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Paco Nathan edited this page Nov 27, 2013 · 16 revisions

Exelixi is a distributed framework for running genetic algorithms at scale. The framework is based on Apache Mesos and the code is mostly implemented in Python.

Why build yet another framework for this purpose? Apache Hadoop would be quite a poor fit, due to requirements for in-memory iteration. Apache Spark could fit the problem more closely, in terms of iterative tasks. However, task overhead can become high in proportion to tasks being performed ("small file problem"), plus there is a considerable amount of configuration required at scale. Server-side operations and coprocessors in Apache Cassandra or Apache HBase might also provide a good fit for GA processing, but both of those also require lots of configuration. Moreover, many of the features for these more heavyweight frameworks are not needed, plus it helps to have some lightweight messaging available among the shards -- which these existing frameworks lack.

On the one hand, Exelixi provides the basis for a tutorial for building distributed frameworks in Apache Mesos. On the other hand, it provides a general-purpose GA platform that emphasizes scalability and fault tolerance, while leveraging the wealth of available Python analytics packages.

Quick Start

More details are given below about customizing this framework for solving specific GA problems. The following instructions will help you get started quickly, running Exelixi either on Apache Mesos or in standalone mode.

System Dependencies

Usage for Apache Mesos launch

First, launch an Apache Mesos cluster. The following instructions are based on using the Elastic Mesos service, which uses Ubuntu Linux servers running on Amazon AWS. However, the basic outline of steps should apply in the general case.

Once you have confirmation that your cluster is running -- Elastic Mesos sends you an email messages with a list of masters and slaves -- then use ssh to login on any of the masters:

ssh -A -l ubuntu <master-public-ip>

You must install the Python bindings for Apache Mesos, In this instance the Apache Mesos version is 0.14.0-rc4, so you must install the Python egg for that exact release. Also, you need to install the Exelixi source.

On the master, download the master branch of the Exelixi code repo on GitHub and install the required libraries:

wget https://github.com/ceteri/exelixi/archive/master.zip ; \
unzip master.zip ; \
cd exelixi-master ; \
./bin/local_install.sh

You can test the installation at any point simply by attempting to import the mesos package into Python:

python -c 'import mesos'

If there is no ImportError exception thrown, then your installation should be complete. Next, run the installation commands on each of the slaves:

python ./src/exelixi.py -n localhost:5050 | ./bin/install.sh

Great, ready to roll! Now launch the Framework, which in turn launches the Executors remotely on slave nodes. In the following case, it runs on two slave nodes:

python ./src/exelixi.py -m localhost:5050 -e 2

If everything runs successfully, the log should conclude with a final line:

all tasks done, and all messages received; exiting

See a GitHub gist for an example of a successful run.

Usage for Standalone Mode

To get started quickly on a single node (i.e., your laptop) in standalone mode simply follow two steps. First, launch one Executor locally:

nohup ./src/exelixi.py -p 9311 &

Then launch a Framework to run the default GA as an example:

./src/exelixi.py -s localhost:9311

Note that there are trade-offs regarding standalone mode. Pros: simple to test the customization of a GA quickly, without requiring an Apache Mesos cluster. Cons: difficult to configure and manage a GA in production at scale, since it lacks features for security and fault tolerance.

Implementation

Components

FeatureFactory: a base class for configuration and customization of the GA problem to be solved, which generates and evaluates feature sets

Individual: an candidate solution, represented by a feature set plus a fitness value obtained by applying a fitness function to that feature set

Population: a collection of Individuals, which in turn breed other Individuals

FossilRecord: an archive of Individuals that did not survive, persisted to durable storage and used to limit ergodic behaviors in search -- and also used for analysis after an algorithm run terminates

Executor: a service running on a slave node in the cluster, responsible for computing shards of the Population

Framework: a long-running process that maintains state for the system parameters and models parameters, obtains resources for the Executors, coordinates Executors through successive generations, and reports results; also handles all of the user interaction

Class: FeatureFactory

To implement a GA in Exelixi, subclass the FeatureFactory class (copy/edit src/run.py) to customize the following operations:

  • handle serializing/deserializing a feature set
  • randomly generate a feature set
  • calculate (or approximate) a fitness function
  • mutate a feature set
  • crossover a pair of parents to produce a child
  • test the terminating condition

Then customize the model parameters:

  • n_gen: maximum number of generations
  • n_pop: maximum number of "live" Individuals at any point
  • max_pop: maximum number of Individuals explored in the feature space during an algorithm run
  • term_limit: a threshold used for testing the terminating condition
  • hist_granularity: number of decimal places in fitness values used to construct the fitness histogram
  • selection_rate: fraction of "most fit" Individuals selected as parents in each generation
  • mutation_rate: random variable for applying mutation to an Individual retained for diversity

In general, the other classes cover most use cases and rarely need modifications.

Class: Individual

An Individual represents a candidate solution. Individuals get persisted in durable storage as key/value pairs. The value consists of a tuple [fitness value, generation, feature set] and a unique key is constructed from a SHA-3 digest of the JSON representing the feature set.

Let's consider how to persist an Individual in the Fossil Record given:

  • a UUID as a job's unique prefix, e.g., 048e9fae50c311e3a4cd542696d7e175
  • a unique key, e.g., BC19234D
  • a fitness value, e.g., 0.5654
  • a generation number, e.g., 231
  • JSON representing a feature set, e.g., (1, 5, 2)

In that case, the Individual would be represented in tab-separated format (TSV) as the pair:

hdfs://048e9fae50c311e3a4cd542696d7e175/0b799066c39a673d84133a484c2bf9a6b55eae320e33e0cc7a4ade49, [0.5654, 231, [1, 5, 2]]

Class: Framework

A Framework is a long-running process that:

  • parses command-line options from the user
    • n_exe: number of allocated Executors
    • exe_url: download URL for Executor tarball (customized Python classes)
  • generates a UUID for each attempted algorithm run
  • maintains operational state (e.g., system parameters) in Zookeeper
    • list of Executor endpoints from Apache Mesos
    • prefix: unique directory prefix in HDFS based on generated UUID
    • current_gen: current generation count
  • receives logical state (e.g., model parameters) from customized Python classes
  • initializes the pool of Executors
  • iterates through the phases of each generation (selection/mutation, breeding, evaluation)
  • restores state for itself or for any Executor after a failure
  • enumerates results at any point -- including final results after an algorithm run terminates

Resources allocated for each Executor must be sufficient to support a Population shard of n_pop / n_exe Individuals.

Class: Executor

An Executor is a service running on a Apache Mesos slave that:

  • maintains operational state (e.g., system parameters) in memory
    • prefix: unique directory prefix in HDFS based on generated UUID
    • shard_id: unique identifier for this shard
  • implements an in-memory distributed cache backed by HDFS (with write-behinds and checkpoints)
  • provides a lookup service for past/present Individuals in the feature space via a bloom filter
  • generates a shard as a pool of "live" Individuals at initialization or recovery
  • maintains a shard of "live" Individuals in memory
  • enumerates the Individuals in the shard of the Population at any point
  • calculates a partial histogram for the distribution of fitness
  • shuffles the local Population among neighboring Executors via a hash ring
  • applies a filter to "live" Individuals to select parents for the next generation
  • handles mutation, breeding, and evaluation of "live" Individuals
  • persists serialized Individuals to durable storage (write-behinds)
  • recovers a shard from the last checkpoint, after failures

The lookup service which implements the distributed hash table in turn leverages a hash ring to distribute Individuals among neighboring shards of the Population and a bloom filter for a fast, space-efficient, probabilistic set membership function which has no false negatives but allows rare false positives. The hash ring helps to "shuffle" the genes of the Population among different shards, to enhance the breeding pair selection. In essence, this aspect allows for GA problems to scale-out horizontally. The bloom filter introduces a small rate of false positives in the Individual lookup (data loss), as a trade-off for large performance gains. This also forces a predefined limit on the number of Individuals explored in the feature space during an algorithm run.

REST services and internal tasks for the Executors are implement using gevent, a coroutine library that provides concurrency on top of libevent.

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