Running

Default run

Once the toolbox is installed you can run the default modeling experiment as follows:

1. Make sure that you are in the toolbox root directory and you have run 'startup.m' (see above)
2. Type 'go' and press enter.
3. The toolbox will start to model the Academic2DTwice simulator. This simulator has 2 inputs and 2 outputs, and will be modeled using Rational functions, scored using crossvalidation, and samples selected using the gradient sample selection method.
4. To see the exact settings used open config/default.xml. Feel free to edit this file and play around with the different options.

Running different examples

The examples directory contains many example simulators that you can use to test the toolbox with. These examples range from predefined functions, to datasets from various domains, to native simulation code. If you want to try one of the examples, open default.xml and edit the Simulator tag to suit your needs.

See the configuration section on information about the possible options. If you want to add your own example see Adding an example.

If you have updated defaul.xml then simply run 'go' to run the example (making sure that the toolbox is in your Matlab path of course).

Other usages of 'go' are as follows:

	"go"
     	"go('MyConfigFile.xml')"
     	"go('MyConfigFile.xml',xValues, yValues)"
     	"go('MyConfigFile.xml',xValues, yValues, options)"
  
     With options a cell array containing one or more of:
     	"-merge" : merge MyConfigFile.xml with the default configuration
		   Note: the merging process does not support all possible cases,
		         in case of problems, do not specify the "-merge" parameter.

     NB: the default configuraiton file is /path/to/M3/config/default.xml

Debugging

To aid understanding and debugging you should set the console logging handler to FINE (or even FINER, FINEST) as follows: (by default it is set to INFO)

<Option key="java.util.logging.ConsoleHandler.level" value="FINE"/>

Remember to always check the log file first! When reporting problems please attach your log file and the xml configuration file you used.

Output

Output is stored in the directory specified in the ContextConfig of the configuration file (by default this is set to "output"). After completion of a M3-Toolbox run, the following files and directories can be found there:

• config.xml: The xml file that was used by this run. Can be used to reproduce the entire modeling process for that run.
• randstate.dat: contains states of the random number generators, so that it becomes possible to deterministically repeat a modeling loop.
• samples.txt: a list of all the samples that were evaluated and their outputs.
• profilers: contains information and plots about convergence rates, resource usage, and so on.
• best: contains the best models that were constructed during the run and also contains plots of these models. Is continuously updated as the modeling progresses.
• models_outputname: contains a history of all the models and plots for each output that was modelled.

Memory

Note: By default Matlab only allocates about 117MB memory space for the Java Virtual Machine. If you would like to increase this limit (which you should) please follow the instructions here.