Install and run COMETS

These instructions are relevant for COMETS version 2.0.0 and up. The instruction for older versions are here.

In order to run COMETS you must have Java, version 1.8 or higher, and Gurobi, version 8.1.0, installed on your system.

Java can be downloaded and installed from here. Gurobi is here.

Please make sure that after registering and installing Gurobi, you obtain a license.

Installing COMETS

The easiest way to install COMETS is to simply run the installer found on the download page.

If for any reason you wish to install COMETS manually, please follow the instructions below.

Windows:

COMETS for Windows is distributed as an archived .zip file. To extract it double-click on it or right-click and choose Extract All… This will create a directory COMETS_X.Y.Z_win\comets_X.Y.Z, where X.Y.Z is the version number.

The directory contains INSTALL file. Read this file and follow the instructions to install COMETS.

Linux:

COMETS for Linux is distributed as an archived COMETS_X.Y.Z.tar.gz file, where X.Y.Z is the version number. To extract it, run it in a terminal:

$tar -zxvf COMETS_X.Y.Z.tar.gz

where X.Y.Z are replaced with the version numbers.

This will create a directory COMETS_X.Y.Z/comets_X.Y.Z. It contains INSTALL file. To install COMETS read the INSTALL file.

Mac:

COMETS for Linux is distributed as an archived COMETS_X.Y.Z_mac.tar.gz file, where X.Y.Z is the version number. To extract it, run it in a terminal:

$tar -zxvf COMETS_X.Y.Z_mac.tar.gz

where X.Y.Z are replaced with the version numbers.

This will create a directory COMETS_X.Y.Z_mac/comets_X.Y.Z. It contains INSTALL file. To install COMETS read the INSTALL file.

Running COMETS

The instructions for running COMETS are in the RUNNING_COMETS file in the comets_X.Y.Z directory.

The comets_X.Y.Z/layouts_and_models directory contains three examples of layouts and two models. The model_CSP_petri_dish_circles is an example of a two dimensional layout with a toy model model_CSP. The model_CSP_3D_layout is a three dimensional layout with the same toy model.

The Ecoli_colony_layout is a layout for growth of an E.coli colony in two dimensions. The corresponding model is in the EC_ijo1366_model file. A detailed description of running this layout and model is here.