high performance computing on graphics processing units: hgpu.org

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hgpu.org » Applications » Biology

GPU Accelerated RNA Folding Algorithm

Guillaume Rizk, Dominique Lavenier

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Tags: Algorithms, Bioinformatics, Biology, CUDA, nVidia, nVidia GeForce GTX 280, Tesla C870

December 17, 2010 by hgpu

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

AutoDock-GPU: AutoDock for GPUs and other accelerators

Architecting Tensor Core-Based Reductions for Irregular Molecular Docking Kernels

NCCLX: collective communication framework

Collective Communication for 100k+ GPUs

Tutoring LLM into a Better CUDA Optimizer

Kernel Library for LLM Serving

Compiler and Runtime Systems for Generative AI Models

Adaptivity in AdaptiveCpp: Optimizing Performance by Leveraging Runtime Information During JIT-Compilation

Neptune: Advanced ML Operator Fusion for Locality and Parallelism on GPUs

Genten: Software for Generalized Tensor Decompositions by Sandia National Laboratories

A Performance Portable Matrix Free Dense MTTKRP in GenTen

Interleaved Learning and Exploration: A Self-Adaptive Fuzz Testing Framework for MLIR

Pinocchio: PINpointing Orbit Crossing Collapsed Hierarchical Objects

Accelerating cosmological simulations on GPUs: a portable approach using OpenMP

KernelCoder: trained on a curated dataset of reasoning traces and CUDA kernel pairs

ConCuR: Conciseness Makes State-of-the-Art Kernel Generation

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high performance computing on graphics processing units: hgpu.org

Applications

GPU Accelerated RNA Folding Algorithm

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

Recent source codes

AutoDock-GPU: AutoDock for GPUs and other accelerators

NCCLX: collective communication framework

Tutoring LLM into a Better CUDA Optimizer

Kernel Library for LLM Serving

Adaptivity in AdaptiveCpp: Optimizing Performance by Leveraging Runtime Information During JIT-Compilation

Neptune: Advanced ML Operator Fusion for Locality and Parallelism on GPUs

Genten: Software for Generalized Tensor Decompositions by Sandia National Laboratories

Interleaved Learning and Exploration: A Self-Adaptive Fuzz Testing Framework for MLIR

Pinocchio: PINpointing Orbit Crossing Collapsed Hierarchical Objects

KernelCoder: trained on a curated dataset of reasoning traces and CUDA kernel pairs

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