high performance computing on graphics processing units: hgpu.org

ClawHMMER: A Streaming HMMer-Search Implementation

Daniel R. Horn, Mike Houston, Pat Hanrahan

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Tags: ATI, ATI Radeon X800, Bioinformatics, Biology, Brook, nVidia, nVidia GeForce 6800 Ultra, nVidia GeForce 7800 GTX, Pattern Search

November 30, 2010 by hgpu

GPU-BLAST: Using graphics processors to accelerate protein sequence alignment

Panagiotis D. Vouzis, Nikolaos V. Sahinidis

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Tags: Bioinformatics, Biology, BLAST, CUDA, nVidia, Package, Sequence alignment, Tesla C2050

November 30, 2010 by hgpu

Highly accelerated feature detection in proteomics data sets using modern graphics processing units

Rene Hussong, Barbara Gregorius, Andreas Tholey, Andreas Hildebrandt

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Tags: Bioinformatics, Biology, CUDA, nVidia, Package, Tesla C870

November 28, 2010 by hgpu

A Massively Parallel Architecture for Bioinformatics

Gerd Pfeiffer, Stefan Baumgart, Jan Schroder, Manfred Schimmler

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Tags: Algorithms, Bioinformatics, Biology, FPGA, MapReduce

November 27, 2010 by hgpu

Parallel reconstruction of neighbor-joining trees for large multiple sequence alignments using CUDA

Yongchao Liu, Bertil Schmidt, Douglas L. Maskell

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Tags: Bioinformatics, Biology, CUDA, nVidia, nVidia GeForce GTX 280, Sequence alignment, Smith-Waterman algorithm

November 27, 2010 by hgpu

Implications of the Turing completeness of reaction-diffusion models, informed by GPGPU simulations on an XBox 360: cardiac arrhythmias, re-entry and the Halting problem

Simon Scarle

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Tags: Biology, Heart, Medicine, Visualization, Xbox 360

November 27, 2010 by hgpu

CUDA-MEME: Accelerating Motif Discovery in Biological Sequences Using CUDA-enabled Graphics Processing Units

Yongchao Liu, Bertil Schmidt, Weiguo Liu, Douglas L. Maskell

Tags: Biology, CUDA, nVidia, nVidia GeForce GTX 280, Pattern recognition

November 27, 2010 by hgpu

Performance Analysis of IBM Cell Broadband Engine on Sequence Alignment

Yang Song, Gregory M. Striemer, Ali Akoglu

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Tags: Bioinformatics, Biology, Cell processor, CUDA, nVidia, Sequence alignment, Smith-Waterman algorithm, Tesla C870

November 27, 2010 by hgpu

Accelerating leukocyte tracking using CUDA: A case study in leveraging manycore coprocessors

M. Boyer, D. Tarjan, S. T. Acton, K. Skadron

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Tags: Biology, CUDA, Microscopy, nVidia, nVidia GeForce GTX 280

November 26, 2010 by hgpu

Many-core algorithms for statistical phylogenetics

Marc A. Suchard, Andrew Rambaut

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Tags: Bioinformatics, Biology, CUDA, Genetics, nVidia, nVidia GeForce GTX 280

November 23, 2010 by hgpu

A Parallel Algorithm for Error Correction in High-Throughput Short-Read Data on CUDA-Enabled Graphics Hardware

Haixiang Shi, Bertil Schmidt, Weiguo Liu, Wolfgang Muller-Wittig

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Tags: Biology, Computer science, CUDA, Error recovery, nVidia, Package

November 22, 2010 by hgpu

Parallel Position Weight Matrices Algorithms

Mathieu Giraud, Jean-Stephane Varre

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Tags: Biology, Computer science, CUDA, nVidia, nVidia GeForce 8800, nVidia GeForce GTX 280, Package

November 22, 2010 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

ClawHMMER: A Streaming HMMer-Search Implementation

GPU-BLAST: Using graphics processors to accelerate protein sequence alignment

Highly accelerated feature detection in proteomics data sets using modern graphics processing units

A Massively Parallel Architecture for Bioinformatics

Parallel reconstruction of neighbor-joining trees for large multiple sequence alignments using CUDA

Implications of the Turing completeness of reaction-diffusion models, informed by GPGPU simulations on an XBox 360: cardiac arrhythmias, re-entry and the Halting problem

CUDA-MEME: Accelerating Motif Discovery in Biological Sequences Using CUDA-enabled Graphics Processing Units

Performance Analysis of IBM Cell Broadband Engine on Sequence Alignment

Accelerating leukocyte tracking using CUDA: A case study in leveraging manycore coprocessors

Many-core algorithms for statistical phylogenetics

A Parallel Algorithm for Error Correction in High-Throughput Short-Read Data on CUDA-Enabled Graphics Hardware

Parallel Position Weight Matrices Algorithms

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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