high performance computing on graphics processing units: hgpu.org

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hgpu.org » Applications » Biology

Efficient Implementation of MrBayes on multi-GPU

Jie Bao, Hongju Xia, Jianfu Zhou, Xiaoguang Liu, Gang Wang

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Tags: Bayesian, Biology, CUDA, GPU cluster, nVidia, nVidia GeForce GTX 480, Package, Task scheduling

January 28, 2013 by hgpu

The effects of nutrient chemotaxis on bacterial aggregation patterns with non-linear degenerate cross diffusion

J. Francisco Leyva, Carlos Malaga, Ramon G. Plaza

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Tags: Biological Physics, Biology, CUDA, Numerical simulation, nVidia, Tesla C2070

January 23, 2013 by hgpu

Burrows-Wheeler Aligner: A Parallel Approach

Sheridan Lee Wright

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Tags: Algorithms, Bioinformatics, Biology, CUDA, MPI, nVidia, Sequence alignment, Thesis

January 16, 2013 by hgpu

Acceleration of Selective Cationic Antibacterial Peptides computation: A comparison of FPGA and GPU approaches

D. Garcia-Ordaz, M. Arias-Estrada, M. Nuno-Maganda, C. Polanco, G. Del Rio

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Tags: Bioinformatics, Biology, CUDA, FPGA, nVidia, nVidia GeForce GT 230 M, nVidia GeForce GTX 480, Tesla M2070

January 13, 2013 by hgpu

Optimizations in Bioinformatics using GPU Processing on Binary Data

Manuel Belmadani

Tags: Algorithms, Bioinformatics, Biology, CUDA, nVidia, nVidia GeForce GTX 285

January 8, 2013 by hgpu

GPU-Optimized Coarse-Grained MD Simulations of Protein and RNA Folding and Assembly

Andrew J. Proctor, Tyson J. Lipscomb, Anqi Zou, Joshua A. Anderson, Samuel S. Cho

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Tags: Bioinformatics, Biology, CUDA, Macromolecule, Molecular dynamics, nVidia, RNA, Tesla C2070

January 8, 2013 by hgpu

Long Timestep Molecular Dynamics on the Graphical Processing Unit

James C. Sweet, Ronald J. Nowling, Trevor Cickovski, Christopher R. Sweet, Vijay S. Pande, Jesus A. Izaguirre

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Tags: Biology, Chemistry, CUDA, Molecular dynamics, nVidia, nVidia GeForce GTX 580, OpenCL, Package

January 4, 2013 by hgpu

High performance bioinformatics and computational biology on general-purpose graphics processing units

Cheng Ling

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Tags: Bioinformatics, Biology, Computational biology, CUDA, FPGA, nVidia, nVidia GeForce 8800 GTX, nVidia GeForce GTX 460, Sequence alignment, Thesis

January 3, 2013 by hgpu

Radionuclides migration modelling using artificial neural networks and parallel computing

O.S. Hilko, S.P. Kundas, I.A. Gishkeluk

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Tags: Algorithms, Biology, CUDA, MPI, Neural networks, nVidia, nVidia GeForce 9500 GT, nVidia GeForce 9800 GT, nVidia GeForce GT 220 M

December 29, 2012 by hgpu

Bioinformatics Sequence Comparisons on Manycore Processors

Tuan Tu Tran

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Tags: ATI, ATI Radeon HD 5870, Bioinformatics, Biology, nVidia, nVidia GeForce GTX 480, OpenCL, Review, Sequence matching, Thesis

December 25, 2012 by hgpu

Efficient reconstruction of biological networks via transitive reduction on general purpose graphics processors

Dragan Bosnacki, Maximilian R Odenbrett, Anton Wijs, Willem Ligtenberg, Peter Hilbers

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Tags: Algorithms, Bioinformatics, Biology, CUDA, nVidia, nVidia GeForce GTX 480, Package

November 23, 2012 by hgpu

G-SNPM – A GPU-based SNP mapping tool

Alessandro Orro, Andrea Manconi, Emanuele Manca, Giuliano Armano, Luciano Milanesi

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Tags: Algorithms, Bioinformatics, Biology, CUDA, Next-Generation sequencing, nVidia, nVidia GeForce GTX 480, Package, Python, Smith-Waterman algorithm

November 14, 2012 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

Applications

Efficient Implementation of MrBayes on multi-GPU

The effects of nutrient chemotaxis on bacterial aggregation patterns with non-linear degenerate cross diffusion

Burrows-Wheeler Aligner: A Parallel Approach

Acceleration of Selective Cationic Antibacterial Peptides computation: A comparison of FPGA and GPU approaches

Optimizations in Bioinformatics using GPU Processing on Binary Data

GPU-Optimized Coarse-Grained MD Simulations of Protein and RNA Folding and Assembly

Long Timestep Molecular Dynamics on the Graphical Processing Unit

High performance bioinformatics and computational biology on general-purpose graphics processing units

Radionuclides migration modelling using artificial neural networks and parallel computing

Bioinformatics Sequence Comparisons on Manycore Processors

Efficient reconstruction of biological networks via transitive reduction on general purpose graphics processors

G-SNPM – A GPU-based SNP mapping tool

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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