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Massively parallel read mapping on GPUs with PEANUT

Johannes Koster, Sven Rahmann

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Tags: Computer science, Data Structures and Algorithms, nVidia, nVidia GeForce GTX 580, nVidia GeForce GTX 780, OpenCL, Package, Python

March 10, 2014 by hgpu

Data Structures and Algorithms for Counting Problems on Graphs using GPU

Amlan Chatterjee, Sridhar Radhakrishnan, John K. Antonio

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Tags: Algorithms, Computer science, CUDA, Data Structures and Algorithms, nVidia, Tesla C1060, Tesla C2050, Tesla C2070

July 16, 2013 by hgpu

ACL2 Meets the GPU: Formalizing a CUDA-based Parallelizable All-Pairs Shortest Path Algorithm in ACL2

David S. Hardin, Samuel S. Hardin

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Tags: Computer science, CUDA, Data Structures and Algorithms, Logic in Computer Science, nVidia, nVidia GeForce GT 650 M

May 1, 2013 by hgpu

A Novel Data Structure for Particle System Simulation based on GPU with the Use of Neighborhood Grids

Mark Joselli, Jose Ricardo Silva Junior, Marcelo Zamith, Esteban Clua, Eduardo Soluri

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Tags: Cellular automata, Computer science, CUDA, Data Structures and Algorithms, Hashing, nVidia, nVidia GeForce GTX 480, Particle simulation, Visualization

March 23, 2013 by hgpu

GPU Accelerated Multiple Deoxyribose Nucleic Acid Sequence Parallel Matching

Gang Liao, Qi Sun, Longfei Ma, Zhihui Qin

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Tags: Algorithms, Bioinformatics, Computer science, CUDA, Data Structures and Algorithms, nVidia, nVidia GeForce GTX 680, Sequence matching, Suffix trees

March 18, 2013 by hgpu

Parallel Peeling Algorithms

Jiayang Jiang, Michael Mitzenmacher, Justin Thaler

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Tags: Algorithms, Computer science, CUDA, Data Structures and Algorithms, nVidia, Tesla C2070

March 2, 2013 by hgpu

Efficient Parallel and External Matching

Marcel Birn, Vitaly Osipov, Peter Sanders, Christian Schulz, Nodari Sitchinava

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Tags: Algorithms, Computer science, CUDA, Data Structures and Algorithms, MapReduce, Memory model, nVidia, nVidia GeForce GTX 480

February 23, 2013 by hgpu

A structural analysis of the A5/1 state transition graph

Andreas Beckmann, Jaroslaw Fedorowicz, Jorg Keller, Ulrich Meyer

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Tags: Algorithms, Computer science, CUDA, Data Structures and Algorithms, nVidia, nVidia GeForce GTX 580, Security, Stream Ciphers, Tesla C1060

October 25, 2012 by hgpu

Performance Evaluation of Concurrent Lock-free Data Structures on GPUs

Prabhakar Misra, Mainak Chaudhuri

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Tags: Computer science, CUDA, Data Structures and Algorithms, nVidia, Performance, Tesla C2070

September 8, 2012 by hgpu

Approximate Principal Direction Trees

Mark McCartin-Lim, Andrew McGregor, Rui Wang

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Tags: Computer science, Data Structures and Algorithms, Machine learning, nVidia, nVidia GeForce GTX 470

June 25, 2012 by hgpu

Adaptive fast multipole methods on the GPU

Anders Goude, Stefan Engblom

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Tags: Computer science, CUDA, Data Structures and Algorithms, Fast multipole method, nVidia, Package, Tesla C2075

May 23, 2012 by hgpu

Multi-target vectorization with MTPS C++ generic library

Wilfried Kirschenmann, Laurent Plagne, Stephane Vialle

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Tags: Computer science, CUDA, Data Structures and Algorithms, nVidia, nVidia Quadro FX 5800

March 22, 2012 by hgpu

CLUEstering: a high-performance density-based clustering library for scientific computing

PyOMP: OpenMP for Python in Numba

PyOMP: Parallel programming for CPUs and GPUs with OpenMP and Python

GPPerf: Energy-Aware GPU Performance Prediction and Optimization Framework

Understanding GEMM Performance and Energy on NVIDIA Ada Lovelace: A Machine Learning-Based Analytical Approach

HiRep

Scaling SU(2) to 1000 GPUs using HiRep

Gaia AVU-GSR

Performance portability via C++ PSTL, SYCL, OpenMP, and HIP: the Gaia AVU-GSR case study

gpuPairHMM: Ultra-fast GPU-based PairHMM for DNA Variant Calling

gpuPairHMM: High-speed Pair-HMM Forward Algorithm for DNA Variant Calling on GPUs

See all packages

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high performance computing on graphics processing units: hgpu.org

Massively parallel read mapping on GPUs with PEANUT

Data Structures and Algorithms for Counting Problems on Graphs using GPU

ACL2 Meets the GPU: Formalizing a CUDA-based Parallelizable All-Pairs Shortest Path Algorithm in ACL2

A Novel Data Structure for Particle System Simulation based on GPU with the Use of Neighborhood Grids

GPU Accelerated Multiple Deoxyribose Nucleic Acid Sequence Parallel Matching

Parallel Peeling Algorithms

Efficient Parallel and External Matching

A structural analysis of the A5/1 state transition graph

Performance Evaluation of Concurrent Lock-free Data Structures on GPUs

Approximate Principal Direction Trees

Adaptive fast multipole methods on the GPU

Multi-target vectorization with MTPS C++ generic library

Recent source codes

tdg-benchs: benchmarks used to test the performance of taskgraph

SW#SYCL

LLOR: Automatic Repair of OpenMP Programs

Solomon: Simple Off-LOading Macros Orchestrating multiple Notations

CLUEstering: a high-performance density-based clustering library for scientific computing

PyOMP: OpenMP for Python in Numba

GPPerf: Energy-Aware GPU Performance Prediction and Optimization Framework

HiRep

Gaia AVU-GSR

gpuPairHMM: Ultra-fast GPU-based PairHMM for DNA Variant Calling

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