GPU Programming for Molecular Modeling Workshop - Urbana, Aug. 6-8, 2010
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
- 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.
