PGENESIS Tutorial - GUM'02
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Table of Contents
PGENESIS Tutorial - GUM'02
What is PGENESIS?
History
Tutorial Outline
PGENESIS Installation
Installation: Requirements
Installation: GENESIS
Installation: ssh
Installation: PVM
Installation: PGENESIS
Installation: Simple
Installation: Complex
The "pgenesis" Startup Script (1)
The "pgenesis" Startup Script (2)
PGENESIS Functionality
How PGENESIS Runs in Parallel
How PGENESIS Runs in Parallel
Nodes and Zones
Every node in its own zone
All nodes in one zone
Hybrid schemes
Nodes have distinct namespaces
GENESIS Terminology
Who am I?
Styles of Parallel Scripts
Explicit Synchronization
Implicit Synchronization
Remote Function Calls (1)
Remote Function Calls (2)
Remote Function Calls (3)
Threads
Asynchronous Calls (1)
Asynchronous Calls (2)
Asynchronous Calls (3)
Asynchronous Calls (4)
Advice about Barriers (1)
Advice about Barriers (2)
Commands for Network Creation
Parallel I/O: Display
Interaction with Xodus
Parallel I/O: Writing a File
Tips for Avoiding Deadlocks
Motivation
How PGENESIS Fits into Schedule
How PGENESIS Fits into Schedule
Adding Custom "C" Code
Modifiable Parameters
Limitations of PGENESIS
Parameter Searching with PGENESIS
Model Characteristics
Trivial Model
Master/Worker Paradigm (1)
Master/Worker Paradigm (2)
Commands for Optimization
Choose a Search Strategy
A Parallel Genetic Algorithm
Parameter Representation
Main Script
Master Conducts the Search
Master Conducts the Search
Workers Evaluate Individuals
Workers Evaluate Individuals
Master Integrates the Results (1)
Master Integrates the Results (2)
A More Realistic Model
Improved Parameter Representation
Crossover Mutations
Main Script (1)
Main Script (2)
Main Script (3)
Parameters Are Customizable
Worker Evaluates Individuals (1)
Worker Evaluates Individuals (2)
Tuning Search
Large Networks with PGENESIS
Parallel Network Creation
Goals of decomposition
Load balancing
Minimizing communication
Orient_tut Example
Non-scalable decomposition
Scalable decomposition (1)
Scalable decomposition (2)
Scalable decomposition (3)
Case Study: Cerebellar Model
Cell Populations & Connectivity
3-D Representation of Network
Model Partitioning
Timings on 128 Processors of T3E
Timings vs. Model Size
Timings on Workstation Network
Significant Overhead on Cluster
Scaling Up
Getting Cycles
The High End
Parallel Script Development
Parallel Script Development
Resource Limits and Other Tips
Reducing Synchronization Delay
Reducing Synchronization Delay
Parallel I/O
Performance Monitoring (1)
Performance Monitoring (2)
Performance Monitoring (3)
Comparisons and Summary
Alternatives to PGENESIS (1)
Alternatives to PGENESIS (2)
Summary
Discussion
References
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