GPU Programming for Molecular Modeling Workshop Program

Program

Subjects

  • Introduction - Domains of use
  • Key GPU programming and algorithm review
  • GPU programming patterns that arise in many programs
  • Detailed lectures on GPU molecular modeling algorithms

Example code and papers

Schedule

Location:
  • 3269 Beckman Institute

Friday, 8/6: Last day of NSF-funded Virtual School of Computational Science and Engineering

7:00-8:00 pm Introductory lecture, participant introductions (John Stone) [PDF]
8:00-9:00 Participant Project Presentations and Group Discussion
D. Lynch [PDF]
F. Foertter

 

Saturday, 8/7:

  Morning
9:00-10:30 Lectures:
GPU Particle-Grid Algorithms: Electrostatics (John Stone) [PDF]
GPU Particle-Particle Algorithms: Non-bonded Force Calculation (David Hardy) [PDF]
10:30-10:45  Coffee Break
10:45-12:00 Lectures:
GPU Histogramming: Radial Distribution Functions (John Stone)[PDF]
CUDA Algorithms for Stochastic Simulation of Biochemical Reactions (Andrew Magis) [PDF]
 12:00-2:00 Lunch Break
  Afternoon
2:00-3:00 Participant Project Presentations and Group Discussion
Victor Ovchinnikov [PDF]
Cinque Soto [PDF]
Avi Purkayastha [PDF]
Tyler Luchko [PDF]
3:00-3:15 Coffee Break
3:15-5:00 Participant Project Presentations and Group Discussion
Ryan Bubinski [PDF]
Nathan Ellingwood [PDF]
William French [PDF]

 

Sunday, 8/8:

  Morning
9:00-10:30 Lectures:
Single-Node Multi-GPU Algorithms: Molecular Orbitals (John Stone) [PDF]
NAMD: Molecular Dynamics on GPU Clusters (Jim Phillips) [PDF]
10:30-10:45  Coffee Break
10:45-12:00 Laboratory: GPU Programming Project Laboratory
12:00-2:00 Lunch Break
  Afternoon
2:00-3:00 Participant Project Presentations and Group Discussion
Li Wan [PDF]
Trevor Gokey [PDF]
3:00-3:15   Coffee Break
3:15-5:00 Participant Project Presentations and Group Discussion

 

Note: program subject to change.