Command line options of CompuCell3D

Although most users run CC3D using Player GUI sometimes it is very convenient to run CC3D using command line options. CC3D allows to invoke Player directly from command line which is convenient because if saves several clicks and if you run many simulations this might be quite convenient.

Remark: On Windows we use .bat extension for run scripts and on Linux/OSX it is .sh. Otherwise all the material in this section applies to all the platforms.

CompuCell3D Player Command Line Options

The command line options for running simulation with the player are as follows:

compucell3d.bat [options]

Options are:

-i <simulation file> - users specify .cc3d simulation file they want to run.

-s <screenshotDescriptionFileName> - name of the file containing description of screenshots to be taken with the simulation. Usually this file is prepared using Player by switching to different views, clickin camera button and saving screenshot description file from the Player File menu.

-o <customScreenshotDirectoryName> - allows users to specify where screenshots will be written. Overrides default settings.

--noOutput - instructs CC3D not to store any screenshots. Overrides Player settings.

--exitWhenDone - instructs CC3D to exit at the end of simulation. Overrides Player settings.

-h, --help - prints command line usage on the screen

Example command may look like (windows):

compucell3d.bat –i Demos\Models\cellsort\cellsort_2D\cellsort_2d.cc3d --noOutput

or on linux: –i Demos/Models/cellsort/cellsort_2D/cellsort_2d.cc3d --noOutput

and OSX:

compucell3d.command –i Demos/Models/cellsort/cellsort_2D/cellsort_2d.cc3d --noOutput

Running CompuCell3D in a GUI-Less Mode - Command Line Options.

Sometimes when you want to run CC3D on a cluster you will have to use runScript.bat which allows running CC3D simulations without invoking GUI. However, all the screenshots will be still stored.

Remark: current version of this script does not handle properly relative paths so it has to be run from the installation directory of CC3D i.e. you have to cd into this directory prior to runnit runScript.bat. Another solution is to use full paths.

The output of this script is in the form of vtk files which can be subsequently replayed in the Player (and one can take screenshots then). By default all fields present in the simulation are stored in the vtk file. If users want to remove some of the fields from being stored in the vtk format they have to pass this information in the Python script:


Storing entire fields (as opposed to storing screenshots) preserves exact snapshots of the simulation and allows result postprocessing. In addition to the vtk files runScript stores lattice description file with .dml` extension which users open in the Player (File->Open Lattice Description Summary File…) if they want to reply generated vtk files.

The format of the command (windows):

runScript.bat [options]

linux: [options]


runScript.command [options]

The command line options for runScript.bat are as follows:

-i <simulation file> - users specify .cc3d simulation file they want to run.

-c <outputFileCoreName> - allows users to specify core name for the vtk files. The default name for vtk files is Step

-o <customVtkDirectoryName> - allows users to specify where vtk files and the .dml file will be written. Overrides default settings

-f <frequency> or –outputFrequency=<frequency> - allows to specify how often vtk files are stored to the disk. Those files tend to be quite large for bigger simulations so storing them every single MCS (default setting) slows down simulation considerably and also uses a lot of disk space.

--noOutput - instructs CC3D not to store any output. This option makes little sense in most cases.

-h, --help - prints command line usage on the screen

Example command may look as follows(windows):

runScript.bat –i Demos\CompuCellPythonTutorial\InfoPrinter\cellsort_2D_info_printer.cc3d –f 10 –o Demos\CompuCellPythonTutorial\InfoPrinter\screenshots –c infoPrinter

linux: –i Demos/CompuCellPythonTutorial/InfoPrinter/cellsort_2D_info_printer.cc3d –f 10 –o Demos/CompuCellPythonTutorial/InfoPrinter/screenshots –c infoPrinter


runScript.command –i Demos/CompuCellPythonTutorial/InfoPrinter/cellsort_2D_info_printer.cc3d –f 10 –o Demos/CompuCellPythonTutorial/InfoPrinter/screenshots –c infoPrinter