high performance computing on graphics processing units: hgpu.org

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Highly efficient mapping of the Smith-Waterman algorithm on CUDA-compatible GPUs

K. Dohi, K. Benkridt, C. Ling, T. Hamada, Y. Shibata

Tags: Bioinformatics, Biology, CUDA, nVidia, Sequence alignment, Smith-Waterman algorithm

May 31, 2011 by hgpu

Fast Parallel Markov Clustering in Bioinformatics Using Massively Parallel Graphics Processing Unit Computing

Alhadi Bustamam, Kevin Burrage, Nicholas A. Hamilton

Tags: Bioinformatics, Biology, CUDA, MPI, nVidia, Sparse matrix

May 30, 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

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

May 10, 2011 by hgpu

GPU Based Parallel Computing on Blast Program

Huang Lican, Hu Ya

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Tags: Bioinformatics, Biology, BLAST, Sequence alignment

May 7, 2011 by hgpu

GPU acceleration for statistical gene classification

Alfredo Benso, Stefano Di Carlo, Gianfranco Politano, Alessandro Savino

Tags: Bioinformatics, Biology, CUDA, Genetics, nVidia

May 5, 2011 by hgpu

Accelerating scientific applications using GPU’s

M. Taher

Tags: Bioinformatics, Biology, Computer science, CUDA, FFT, nVidia, Security, Sequence alignment

May 3, 2011 by hgpu

Accelerating DNA analysis applications on GPU clusters

A. Tumeo, O. Villa

Tags: Bioinformatics, Biology, GPU cluster, MPI, nVidia, Tesla C1060

April 28, 2011 by hgpu

Pathological Image Analysis Using the GPU: Stroma Classification for Neuroblastoma

Antonio Ruiz, Olcay Sertel, Manuel Ujaldon, Umit Catalyurek, Joel Saltz, Metin Gurcan

Tags: Algorithms, Bioinformatics, Image processing, Medicine

April 26, 2011 by hgpu

Parallel Approaches for SWAMP Sequence Alignment

Shannon Steinfadt, Kevin Schaffer

Tags: Bioinformatics, Biology, Cell processor, FPGA, nVidia, Sequence alignment, Smith-Waterman algorithm

April 19, 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

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

Highly efficient mapping of the Smith-Waterman algorithm on CUDA-compatible GPUs

Fast Parallel Markov Clustering in Bioinformatics Using Massively Parallel Graphics Processing Unit Computing

Fast network centrality analysis using GPUs

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

GPU Based Parallel Computing on Blast Program

GPU acceleration for statistical gene classification

Accelerating scientific applications using GPU’s

Accelerating DNA analysis applications on GPU clusters

Pathological Image Analysis Using the GPU: Stroma Classification for Neuroblastoma

Parallel Approaches for SWAMP Sequence Alignment

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

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

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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