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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