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DeepProf: Performance Analysis for Deep Learning Applications via Mining GPU Execution Patterns

Jiazhen Gu, Huan Liu, Yangfan Zhou, Xin Wang

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Tags: Computer science, CUDA, Deep learning, nVidia, nVidia GeForce GTX 1080 Ti, Performance, Suffix trees

July 14, 2017 by hgpu

Extracting Maximal Exact Matches on GPU

Anas Abu-Doleh, Kamer Kaya, Mohamed Abouelhoda, Umit V. Catalyurek

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Tags: Algorithms, Bioinformatics, Computer science, CUDA, Indexing, nVidia, Suffix trees, Tesla K20

August 2, 2014 by hgpu

Parallelization of DNA alignment algorithms using GPUs

Gustavo Encarnacao

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Tags: Algorithms, Bioinformatics, Biology, CUDA, nVidia, nVidia GeForce GTX 580, Sequence matching, Suffix trees

March 7, 2014 by hgpu

GPU Accelerated Multiple Deoxyribose Nucleic Acid Sequence Parallel Matching

Gang Liao, Qi Sun, Longfei Ma, Zhihui Qin

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Tags: Algorithms, Bioinformatics, Computer science, CUDA, Data Structures and Algorithms, nVidia, nVidia GeForce GTX 680, Sequence matching, Suffix trees

March 18, 2013 by hgpu

A Dynamic Approach to Weighted Suffix Tree Construction Algorithm

Binay Kumar Pandey, Rajdeep Niyogi, Ankush Mittal

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Tags: Algorithms, Cluster computing, Computer science, CUDA, nVidia, nVidia Quadro FX 3700, Suffix trees

December 11, 2011 by hgpu

Advantages and GPU implementation of high-performance indexed DNA search based on suffix arrays

Gustavo Encarnacao, Nuno Sebastiao, Nuno Roma

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Tags: Bioinformatics, Biology, CUDA, nVidia, nVidia GeForce GTX 580, Suffix trees

November 13, 2011 by hgpu

Parallel Lexicographic Names Construction with CUDA

Weidong Sun, Zongmin Ma

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Tags: Code generation, Computer science, CUDA, nVidia, nVidia GeForce 9600 GSO, Suffix trees

April 16, 2011 by hgpu

Size Matters: Space/Time Tradeoffs to Improve GPGPU Applications Performance

Abdullah Gharaibeh, Matei Ripeanu

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

February 27, 2011 by hgpu

Fast Exact String Matching on the GPU

Michael C. Schatz, Cole Trapnell

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Tags: Algorithms, Computational biology, Computer science, CUDA, nVidia, nVidia GeForce 8800 GTX, Package, Search, String matching, Suffix trees

February 20, 2011 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

Over-synchronization in GPU Programs

profile_util: simple C++ library to report memory, timing, thread affinity

Profile Util library: A quick and easy way to get MPI, OpenMP and GPU runtime information

MaC: Mamba CPU performance predictor

MambaCPU: Enhanced Correlation Mining with State Space Models for CPU Performance Prediction

Mixed-precision finite element kernels

Mixed-precision finite element kernels and assembly: Rounding error analysis and hardware acceleration

SHMT: The Simultaneous and Heterogenous Multithreading project

General-Purpose Computing on Tensor Processors

Superpipeline: A Universal Approach for Reducing GPU Memory Usage in Large Models

EnergyUCB-Bandit

Online Energy Optimization in GPUs: A Multi-Armed Bandit Approach

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high performance computing on graphics processing units: hgpu.org

DeepProf: Performance Analysis for Deep Learning Applications via Mining GPU Execution Patterns

Extracting Maximal Exact Matches on GPU

Parallelization of DNA alignment algorithms using GPUs

GPU Accelerated Multiple Deoxyribose Nucleic Acid Sequence Parallel Matching

A Dynamic Approach to Weighted Suffix Tree Construction Algorithm

Advantages and GPU implementation of high-performance indexed DNA search based on suffix arrays

Parallel Lexicographic Names Construction with CUDA

Size Matters: Space/Time Tradeoffs to Improve GPGPU Applications Performance

Fast Exact String Matching on the GPU

Optimizing data intensive GPGPU computations for DNA sequence alignment

Recent source codes

Kokkidio: Kokkos+Eigen - write fast, readable multi-platform code

LLaMA-Inference-Bench

MATAR

Over-synchronization in GPU Programs

profile_util: simple C++ library to report memory, timing, thread affinity

MaC: Mamba CPU performance predictor

Mixed-precision finite element kernels

SHMT: The Simultaneous and Heterogenous Multithreading project

Superpipeline: A Universal Approach for Reducing GPU Memory Usage in Large Models

EnergyUCB-Bandit

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