Running Compucell form command line

The linux install has a script located in cc3d-3.6.2 called runScript.sh that is required to run CompuCell3D from the command line. I'm not sure how you guys do things in windows, but scripting CompuCell3D in linux is easy.

Here is an instance of running an example scripts supplied in /opt/cc3d-3.6.2/examples_PythonTutorial with no GUI on Ubuntu 12.04.

sudo sh /opt/cc3d-3.6.2/runScript.sh
-i /opt/cc3d-3.6.2/examples_PythonTutorial/cellsort_2D_with_py_plugin/cellsort_2D_with_py_plugin.cc3d

I have to throw the sudo in there to get it to work right out of the box, but it does. :->

I am having a similar issue.

compucell3d.bat -i "mysimulation" works fine, but attempting to set the output directory like

compucell3d.bat -i "mysimulation" -o "outputdir" causes the player to hang because it can't find the output directory.

Likewise, the --exitWhenDone option does not work. Have these problems been fixed? The inability to specify a custom output directory is very frustrating and prevents me from automating everything, on a windows machine at least.

Hi Dan,

The Ubuntu 12.04 binaries work for doing this in case you *really* need to get it automated quickly. I'm not so sure about doing it batch style in windows, though. I am in the process of *compiling from source* for my linux machine because the OpenCL example Demos that are included with the Windows executables are absent from the .deb file I installed, for understandable reasons (Linux distros are pretty heterogeneous).

As a fellow user, my recommendation would be for you to install linux ( Ubuntu is good ) and compile from source as described at the page http://www.compucell3d.org/SourceCode. That is the beauty of open source software. If there is any problem with an executable, you can fix it! Also, if you are playing around with the Demos with Ubuntu 12.04, be mindful that you will probably need to move the files in /opt/sundials-*/lib to /usr/lib or mess around with swig so the steppables know where to look for the sbml ode solver functions. The program exits with a Seg Fault, but it gets the right answers, so fixing it is a lower priority.