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SWPS3 – fast multi-threaded vectorized Smith-Waterman for IBM Cell/B.E. and x86/SSE2

Adam Szalkowski, Christian Ledergerber, Philipp Kraehenbuehl, Christophe Dessimoz

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Tags: Biology, Cell processor, CUDA, nVidia, nVidia GeForce 8800 GTX, Optimization, Package, Sequence alignment, Smith-Waterman algorithm

December 12, 2010 by hgpu

Exploring Parallel Algorithms for Volumetric Mass-Spring-Damper Models in CUDA

Allan Rasmusson, Jesper Mosegaard, Thomas S. Sorensen

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Tags: Biology, CUDA, Medicine, nVidia, nVidia GeForce 8800 GTX

December 12, 2010 by hgpu

High performance computing for deformable image registration: Towards a new paradigm in adaptive radiotherapy

Sanjiv S. Samant, Junyi Xia, P, John D. Owens

Tags: Biology, Computed tomography, CT, CUDA, Image reconstruction, Image registration, Medicine, nVidia, nVidia GeForce 8800 GTX, Radiotherapy

December 11, 2010 by hgpu

Initial Experiences Porting a Bioinformatics Application to a Graphics Processor

Maria Charalambous, Pedro Trancoso, Alexandros Stamatakis

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Tags: Bioinformatics, Biology, Brook, nVidia, nVidia GeForce FX 5700

December 10, 2010 by hgpu

Performance evaluation of image processing algorithms on the GPU

Daniel Castano-Diez, Dominik Moser, Andreas Schoenegger, Sabine Pruggnaller, Achilleas S S. Frangakis

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Tags: Biology, CUDA, Image processing, Medicine, nVidia, nVidia Quadro FX 5600, Pattern recognition, Tomography

December 7, 2010 by hgpu

GPU-MEME: Using Graphics Hardware to Accelerate Motif Finding in DNA Sequences

Chen Chen, Bertil Schmidt, Liu Weiguo, Wolfgang Muller-Wittig

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Tags: Bioinformatics, Biology, GLSL, nVidia, nVidia GeForce 8800 GTX, OpenGL, Package, Pattern recognition

December 6, 2010 by hgpu

Implementation and performance evaluation of reconstruction algorithms on graphics processors

D. Castanodiez, H. Mueller, A. Frangakis

Tags: Biology, Electron microscopy, Image processing

December 6, 2010 by hgpu

Hierarchical clustering of gene expression profiles with graphics hardware acceleration

Q. Zhang, Y. Zhang

Tags: Biology, Genetics, Pattern recognition

December 4, 2010 by hgpu

Locality and parallelism optimization for dynamic programming algorithm in bioinformatics

Guangming Tan, Shengzhong Feng, Ninghui Sun

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Tags: Algorithms, Bioinformatics, Biology, Programming techniques

December 2, 2010 by hgpu

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

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

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high performance computing on graphics processing units: hgpu.org

SWPS3 – fast multi-threaded vectorized Smith-Waterman for IBM Cell/B.E. and x86/SSE2

Exploring Parallel Algorithms for Volumetric Mass-Spring-Damper Models in CUDA

High performance computing for deformable image registration: Towards a new paradigm in adaptive radiotherapy

Initial Experiences Porting a Bioinformatics Application to a Graphics Processor

Performance evaluation of image processing algorithms on the GPU

GPU-MEME: Using Graphics Hardware to Accelerate Motif Finding in DNA Sequences

Implementation and performance evaluation of reconstruction algorithms on graphics processors

Hierarchical clustering of gene expression profiles with graphics hardware acceleration

Locality and parallelism optimization for dynamic programming algorithm in bioinformatics

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

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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