high performance computing on graphics processing units: hgpu.org

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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

Simulating spiking neural networks on massively parallel graphical processing units using a code generation approach with GeNN

Esin Yavuz, James Turner, Thomas Nowotny

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Tags: Bioinformatics, Biology, Code generation, CUDA, Neural networks, Neuroscience, nVidia, Package, Tesla C2070

July 28, 2014 by hgpu

Performance Efficient DNA Sequence Detection on GPU Using Parallel Pattern Matching Approach

Rahul Shirude, Valmik B. Nikam, B.B. Meshram

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Tags: Bioinformatics, Biology, CUDA, nVidia, nVidia GeForce GTX Titan, RNA, Sequence alignment, String matching, Tesla K20

July 26, 2014 by hgpu

A Multi-GPU Compute Solution for Optimized Genomic Selection Analysis

Trevor DeVore

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Tags: Bayesian, Bioinformatics, Biology, CUDA, Heterogeneous systems, nVidia, Tesla K20, Tesla K40, Thesis

July 23, 2014 by hgpu

Over-synchronization in GPU Programs

profile_util: simple C++ library to report memory, timing, thread affinity

Profile Util library: A quick and easy way to get MPI, OpenMP and GPU runtime information

MaC: Mamba CPU performance predictor

MambaCPU: Enhanced Correlation Mining with State Space Models for CPU Performance Prediction

Mixed-precision finite element kernels

Mixed-precision finite element kernels and assembly: Rounding error analysis and hardware acceleration

SHMT: The Simultaneous and Heterogenous Multithreading project

General-Purpose Computing on Tensor Processors

Superpipeline: A Universal Approach for Reducing GPU Memory Usage in Large Models

EnergyUCB-Bandit

Online Energy Optimization in GPUs: A Multi-Armed Bandit Approach

See all packages

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high performance computing on graphics processing units: hgpu.org

Applications

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

Simulating spiking neural networks on massively parallel graphical processing units using a code generation approach with GeNN

Performance Efficient DNA Sequence Detection on GPU Using Parallel Pattern Matching Approach

A Multi-GPU Compute Solution for Optimized Genomic Selection Analysis

Recent source codes

Kokkidio: Kokkos+Eigen - write fast, readable multi-platform code

LLaMA-Inference-Bench

MATAR

Over-synchronization in GPU Programs

profile_util: simple C++ library to report memory, timing, thread affinity

MaC: Mamba CPU performance predictor

Mixed-precision finite element kernels

SHMT: The Simultaneous and Heterogenous Multithreading project

Superpipeline: A Universal Approach for Reducing GPU Memory Usage in Large Models

EnergyUCB-Bandit

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