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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

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

SCELib3.0: The new revision of SCELib, the parallel computational library of molecular properties in the Single Center Approach

N. Sanna, I. Baccarelli, G. Morelli

Tags: Biology, Chemistry, CUDA, Molecular modeling, nVidia

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

Accelerating phase unwrapping and affine transformations for optical quadrature microscopy using CUDA

Perhaad Mistry, Sherman Braganza, David Kaeli, Miriam Leeser

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Tags: Biology, CUDA, Genetics, Image processing, nVidia, nVidia GeForce 8800 GTX

January 6, 2011 by hgpu

MSCCL++: A GPU-driven communication stack for scalable AI applications

MSCCL++: Rethinking GPU Communication Abstractions for Cutting-edge AI Applications

Benchmark compute shader of Unity against InteropUnityCUDA

InteropUnityCUDA: A Tool for Interoperability Between Unity and CUDA

Data-efficient LLM Fine-tuning for Code Generation

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

DeepCompile: A Compiler-Driven Approach to Optimizing Distributed Deep Learning Training

Large Language Model Powered C-to-CUDA Code Translation: A Novel Auto-Parallelization Framework

GigaAPI: a user-space API that simplifies multi-GPU programming, bridging the gap between the capabilities of parallel GPU systems and the ability of developers to harness their full potential

GigaAPI for GPU Parallelization

Coccinelle: a C code transformation engine using SmPL for matches, refactorings, and bug fixing

Advances in Semantic Patching for HPC-oriented Refactorings with Coccinelle

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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

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

SCELib3.0: The new revision of SCELib, the parallel computational library of molecular properties in the Single Center Approach

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

Accelerating phase unwrapping and affine transformations for optical quadrature microscopy using CUDA

Recent source codes

MSCCL++: A GPU-driven communication stack for scalable AI applications

Benchmark compute shader of Unity against InteropUnityCUDA

Data-efficient LLM Fine-tuning for Code Generation

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

Large Language Model Powered C-to-CUDA Code Translation: A Novel Auto-Parallelization Framework

GigaAPI: a user-space API that simplifies multi-GPU programming, bridging the gap between the capabilities of parallel GPU systems and the ability of developers to harness their full potential

Coccinelle: a C code transformation engine using SmPL for matches, refactorings, and bug fixing

DuoReduce: MLIR's benchmark

Shamrock: Multi-GPU hydrodynamics for astrophysics

LLMPerf: GPU Performance Modeling meets Large Language Models

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