high performance computing on graphics processing units: hgpu.org

hgpu.org » Applications » Biology

Integrative multicellular biological modeling: a case study of 3D epidermal development using GPU algorithms

Scott Christley, Briana Lee, Xing Dai, Qing Nie

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Tags: Biology, CUDA, nVidia, nVidia GeForce GTX 285

December 15, 2010 by hgpu

Scalable and Interactive Segmentation and Visualization of Neural Processes in EM Datasets

Won-ki Jeong, Johanna Beyer, Student Member, Markus Hadwiger, Amelio Vazquez, Student Member, Hanspeter Pfister, Senior Member, Ross T. Whitaker

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Tags: Biology, Electron microscopy, Neuroscience, nVidia, nVidia Quadro FX 5800, Rendering, Tesla C1060

December 15, 2010 by hgpu

Scalable and highly parallel implementation of Smith-Waterman on graphics processing unit using CUDA

Ali Akoglu, Gregory Striemer

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

December 15, 2010 by hgpu

Real-world comparison of CPU and GPU implementations of SNPrank: a network analysis tool for GWAS

Nicholas A. Davis, Ahwan Pandey, B. A. McKinney

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Tags: Bioinformatics, Biology, CUDA, Genetics, Medicine, nVidia, Package, Tesla M1060

December 13, 2010 by hgpu

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

Efficient GPU Implementation of Multi-Precision Integer Division

ParEval: A Parallel Code Evaluation Benchmark

ParEval-Repo: A Benchmark Suite for Evaluating LLMs with Repository-level HPC Translation Tasks

FlashSparse: Minimizing Computation Redundancy for Fast Sparse Matrix Multiplications on Tensor Cores

Libra: Synergizing CUDA and Tensor Cores for High-Performance Sparse Matrix Multiplication

exa-AMD: Exascale Accelerated Materials Discovery

Accelerated discovery and design of Fe-Co-Zr magnets with tunable magnetic anisotropy through machine learning and parallel computing

WiLLM: An Open Wireless LLM Communication System

Vcc: the Vulkan Clang Compiler

No More Shading Languages: Compiling C++ to Vulkan Shaders

hpcbench: A set of benchmarking utilities for biomolecular simulation tools

Engineering Supercomputing Platforms for Biomolecular Applications

HPCTransCompile: An AI Compiler Generated Dataset for High-Performance CUDA Transpilation and LLM Preliminary Exploration

chemtrain: Training Molecular Dynamics Potentials in JAX

chemtrain-deploy: A parallel and scalable framework for machine learning potentials in million-atom MD simulations

microSYCL: SYCL micro-benchmarks repository

Exploring SYCL as a Portability Layer for High-Performance Computing on CPUs

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high performance computing on graphics processing units: hgpu.org

Applications

Integrative multicellular biological modeling: a case study of 3D epidermal development using GPU algorithms

Scalable and Interactive Segmentation and Visualization of Neural Processes in EM Datasets

Scalable and highly parallel implementation of Smith-Waterman on graphics processing unit using CUDA

Real-world comparison of CPU and GPU implementations of SNPrank: a network analysis tool for GWAS

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

Recent source codes

Efficient GPU Implementation of Multi-Precision Integer Division

ParEval: A Parallel Code Evaluation Benchmark

FlashSparse: Minimizing Computation Redundancy for Fast Sparse Matrix Multiplications on Tensor Cores

exa-AMD: Exascale Accelerated Materials Discovery

WiLLM: An Open Wireless LLM Communication System

Vcc: the Vulkan Clang Compiler

hpcbench: A set of benchmarking utilities for biomolecular simulation tools

HPCTransCompile: An AI Compiler Generated Dataset for High-Performance CUDA Transpilation and LLM Preliminary Exploration

chemtrain: Training Molecular Dynamics Potentials in JAX

microSYCL: SYCL micro-benchmarks repository

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