1. The Design of a Grid Computing System for Drug Discovery and Design
David Gobaud
Computational Drug Discovery
Stanford University
14 March 2006

2. Outline Overview Network Topology Structure Summary
Resource Management Agent
Job Submission Client
Scheduler Node
Execution Node
Experimental Results
Questions

3. Overview
Novel Grid computing system for drug discovery and design (DDG)
Use idle resources donated by nodes over the internet
P2P technology
Hybrid resource management architecture
Avoid master/slave problems

4. Network Topology Centralized + Decentralized P2P
Clusters that wish to compute join DDG and become execution nodes
Grouped into Virtual Organizations (VO) by structures and interests
Communicate via Resource Management Agents (RMA) in P2P mode
One peer fails – other peers can compensate
Each local RMA captures and maintains resource info of a VO

5. Structure Summary
End-users submit protein molecule files to DDG via web portal
End-users create job request template for a new application
Specify QoS requirements
Job submitted to Scheduler Node by Submission Node
DDG provides a distributed repository where execution nodes publish their real-time workload info

6. Structure Summary Scheduler Node
Divide job into many parallel sub-jobs
Query repository to find and allocate execution nodes for sub-jobs to satisfy QoS requirements
Combine results from sub-jobs into whole docking result
Return result to submission node which informs the user the job is complete

7. High-Level Workflow of DDG

8. Experimental Results
Feasibility and performance evaluated by protein molecules docking experiments
Many DBs used – Specs, ACD, CNPP, and NCBI
20 PC LAN
1Ghz Pentium IVs
256 Mb RAM
40 Gb hard drives
100 Mb/sec Ethernet
SGI Origin 3800 cluster of 64 processors
SUNWAY cluster of 32 processors
SUNWAY cluster of 64 processors
SUNWAY cluster of 256 processors

9. Experimental Results – Running Time

10. Experimental Results – Robustness
20 PCs each receiving 100 protein molecules to dock
Some PCs randomly shut down
After P2P network stabilized fraction of molecules that could not be processed measures
Molecule docking failure rate almost equal to nodes failure rate as expected
No significant resource scheduling failure -> Robust

11. Questions Why are failed docking computations not rescheduled?
What type of network topology does use?