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On the design of architecture-aware algorithms for emerging applications

Seunghwa Kang

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Tags: Algorithms, Benchmarking, Biology, Cell processor, Computational biology, CUDA, Image processing, MapReduce, nVidia, Package, Tesla C1060, Thesis

December 2, 2011 by hgpu

Bit-Parallel Multiple Pattern Matching

Tuan Tu Tran, Mathieu Giraud, Jean-Stephane Varre

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Tags: Algorithms, ATI, ATI Radeon HD 5870, Biology, Computational biology, nVidia, nVidia GeForce GTX 480, OpenCL

November 10, 2011 by hgpu

GPU Computations in Heterogeneous Grid Environments

Marcus Hinders

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Tags: ATI, ATI Radeon HD 5870, Biology, Computational biology, Computer science, Grid, Heterogeneous systems, nVidia, nVidia GeForce 8600 GT, nVidia GeForce GTX 280, OpenCL, Thesis

October 30, 2011 by hgpu

Computational Biology and Applied Bioinformatics

Heitor Silverio Lopes, Leonardo Magalhaes Cruz

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Tags: Bioinformatics, Biology, Book, Computational biology, CUDA, nVidia, Review, Sequence alignment, Spectrometry

October 23, 2011 by hgpu

GPU Computation in Bioinspired Algorithms: A Review

M. G. Arenas, A. M. Mora, G. Romero and P. A. Castillo

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Tags: Algorithms, ATI, Bioinformatics, Biology, Computational biology, CUDA, nVidia, OpenCL, Overview, Review

September 8, 2011 by hgpu

Rapid RNA Folding: Analysis and Acceleration of the Zuker Recurrence

Arpith C. Jacob, Jeremy D. Buhler, Roger D. Chamberlain

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Tags: Algorithms, Bioinformatics, Biology, Computational biology, CUDA, FPGA, nVidia, nVidia GeForce GTX 280, RNA, Tesla C870

August 27, 2011 by hgpu

Parallelizing the Cellular Potts Model on graphics processing units

Jose J. Tapia, Roshan M. D'Souza

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Tags: Biology, Computational biology, CUDA, nVidia, Tesla C1060

July 22, 2011 by hgpu

Size Matters: Space/Time Tradeoffs to Improve GPGPU Applications Performance

Abdullah Gharaibeh, Matei Ripeanu

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Tags: Bioinformatics, Biology, Computational biology, CUDA, nVidia, nVidia GeForce 8800 GTX, Package, Sequence alignment, Short read mapping, Suffix trees

February 27, 2011 by hgpu

Fast Exact String Matching on the GPU

Michael C. Schatz, Cole Trapnell

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Tags: Algorithms, Computational biology, Computer science, CUDA, nVidia, nVidia GeForce 8800 GTX, Package, Search, String matching, Suffix trees

February 20, 2011 by hgpu

A parameterisable and scalable Smith-Waterman algorithm implementation on CUDA-compatible GPUs

Cheng Ling, Khaled Benkrid, Tsuyoshi Hamada

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Tags: Bioinformatics, Biology, Computational biology, CUDA, nVidia, nVidia GeForce 8800 GTX, Sequence alignment, Smith-Waterman algorithm

January 4, 2011 by hgpu

Analysis of a Computational Biology Simulation Technique on Emerging Processing Architectures

Jeremy S. Meredith, Sadaf R. Alam, Jeffrey S. Vetter

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Tags: Biology, Cell processor, Cg, Computational biology, Molecular dynamics, nVidia, nVidia GeForce 7900 GTX

January 2, 2011 by hgpu

Source-to-Source Optimization of CUDA C for GPU Accelerated Cardiac Cell Modeling

Fred V. Lionetti, Andrew D. McCulloch, Scott B. Baden

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Tags: Computational biology, Computer science, CUDA, High-level Languages, nVidia, nVidia GeForce GTX 295, Optimization

December 29, 2010 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

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high performance computing on graphics processing units: hgpu.org

On the design of architecture-aware algorithms for emerging applications

Bit-Parallel Multiple Pattern Matching

GPU Computations in Heterogeneous Grid Environments

Computational Biology and Applied Bioinformatics

GPU Computation in Bioinspired Algorithms: A Review

Rapid RNA Folding: Analysis and Acceleration of the Zuker Recurrence

Parallelizing the Cellular Potts Model on graphics processing units

Size Matters: Space/Time Tradeoffs to Improve GPGPU Applications Performance

Fast Exact String Matching on the GPU

A parameterisable and scalable Smith-Waterman algorithm implementation on CUDA-compatible GPUs

Analysis of a Computational Biology Simulation Technique on Emerging Processing Architectures

Source-to-Source Optimization of CUDA C for GPU Accelerated Cardiac Cell Modeling

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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