high performance computing on graphics processing units: hgpu.org

Applications

hgpu.org » Applications » Biology

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

Pooya Zandevakili, Ming Hu, Zhaohui Qin

View

Download (PDF)

Source codes

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

View

Download (PDF)

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

View

Download (PDF)

Source codes

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

View

Download (PDF)

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

View

Download (PDF)

Source codes

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

View

Download (PDF)

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,

View

Download (PDF)

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

View

Download (PDF)

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

View

Download (PDF)

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

View

Download (PDF)

Source codes

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

A GPU-Based Implementation of Differential Evolution for Solving the Gene Regulatory Network Model Inference Problem

Luis E. Ramirez-Chavez, Carlos A. Coello Coello, Eduardo Rodriguez-Tello

View

Download (PDF)

Tags: Bioinformatics, Biology, CUDA, Differential equations, Differential evolution, nVidia, nVidia GeForce GTX 460, Optimization

January 23, 2012 by hgpu

Accelerated Large-Scale Multiple Sequence Alignment

Scott Lloyd, Quinn O. Snell

View

Download (PDF)

Source codes

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

January 19, 2012 by hgpu

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

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

Optical flow algorithms for SYCL

SYCL in the edge: performance and energy evaluation for heterogeneous acceleration

OpenMP5-Offload-OpenMC-Intel-PVC

Distributed OpenMP Offloading of OpenMC on Intel GPU MAX Accelerators

See all packages

* * *

high performance computing on graphics processing units: hgpu.org

Applications

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

A GPU-Based Implementation of Differential Evolution for Solving the Gene Regulatory Network Model Inference Problem

Accelerated Large-Scale Multiple Sequence Alignment

Recent source codes

QArray

Celerity: High-level C++ for Accelerator Clusters

CIFAR-10 Airbench: 94% on CIFAR-10 in 3.29 second

gpu_tracker: Context manager and CLI that tracks the computational-resource-usage of a code block or shell command, particularly the GPU usage

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

Optical flow algorithms for SYCL

OpenMP5-Offload-OpenMC-Intel-PVC

Most viewed papers (last 30 days)