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Scalable Peer-to-peer Network for Biological Simulations
Shun-Yun Hu
2005/05/26
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Outline
Introduction Voronoi-based Overlay Network (VON) Protein Folding Problem Conclusion
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A Look at Simulations
Simulations are important tools in scientific research
Larger scale and higher resolution (more accurate and detailed simulations) are constantly sought
However, computational resource can be limited
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An Untapped Potential
300 Million PCs on the Internet (2000 est.)
Up to 80% to 90% of CPU is wasted
Large supply of computing resource, growing rapidly
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An Example: SETI@Home
Search for Extraterrestrial Intelligence (SETI) UC Berkeley Project launched in May 1999
PC User downloads a screen saver Calculations are done using idle CPU time
2005/03 statistics (in 6 years) 5.3 M world-wide participants 2.2 M years of single-processor CPU 54 teraflop machine (current top 3: 70.72, 51.87, 35.86)
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Simulation: Folding@Home
Stanford Project launched in Sept. 2000 Seeks to determine protein’s 3D structure
Screensaver that downloads “work units” 2002 Statistics:
30,000 volunteers 1 M days of single-processor CPU
Published 23 papers in: Science, Nature, Nature Structural Biology, PNAS, JMB, etc.
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The Grand Question
Can we build the ultimate simulator for large-scale simulation utilizing millions of computers world-wide?
Potential applications: Nuclear reaction Star clusters Atomic-scale modeling in material science Weather, earthquakes Biology (protein, ecosystem, brain, ...)
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Current Limitations
Current methodology: Client-server model (master & slaves) clients request “work unit” to process Communication is minimized Clients do not communicate
Issues: Only suitable for “embarrassingly parallel” simulations Sophisticated server-side algorithm and management required
An alternative: peer-to-peer (P2P) computing
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What is Peer-to-Peer (P2P)?
[Stoica et al. 2003] Distributed systems without any centralized control
or hierarchical organization Runs software with equivalent functionality
Examples File-sharing: Napster, Gnutella, eDonkey VoIP: Skype DHT: Chord, CAN, Pastry
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Peer-to-Peer Overlay
A P2P overlay network source: [Keller & Simon 2003]
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Promise & Challenge of P2P
Promises Growing resource, decentralized
Scalable Commodity hardware Affordable
Challenges Topology maintenance dynamic join/leave Efficient content retrieval no global knowledge
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A Simulation Scenario
How can we utilize P2P for simulation-purpose?Answer: depends on what you want to simulate
We observe that many simulations… are spatially-oriented (i.e. based on coordinate systems) run in discrete time-steps require synchronization at each time-step exhibit localized interaction (i.e. short-range interaction)
example: molecular dynamics (MD) simulation
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Scenario Defined for P2P
Many simulated entities (nodes) on a 2D plane ( > 1,000) Positions (coordinates) may change at each time-step How to synchronize positions with those in Area of Interest
(AOI)?
Area of Interest
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P2P Design Goals
Observation: the contents are information from AOI neighbors P2P content discovery is a neighbor discovery problem
Solve the Neighbor Discovery Problem in a fully-distributed, message-efficient manner.
Specific goals: Scalable Limit & minimize message traffics Fast Direct connection with AOI neighbors
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Outline
Introduction Voronoi-based Overlay Network (VON) Protein Folding Problem Conclusion
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Voronoi Diagram
2D Plane partitioned into regions by sites, each region contains all the points closest to its site
Can be used to find k-nearest neighbor easily
Neighbors
Site
Region
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Design Concepts
Identify enclosing and boundary neighbors Each node constructs a Voronoi of all AOI neighbors Enclosing neighbors are minimally maintained Mutual collaboration in neighbor discovery
Circle Area of Interest (AOI)
White self
Yellow enclosing neighbor (E.N.)
L. Blue boundary neighbor (B.N.)
Pink E.N. & B.N.
Green AOI neighbor
D. Blue unknown neighbor
Use Voronoi to solve the neighbor discovery problem
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Procedure (JOIN)
1) Joining node sends coordinates to any existing node
Join request is forwarded to acceptor
2) Acceptor sends back its own neighbor list
joining node connects with other nodes on the list
Acceptor’s region
Joining node
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Procedure (MOVE)
1) Positions sent to all neighbors, mark messages to B.N.
B.N. checks for overlaps between mover’s AOI and its E.N.
2) Connect to new nodes upon notification by B.N.
Disconnect any non-overlapped neighbor
Boundary neighbors
New neighbors
Non-overlapped neighbors
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Outline
Introduction Voronoi-based Overlay Network (VON) Protein Folding Problem Conclusion
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Protein Folding Problem
Find native state (lowest free energy) 3D structure given a 1D sequence of amino acids
Timescale limitation of classical MD methods Secondary structure folds in 0.1 ~ 10 s Small protein folds in tens of s Current record: 1s (villin headpiece) full-atomic simulation of 1 ns takes one CPU day 1,000 ~ 10,000 gap (it might take decades)
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Folding@Home Parallelization Dynamics of complex
system involves crossing of free energy barriers
Most time is spent in free energy minimum “waiting”
Possible to simulate using trajectories much shorter than folding time
“ensemble dynamics” (same coords, different velocities)
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Outline
Introduction Voronoi-based Overlay Network (VON) Protein Folding Problem Conclusion
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Summary
Idle CPU and networks are untapped potential resources for large-scale simulation
Current approaches do not support simulations that require frequent synchronization / updates
A promising solution: Voronoi-based P2P Overlay Leverage knowledge of each peer to maintain topology Properties: scalable, efficient, fully-distributed Enable simulations with frequent localized synchronization
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Acknowledgements Dr. Jui-Fa Chen (陳瑞發老師 ) Dr. Wei-Chuan Lin (林偉川老師 ) Members of the Alpha Lab, TKU CS
Guan-Ming Liao (廖冠名 ) Dr. Chin-Kun Hu (胡進錕老師 ) LSCP, Institute of Physics, Academia Sinica
Joaquin Keller (France Telecomm R&D, Solipsis) Bart Whitebook(butterfly.net) Jon Watte (there.com)
Dr. Wen-Bing Horng (洪文斌老師 ) Dr. Jiung-yao Huang (黃俊堯老師 )