high performance computing on graphics processing units: hgpu.org

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hgpu.org » Applications » Biology

GPU-Accelerated DNA Distance Matrix Computation

Zhi Ying, Xinhua Lin, Simon Chong-Wee See, Minglu Li

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Tags: ATI, ATI Radeon HD 5850, Bioinformatics, Biology, Genetics, nVidia, OpenCL, Performance, Tesla C2050

October 3, 2011 by hgpu

Large Scale DNA Sequence Alignment and Kernel Method Implemented with GPUs

Songwen Pei, Wenhao Wang, Gang Wei, Baifeng Wu

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Tags: Algorithms, ATI, ATI Radeon HD 4870, Bioinformatics, Biology, Brook, Sequence alignment

October 1, 2011 by hgpu

Manycore high-performance computing in bioinformatics

Jean-Stephane Varre, Bertil Schmidt, Stephane Janot, Mathieu Giraud

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Tags: Algorithms, Bioinformatics, Biology, CUDA, nVidia, OpenCL, Review, RNA, Sequence alignment

September 26, 2011 by hgpu

Accelerating reaction-diffusion simulations with general-purpose graphics processing units

Matthias Vigelius, Aidan Lane, Bernd Meyer

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Tags: Algorithms, Bioinformatics, Biology, CUDA, nVidia, Package, Rendering, Stochastic simulation

September 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

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

EpiGPU

Gibran Hemani, Athanasios Theocharidis, Wenhua Wei, Chris Haley

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Tags: ATI, Biology, Genetics, nVidia, OpenCL

August 21, 2011 by hgpu

Visual Computing in Biology and Medicine: Interactive visual analysis of contrast-enhanced ultrasound data based on small neighborhood statistics

Paolo Angelelli, Kim Nylund, Odd Helge Gilja, Helwig Hauser

Tags: Biology, Medicine, OpenCL, Ultrasound, Visualization

August 21, 2011 by hgpu

FPGA acceleration of rigid-molecule docking codes

Bharat Sukhwani, Martin C. Herbordt

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Tags: Biology, Biomolecules, CUDA, FPGA, Molecular modeling, nVidia, Performance, Tesla C1060

August 15, 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

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

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high performance computing on graphics processing units: hgpu.org

Applications

GPU-Accelerated DNA Distance Matrix Computation

Large Scale DNA Sequence Alignment and Kernel Method Implemented with GPUs

Manycore high-performance computing in bioinformatics

Accelerating reaction-diffusion simulations with general-purpose graphics processing units

GPU Computation in Bioinspired Algorithms: A Review

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

EpiGPU

Visual Computing in Biology and Medicine: Interactive visual analysis of contrast-enhanced ultrasound data based on small neighborhood statistics

FPGA acceleration of rigid-molecule docking codes

Network-on-Chip Hardware Accelerators for Biological Sequence Alignment

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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