high performance computing on graphics processing units: hgpu.org

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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

MSA-CUDA: Multiple Sequence Alignment on Graphics Processing Units with CUDA

Yongchao Liu, Bertil Schmidt, Douglas L. Maskell

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Tags: Bioinformatics, Biology, CUDA, nVidia, nVidia GeForce GTX 280, Sequence alignment

November 21, 2010 by hgpu

Patient-Specific Non-Linear Finite Element Modelling for Predicting Soft Organ Deformation in Real-Time; Application to Non-Rigid Neuroimage Registration

Adam Wittek, Grand Joldes, Mathieu Couton, Simon K. Warfield, Karol Miller

Tags: Biology, Medicine, nVidia, Surgical simulation, Tesla C870

November 20, 2010 by hgpu

Ultra-fast FFT protein docking on graphics processors

David W. Ritchie, Vishwesh Venkatraman

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

November 19, 2010 by hgpu

Acceleration of the Smith-Waterman Algorithm using Single and Multiple Graphics Processors

Ali Khajeh-Saeed, Stephen Poole, J. Blair Perot

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Tags: Bioinformatics, Biology, CUDA, nVidia, nVidia GeForce 9800 GT, nVidia GeForce 9800 GTX, nVidia GeForce GTX 295, Sequence matching, Smith-Waterman algorithm

November 18, 2010 by hgpu

GPU-enabled FREALIGN: Accelerating single particle 3D reconstruction and refinement in Fourier space on graphic processors

Xueming Li, Nikolaus Grigorieff, Yifan Cheng

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Tags: Biology, CUDA, Electron microscopy, Image reconstruction, nVidia, Package

November 18, 2010 by hgpu

Low cost, high performance GPU computing solution for atomic resolution cryoEM single-particle reconstruction

Xiaokang Zhang, Xing Zhang, Z. Hong Zhou

Tags: Biology, Cryo-EM, CUDA, Image reconstruction, nVidia

November 18, 2010 by hgpu

An adaptive Expectation-Maximization algorithm with GPU implementation for electron cryomicroscopy

Hemant D. Tagare, Andrew Barthel, Fred J. Sigworth

Tags: Algorithms, Biology, Cryo-EM, CUDA, Image reconstruction, nVidia

November 18, 2010 by hgpu

Fast free-form deformation using graphics processing units

Marc Modat, Gerard R. Ridgway, Zeike A. Taylor, Manja Lehmann, Josephine Barnes, David J. Hawkes, Nick C. Fox, Sebastien Ourselin

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Tags: Biology, CUDA, Image processing, Medicine, nVidia, nVidia GeForce 8800 GTX, Package

November 17, 2010 by hgpu

permGPU: Using graphics processing units in RNA microarray association studies

Ivo Shterev, Sin H. Jung, Stephen George, Kouros Owzar

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

November 17, 2010 by hgpu

Alignator: A GPU powered software package for robust fiducial-less alignment of cryo tilt-series

Daniel Castano-Diez, Margot Scheffer, Ashraf Al-Amoudi, Achilleas S. Frangakis

Tags: Biology, Cryo-electron tomography, Image alignment, Image processing

November 17, 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

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

Parallel Position Weight Matrices Algorithms

MSA-CUDA: Multiple Sequence Alignment on Graphics Processing Units with CUDA

Patient-Specific Non-Linear Finite Element Modelling for Predicting Soft Organ Deformation in Real-Time; Application to Non-Rigid Neuroimage Registration

Ultra-fast FFT protein docking on graphics processors

Acceleration of the Smith-Waterman Algorithm using Single and Multiple Graphics Processors

GPU-enabled FREALIGN: Accelerating single particle 3D reconstruction and refinement in Fourier space on graphic processors

Low cost, high performance GPU computing solution for atomic resolution cryoEM single-particle reconstruction

An adaptive Expectation-Maximization algorithm with GPU implementation for electron cryomicroscopy

Fast free-form deformation using graphics processing units

permGPU: Using graphics processing units in RNA microarray association studies

Alignator: A GPU powered software package for robust fiducial-less alignment of cryo tilt-series

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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