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Accurate Sequence Alignment using Distributed Filtering on GPU Clusters

Reza Farivar, Shivaram Venkataraman, Yanen Li, Ellick Chan, Abhishek Verma, Roy H. Campbell

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Tags: Bioinformatics, Biology, CUDA, Filtering, GPU cluster, nVidia, Sequence alignment, Tesla S1070

December 26, 2011 by hgpu

GPU Accelerated PK-means Algorithm for Gene Clustering

Wuchao Situ, Yau-King Lam, Yi Xiao, P.W.M. Tsang, Chi-Sing Leung

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Tags: Algorithms, Biology, Clustering, CUDA, Genetics, nVidia, nVidia GeForce GTX 260

December 20, 2011 by hgpu

An Efficient Simulation Environment for Modeling Large-Scale Cortical Processing

Micah Richert, Jayram Moorkanikara Nageswaran, Nikil Dutt, Jeffrey L. Krichmar

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Tags: Biology, CUDA, Neural networks, Neuroscience, nVidia, Package, Tesla C1060

December 19, 2011 by hgpu

A Novel Multi-GPU Neural Simulator

C. M. Thibeault, R. Hoang, F. C. Harris Jr.

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Tags: Biology, Biophysics, CUDA, Neuroscience, nVidia, nVidia GeForce GTX 480

December 14, 2011 by hgpu

Fast extraction of neuron morphologies from large-scale SBFSEM image stacks

Stefan Lang, Panos Drouvelis, Enkelejda Tafaj, Peter Bastian, Bert Sakmann

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Tags: Algorithms, Biology, CUDA, Electron microscopy, Image processing, Microscopy, Neuroscience, nVidia, Tesla C1060

December 8, 2011 by hgpu

GPU-Euler: Sequence Assembly Using GPGPU

Syed F. Mahmood, Huzefa Rangwala

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Tags: Biology, CUDA, Genetics, nVidia, nVidia Quadro FX 5800

December 5, 2011 by hgpu

kNN Query Processing in Metric Spaces Using GPUs

Ricardo J. Barrientos, Jose I. Gomez, Christian Tenllado, Manuel Prieto Matias, Mauricio Marin

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Tags: Algorithms, Biology, Computational biology, CUDA, Databases, Information Retrieval, nVidia, nVidia GeForce GTX 280

December 4, 2011 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

Parallel-META: A high-performance computational pipeline for metagenomic data analysis

Xiaoquan Su, Jian Xu, Kang Ning

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Tags: Biology, Databases, Genetics, nVidia, Optimization, Tesla C2070

December 2, 2011 by hgpu

Parallelized agent-based simulation on CPU and graphics hardware for spatial and stochastic models in biology

Martin Falk, Michael Ott, Thomas Ertl, Michael Klann, Heinz Koeppl

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Tags: Biology, CUDA, nVidia, nVidia GeForce GTX 465, Programming techniques

November 24, 2011 by hgpu

A Parallel Deconvolution Algorithm in Perfusion Imaging

Fan Zhu, David Rodriguez Gonzalez, Trevor Carpenter, Malcolm Atkinson, Joanna Wardlaw

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Tags: Algorithms, Biology, CUDA, Medicine, nVidia, nVidia GeForce GTX 280, Performance, Tesla C1060

November 23, 2011 by hgpu

Accelerating Protein Sequence Search in a Heterogeneous Computing System

Shucai Xiao, Heshan Lin, Wu-chun Feng

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Tags: Algorithms, Bioinformatics, Biology, BLAST, Databases, Heterogeneous systems, nVidia, Optimization, Tesla C1060, Tesla C2050

November 23, 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

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high performance computing on graphics processing units: hgpu.org

Accurate Sequence Alignment using Distributed Filtering on GPU Clusters

GPU Accelerated PK-means Algorithm for Gene Clustering

An Efficient Simulation Environment for Modeling Large-Scale Cortical Processing

A Novel Multi-GPU Neural Simulator

Fast extraction of neuron morphologies from large-scale SBFSEM image stacks

GPU-Euler: Sequence Assembly Using GPGPU

kNN Query Processing in Metric Spaces Using GPUs

On the design of architecture-aware algorithms for emerging applications

Parallel-META: A high-performance computational pipeline for metagenomic data analysis

Parallelized agent-based simulation on CPU and graphics hardware for spatial and stochastic models in biology

A Parallel Deconvolution Algorithm in Perfusion Imaging

Accelerating Protein Sequence Search in a Heterogeneous Computing System

Recent source codes

PELSI: Power-Efficient Layer-Switched Inference

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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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