cellular modelling, Computational modelling, Computer science, CUDA, nVidia, Package

October 28, 2010 by hgpu

Code Generation for Cryptographic Kernels using Multi-word Modular Arithmetic on GPU

GSParLib

GSParLib: A multi-level programming interface unifying OpenCL and CUDA for expressing stream and data parallelism

Keras Sig: Efficient Path Signature Computation on GPU in Keras 3

KSig: GPU-accelerated computation of popular time series kernels

A User’s Guide to KSig: GPU-Accelerated Computation of the Signature Kernel

IterApp: Iterative Application Skeleton

Boosting Performance of Iterative Applications on GPUs: Kernel Batching with CUDA Graphs

SCALE-Ahead-Of-Time Compilation of CUDA for AMD GPUs

LeetDecoding: A PyTorch Library for Exponentially Decaying Causal Linear Attention with CUDA Implementations

Anari-visionaray

Data Parallel Visualization and Rendering on the RAMSES Supercomputer with ANARI

PROM: an open-source software framework to enhance the robustness and performance of predictive models against such changes during deployment

Enhancing Deployment-Time Predictive Model Robustness for Code Analysis and Optimization

DeepSpeed: a deep learning optimization library that makes distributed training and inference easy, efficient, and effective

Scalable Access-Pattern Aware I/O Acceleration and Multi-Tiered Data Management for HPC and AI Workloads

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high performance computing on graphics processing units: hgpu.org

Packages

High-throughput sequence alignment using Graphics Processing Units

Optimizing data intensive GPGPU computations for DNA sequence alignment

Mars: a MapReduce framework on graphics processors

Exploiting graphics processing units for computational biology and bioinformatics

Accelerating molecular dynamic simulation on graphics processing units

A performance study of general-purpose applications on graphics processors using CUDA

GPU-based Video Feature Tracking and Matching

The Heisenberg spin glass model on GPU: myths and actual facts

CUDA compatible GPU cards as efficient hardware accelerators for Smith-Waterman sequence alignment

GpuCV: A GPU-Accelerated Framework for Image Processing and Computer Vision

The gputools package enables GPU computing in R

High performance cellular level agent-based simulation with FLAME for the GPU

Recent source codes

Code Generation for Cryptographic Kernels using Multi-word Modular Arithmetic on GPU

GSParLib

Keras Sig: Efficient Path Signature Computation on GPU in Keras 3

KSig: GPU-accelerated computation of popular time series kernels

IterApp: Iterative Application Skeleton

SCALE-Ahead-Of-Time Compilation of CUDA for AMD GPUs

LeetDecoding: A PyTorch Library for Exponentially Decaying Causal Linear Attention with CUDA Implementations

Anari-visionaray

PROM: an open-source software framework to enhance the robustness and performance of predictive models against such changes during deployment

DeepSpeed: a deep learning optimization library that makes distributed training and inference easy, efficient, and effective

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