high performance computing on graphics processing units: hgpu.org

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Accelerating reaction-diffusion simulations with general-purpose graphics processing units

Matthias Vigelius, Aidan Lane, Bernd Meyer

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Tags: Algorithms, Bioinformatics, Biology, CUDA, nVidia, Package, Rendering, Stochastic simulation

September 23, 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

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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

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

July 1, 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

cuGWAM: Genome-wide association multifactor dimensionality reduction using CUDA-enabled high-performance graphics processing unit

Min-Seok Kwon, Kyunga Kim, Sungyoung Lee, Taesung Park

Source codes

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

June 9, 2011 by hgpu

GENIE: a software package for gene-gene interaction analysis in genetic association studies using multiple GPU or CPU cores

Satish Chikkagoudar, Kai Wang, Mingyao Li

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Tags: Biology, CUDA, Genetics, nVidia, nVidia Quadro FX 1800, Package, Tesla C1060

June 7, 2011 by hgpu

Fast network centrality analysis using GPUs

Zhiao Shi, Bing Zhang

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Tags: All-Pairs Distance, Bioinformatics, Biology, CUDA, nVidia, Package, Tesla C2050

May 13, 2011 by hgpu

Exact and complete short-read alignment to microbial genomes using Graphics Processing Unit programming

Jochen Blom, Tobias Jakobi, Daniel Doppmeier, Sebastian Jaenicke, Jorn Kalinowski, Jens Stoye, Alexander Goesmann

Source codes

Tags: Algorithms, Bioinformatics, Biology, CUDA, Next-Generation sequencing, nVidia, Package

May 10, 2011 by hgpu

CUDA-BLASTP: Accelerating BLASTP on CUDA-Enabled Graphics Hardware

Weiguo Liu, Bertil Schmidt, Wolfgang Muller-Wittig

Source codes

Tags: Bioinformatics, Biology, BLAST, CUDA, nVidia, nVidia GeForce GTX 295, Package, Sequence alignment

April 18, 2011 by hgpu

Exact and complete short read alignment to microbial genomes using GPU programming

Jochen Blom, Tobias Jakobi, Daniel Doppmeier, Sebastian Jaenicke, Jorn Kalinowski, Jens Stoye, Alexander Goesmann

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Tags: Bioinformatics, Biology, CUDA, Next-Generation sequencing, nVidia, nVidia GeForce GTX 280, Package

April 11, 2011 by hgpu

DecGPU: distributed error correction on massively parallel graphics processing units using CUDA and MPI

Yongchao Liu, Bertil Schmidt, Douglas Maskell

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Tags: Bioinformatics, Biology, CUDA, MPI, Next-Generation sequencing, nVidia, OpenMP, Package, Tesla S1070

April 11, 2011 by hgpu

Poster: GPU-accelerated rigid body fitting of atomic structures into electron density maps

Edward W. Lowe Jr., Nils Woetzel, Jens Meiler

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Tags: ATI, ATI Radeon HD 5970, Biology, Cryo-EM, Molecular modeling, nVidia, nVidia GeForce GTX 470, OpenCL, Package, Poster, Tesla C1060, Tesla C2050

April 1, 2011 by hgpu

Coccinelle: a C code transformation engine using SmPL for matches, refactorings, and bug fixing

Advances in Semantic Patching for HPC-oriented Refactorings with Coccinelle

DuoReduce: MLIR's benchmark

Hardware-Assisted Software Testing and Debugging for Heterogeneous Computing

Shamrock: Multi-GPU hydrodynamics for astrophysics

The Shamrock code: I- Smoothed Particle Hydrodynamics on GPUs

LLMPerf: GPU Performance Modeling meets Large Language Models

Hercules: A Compiler for Productive Programming of Heterogeneous Systems

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high performance computing on graphics processing units: hgpu.org

Packages

Accelerating reaction-diffusion simulations with general-purpose graphics processing units

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

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

Protein alignment algorithms with an efficient backtracking routine on multiple GPUs

cuGWAM: Genome-wide association multifactor dimensionality reduction using CUDA-enabled high-performance graphics processing unit

GENIE: a software package for gene-gene interaction analysis in genetic association studies using multiple GPU or CPU cores

Fast network centrality analysis using GPUs

Exact and complete short-read alignment to microbial genomes using Graphics Processing Unit programming

CUDA-BLASTP: Accelerating BLASTP on CUDA-Enabled Graphics Hardware

Exact and complete short read alignment to microbial genomes using GPU programming

DecGPU: distributed error correction on massively parallel graphics processing units using CUDA and MPI

Poster: GPU-accelerated rigid body fitting of atomic structures into electron density maps

Recent source codes

Coccinelle: a C code transformation engine using SmPL for matches, refactorings, and bug fixing

DuoReduce: MLIR's benchmark

Shamrock: Multi-GPU hydrodynamics for astrophysics

LLMPerf: GPU Performance Modeling meets Large Language Models

Hercules: A Compiler for Productive Programming of Heterogeneous Systems

Celerity Runtime: High-level C++ for Accelerator Clusters

wgpy: WebGL accelerated numpy-compatible array library for web browser

Microbenchmarking OpenMP target offload with Catch2

SUperman: Highly Efficient Permanent Computation Library

TransCL: An Automatic CUDA-to-OpenCL Programs Transformation Framework

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