GPU Programming for Molecular Modeling Workshop - Aug. 2-4, 2013

Program

Location:
  • 3269 Beckman Institute

Friday, August 2: Last day of NSF-funded VSCSE "Proven Algorithmic Techniques for Many-core Processors" Summer School

  Evening
7:00-8:00 Introductory lecture, participant introductions (All instructors) [PDF]
8:00-8:15 Participants Given ORNL Titan Login Keys
8:15-8:30 ORNL Titan Usage and Documentation Overview
8:30-9:00 Overview of GPU Computing in Molecular Modeling (John Stone) [PDF]

 

Saturday, August 3:

  Morning
9:00-10:30

Lectures:
Heterogenous Computing on Titan (Fernanda Foertter, Oak Ridge Leadership Computing Facility) [PDF]

10:30-10:45 Coffee Break
10:45-12:00

Lectures:
GPU Particle-Particle Algorithms: Non-bonded Force Calculation (David Hardy) [PDF]
GPU-Accelerated Quantum Chemistry (Ivan Ufimtsev, Stanford University) [PDF]

 12:00-2:00 Lunch Break
  Afternoon
2:00-3:00 Participant Project Presentations and Group Discussion
P1: "GOMC GPU Optmized Monte Carlo", Jason Mick, Kamel Rushaidat, Yuanzhe Li, Wayne State U. [PDF]
3:00-3:15 Coffee Break
3:15-5:00 Participant Project Presentations and Group Discussion
P2: "Structure, dynamics and assembly mechanism of the capsid of HIV-1 virus by solid state NMR, Transmission Electron Microscopy and Monte Carlo simulation", Bo Chen, U. Central Florida. [PDF]
P3: "GPU-Accelerated 3-Dimensional Reaction Diffusion Systems", John Holmen, Kettering U. [PDF]
P4: "Brownian dynamics of obstructions in Lattice Microbes", Tyler Earnest, U. Illinois. [PDF]

 

Sunday, August 4:

  Morning
9:00-10:30

Lectures:
Lattice Microbes: CUDA Algorithms for Stochastic Simulation of Biochemical Reactions (Mike Hallock / Joseph Peterson) [PDF]
NAMD: GPU-Accelerated Petascale Molecular Dynamics Simulations on Titan and Blue Waters (Jim Phillips) [PDF]

10:30-10:45  Coffee Break
10:45-12:00 GPU Particle-Grid Algorithms: Molecular Surfaces and Synthetic Density Maps (John Stone) [PDF]
Laboratory: GPU Programming Project Laboratory
12:00-2:00 Lunch Break
  Afternoon
2:00-3:00 Participant Project Presentations and Group Discussion
P5:"Computer Simulations of DNA Driven Nanoparticle Assemblies", Fernando Vargas-Lara, National Institute of Standards and Technology. [PDF]
P6:"Molecular Dynamics of Polymer Nano-composites", Beatriz Pazmino, Wesleyan U. [PDF]
P7:"All-atom Normal Mode Analysis (NMA)", Dongsheng Lei, Lawrence Berkeley National Laboratory. [PDF]
P8:"Transmission Electron Tomography 3D Reconstruction by IPET Method", Xing Zhang, Lawrence Berkeley National Laboratory. [PDF]
P9:"Multiscale Investigation of Biomolecular Systems Dynamics", Mert Gur, U. Pittsburgh. [PDF]
3:00-3:15 Coffee Break
3:15-5:00 Presentation Award, Group Discussion, and Evaluation Surveys

 

Note: program subject to change.

Our thanks the Oak Ridge Leadership Computing Facility for providing resources and training.