high performance computing on graphics processing units: hgpu.org

Applications

Finding Longest Common Subsequences by GPU-Based Parallel Ant Colony Optimization

David Markvica

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Tags: Algorithms, Biology, Computational biology, Computer science, Heterogeneous systems, Metaheuristics, nVidia, nVidia GeForce GTX 560 Ti, OpenCL, Optimization, Pattern recognition, Thesis

October 27, 2014 by hgpu

On the Efficiency of CPU and Hybrid CPU-GPU Systems in Computational Biology Tasks

Nikolay Pydiura, Pavel Karpov, Yaroslav Blume

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Tags: AMD Radeon R9 280, ATI, Biology, Computational biology, CUDA, Molecular dynamics, nVidia, nVidia GeForce GTX 480, OpenCL

October 25, 2014 by hgpu

Massively parallel read mapping on GPUs with the q-group index and PEANUT

Johannes Koster, Sven Rahmann

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Tags: Algorithms, Bioinformatics, Biology, nVidia, nVidia GeForce GTX 780, OpenCL

October 20, 2014 by hgpu

Accelerating Protein Coordinate Conversion using GPUs

Mahsa Bayati, Jaydeep P. Bardhan, David M. King, Miriam Leeser

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Tags: Algorithms, Bioinformatics, Biology, CUDA, nVidia, Tesla C2075

October 10, 2014 by hgpu

MEGAHIT: An ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph

Dinghua Li, Chi-Man Liu, Ruibang Luo, Kunihiko Sadakane, Tak-Wah Lam

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Tags: Biology, CUDA, Genomics, nVidia, Package, Tesla K40

September 29, 2014 by hgpu

Calculation of Force Field Grids for Molecular Docking Using Graphics Processing Unit

Mikhail A. Farkov

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Tags: Algorithms, Bioinformatics, Biology, CUDA, molecular docking, nVidia, nVidia GeForce GT 440, Tesla K20, Tesla M2090

September 24, 2014 by hgpu

A Software Framework for the Detection and Classification of Biological Targets in Bio-Nano Sensing

Abdul Hafeez

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Tags: Biology, Biophysics, CUDA, Distributed computing, Filtering, nVidia, nVidia Quadro FX 580, Sensing, Thesis

September 19, 2014 by hgpu

Machine learning for ultrafast X-ray diffraction patterns on large-scale GPU clusters

Tomas Ekeberg, Stefan Engblom, Jing Liu

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Tags: Algorithms, Biological Physics, Biology, Biomolecules, Cluster computing, Computational Complexity, CUDA, GPU cluster, Machine learning, nVidia, nVidia GeForce GTX 680, OpenMPI

September 16, 2014 by hgpu

Parallel Computation of Non-Bonded Interactions in Drug Discovery: Nvidia GPUs vs. Intel Xeon Phi

Jianbin Fang, Ana Lucia Varbanescu, Baldomero Imbernon, Jose M. Cecilia, Horacio Perez-Sanchez

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Tags: Bioinformatics, Biology, CUDA, Electrostatics, Intel Xeon Phi, nVidia, Performance, Pharmaceuticals, Tesla K20

September 13, 2014 by hgpu

A Reduction of the Elastic Net to Support Vector Machines with an Application to GPU Computing

Quan Zhou, Wenlin Chen, Shiji Song, Jacob R. Gardner, Kilian Q. Weinberger, Yixin Chen

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Tags: Algorithms, Biology, CUDA, Genetics, Machine learning, Neuroscience, nVidia, nVidia GeForce GTX Titan, Statistics

September 9, 2014 by hgpu

Convex Clustering: An Attractive Alternative to Hierarchical Clustering

Gary K. Chen, Eric Chi, John Ranola, Kenneth Lange

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Tags: Algorithms, Bioinformatics, Biology, Cluster analysis, Clustering, Genomics, Hierarchical clustering, nVidia, OpenCL, Package, Tesla C2050

September 9, 2014 by hgpu

Faster sequence alignment through GPU-accelerated restriction of the seed-and-extend search space

Richard Wilton, Tamas Budavari, Ben Langmead, Sarah Wheelan, Steven L. Salzberg, Alex Szalay

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Tags: Bioinformatics, Biology, CUDA, nVidia, Sequence alignment, Tesla K20

August 10, 2014 by hgpu

Mutual-Supervised Learning for Sequential-to-Parallel Code Translation

Hardware Compute Partitioning on NVIDIA GPUs for Composable Systems

KISim: Kubernetes Intelligent Scheduling Simulator

KIS-S: A GPU-Aware Kubernetes Inference Simulator with RL-Based Auto-Scaling

Efficient GPU Implementation of Multi-Precision Integer Division

exa-AMD: Exascale Accelerated Materials Discovery

Accelerated discovery and design of Fe-Co-Zr magnets with tunable magnetic anisotropy through machine learning and parallel computing

ParEval: A Parallel Code Evaluation Benchmark

ParEval-Repo: A Benchmark Suite for Evaluating LLMs with Repository-level HPC Translation Tasks

FlashSparse: Minimizing Computation Redundancy for Fast Sparse Matrix Multiplications on Tensor Cores

Libra: Synergizing CUDA and Tensor Cores for High-Performance Sparse Matrix Multiplication

WiLLM: An Open Wireless LLM Communication System

Vcc: the Vulkan Clang Compiler

No More Shading Languages: Compiling C++ to Vulkan Shaders

hpcbench: A set of benchmarking utilities for biomolecular simulation tools

Engineering Supercomputing Platforms for Biomolecular Applications

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high performance computing on graphics processing units: hgpu.org

Applications

Finding Longest Common Subsequences by GPU-Based Parallel Ant Colony Optimization

On the Efficiency of CPU and Hybrid CPU-GPU Systems in Computational Biology Tasks

Massively parallel read mapping on GPUs with the q-group index and PEANUT

Accelerating Protein Coordinate Conversion using GPUs

MEGAHIT: An ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph

Calculation of Force Field Grids for Molecular Docking Using Graphics Processing Unit

A Software Framework for the Detection and Classification of Biological Targets in Bio-Nano Sensing

Machine learning for ultrafast X-ray diffraction patterns on large-scale GPU clusters

Parallel Computation of Non-Bonded Interactions in Drug Discovery: Nvidia GPUs vs. Intel Xeon Phi

A Reduction of the Elastic Net to Support Vector Machines with an Application to GPU Computing

Convex Clustering: An Attractive Alternative to Hierarchical Clustering

Faster sequence alignment through GPU-accelerated restriction of the seed-and-extend search space

Recent source codes

Mutual-Supervised Learning for Sequential-to-Parallel Code Translation

Hardware Compute Partitioning on NVIDIA GPUs for Composable Systems

KISim: Kubernetes Intelligent Scheduling Simulator

Efficient GPU Implementation of Multi-Precision Integer Division

exa-AMD: Exascale Accelerated Materials Discovery

ParEval: A Parallel Code Evaluation Benchmark

FlashSparse: Minimizing Computation Redundancy for Fast Sparse Matrix Multiplications on Tensor Cores

WiLLM: An Open Wireless LLM Communication System

Vcc: the Vulkan Clang Compiler

hpcbench: A set of benchmarking utilities for biomolecular simulation tools

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