high performance computing on graphics processing units: hgpu.org

Applications

Improving the Mapping of Smith-Waterman Sequence Database Searches onto CUDA-Enabled GPUs

Liang-Tsung Huang, Chao-Chin Wu, Lien-Fu Lai, Yun-Ju Li

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Tags: Bioinformatics, Biology, CUDA, Databases, nVidia, Sequence alignment, Smith-Waterman algorithm, Tesla C1060, Tesla K20

June 30, 2015 by hgpu

Concurrent Task Execution on the Intel Xeon Phi

Yucheng Zhu

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Tags: Bioinformatics, Biology, Computer science, CUDA, Intel Xeon Phi, nVidia, OpenMP, Sequence alignment, Smith-Waterman algorithm, Tesla K20, Thesis

June 22, 2015 by hgpu

Comparative Study of the Parallelization of the Smith-Waterman Algorithm on OpenMP and Cuda C

Amadou Chaibou, Oumarou Sie

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Tags: Bioinformatics, Biology, CUDA, nVidia, nVidia GeForce GTX 670, OpenMP, Sequence alignment, Smith-Waterman algorithm

June 22, 2015 by hgpu

Implementation of K-shortest Path Algorithm in GPU Using CUDA

Avadhesh Pratap Singh, Dhirendra Pratap Singh

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Tags: Bioinformatics, Biology, Computer science, CUDA, nVidia, Sequence alignment, Tesla C2075

June 7, 2015 by hgpu

Genetically Improved BarraCUDA

W. B. Langdon, Brian Yee Hong Lam

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Tags: Algorithms, Benchmarking, Biology, CUDA, Genomics, nVidia, nVidia GeForce GT 730, Package, Tesla K20, Tesla K40, Tesla K80

June 1, 2015 by hgpu

Flexible, Fast and Accurate Sequence Alignment Profiling on GPGPU with PaSWAS

Sven Warris, Feyruz Yalcin, Katherine J. L. Jackson, Jan Peter Nap

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Tags: Bioinformatics, Biology, CUDA, nVidia, nVidia GeForce GTX 285, nVidia GeForce GTX 295, Package, Sequence alignment, Smith-Waterman algorithm, Tesla C1060

April 7, 2015 by hgpu

Accelerating complex brain-model simulations on GPU platforms

H.A. Du Nguyen, Zaid Al-Ars, Georgios Smaragdos, Christos Strydis

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Tags: Biology, CUDA, nVidia, nVidia GeForce GT 640, nVidia GeForce GTX 480, Tesla C2075, Tesla K20

March 30, 2015 by hgpu

Real-time multi-view deconvolution

Benjamin Schmid, Jan Huisken

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Tags: Biology, CUDA, Microscopy, nVidia, nVidia GeForce GTX Titan, Package

March 30, 2015 by hgpu

Arioc: high-throughput read alignment with GPU-accelerated exploration of the seed-and-extend search space

Richard Wilton, Tamas Budavari, Ben Langmead, Sarah J. Wheelan, Steven L. Salzberg, Alexander S. Szalay

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

March 28, 2015 by hgpu

Parallelization, Scalability, and Reproducibility in Next-Generation Sequencing Analysis

Johannes Koster

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Tags: Algorithms, Bayesian, Bioinformatics, Biology, Filtering, Next-Generation sequencing, nVidia, nVidia GeForce GTX 580, nVidia GeForce GTX 780, OpenCL, Package, Thesis

March 23, 2015 by hgpu

Implementation of Smith-Waterman algorithm in OpenCL for GPUs

Dzmitry Razmyslovich, Guillermo Marcus, Markus Gipp, Marc Zapatka, Andreas Szillus

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Tags: Bioinformatics, Biology, nVidia, nVidia GeForce GTX 480, OpenCL, Package, Sequence alignment, Smith-Waterman algorithm

February 27, 2015 by azhar ali

NMF-mGPU: non-negative matrix factorization on multi-GPU systems

Edgardo Mejia-Roa, Daniel Tabas-Madrid, Javier Setoain, Carlos Garcia, Francisco Tirado, Alberto Pascual-Montano

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Tags: Algorithms, Bioinformatics, Biology, CUDA, Factorization, GPU cluster, MPI, Nonnegative matrix factorization, nVidia, Package, Tesla C1060

February 19, 2015 by hgpu

SimSYCL: Synchronous, single-threaded, library-only SYCL implementation for debugging and verification

SimSYCL: A SYCL Implementation Targeting Development, Debugging, Simulation and Conformance

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

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

94% on CIFAR-10 in 3.29 Seconds on a Single GPU

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

See all packages

* * *

high performance computing on graphics processing units: hgpu.org

Applications

Improving the Mapping of Smith-Waterman Sequence Database Searches onto CUDA-Enabled GPUs

Concurrent Task Execution on the Intel Xeon Phi

Comparative Study of the Parallelization of the Smith-Waterman Algorithm on OpenMP and Cuda C

Implementation of K-shortest Path Algorithm in GPU Using CUDA

Genetically Improved BarraCUDA

Flexible, Fast and Accurate Sequence Alignment Profiling on GPGPU with PaSWAS

Accelerating complex brain-model simulations on GPU platforms

Real-time multi-view deconvolution

Arioc: high-throughput read alignment with GPU-accelerated exploration of the seed-and-extend search space

Parallelization, Scalability, and Reproducibility in Next-Generation Sequencing Analysis

Implementation of Smith-Waterman algorithm in OpenCL for GPUs

NMF-mGPU: non-negative matrix factorization on multi-GPU systems

Recent source codes

SimSYCL: Synchronous, single-threaded, library-only SYCL implementation for debugging and verification

GPU plugin for PySCF

QArray

Celerity: High-level C++ for Accelerator Clusters

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

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

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

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