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Towards microsecond biological molecular dynamics simulations on hybrid processors

Scott Hampton, Pratul K. Agarwal, Sadaf R. Alam, Paul S. Crozier

Tags: Bioinformatics, Biology, CUDA, Molecular dynamics, nVidia, Tesla C1060, Tesla C2050

January 19, 2011 by hgpu

Optimal Utilization of Heterogeneous Resources for Biomolecular Simulations

Scott S. Hampton, Sadaf R. Alam, Paul S. Crozier, Pratul K. Agarwal

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Tags: Bioinformatics, Biology, CUDA, Molecular dynamics, nVidia, Tesla C1060, Tesla C2050

January 19, 2011 by hgpu

Real-Time Non-rigid Registration of Medical Images on a Cooperative Parallel Architecture

Yixun Liu, Andriy Fedorov, Ron Kikinis, Nikos Chrisochoides

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Tags: Bioinformatics, CUDA, Image registration, Medicine, nVidia, nVidia GeForce 8800 GT

January 17, 2011 by hgpu

Fast Genetic Programming on GPUs

Simon Harding, Wolfgang Banzhaf

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Tags: Bioinformatics, Biology, DirectX, Genetics, nVidia, nVidia GeForce 7300

January 15, 2011 by hgpu

GPU accelerated biochemical network simulation

Yanxiang Zhou, Juliane Liepe, Xia Sheng, Michael P. H. Stumpf, Chris Barnes

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Tags: Bioinformatics, Biology, CUDA, GPU cluster, nVidia, Package, Tesla C2050

January 13, 2011 by hgpu

Rapid evaluation and evolution of neural models using graphics card hardware

Thomas F. Clayton, Leena N. Patel, Gareth Leng, Alan F. Murray, Iain A.B. Lindsay

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Tags: Algorithms, Bioinformatics, Biology, CUDA, Evolutionary Computations, nVidia, nVidia GeForce 8800 GTX

January 13, 2011 by hgpu

Automated image alignment for 2D gel electrophoresis in a high-throughput proteomics pipeline

Andrew W. Dowsey, Michael J. Dunn, Guang-Zhong Z. Yang

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Tags: Bioinformatics, Biology, Cg, Image alignment, nVidia, nVidia GeForce 6800 Ultra, Package

January 11, 2011 by hgpu

Fast binding site mapping using GPUs and CUDA

Bharat Sukhwani, Martin C. Herbordt

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Tags: Bioinformatics, Biology, CUDA, Molecular dynamics, nVidia, Tesla C1060

January 11, 2011 by hgpu

Quality-score guided error correction for short-read sequencing data using CUDA

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

Tags: Bioinformatics, Biology, CUDA, Error recovery, Genetics, nVidia

January 11, 2011 by hgpu

CBESW: sequence alignment on the Playstation 3

Adrianto Wirawan, Chee Keong K. Kwoh, Nim Tri T. Hieu, Bertil Schmidt

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Tags: Algorithms, Bioinformatics, Biology, BLAST, Cell processor, CUDA, nVidia, nVidia GeForce 8800 GTX, Package, Playstation, Sequence alignment, Smith-Waterman algorithm

January 8, 2011 by hgpu

FPGA acceleration of the phylogenetic likelihood function for Bayesian MCMC inference methods

Stephanie Zierke, Jason Bakos

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Tags: Bioinformatics, Biology, FPGA

January 7, 2011 by hgpu

A parameterisable and scalable Smith-Waterman algorithm implementation on CUDA-compatible GPUs

Cheng Ling, Khaled Benkrid, Tsuyoshi Hamada

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Tags: Bioinformatics, Biology, Computational biology, CUDA, nVidia, nVidia GeForce 8800 GTX, Sequence alignment, Smith-Waterman algorithm

January 4, 2011 by hgpu

Code Generation for Cryptographic Kernels using Multi-word Modular Arithmetic on GPU

GSParLib

GSParLib: A multi-level programming interface unifying OpenCL and CUDA for expressing stream and data parallelism

Keras Sig: Efficient Path Signature Computation on GPU in Keras 3

KSig: GPU-accelerated computation of popular time series kernels

A User’s Guide to KSig: GPU-Accelerated Computation of the Signature Kernel

IterApp: Iterative Application Skeleton

Boosting Performance of Iterative Applications on GPUs: Kernel Batching with CUDA Graphs

SCALE-Ahead-Of-Time Compilation of CUDA for AMD GPUs

LeetDecoding: A PyTorch Library for Exponentially Decaying Causal Linear Attention with CUDA Implementations

Anari-visionaray

Data Parallel Visualization and Rendering on the RAMSES Supercomputer with ANARI

PROM: an open-source software framework to enhance the robustness and performance of predictive models against such changes during deployment

Enhancing Deployment-Time Predictive Model Robustness for Code Analysis and Optimization

DeepSpeed: a deep learning optimization library that makes distributed training and inference easy, efficient, and effective

Scalable Access-Pattern Aware I/O Acceleration and Multi-Tiered Data Management for HPC and AI Workloads

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high performance computing on graphics processing units: hgpu.org

Towards microsecond biological molecular dynamics simulations on hybrid processors

Optimal Utilization of Heterogeneous Resources for Biomolecular Simulations

Real-Time Non-rigid Registration of Medical Images on a Cooperative Parallel Architecture

Fast Genetic Programming on GPUs

GPU accelerated biochemical network simulation

Rapid evaluation and evolution of neural models using graphics card hardware

Automated image alignment for 2D gel electrophoresis in a high-throughput proteomics pipeline

Fast binding site mapping using GPUs and CUDA

Quality-score guided error correction for short-read sequencing data using CUDA

CBESW: sequence alignment on the Playstation 3

FPGA acceleration of the phylogenetic likelihood function for Bayesian MCMC inference methods

A parameterisable and scalable Smith-Waterman algorithm implementation on CUDA-compatible GPUs

Recent source codes

Code Generation for Cryptographic Kernels using Multi-word Modular Arithmetic on GPU

GSParLib

Keras Sig: Efficient Path Signature Computation on GPU in Keras 3

KSig: GPU-accelerated computation of popular time series kernels

IterApp: Iterative Application Skeleton

SCALE-Ahead-Of-Time Compilation of CUDA for AMD GPUs

LeetDecoding: A PyTorch Library for Exponentially Decaying Causal Linear Attention with CUDA Implementations

Anari-visionaray

PROM: an open-source software framework to enhance the robustness and performance of predictive models against such changes during deployment

DeepSpeed: a deep learning optimization library that makes distributed training and inference easy, efficient, and effective

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