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Performance Analysis of IBM Cell Broadband Engine on Sequence Alignment

Yang Song, Gregory M. Striemer, Ali Akoglu

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Tags: Bioinformatics, Biology, Cell processor, CUDA, nVidia, Sequence alignment, Smith-Waterman algorithm, Tesla C870

November 27, 2010 by hgpu

Acceleration of the Smith-Waterman Algorithm using Single and Multiple Graphics Processors

Ali Khajeh-Saeed, Stephen Poole, J. Blair Perot

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Tags: Bioinformatics, Biology, CUDA, nVidia, nVidia GeForce 9800 GT, nVidia GeForce 9800 GTX, nVidia GeForce GTX 295, Sequence matching, Smith-Waterman algorithm

November 18, 2010 by hgpu

CUDASW++ 2.0: enhanced Smith-Waterman protein database search on CUDA-enabled GPUs based on SIMT and virtualized SIMD abstractions

Yongchao Liu, Bertil Schmidt, Douglas Maskell

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Tags: Bioinformatics, Biology, Computational biology, CUDA, nVidia, nVidia GeForce GTX 280, nVidia GeForce GTX 295, Package, Smith-Waterman algorithm

November 6, 2010 by hgpu

CUDASW++: optimizing Smith-Waterman sequence database searches for CUDA-enabled graphics processing units

Yongchao Liu, Douglas Maskell, Bertil Schmidt

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Tags: Bioinformatics, Biology, Computational biology, CUDA, nVidia, nVidia GeForce GTX 280, nVidia GeForce GTX 295, Package, Smith-Waterman algorithm

November 4, 2010 by hgpu

GPU Accelerated Smith-Waterman

Yang Liu, Wayne Huang, John Johnson, Sheila Vaidya

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Tags: Bioinformatics, Biology, Computational biology, Computer science, GLSL, nVidia, nVidia GeForce 7800 GTX, OpenGL, Smith-Waterman algorithm

November 1, 2010 by hgpu

Bio-sequence database scanning on a GPU

Weiguo Liu, B. Schmidt, G. Voss, A. Schroder, W. Muller-Wittig

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Tags: Biology, Computational biology, GLSL, nVidia, nVidia GeForce 6800 GTO, nVidia GeForce 7800 GTX, OpenGL, Smith-Waterman algorithm

October 30, 2010 by hgpu

An efficient implementation of Smith Waterman algorithm on GPU using CUDA, for massively parallel scanning of sequence databases

Lukasz Ligowski, Witold Rudnicki

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Tags: Bioinformatics, Biology, Computational biology, Computer science, CUDA, nVidia, nVidia GeForce 9800 GX2, Sequence alignment, Smith-Waterman algorithm

October 28, 2010 by hgpu

CUDA compatible GPU cards as efficient hardware accelerators for Smith-Waterman sequence alignment

Svetlin Manavski, Giorgio Valle

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

October 28, 2010 by hgpu

Sequence alignment with GPU: Performance and design challenges

Gregory M. Striemer, Ali Akoglu

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Tags: Bioinformatics, Biology, Computational biology, Computer science, CUDA, nVidia, Package, Sequence alignment, Smith-Waterman algorithm, Tesla C870

October 27, 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

Performance Analysis of IBM Cell Broadband Engine on Sequence Alignment

Acceleration of the Smith-Waterman Algorithm using Single and Multiple Graphics Processors

CUDASW++ 2.0: enhanced Smith-Waterman protein database search on CUDA-enabled GPUs based on SIMT and virtualized SIMD abstractions

CUDASW++: optimizing Smith-Waterman sequence database searches for CUDA-enabled graphics processing units

GPU Accelerated Smith-Waterman

Bio-sequence database scanning on a GPU

An efficient implementation of Smith Waterman algorithm on GPU using CUDA, for massively parallel scanning of sequence databases

CUDA compatible GPU cards as efficient hardware accelerators for Smith-Waterman sequence alignment

Sequence alignment with GPU: Performance and design challenges

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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