high performance computing on graphics processing units: hgpu.org

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Protein alignment algorithms with an efficient backtracking routine on multiple GPUs

Jacek Blazewicz, Wojciech Frohmberg, Michal Kierzynka, Erwin Pesch, Pawel Wojciechowski

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Tags: Bioinformatics, Biology, CUDA, nVidia, nVidia GeForce GTX 280, nVidia GeForce GTX 480, Package, Sequence alignment, Tesla S1070

June 21, 2011 by hgpu

The accelerating implementation of BLAST with stream processor

Gang Wei, Chao Ma, Songwen Pei, Baifeng Wu

Tags: ATI, ATI Radeon HD 4850, Bioinformatics, Biology, BLAST, Brook, Sequence alignment

June 15, 2011 by hgpu

The scoring sequences on profile Hidden Markov Models with delete states elimination by GPUs

Jun Li, Yanhui Li, Shuangping Chen

Tags: Bioinformatics, Computer science, nVidia, nVidia GeForce 9800 GTX, Sequence alignment

June 10, 2011 by hgpu

Highly efficient mapping of the Smith-Waterman algorithm on CUDA-compatible GPUs

K. Dohi, K. Benkridt, C. Ling, T. Hamada, Y. Shibata

Tags: Bioinformatics, Biology, CUDA, nVidia, Sequence alignment, Smith-Waterman algorithm

May 31, 2011 by hgpu

GPU Based Parallel Computing on Blast Program

Huang Lican, Hu Ya

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Tags: Bioinformatics, Biology, BLAST, Sequence alignment

May 7, 2011 by hgpu

Accelerating scientific applications using GPU’s

M. Taher

Tags: Bioinformatics, Biology, Computer science, CUDA, FFT, nVidia, Security, Sequence alignment

May 3, 2011 by hgpu

Parallel Approaches for SWAMP Sequence Alignment

Shannon Steinfadt, Kevin Schaffer

Tags: Bioinformatics, Biology, Cell processor, FPGA, nVidia, Sequence alignment, Smith-Waterman algorithm

April 19, 2011 by hgpu

CUDA-BLASTP: Accelerating BLASTP on CUDA-Enabled Graphics Hardware

Weiguo Liu, Bertil Schmidt, Wolfgang Muller-Wittig

Source codes

Tags: Bioinformatics, Biology, BLAST, CUDA, nVidia, nVidia GeForce GTX 295, Package, Sequence alignment

April 18, 2011 by hgpu

Accelerating global sequence alignment using CUDA compatible multi-core GPU

T.R.P. Siriwardena, D.N. Ranasinghe

Tags: Bioinformatics, Biology, CUDA, nVidia, Sequence alignment

April 10, 2011 by hgpu

On accelerating iterative algorithms with CUDA: A case study on Conditional Random Fields training algorithm for biological sequence alignment

Zhihui Du, Zhaoming Yin, Wenjie Liu, D. Bader

Tags: Bioinformatics, Biology, CUDA, nVidia, Sequence alignment

April 8, 2011 by hgpu

A Hybrid Computational Grid Architecture for Comparative Genomics

A. Singh, Chen Chen, Weiguo Liu, W. Mitchell, B. Schmidt

Tags: Bioinformatics, Biology, Genetics, Sequence alignment

April 6, 2011 by hgpu

The optimization of parallel Smith-Waterman sequence alignment using on-chip memory of GPGPU

Qian Zhang, Hong An, Gu Liu, Wenting Han, Ping Yao, Mu Xu, Xiaoqiang Li

Tags: Bioinformatics, Biology, CUDA, nVidia, Sequence alignment, Smith-Waterman algorithm

April 4, 2011 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

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