Running example models and using a cluster

The purpose of these tutorials is to learn how to run the example growth simulations included in GFtbox. It is assumed that you have already downloaded the GFtbox software.

Getting Started

1) Explaining the tools. In these tutorials, we will be using GFtboxCommand and ClusterMonitor. This section explains the purpose of these functions.

2) Running a growth simulation for an example model. This section demonstrates how to use GFtboxCommand to run a growth simulation. The model used for the simulation is an example model included with the GFtbox.

3) Altering the simulation parameters. Following on from part 2, here we show how to adjust a simulation parameter within GFtboxCommand. Specifically, we alter the value of dt, the temporal resolution of the simulation, and show how it can be used to verify the correctness of the value specified.

4) Altering the model parameters. Finally, we demonstrate how a number of model parameters can be varied by specifying a range of values for each model argument. We show how the computationally expensive task of simulating all combinations of specified ranges can be more efficient if a computer cluster is used via the ClusterMonitor tool.

1 Explaining the tools

ClusterMonitor

Provides a graphical interface for managing simulations running remotely on a computer cluster. Allows you to see which projects are present and running on the cluster, to retrieve the completed projects, to generate images of the simulations at specified stages of growth, and to remove projects from the cluster. - Will say that Terminal or SSH does same thing, and can still be useful

4 Altering the model parameters

3 - Will show dt changed individually, submitted as a range, submitted to a cluster