high performance computing on graphics processing units: hgpu.org

hgpu.org » Biology

Neurokernel: An Open Scalable Software Framework for Emulation and Validation of Drosophila Brain Models on Multiple GPUs

Lev E. Givon, Aurel A. Lazar

View

Download (PDF)

Source codes

Tags: Biology, CUDA, Neuroscience, nVidia, Package, Python

November 18, 2013 by hgpu

Graphics Processing Unit-Accelerated Quantitative Trait Loci Detection

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

View

Download (PDF)

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

View

Download (PDF)

Source codes

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

View

Download (PDF)

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

View

Download (PDF)

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

View

Download (PDF)

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

View

Download (PDF)

Source codes

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

View

Download (PDF)

Source codes

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

View

Download (PDF)

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

October 12, 2013 by hgpu

Enabling the use of Heterogeneous Computing for Bioinformatics

Ramakrishna Bijanapalli Chakri

View

Download (PDF)

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

View

Download (PDF)

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

View

Download (PDF)

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

September 28, 2013 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

See all packages

* * *

high performance computing on graphics processing units: hgpu.org

Neurokernel: An Open Scalable Software Framework for Emulation and Validation of Drosophila Brain Models on Multiple GPUs

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

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

Most viewed papers (last 30 days)