high performance computing on graphics processing units: hgpu.org

hgpu.org » Bioinformatics

Two-Level Approach to Efficient Visualization of Protein Dynamics

Ove Daae Lampe, I. Viola, N. Reuter, H. Hauser

Tags: Bioinformatics, Biology, Molecular dynamics, Rendering, Visualization

August 31, 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

Fine-grain Parallelism using Multi-core, Cell/BE, and GPU Systems

Frederico Pratas, Pedro Trancoso, Leonel Sousa, Alexandros Stamatakis, Guochun Shi, Volodymyr Kindratenko

Tags: Bioinformatics, Biology, Cell processor, CUDA, Molecular dynamics, nVidia

August 25, 2011 by hgpu

Network-on-Chip Hardware Accelerators for Biological Sequence Alignment

Souradip Sarkar, Gaurav Ramesh Kulkarni, Partha Pratim Pande, Ananth Kalyanaraman

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Tags: Algorithms, Bioinformatics, Biology, FPGA, Sequence alignment

August 12, 2011 by hgpu

Unifying stream based and reconfigurable computing to design application accelerators

Bruno Francisco, Frederico Pratas, Leonel Sousa

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Tags: Bioinformatics, Biology, Computer science, Data parallelism, FPGA, nVidia, nVidia GeForce GTX 285

August 2, 2011 by hgpu

High-Throughput Sequence Translation Using CUDA

Sun Wei-dong, Ma Zong-min

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

July 25, 2011 by hgpu

A Coarse Grain Reconfigurable Architecture for sequence alignment problems in bio-informatics

Pei Liu, A. Hemani

Tags: Algorithms, Bioinformatics, Biology, FPGA, Sequence alignment, Smith-Waterman algorithm

July 25, 2011 by hgpu

On the Robust Mapping of Dynamic Programming onto a Graphics Processing Unit

Shucai Xiao, A.M. Aji, Wu-chun Feng

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Tags: Algorithms, Bioinformatics, Biology, Cell processor, CUDA, Data parallelism, nVidia, nVidia GeForce GTX 280, Sequence alignment, Smith-Waterman algorithm

July 23, 2011 by hgpu

Harnessing the power of idle GPUs for acceleration of biological sequence alignment

Fumihiko Ino, Yuki Kotani, Yuma Munekawa, Kenichi Hagihara

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Tags: Bioinformatics, Biology, CUDA, nVidia, nVidia GeForce 7900 GTX, nVidia GeForce 7950 GX2, nVidia GeForce 8800 GTX, OpenGL, Sequence alignment

July 12, 2011 by hgpu

An Adaptive Hybrid Multiprocessor technique for bioinformatics sequence alignment

T. Bonny, M.A. Zidan, K.N. Salama

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Tags: Bioinformatics, Biology, CUDA, nVidia, nVidia Quadro FX 4800, Sequence alignment, Smith-Waterman algorithm

July 7, 2011 by hgpu

Striped Smith-Waterman speeds database searches six times over other SIMD implementations

M. Farrar

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Tags: Algorithms, Bioinformatics, Biology, Sequence alignment, Smith-Waterman algorithm

July 6, 2011 by hgpu

Six-fold speed-up of Smith-Waterman sequence database searches using parallel processing on common microprocessors

Torbjorn Rognes, Erling Seeberg

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Tags: Algorithms, Bioinformatics, Biology, Sequence alignment, Smith-Waterman algorithm

July 6, 2011 by hgpu

Over-synchronization in GPU Programs

profile_util: simple C++ library to report memory, timing, thread affinity

Profile Util library: A quick and easy way to get MPI, OpenMP and GPU runtime information

MaC: Mamba CPU performance predictor

MambaCPU: Enhanced Correlation Mining with State Space Models for CPU Performance Prediction

Mixed-precision finite element kernels

Mixed-precision finite element kernels and assembly: Rounding error analysis and hardware acceleration

SHMT: The Simultaneous and Heterogenous Multithreading project

General-Purpose Computing on Tensor Processors

Superpipeline: A Universal Approach for Reducing GPU Memory Usage in Large Models

EnergyUCB-Bandit

Online Energy Optimization in GPUs: A Multi-Armed Bandit Approach

See all packages

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high performance computing on graphics processing units: hgpu.org

Two-Level Approach to Efficient Visualization of Protein Dynamics

Rapid RNA Folding: Analysis and Acceleration of the Zuker Recurrence

Fine-grain Parallelism using Multi-core, Cell/BE, and GPU Systems

Network-on-Chip Hardware Accelerators for Biological Sequence Alignment

Unifying stream based and reconfigurable computing to design application accelerators

High-Throughput Sequence Translation Using CUDA

A Coarse Grain Reconfigurable Architecture for sequence alignment problems in bio-informatics

On the Robust Mapping of Dynamic Programming onto a Graphics Processing Unit

Harnessing the power of idle GPUs for acceleration of biological sequence alignment

An Adaptive Hybrid Multiprocessor technique for bioinformatics sequence alignment

Striped Smith-Waterman speeds database searches six times over other SIMD implementations

Six-fold speed-up of Smith-Waterman sequence database searches using parallel processing on common microprocessors

Recent source codes

Kokkidio: Kokkos+Eigen - write fast, readable multi-platform code

LLaMA-Inference-Bench

MATAR

Over-synchronization in GPU Programs

profile_util: simple C++ library to report memory, timing, thread affinity

MaC: Mamba CPU performance predictor

Mixed-precision finite element kernels

SHMT: The Simultaneous and Heterogenous Multithreading project

Superpipeline: A Universal Approach for Reducing GPU Memory Usage in Large Models

EnergyUCB-Bandit

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