high performance computing on graphics processing units: hgpu.org

Applications

hgpu.org » Applications » Biology

LNA: Fast Protein Classification Using A Laplacian Characterization of Tertiary Structure

Nicolas Bonnel, Pierre-Francois Marteau

View

Download (PDF)

Tags: Algorithms, Benchmarking, Biology, Databases, nVidia, OpenCL, Tesla M2050

January 18, 2012 by hgpu

CPU-GPU hybrid accelerating the Zuker algorithm for RNA secondary structure prediction application

Guoqing Lei, Yong Dou, Wen Wan, Fei Xia, Rongchun Li, Meng Ma, Dan Zou

View

Download (PDF)

Tags: Algorithms, Bioinformatics, Biology, CUDA, Hybrid computing, nVidia, nVidia GeForce GTX 580, RNA

January 15, 2012 by hgpu

BarraCUDA – a fast short read sequence aligner using graphics processing units

Petr Klus, Simon Lam, Dag Lyberg, Ming Sin Cheung, Graham Pullan, Ian McFarlane, Giles S. H. Yeo, Brian Y. H. Lam

View

Download (PDF)

Source codes

Tags: Bioinformatics, Biology, CUDA, nVidia, Package, Sequence alignment, Tesla M2050, Tesla M2090

January 13, 2012 by hgpu

Parallel mutual information estimation for inferring gene regulatory networks on GPUs

Haixiang Shi, Bertil Schmidt, Weiguo Liu, Wolfgang Muller-Wittig

View

Download (PDF)

Source codes

Tags: Algorithms, Biology, Computational biology, CUDA, Image processing, Machine learning, nVidia, Package, Tesla C2050

January 13, 2012 by hgpu

Implementation of Virtual Embryology using the Thrust library for CUDA

Anna Aichmayr Markus Dauschan

View

Download (PDF)

Tags: Biology, CUDA, Neural networks, nVidia, Python

January 13, 2012 by hgpu

MetaBinG: Using GPUs to Accelerate Metagenomic Sequence Classification

Peng Jia, Liming Xuan, Lei Liu, Chaochun Wei

View

Download (PDF)

Source codes

Tags: Biology, Computational biology, CUDA, Genetics, nVidia, Package, Tesla C1060

January 11, 2012 by hgpu

Petaflop biofluidics simulations on a two million-core system

Massimo Bernaschi, Satoshi Matsuoka, Mauro Bisson, Massimiliano Fatica, Toshio Endo, Simone Melchionna

View

Download (PDF)

Tags: Algorithms, Biology, CUDA, GPU cluster, Medicine, nVidia, Optimization, Tesla M2050

January 11, 2012 by hgpu

A Parallel Supercomputer Implementation of a Biological Inspired Neural Network and its use for Pattern Recognition

Vincent de Ladurantaye, Jean Lavoie, Jocelyn Bergeron, Maxime Parenteau, Huizhong Lu, Ramin Pichevar, Jean Rouat

View

Download (PDF)

Tags: Biology, CUDA, MPI, Neural networks, nVidia, nVidia GeForce GTX 285, Pattern recognition

January 5, 2012 by hgpu

Building Human Brain Network in 3D Coefficient Map Determined by X-ray Microtomography

Ryuta Mizutani, Akihisa Takeuchi, Kentaro Uesugi, Susumu Takekoshi, Naoya Nakamura, Yoshio Suzuki

View

Download (PDF)

Source codes

Tags: Biology, CUDA, Image reconstruction, Medicine, nVidia, nVidia GeForce GTX 470, Package, Tomography

December 30, 2011 by hgpu

Accurate Sequence Alignment using Distributed Filtering on GPU Clusters

Reza Farivar, Shivaram Venkataraman, Yanen Li, Ellick Chan, Abhishek Verma, Roy H. Campbell

View

Download (PDF)

Tags: Bioinformatics, Biology, CUDA, Filtering, GPU cluster, nVidia, Sequence alignment, Tesla S1070

December 26, 2011 by hgpu

GPU Accelerated PK-means Algorithm for Gene Clustering

Wuchao Situ, Yau-King Lam, Yi Xiao, P.W.M. Tsang, Chi-Sing Leung

View

Download (PDF)

Tags: Algorithms, Biology, Clustering, CUDA, Genetics, nVidia, nVidia GeForce GTX 260

December 20, 2011 by hgpu

An Efficient Simulation Environment for Modeling Large-Scale Cortical Processing

Micah Richert, Jayram Moorkanikara Nageswaran, Nikil Dutt, Jeffrey L. Krichmar

View

Download (PDF)

Source codes

Tags: Biology, CUDA, Neural networks, Neuroscience, nVidia, Package, Tesla C1060

December 19, 2011 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

* * *

high performance computing on graphics processing units: hgpu.org

Applications

LNA: Fast Protein Classification Using A Laplacian Characterization of Tertiary Structure

CPU-GPU hybrid accelerating the Zuker algorithm for RNA secondary structure prediction application

BarraCUDA – a fast short read sequence aligner using graphics processing units

Parallel mutual information estimation for inferring gene regulatory networks on GPUs

Implementation of Virtual Embryology using the Thrust library for CUDA

MetaBinG: Using GPUs to Accelerate Metagenomic Sequence Classification

Petaflop biofluidics simulations on a two million-core system

A Parallel Supercomputer Implementation of a Biological Inspired Neural Network and its use for Pattern Recognition

Building Human Brain Network in 3D Coefficient Map Determined by X-ray Microtomography

Accurate Sequence Alignment using Distributed Filtering on GPU Clusters

GPU Accelerated PK-means Algorithm for Gene Clustering

An Efficient Simulation Environment for Modeling Large-Scale Cortical Processing

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

Most viewed papers (last 30 days)