high performance computing on graphics processing units: hgpu.org

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BarraCUDA – a fast short read sequence aligner using graphics processing units

Petr Klus, Simon Lam, Dag Lyberg, Ming Sin Cheung, Graham Pullan, Ian McFarlane, Giles S. H. Yeo, Brian Y. H. Lam

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Tags: Bioinformatics, Biology, CUDA, nVidia, Package, Sequence alignment, Tesla M2050, Tesla M2090

January 13, 2012 by hgpu

Accurate Sequence Alignment using Distributed Filtering on GPU Clusters

Reza Farivar, Shivaram Venkataraman, Yanen Li, Ellick Chan, Abhishek Verma, Roy H. Campbell

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Tags: Bioinformatics, Biology, CUDA, Filtering, GPU cluster, nVidia, Sequence alignment, Tesla S1070

December 26, 2011 by hgpu

Achieving High Throughput Sequencing with Graphics Processing Units

Su Chen, Chaochao Zhang, Feng Shen, Ling Bai, Hai Jiang, Damir Herman

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Tags: Algorithms, Bioinformatics, Computer science, CUDA, nVidia, Sequence alignment, Tesla C2050

December 10, 2011 by hgpu

Accelerating Protein Sequence Search in a Heterogeneous Computing System

Shucai Xiao, Heshan Lin, Wu-chun Feng

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Tags: Algorithms, Bioinformatics, Biology, BLAST, Databases, Heterogeneous systems, nVidia, Optimization, Tesla C1060, Tesla C2050

November 23, 2011 by hgpu

Application of GPGPU for Acceleration of Short DNA Sequence Alignment in Unipro UGENE Project

Konstantin Okonechinkov, German Grekhov, Konstantin Stepanyuk, Mikhail Fursov

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Tags: Algorithms, Bioinformatics, Biology, nVidia, OpenCL, Package, Sequence alignment, Tesla C1060, Tesla C2070

November 22, 2011 by hgpu

Using Graphics Processors for a High Performance Normalization of Gene Expressions

Andres Rodriguez, Oswaldo Trelles, Manuel Ujaldon

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Tags: Bioinformatics, Biology, CUDA, nVidia, nVidia GeForce 9800 GX2

November 22, 2011 by hgpu

Parallel Approach for Longest Common Subsequence problem on GPU

Raik Issaoui, Amine Draief, Abdelfettah Belghith

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Tags: Algorithms, Bioinformatics, Biology, CUDA, nVidia, nVidia GeForce GT 430, OpenCL, Sequence matching

November 16, 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

Molecular Docking on FPGA and GPU Platforms

I. Pechan, B. Feher

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Tags: Algorithms, Bioinformatics, Biology, CUDA, FPGA, nVidia, nVidia GeForce GT 220, nVidia GeForce GTX 260

November 13, 2011 by hgpu

GSNP: A DNA Single-Nucleotide Polymorphism Detection System with GPU Acceleration

Mian Lu, Jiuxin Zhao, Qiong Luo, Bingqiang Wang, Shaohua Fu, Zhe Lin

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Tags: Bioinformatics, Biology, Compression, nVidia, Package, Sorting, Tesla M2050

November 12, 2011 by hgpu

Improving CUDASW++, a Parallelization of Smith-Waterman for CUDA Enabled Devices

Doug Hains, Zach Cashero, Mark Ottenberg, Wim Bohm, Sanjay Rajopadhye

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Tags: Algorithms, Bioinformatics, Biology, CUDA, nVidia, Sequence alignment, Smith-Waterman algorithm, Tesla C1060, Tesla C2050

November 5, 2011 by hgpu

Effective Parallelization of Non-bonded Interactions Kernel for Virtual Screening on GPUs

Gines D. Guerrero, Horacio Perez-Sanchez, Wolfgang Wenzel, Jose M. Cecilia, Jose M. Garcia

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Tags: Bioinformatics, Biology, CUDA, nVidia, Optimization, Pharmaceuticals, Tesla C1060

October 30, 2011 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

See all packages

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high performance computing on graphics processing units: hgpu.org

BarraCUDA – a fast short read sequence aligner using graphics processing units

Accurate Sequence Alignment using Distributed Filtering on GPU Clusters

Achieving High Throughput Sequencing with Graphics Processing Units

Accelerating Protein Sequence Search in a Heterogeneous Computing System

Application of GPGPU for Acceleration of Short DNA Sequence Alignment in Unipro UGENE Project

Using Graphics Processors for a High Performance Normalization of Gene Expressions

Parallel Approach for Longest Common Subsequence problem on GPU

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

Molecular Docking on FPGA and GPU Platforms

GSNP: A DNA Single-Nucleotide Polymorphism Detection System with GPU Acceleration

Improving CUDASW++, a Parallelization of Smith-Waterman for CUDA Enabled Devices

Effective Parallelization of Non-bonded Interactions Kernel for Virtual Screening on GPUs

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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