Problems Installing or running CompuCell3D and Twedit ++


Installation Issues

If you are facing any problem with installation please contact CompuCell3D developer T.J. at . Usually, it is an minor issue that can be solved easily.

To report any bugs, or to ask questions, please visit our Q&A page: Reddit_CompuCell3D.

CC3D suddenly stops working !!!!!

If CC3D (Player) suddenly stops working, and doesn't give any useful information as to why, then it is likely the problem is corrupted configuration files called _settings.sqlite. These file contain Player's preferences like the windows' layouts, recent file lists, cell colors etc. To correct this problem you need to delete this file in the Project that is having the problem and also delete the global file. The Project's copy will be in the Simulation folder;


The global copy is in a hidden file. On Windows the file is;


On Linux the file is;


On Mac the file is;


By default, Mac hides hidden folders and files (those that begin with a "."). To show hidden files:

  1. In Finder, open up your Macintosh hard drive folder
  2. Press Command+Shift+Dot
  3. Your hidden files will become visible. Repeat step 2 to hide them again!

On all platforms, you can either delete both of these files or simply rename them so that CC3D can't find them. Renaming them has the advantage that you can recover the files if it turns out they were not the problem.

Updating an old CC3D version 3.x to CC3D version 4.x

Significant changes were made in CompuCell3D when we created version 4 compared to version 3. The most obvious change is that we have updated to Python 3.x instead of the previous Python 2.x. The biggest consequence of that is changes in the Python print statement. Python 3.x requires parenthesis around the arguments to print. So a print command in CC3D 3.x (Python 2.x) like:

print "mcs=",mcs

is now:


For details on the other changes in CC3D 4.x compared to 3.x please see transitioning_to_cc3d_4 .

CC3D Reddit forum

The CC3D team maintains a Reddit for questions and suggestion. This is a good place to ask for help or suggest new features.

The entries in the old AllAnswered forum (through April 2019) are available at CC3D AllAnswered archive.html. The text of the questions and answers is there but the linked files have not yet been moved. In the short term, if you need one of the linked files please ask for it on the Reddit forum.

Mac security problems

If you are using Mac OS 10.15.x you may have problems running CompuCell3D because of Apple's increasingly onerous security measures. This problem should be fixed in CompuCell3d release 4.2.0 (May 2, 2020). If you encounter problems please contact us at <jsluka AT iu DOT edu>.

Can't run the Demos?

If you have trouble running the CompuCell3D demos in the Demos folder in the distribution, check if you have write access to the Demos folder. CC3D will attempt to write the _settings.sqlite file in the Demo's Simulation folder and that requires write access. If you can't get write access to the demos folder you can just copy the particular Demo's entire folder to your workspace and run it from there.

CompuCell3D: Problems_and_bugs (last edited 2021-01-21 21:52:39 by JamesSluka)