Problems Installing or running CompuCell3D and Twedit ++

Index

• Installation Issues?

• CC3D was working but has suddenly stopped working?

  • Delete the two _settings.sqlite files

  • Reset the CC3D / Player Settings dialog

  • Random crashes when using PixelTracker Plugin and multiple CPUs

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

• CC3D Reddit forum

• Problems with security on Mac's

• Can't run the demos distribtued with CompuCell3D?

Report Bugs and Request New Features

• To Report issue navigate to Report CC3D Issue

• More information on how to report a but can be found here How to report a bug?

• You can participate in CC3D's GitHub discussion at CompuCell3D GitHub Discussions .

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.
You can also search old messages to see if someone else has already asked your question.

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.

Installation Issues

If you are facing any problem with installation please post to Reddit_CompuCell3D. Often, 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 !!!!!

Delete the two _settings.sqlite files

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;

 C:\Users\<USERNAME>\<PATH_TO_PROJECT>\<PROJECT_NAME>\Simulation\_settings.sqlite 

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

 C:\Users\<USERNAME>\.compucell3d_py3\_settings.sqlite 

On Linux the file is;

 /home/<USERNAME>/.compucell3d_py3/_settings.sqlite 

On Mac the file is;

 /Users/<USERNAME>/.compucell3d_py3/_settings.sqlite 

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.

Reset the CC3D / Player Settings dialog

After doing the above (deleting both .sqlite files),

1. Open Player (CC3D) but do not load a simulation.
2. Go to the menu “Tools” “Configuration…” settings window.
3. Select the first tab “Output” (especially if the dialog opened on the “Cells/Colors” tab).
4. Close the Dialog with “Ok”
5. Exit Player.

Now try to run your simulation.

Random crashes when using PixelTracker Plugin and multiple CPUs

On some platforms there is a random error that occurs when the PixelTracker plugin is used with multiple CPUs. The simulation will crash at random and unpredictable places and will not provide any useful debugging information. This only happens when several "Processors" (CPUs) are requested in the XML, typically 8 or more.

 <Metadata> 
    <NumberOfProcessors>8</NumberOfProcessors> 
 </Metadata> 

The problem can usually be resolved by not loading PixelTracker plugin if you don't actually need it, or by reducing the number of processors.

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:

print("mcs=",mcs)

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

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 <tjsego 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.