CompuCell3D
Index
Installation Issue?
If you are facing any problem with installation please contact CompuCell3D developer T.J. at tjsego@iu.edu . 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.
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 Indiana DOT edu>.
Running CC3D 4.2.2 Amazon Web Services (AWS)
To install CC3D 4.2.2 on AWS servers, please search for image called
cc3d_4.2.2
and follow the instructions at Running CC3D on AWS cloud. Make sure to replace CC3D version described in this manual with the current version.
CC3D Version 4.2.3 (Aug 22 2020)
We are pleased to announce new version 4.221 of our software CompuCell3D. This a bug-fix release that includes the following features and bug-fixes:
Improvements and new features
- Added on_stop function to steppable - called if user stops the simulation
- Added ability to open zipped project from both Player and Twedit++
- Improved commenting / uncommenting of XML scripts
- Added more natural syntax to refer to cell types
e.g., self.cell_type.Condensing
- Added pre-check for cell types and fields
- Added Add Steppable ... function to CC3D Python menu, making it easier to add steppables in Twedit
Multiple bug fixes including
- Fixed settings handling in Twedit++
- Fixed display of line numbers in Twedit++
- Fixed issues with 2.5D simulations where dim z=2
- Fixed behavior of cell_list_by_cell type when using nested loops
- Improved random seed generation (matters if two identical simulations are started within less than a second of each other)
Known Issues
- GPU solvers on OSX 10.14 or higher may not work properly
Binary distribution packages
Windows - 32-bit and 64-bit
CompuCell3D 4.2.3 - Windows (select one of the exe files) Download
Note: If CC3D does not run properly on your machine with NVidia card you can try non-gpu version of the binaries - in this case get setup-no-gpu-xxx.exe file. xxx stands for version number and revision number of current CC3D
IMPORTANT: If after installation of new CC3D you encounter problems on Windows. Please manually remove the directory where CC3D is installed and try using installer again. This is a one-time inconvenience associated with the transition to the new ways of storing Player settings. You may also need to remove _settings.sqlite file in the Simulation subfolder of the .cc3d project folder
Mac OS X - binaries
CompuCell3D 4.2.3 - Mac OS X Download
(Note: Don't download the version using the green box, scroll down to the directly listing and download the .zip file.)
Installation Instructions for Mac OSX Binaries (not needed if you download the binary above)
Linux
We are providing binaries for 64 bit Ubuntu and RedHat (you should not need to compile anything)
CompuCell3D 4.2.3 - Linux (Ubuntu/RedHat) Download
CC3D Version 4.2.2 (July 25, 2020)
We are pleased to announce new version 4.221 of our software CompuCell3D. This a bug-fix release that includes the following features and bug-fixes:
Improvements and new features
- Added ability top open zipped .cc3d project directly from Twedit++ - no need to do unzipping using 3rd party tools
- Added saving of simulation layout on simulation stop or simulation finish events
- Added automatic zip file name fill-in in Twedit++ when zipping .cc3d project
- Added Simulation menu action to reset global settings - as of now users can reset simulation-specific and global settings directly from Player menu
- Added option to reset Twedit++ settings directly from Twedit++ GUI
Multiple bug fixes including
- Fixed saving of windows layout - including plots and steering panel
- Fixed screenshot color issues - as of now coloring is based on specification inside screenshot description file, and not on current player settings
- Fixed handling of secretion in ReactionDiffusionSolverFE
- Fixed "Check for New Version" functionality in the player
- Fixed behavior of simulations that use plots but are run in gui-less mode
- Fixed Twedit++ zoom in / zoom out issues
- Fixed CC3D version printout issues
Known Issues
- GPU solvers on OSX 10.14 or higher may not work properly
Binary distribution packages
Windows - 32-bit and 64-bit
CompuCell3D 4.2.2 - Windows (select one of the exe files) Download
Note: If CC3D does not run properly on your machine with NVidia card you can try non-gpu version of the binaries - in this case get setup-no-gpu-xxx.exe file. xxx stands for version number and revision number of current CC3D
IMPORTANT: If after installation of new CC3D you encounter problems on Windows. Please manually remove the directory where CC3D is installed and try using installer again. This is a one-time inconvenience associated with the transition to the new ways of storing Player settings. You may also need to remove _settings.sqlite file in the Simulation subfolder of the .cc3d project folder
Mac OS X - binaries
CompuCell3D 4.2.2 - Mac OS X Download
(Note: Don't download the version using the green box, scroll down to the directly listing and download the .zip file.)
Installation Instructions for Mac OSX Binaries (not needed if you download the binary above)
Linux
We are providing binaries for 64 bit Ubuntu and RedHat (you should not need to compile anything)
CompuCell3D 4.2.2 - Linux (Ubuntu/RedHat) Download
Older Releases
CC3D Version 4.2.1 (June 8, 2020)
We are pleased to announce new version 4.2.1 of our software CompuCell3D. This a bug-fix release that includes the following features and bug-fixes:
Improvements and new features
Added new convenience function to FieldSecretor class to compute total concentration "seen" by a cell as well as total amount of field in the entire lattice
Multiple bug fixes including
- Fixed Replay of saved simulation snapshots
- Fixed simulation shutdown function call sequence to avoid crashes after last MCS was not a multiple of screen update frequency
Known Issues
- GPU solvers on OSX 10.14 or higher may not work properly
Binary distribution packages
Windows - 32-bit and 64-bit
CompuCell3D 4.2.1 - Windows (select one of the exe files) Download
Note: If CC3D does not run properly on your machine with NVidia card you can try non-gpu version of the binaries - in this case get setup-no-gpu-xxx.exe file. xxx stands for version number and revision number of current CC3D
IMPORTANT: If after installation of new CC3D you encounter problems on Windows. Please manually remove the directory where CC3D is installed and try using installer again. This is a one-time inconvenience associated with the transition to the new ways of storing Player settings. You may also need to remove _settings.sqlite file in the Simulation subfolder of the .cc3d project folder
Mac OS X - binaries
CompuCell3D 4.2.1 - Mac OS X Download
(Note: Don't download the version using the green box, scroll down to the directly listing and download the .zip file.)
Installation Instructions for Mac OSX Binaries (not needed if you download the binary above)
Linux
We are providing binaries for 64 bit Ubuntu and RedHat (you should not need to compile anything)
CompuCell3D 4.2.1 - Linux (Ubuntu/RedHat) Download