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On continuous maximum flow image segmentation algorithm

Laszlo Marak

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Tags: Algorithms, Biology, Materials Science, nVidia, nVidia GeForce GTX 470, OpenCL, Tesla C2050, Thesis, Tomography

March 2, 2013 by hgpu

Burrows-Wheeler Aligner: A Parallel Approach

Sheridan Lee Wright

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Tags: Algorithms, Bioinformatics, Biology, CUDA, MPI, nVidia, Sequence alignment, Thesis

January 16, 2013 by hgpu

High performance bioinformatics and computational biology on general-purpose graphics processing units

Cheng Ling

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Tags: Bioinformatics, Biology, Computational biology, CUDA, FPGA, nVidia, nVidia GeForce 8800 GTX, nVidia GeForce GTX 460, Sequence alignment, Thesis

January 3, 2013 by hgpu

Bioinformatics Sequence Comparisons on Manycore Processors

Tuan Tu Tran

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Tags: ATI, ATI Radeon HD 5870, Bioinformatics, Biology, nVidia, nVidia GeForce GTX 480, OpenCL, Review, Sequence matching, Thesis

December 25, 2012 by hgpu

Massive parallelization of combinatorial statistical genetics analyses porting machine learning methods on general purpose graphics processing units (GPU)

Tony Kam-Thong

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Tags: Biology, CUDA, Genetics, Machine learning, nVidia, nVidia GeForce GTX 295, nVidia GeForce GTX 580, Package, Thesis

September 16, 2012 by hgpu

Algorithms for the mapping of genome sequences in GPGPU

David Seide

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Tags: Biology, CUDA, Genetics, nVidia, nVidia GeForce GTX 280, Sequence alignment, Thesis

August 5, 2012 by hgpu

GPU-Optimized Molecular Dynamics Simulations

Tyson J. Lipscomb

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Tags: Biology, Biomolecules, CUDA, Molecular dynamics, nVidia, nVidia GeForce GTX 480, nVidia GeForce GTX 580, Optimization, Pseudo-random number generators, Review, RNA, Tesla C2070, Thesis

July 8, 2012 by hgpu

LAMMPScuda – a new GPU accelerated Molecular Dynamics Simulations Package and its Application to Ion-Conducting Glasses

Christian Robert Trott

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Tags: Biology, Computational Physics, CUDA, Heterogeneous systems, Molecular dynamics, nVidia, nVidia GeForce GTX 280, nVidia GeForce GTX 470, Package, Physics, Polymer Systems, Tesla C1060, Thesis

February 13, 2012 by hgpu

On the design of architecture-aware algorithms for emerging applications

Seunghwa Kang

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Tags: Algorithms, Benchmarking, Biology, Cell processor, Computational biology, CUDA, Image processing, MapReduce, nVidia, Package, Tesla C1060, Thesis

December 2, 2011 by hgpu

GPU Computations in Heterogeneous Grid Environments

Marcus Hinders

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Tags: ATI, ATI Radeon HD 5870, Biology, Computational biology, Computer science, Grid, Heterogeneous systems, nVidia, nVidia GeForce 8600 GT, nVidia GeForce GTX 280, OpenCL, Thesis

October 30, 2011 by hgpu

Accelerating molecular docking and binding site mapping using FPGAs and GPUs

Bharat Sukhwani

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Tags: Algorithms, Biology, Biomechanics, CUDA, FPGA, Molecular modeling, nVidia, Tesla C1060, Thesis

October 22, 2011 by hgpu

Accelerating the Stochastic Simulation Algorithm using Emerging Architectures

David Dewayne Jenkins

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Tags: Biology, CUDA, Monte Carlo simulation, nVidia, nVidia GeForce 8600 M, Stochastic simulation, Tesla C1060, Tesla C870, Thesis

February 16, 2011 by hgpu

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

DuoReduce: MLIR's benchmark

Hardware-Assisted Software Testing and Debugging for Heterogeneous Computing

See all packages

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high performance computing on graphics processing units: hgpu.org

Theses

On continuous maximum flow image segmentation algorithm

Burrows-Wheeler Aligner: A Parallel Approach

High performance bioinformatics and computational biology on general-purpose graphics processing units

Bioinformatics Sequence Comparisons on Manycore Processors

Massive parallelization of combinatorial statistical genetics analyses porting machine learning methods on general purpose graphics processing units (GPU)

Algorithms for the mapping of genome sequences in GPGPU

GPU-Optimized Molecular Dynamics Simulations

LAMMPScuda – a new GPU accelerated Molecular Dynamics Simulations Package and its Application to Ion-Conducting Glasses

On the design of architecture-aware algorithms for emerging applications

GPU Computations in Heterogeneous Grid Environments

Accelerating molecular docking and binding site mapping using FPGAs and GPUs

Accelerating the Stochastic Simulation Algorithm using Emerging Architectures

Recent source codes

PELSI: Power-Efficient Layer-Switched Inference

Ouroboros: Virtualized Queues for dynamic memory management

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

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