high performance computing on graphics processing units: hgpu.org

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hgpu.org » Applications » Biology

Graphics Processing Unit-Accelerated Quantitative Trait Loci Detection

Guillaume Chapuis, Olivier Filangi, Dominique Lavenier, Jean Michel J. M. Elsen, Pascale Leroy

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

November 16, 2013 by hgpu

Accelerating calculations of RNA secondary structure partition functions using GPUs

Harry A Stern, David H Mathews

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Tags: Bioinformatics, Biology, CUDA, nVidia, Package, RNA, Tesla M2050

November 11, 2013 by hgpu

Computational kinetics of a large scale biological process on GPU workstations: DNA bending

Arnold Peter Ruymgaart

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Tags: Biology, CUDA, Molecular dynamics, nVidia, nVidia GeForce GTX 480, Thesis

November 8, 2013 by hgpu

Communication Optimization for Multi GPU Implementation of Smith-Waterman Algorithm

Sampath Kumar, P. K. Baruah

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Tags: Algorithms, Biology, Computational biology, CUDA, Databases, nVidia, Sequence matching, Smith-Waterman algorithm, Tesla M2050

November 2, 2013 by hgpu

gEMpicker: A Highly Parallel GPU-Accelerated Particle Picking Tool for Cryo-Electron Microscopy

Thai V. Hoang, Xavier Cavin, Patrick Schultz, David W. Ritchie

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Tags: Algorithms, Biology, Cryo-EM, CUDA, Electron microscopy, FFT, Macromolecule, Microscopy, nVidia, Tesla C1060, Tesla C2075

October 24, 2013 by hgpu

cudaMap: a GPU accelerated program for gene expression connectivity mapping

Darragh G McArt, Peter Bankhead, Philip D Dunne, Manuel Salto-Tellez, Peter Hamilton, Shu-Dong Zhang

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

October 17, 2013 by hgpu

High performance sequence mining using pairwise statistical significance

Yuhong Zhang, Feng Chen

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

October 12, 2013 by hgpu

Regional Heritability Advanced Complex Trait Analysis for GPU and Traditional Parallel Architectures

L. Cebamanos, A. Gray, I. Stewart, A. Tenesa

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Tags: Algorithms, Bioinformatics, Biology, CUDA, nVidia, Tesla K20

October 12, 2013 by hgpu

Enabling the use of Heterogeneous Computing for Bioinformatics

Ramakrishna Bijanapalli Chakri

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Tags: Bioinformatics, Biology, CUDA, FPGA, Heterogeneous systems, nVidia, nVidia GeForce GTX 580, Smith-Waterman algorithm, Thesis

October 8, 2013 by hgpu

GPU-powered Simulation Methodologies for Biological Systems

Daniela Besozzi, Giulio Caravagna, Paolo Cazzaniga, Marco Nobile, Dario Pescini, Alessandro Re

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Tags: Biology, Computer science, CUDA, nVidia

October 2, 2013 by hgpu

gEMfitter: A Highly Parallel FFT-Based 3D Density Fitting Tool With GPU Texture Memory Acceleration

Thai V. Hoang, Xavier Cavin, David W. Ritchie

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Tags: Biology, Cryo-EM, CUDA, Electron microscopy, FFT, Macromolecule, Microscopy, nVidia, Tesla C2075

September 28, 2013 by hgpu

Improving Resource Utilization in Heterogeneous CPU-GPU Systems

Michael Boyer

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Tags: Algorithms, ATI, ATI Radeon HD 5870, ATI Radeon HD 7970, Biology, Computer science, CUDA, Heterogeneous systems, nVidia, nVidia GeForce GTX 280, OpenCL, Package, Software Engineering, Thesis

September 23, 2013 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

Graphics Processing Unit-Accelerated Quantitative Trait Loci Detection

Accelerating calculations of RNA secondary structure partition functions using GPUs

Computational kinetics of a large scale biological process on GPU workstations: DNA bending

Communication Optimization for Multi GPU Implementation of Smith-Waterman Algorithm

gEMpicker: A Highly Parallel GPU-Accelerated Particle Picking Tool for Cryo-Electron Microscopy

cudaMap: a GPU accelerated program for gene expression connectivity mapping

High performance sequence mining using pairwise statistical significance

Regional Heritability Advanced Complex Trait Analysis for GPU and Traditional Parallel Architectures

Enabling the use of Heterogeneous Computing for Bioinformatics

GPU-powered Simulation Methodologies for Biological Systems

gEMfitter: A Highly Parallel FFT-Based 3D Density Fitting Tool With GPU Texture Memory Acceleration

Improving Resource Utilization in Heterogeneous CPU-GPU Systems

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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