high performance computing on graphics processing units: hgpu.org

Applications

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

Parallelized Hierarchical Expected Matching Probability for Multiple Sequence Alignment

Kedhar M, DR. M. Rajasekhara Babu, Mayank G, Abhinivesh M

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Tags: Bioinformatics, Biology, CUDA, nVidia, Programming techniques, RNA, Sequence alignment, Tesla C2070

July 12, 2014 by hgpu

Visualization and Correction of Automated Segmentation, Tracking and Lineaging from 5-D Stem Cell Image Sequences

Eric Wait, Mark Winter, Chris Bjornsson, Erzsebet Kokovay, Yue Wang, Susan Goderie, Sally Temple, Andrew Cohen

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Tags: Biology, Computer science, CUDA, Graphics, Image processing, Microscopy, nVidia, nVidia GeForce GTX 430, Visualization

July 11, 2014 by hgpu

gpu_tracker: Context manager and CLI that tracks the computational-resource-usage of a code block or shell command, particularly the GPU usage

gpu_tracker: Python package for tracking and profiling GPU utilization in both desktop and high-performance computing environments

LOOPer: a polyhedral compiler for expressing fast and portable data parallel algorithms

LOOPer: A Learned Automatic Code Optimizer For Polyhedral Compilers

OpenMC Monte Carlo Code

Performance Portable Monte Carlo Particle Transport on Intel, NVIDIA, and AMD GPUs

Polygeist: C/C++ frontend for MLIR

Retargeting and Respecializing GPU Workloads for Performance Portability

Parallel Gaussian process with kernel approximation in CUDA

Optical flow algorithms for SYCL

SYCL in the edge: performance and energy evaluation for heterogeneous acceleration

OpenMP5-Offload-OpenMC-Intel-PVC

Distributed OpenMP Offloading of OpenMC on Intel GPU MAX Accelerators

See all packages

* * *

high performance computing on graphics processing units: hgpu.org

Applications

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

Parallelized Hierarchical Expected Matching Probability for Multiple Sequence Alignment

Visualization and Correction of Automated Segmentation, Tracking and Lineaging from 5-D Stem Cell Image Sequences

Recent source codes

QArray

Celerity: High-level C++ for Accelerator Clusters

CIFAR-10 Airbench: 94% on CIFAR-10 in 3.29 second

gpu_tracker: Context manager and CLI that tracks the computational-resource-usage of a code block or shell command, particularly the GPU usage

LOOPer: a polyhedral compiler for expressing fast and portable data parallel algorithms

OpenMC Monte Carlo Code

Polygeist: C/C++ frontend for MLIR

Parallel Gaussian process with kernel approximation in CUDA

Optical flow algorithms for SYCL

OpenMP5-Offload-OpenMC-Intel-PVC

Most viewed papers (last 30 days)