high performance computing on graphics processing units: hgpu.org

Accelerating Pairwise DNA Sequence Alignment using the CUDA Compatible GPU

H. Khaled, R. El Gohary, N. L. Badr, H. M. Faheem

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Tags: Algorithms, Bioinformatics, Biology, CUDA, nVidia, nVidia GeForce GT 540 M, Sequence alignment, Smith-Waterman algorithm

December 22, 2013 by hgpu

Efficient Multi-GPU Computation of All-Pairs Shortest Paths

Hristo Djidjev, Sunil Thulasidasan, Guillaume Chapuis, Rumen Andonov, Dominique Lavenier

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Tags: Algorithms, Bioinformatics, Biology, CUDA, GPU cluster, nVidia, Tesla C2090

December 18, 2013 by hgpu

Exploiting parallel features of modern computer architectures in bioinformatics

Guillaume Chapuis

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Tags: Algorithms, Bioinformatics, Biology, CUDA, Genetics, nVidia, Path problems, Tesla C2050, Tesla C2090, Thesis

December 16, 2013 by hgpu

Neurokernel: An Open Scalable Software Framework for Emulation and Validation of Drosophila Brain Models on Multiple GPUs

Lev E. Givon, Aurel A. Lazar

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Tags: Biology, CUDA, Neuroscience, nVidia, Package, Python

November 18, 2013 by hgpu

Graphics Processing Unit-Accelerated Quantitative Trait Loci Detection

Guillaume Chapuis, Olivier Filangi, Dominique Lavenier, Jean Michel J. M. Elsen, Pascale Leroy

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Tags: Bioinformatics, Biology, CUDA, nVidia, Tesla C2050

November 16, 2013 by hgpu

Accelerating calculations of RNA secondary structure partition functions using GPUs

Harry A Stern, David H Mathews

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Tags: Bioinformatics, Biology, CUDA, nVidia, Package, RNA, Tesla M2050

November 11, 2013 by hgpu

Computational kinetics of a large scale biological process on GPU workstations: DNA bending

Arnold Peter Ruymgaart

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Tags: Biology, CUDA, Molecular dynamics, nVidia, nVidia GeForce GTX 480, Thesis

November 8, 2013 by hgpu

Communication Optimization for Multi GPU Implementation of Smith-Waterman Algorithm

Sampath Kumar, P. K. Baruah

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Tags: Algorithms, Biology, Computational biology, CUDA, Databases, nVidia, Sequence matching, Smith-Waterman algorithm, Tesla M2050

November 2, 2013 by hgpu

gEMpicker: A Highly Parallel GPU-Accelerated Particle Picking Tool for Cryo-Electron Microscopy

Thai V. Hoang, Xavier Cavin, Patrick Schultz, David W. Ritchie

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Tags: Algorithms, Biology, Cryo-EM, CUDA, Electron microscopy, FFT, Macromolecule, Microscopy, nVidia, Tesla C1060, Tesla C2075

October 24, 2013 by hgpu

cudaMap: a GPU accelerated program for gene expression connectivity mapping

Darragh G McArt, Peter Bankhead, Philip D Dunne, Manuel Salto-Tellez, Peter Hamilton, Shu-Dong Zhang

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Tags: Bioinformatics, Biology, CUDA, nVidia, Package, Tesla C2050

October 17, 2013 by hgpu

High performance sequence mining using pairwise statistical significance

Yuhong Zhang, Feng Chen

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Tags: Algorithms, Bioinformatics, Biology, CUDA, nVidia, Package, Tesla C2050

October 12, 2013 by hgpu

Regional Heritability Advanced Complex Trait Analysis for GPU and Traditional Parallel Architectures

L. Cebamanos, A. Gray, I. Stewart, A. Tenesa

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Tags: Algorithms, Bioinformatics, Biology, CUDA, nVidia, Tesla K20

October 12, 2013 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

Applications

Accelerating Pairwise DNA Sequence Alignment using the CUDA Compatible GPU

Efficient Multi-GPU Computation of All-Pairs Shortest Paths

Exploiting parallel features of modern computer architectures in bioinformatics

Neurokernel: An Open Scalable Software Framework for Emulation and Validation of Drosophila Brain Models on Multiple GPUs

Graphics Processing Unit-Accelerated Quantitative Trait Loci Detection

Accelerating calculations of RNA secondary structure partition functions using GPUs

Computational kinetics of a large scale biological process on GPU workstations: DNA bending

Communication Optimization for Multi GPU Implementation of Smith-Waterman Algorithm

gEMpicker: A Highly Parallel GPU-Accelerated Particle Picking Tool for Cryo-Electron Microscopy

cudaMap: a GPU accelerated program for gene expression connectivity mapping

High performance sequence mining using pairwise statistical significance

Regional Heritability Advanced Complex Trait Analysis for GPU and Traditional Parallel Architectures

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

Most viewed papers (last 30 days)