high performance computing on graphics processing units: hgpu.org

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hgpu.org » Applications » Biology

CUSHAW: a CUDA compatible short read aligner to large genomes based on the Burrows-Wheeler transform

Yongchao Liu, Bertil Schmidt, Douglas L. Maskell

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Tags: Bioinformatics, Biology, CUDA, nVidia, Package, Tesla C2050

June 21, 2012 by hgpu

Parallel Implementation of the Wu-Manber Algorithm Using the OpenCL Framework

Themistoklis K. Pyrgiotis, Charalampos S. Kouzinopoulos, Konstantinos G. Margaritis

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Tags: Algorithms, Biology, Computational biology, Databases, nVidia, nVidia GeForce GTX 280, OpenCL, Pattern Search, Sequence matching

June 20, 2012 by hgpu

GPUmotif: An Ultra-Fast and Energy-Efficient Motif Analysis Program Using Graphics Processing Units

Pooya Zandevakili, Ming Hu, Zhaohui Qin

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Tags: Algorithms, Biochemistry, Biology, Chemistry, Computational biology, Computer science, CUDA, Genetics, nVidia, nVidia GeForce GTX 260, nVidia GeForce GTX 480, Package

June 17, 2012 by hgpu

Range query processing in a multi-GPU environment

Ricardo J. Barrientos, Jose I. Gomez, Christian Tenllado, Manuel Prieto Matias, Mauricio Marin

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Tags: Algorithms, Biology, Computational biology, Computer science, CUDA, Databases, GPU cluster, nVidia, OpenMP, Tesla C1060

June 11, 2012 by hgpu

CUDAICA: GPU optimization of Infomax-ICA EEG analysis

Federico Raimondo, Juan Kamienkowski, Mariano Sigman, Diego Fernandez Slezak

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Tags: Algorithms, Biology, CUBLAS, CUDA, Linear Algebra, Matrix multiplication, Neuroscience, nVidia, nVidia GeForce GTX 560, Package, Tesla C2070

June 11, 2012 by hgpu

Multi-dimensional characterization of electrostatic surface potential computation on graphics processors

Mayank Daga, Wu-chun Feng

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Tags: Algorithms, Biology, Biomolecules, Computational Complexity, CUDA, Electrostatics, Molecular modeling, nVidia, Optimization, Tesla C1060, Tesla C2050

May 12, 2012 by hgpu

GHOSTM: A GPU-Accelerated Homology Search Tool for Metagenomics

Shuji Suzuki, Takashi Ishida, Ken Kurokawa, Yutaka Akiyama

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Tags: Algorithms, Biology, CUDA, Databases, Next-Generation sequencing, nVidia, Package, Tesla S1070

May 10, 2012 by hgpu

Simulating the Spread of Epidemics in Real-world Trading Networks using OpenCL

Martin Clauss

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Tags: Biology, Medicine, nVidia, nVidia GeForce GTX 470, nVidia Quadro 1000 M, OpenCL

May 4, 2012 by hgpu

Design of high-performance parallelized gene predictors in MATLAB

Sylvain Robert Rivard, Jean-Gabriel Mailloux, Rachid Beguenane, Hung Tien Bui,

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Tags: Algorithms, Bioinformatics, Biology, CUDA, FFT, Genetics, nVidia, nVidia GeForce GTX 560

April 13, 2012 by hgpu

An Algorithm for Fast Edit Distance Computation on GPUs

Reza Farivar, Harshit Kharbanda, Shivaram Venkataraman, Roy H. Campbell

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Tags: Algorithms, Bioinformatics, Biology, Computer science, CUDA, nVidia, nVidia GeForce GTX 275, Security, Sequence alignment

March 11, 2012 by hgpu

Multiscale Hemodynamics Using GPU Clusters

Mauro Bisson, Massimo Bernaschi, Simone Melchionna, Sauro Succi, Efthimios Kaxiras

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Tags: Biology, CUDA, Fluid dynamics, GPU cluster, Lattice Boltzmann model, Medicine, nVidia, Tesla C1060

February 17, 2012 by hgpu

LAMMPScuda – a new GPU accelerated Molecular Dynamics Simulations Package and its Application to Ion-Conducting Glasses

Christian Robert Trott

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Tags: Biology, Computational Physics, CUDA, Heterogeneous systems, Molecular dynamics, nVidia, nVidia GeForce GTX 280, nVidia GeForce GTX 470, Package, Physics, Polymer Systems, Tesla C1060, Thesis

February 13, 2012 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

CUSHAW: a CUDA compatible short read aligner to large genomes based on the Burrows-Wheeler transform

Parallel Implementation of the Wu-Manber Algorithm Using the OpenCL Framework

GPUmotif: An Ultra-Fast and Energy-Efficient Motif Analysis Program Using Graphics Processing Units

Range query processing in a multi-GPU environment

CUDAICA: GPU optimization of Infomax-ICA EEG analysis

Multi-dimensional characterization of electrostatic surface potential computation on graphics processors

GHOSTM: A GPU-Accelerated Homology Search Tool for Metagenomics

Simulating the Spread of Epidemics in Real-world Trading Networks using OpenCL

Design of high-performance parallelized gene predictors in MATLAB

An Algorithm for Fast Edit Distance Computation on GPUs

Multiscale Hemodynamics Using GPU Clusters

LAMMPScuda – a new GPU accelerated Molecular Dynamics Simulations Package and its Application to Ion-Conducting Glasses

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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