high performance computing on graphics processing units: hgpu.org

Applications

Analysis of Surface Folding Patterns of DICCCOLS Using the GPU-Optimized Geodesic Field Estimate

Anirban Mukhopadhyay, Chul Woo Lim, Suchendra M. Bhandarkar, Hanbo Chen, Austin New, Tianming Liu, Khaled Rasheed, Thiab Taha

View

Download (PDF)

Tags: Algorithms, Biology, CUDA, Diffusion tensor, Image registration, Neuroscience, nVidia, nVidia GeForce GTX 480

July 7, 2014 by hgpu

Molecular dynamics simulations through GPU video games technologies

Styliani Loukatou, Louis Papageorgiou, Paraskevas Fakourelis, Arianna Filntisi, Eleftheria Polychronidou, Ioannis Bassis, Vasileios Megalooikonomou, Wojciech Makalowski, Dimitrios Vlachakis, Sophia Kossida

View

Download (PDF)

Tags: Bioinformatics, Biology, Chemistry, CUDA, Medicine, Molecular dynamics, nVidia, OpenCL, Physics

July 4, 2014 by hgpu

Exploiting parallel features of modern computer architectures in bioinformatics: applications to genetics, structure comparison and large graph analysis

Guillaume Chapuis

View

Download (PDF)

Tags: Algorithms, Bioinformatics, Biology, CUDA, Genetics, Graph theory, nVidia, Path problems, Tesla C2050, Thesis

July 3, 2014 by hgpu

Parallelizing the cellular potts model on GPU and multi-core CPU: An OpenCL cross-platform study

Chao Yu, Bo Yang

View

Download (PDF)

Tags: ATI, ATI Radeon HD 7870, Biology, Computer science, OpenCL

July 1, 2014 by hgpu

Various String Matching Algorithms for DNA Sequences to Detect Breast Cancer using CUDA Processors

Nagaveni V, G T Raju

View

Download (PDF)

Tags: Algorithms, Bioinformatics, Biology, CUDA, Databases, Medicine, nVidia, String matching, Tesla C2070

June 28, 2014 by hgpu

An efficient parallel algorithm for accelerating computational protein design

Yichao Zhou, Wei Xu, Bruce R. Donald, Jianyang Zeng

View

Download (PDF)

Source codes

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

June 23, 2014 by hgpu

Fast Sequence Alignment Method Using CUDA-enabled GPU

Yeim-Kuan Chang, De-Yu Chen

View

Download (PDF)

Tags: Bioinformatics, Biology, CUDA, nVidia, Sequence alignment, Smith-Waterman algorithm, Tesla C1060

June 19, 2014 by hgpu

GPU-accelerated Computation for Statistical Analysis of the Next-Generation Sequencing Data

Yilan Liu

View

Download (PDF)

Tags: Bioinformatics, Biology, Computer science, CUDA, Next-Generation sequencing, nVidia, nVidia GeForce GTX 770

June 13, 2014 by hgpu

GPU-Accelerated Dynamic Functional Connectivity Analysis for Functional MRI Data Using OpenCL

D. Akgün, Ü. Sakoğlu, M. Mete, J. Esquivel, B. Adinoff

View

Download (PDF)

Tags: Biology, Magnetic resonance imaging, Medicine, MRI, Neuroscience, nVidia, nVidia GeForce GTX 660, OpenCL

June 9, 2014 by hgpu

Massive exploration of perturbed conditions of the blood coagulation cascade through GPU parallelization

Paolo Cazzaniga, Marco S. Nobile, Daniela Besozzi, Matteo Bellini, Giancarlo Mauri

View

Download (PDF)

Tags: Bioinformatics, Biology, Computational biology, CUDA, Differential equations, nVidia, ODEs, Ordinary differential equations, Tesla K20

May 30, 2014 by hgpu

Performance Evaluation of Quicksort with GPU Dynamic Parallelism for Gene-Expression Quantile Normalization

Roberto Pinto Souto, Carla Osthoff, Douglas Augusto, Oswaldo Trelles, Ana Tereza Ribeiro de Vasconcelos

View

Download (PDF)

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

May 29, 2014 by hgpu

GPU-BSM: A GPU-Based Tool to Map Bisulfite-Treated Reads

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

View

Download (PDF)

Source codes

Tags: Bioinformatics, Biology, CUDA, Genetics, nVidia, nVidia GeForce GTX 480, Package, Python, Sequence alignment, Tesla K10, Tesla K20

May 25, 2014 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

Analysis of Surface Folding Patterns of DICCCOLS Using the GPU-Optimized Geodesic Field Estimate

Molecular dynamics simulations through GPU video games technologies

Exploiting parallel features of modern computer architectures in bioinformatics: applications to genetics, structure comparison and large graph analysis

Parallelizing the cellular potts model on GPU and multi-core CPU: An OpenCL cross-platform study

Various String Matching Algorithms for DNA Sequences to Detect Breast Cancer using CUDA Processors

An efficient parallel algorithm for accelerating computational protein design

Fast Sequence Alignment Method Using CUDA-enabled GPU

GPU-accelerated Computation for Statistical Analysis of the Next-Generation Sequencing Data

GPU-Accelerated Dynamic Functional Connectivity Analysis for Functional MRI Data Using OpenCL

Massive exploration of perturbed conditions of the blood coagulation cascade through GPU parallelization

Performance Evaluation of Quicksort with GPU Dynamic Parallelism for Gene-Expression Quantile Normalization

GPU-BSM: A GPU-Based Tool to Map Bisulfite-Treated Reads

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)