high performance computing on graphics processing units: hgpu.org

Applications

hgpu.org » Applications » Biology

PlinkGPU: A Framework for GPU Acceleration of Whole Genome Data Analysis

Jeffrey Poznanovic

View

Download (PDF)

Tags: Bioinformatics, Biology, CUDA, Genetics, nVidia, OpenCL, Tesla S1070

October 13, 2011 by hgpu

Performance improvements for iterative electron tomography reconstruction using graphics processing units (GPUs)

W.J. Palenstijna, K.J. Batenburga, J. Sijbersa

View

Download (PDF)

Tags: Biology, Image reconstruction, Medicine, nVidia GeForce GTX 280, nVidia GeForce GTX 480, Tomography

October 8, 2011 by hgpu

GPGPU-assisted prediction of ion binding sites in proteins

Leonid Uroshlev, Sergei Rahmanov, Ivan Kulakovskiy, Vsevolod Makeev

View

Download (PDF)

Tags: Biology, Biophysics, CUDA, Molecular modeling, nVidia

October 7, 2011 by hgpu

Democratic Population Decisions Result in Robust Policy-Gradient Learning: A Parametric Study with GPU Simulations

Paul Richmond, Lars Buesing, Michele Giugliano, Eleni Vasilaki

View

Download (PDF)

Source codes

Tags: Biology, CUDA, Neuroscience, nVidia, nVidia GeForce GTX 480, Package, Python

October 5, 2011 by hgpu

GPU-Accelerated DNA Distance Matrix Computation

Zhi Ying, Xinhua Lin, Simon Chong-Wee See, Minglu Li

View

Download (PDF)

Tags: ATI, ATI Radeon HD 5850, Bioinformatics, Biology, Genetics, nVidia, OpenCL, Performance, Tesla C2050

October 3, 2011 by hgpu

Large Scale DNA Sequence Alignment and Kernel Method Implemented with GPUs

Songwen Pei, Wenhao Wang, Gang Wei, Baifeng Wu

View

Download (PDF)

Tags: Algorithms, ATI, ATI Radeon HD 4870, Bioinformatics, Biology, Brook, Sequence alignment

October 1, 2011 by hgpu

Manycore high-performance computing in bioinformatics

Jean-Stephane Varre, Bertil Schmidt, Stephane Janot, Mathieu Giraud

View

Download (PDF)

Tags: Algorithms, Bioinformatics, Biology, CUDA, nVidia, OpenCL, Review, RNA, Sequence alignment

September 26, 2011 by hgpu

Accelerating reaction-diffusion simulations with general-purpose graphics processing units

Matthias Vigelius, Aidan Lane, Bernd Meyer

Source codes

Tags: Algorithms, Bioinformatics, Biology, CUDA, nVidia, Package, Rendering, Stochastic simulation

September 23, 2011 by hgpu

GPU Computation in Bioinspired Algorithms: A Review

M. G. Arenas, A. M. Mora, G. Romero and P. A. Castillo

View

Download (PDF)

Tags: Algorithms, ATI, Bioinformatics, Biology, Computational biology, CUDA, nVidia, OpenCL, Overview, Review

September 8, 2011 by hgpu

Two-Level Approach to Efficient Visualization of Protein Dynamics

Ove Daae Lampe, I. Viola, N. Reuter, H. Hauser

Tags: Bioinformatics, Biology, Molecular dynamics, Rendering, Visualization

August 31, 2011 by hgpu

Rapid RNA Folding: Analysis and Acceleration of the Zuker Recurrence

Arpith C. Jacob, Jeremy D. Buhler, Roger D. Chamberlain

View

Download (PDF)

Tags: Algorithms, Bioinformatics, Biology, Computational biology, CUDA, FPGA, nVidia, nVidia GeForce GTX 280, RNA, Tesla C870

August 27, 2011 by hgpu

Fine-grain Parallelism using Multi-core, Cell/BE, and GPU Systems

Frederico Pratas, Pedro Trancoso, Leonel Sousa, Alexandros Stamatakis, Guochun Shi, Volodymyr Kindratenko

Tags: Bioinformatics, Biology, Cell processor, CUDA, Molecular dynamics, nVidia

August 25, 2011 by hgpu

AutoDock-GPU: AutoDock for GPUs and other accelerators

Architecting Tensor Core-Based Reductions for Irregular Molecular Docking Kernels

NCCLX: collective communication framework

Collective Communication for 100k+ GPUs

Tutoring LLM into a Better CUDA Optimizer

Kernel Library for LLM Serving

Compiler and Runtime Systems for Generative AI Models

Adaptivity in AdaptiveCpp: Optimizing Performance by Leveraging Runtime Information During JIT-Compilation

Neptune: Advanced ML Operator Fusion for Locality and Parallelism on GPUs

Genten: Software for Generalized Tensor Decompositions by Sandia National Laboratories

A Performance Portable Matrix Free Dense MTTKRP in GenTen

Interleaved Learning and Exploration: A Self-Adaptive Fuzz Testing Framework for MLIR

Pinocchio: PINpointing Orbit Crossing Collapsed Hierarchical Objects

Accelerating cosmological simulations on GPUs: a portable approach using OpenMP

KernelCoder: trained on a curated dataset of reasoning traces and CUDA kernel pairs

ConCuR: Conciseness Makes State-of-the-Art Kernel Generation

See all packages

* * *

high performance computing on graphics processing units: hgpu.org

Applications

PlinkGPU: A Framework for GPU Acceleration of Whole Genome Data Analysis

Performance improvements for iterative electron tomography reconstruction using graphics processing units (GPUs)

GPGPU-assisted prediction of ion binding sites in proteins

Democratic Population Decisions Result in Robust Policy-Gradient Learning: A Parametric Study with GPU Simulations

GPU-Accelerated DNA Distance Matrix Computation

Large Scale DNA Sequence Alignment and Kernel Method Implemented with GPUs

Manycore high-performance computing in bioinformatics

Accelerating reaction-diffusion simulations with general-purpose graphics processing units

GPU Computation in Bioinspired Algorithms: A Review

Two-Level Approach to Efficient Visualization of Protein Dynamics

Rapid RNA Folding: Analysis and Acceleration of the Zuker Recurrence

Fine-grain Parallelism using Multi-core, Cell/BE, and GPU Systems

Recent source codes

AutoDock-GPU: AutoDock for GPUs and other accelerators

NCCLX: collective communication framework

Tutoring LLM into a Better CUDA Optimizer

Kernel Library for LLM Serving

Adaptivity in AdaptiveCpp: Optimizing Performance by Leveraging Runtime Information During JIT-Compilation

Neptune: Advanced ML Operator Fusion for Locality and Parallelism on GPUs

Genten: Software for Generalized Tensor Decompositions by Sandia National Laboratories

Interleaved Learning and Exploration: A Self-Adaptive Fuzz Testing Framework for MLIR

Pinocchio: PINpointing Orbit Crossing Collapsed Hierarchical Objects

KernelCoder: trained on a curated dataset of reasoning traces and CUDA kernel pairs

Most viewed papers (last 30 days)