Index

Do you want to test CompuCell3D before installing?

We have several CompuCell3D demos deployed for online testing, visit: Repository of nanoHub CompuCell3D Tools.

Installation Issue, Bugs, sudden crashes?

If you encounter any problems with CompuCell3D or Twedit++ please visit this page.

CC3D Version 4.3.1 (Jul 1272022)

We are pleased to announce new version 4.310 of our software CompuCell3D. This release includes multiple bug fixes and new features.

Improvements and new features

Known Issues

Binary distribution packages

Windows - 32-bit and 64-bit

We have a step-by-step installation guide in pdf and docx formats.

Note 1: 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

Note 2:: 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

To install, after downloading installer script open terminal and go to the directory where you downloaded the package (likely Downloads folder) run the following: 

   chmod +x cc3d-installer-osx-4.3.1.0.sh
   ./cc3d-installer-osx-4.3.1.0.sh

CompuCell3D installer will install packages in /Users/<your_login_name>/CompuCell3D

Linux

We are providing binaries for 64 bit Ubuntu and RedHat (you should not need to compile anything)

To install, after downloading installer script open terminal and go to the directory where you downloaded the package (likely Downloads folder) run the following: 

   chmod +x cc3d-installer-linux-4.3.1.0.sh
   ./cc3d-installer-linux-4.3.1.0.sh

CompuCell3D installer will install packages in /home/<your_login_name>/CompuCell3D

Installing directly using conda (for power users only)

If you already have anaconda or miniconda installed on your system you may install compucell3d directly via conda install command. To install version 4.3.0 directly type: 

 conda install -c conda-forge -c compucell3d compucell3d=4.3.1

Note, you need to specify two channels conda-forge and compucell3d in order to get all packages. If you decide to use this way of installing you will need to manually install Demos folder. To start player installed directly via conda you would run: 

python -m cc3d.player5

Speeding up package resolution

You may have noticed that resolving dependencies is relatively slow when using conda commands. There is a relatively simple solution to this. All you need to do is to install mamba package manager in your base conda environment: 

conda activate base
conda install -c conda-forge mamba

Once you have mamba package manager installed you replace conda with mamba to install compucell3d : 

mamba install -c conda-forge -c compucell3d compucell3d=4.3.1

The reason mamba is significantly faster than conda is because mamba is written in C++ and it provides fairly complete replacement for conda functionality

Running CC3D 4.2.5 Amazon Web Services (AWS)

To install CC3D 4.2.5 on AWS servers, please search for image (available in regions us-east-2 and us-west-1) called 

cc3d_4.2.5

or search directly for the following image id: 

ami-03769eff9c88589db

and follow the instructions at Running CC3D on AWS cloud. Make sure to replace CC3D version described in this manual with the current version.

Older Releases

CC3D Version 4.3.0 (Apr 14 2022)

We are pleased to announce new version 4.3.0 of our software CompuCell3D. This release includes multiple bug fixes and new features.

Improvements and new features

Known Issues

Binary distribution packages

Windows - 32-bit and 64-bit

We have a step-by-step installation guide in pdf and docx formats.

Note 1: 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

Note 2:: 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

To install, after downloading installer script open terminal and go to the directory where you downloaded the package (likely Downloads folder) run the following: 

   chmod +x cc3d-installer-osx-4.3.0.2.sh
   ./cc3d-installer-osx-4.3.0.2.sh

CompuCell3D installer will install packages in /Users/<your_login_name>/CompuCell3D

Installing directly using conda (for power users only)

If you already have anaconda or miniconda installed on your system you may install compucell3d directly via conda install command. To install version 4.3.0 directly type: 

 conda install -c conda-forge -c compucell3d compucell3d=4.3.0

Note, you need to specify two channels conda-forge and compucell3d in order to get all packages. If you decide to use this way of installing you will need to manually install Demos folder. To start player installed directly via conda you would run: 

python -m cc3d.player5

Linux

We are providing binaries for 64 bit Ubuntu and RedHat (you should not need to compile anything)

To install, after downloading installer script open terminal and go to the directory where you downloaded the package (likely Downloads folder) run the following: 

   chmod +x cc3d-installer-linux-4.3.0.2.sh
   ./cc3d-installer-linux-4.3.0.2.sh

CompuCell3D installer will install packages in /home/<your_login_name>/CompuCell3D

CC3D Version 4.2.5 (June 12 2021)

We are pleased to announce new version 4.2.5 of our software CompuCell3D. This release includes multiple bug fixes and new features.

Improvements and new features

Multiple bug fixes including

Known Issues

Binary distribution packages

Windows - 32-bit and 64-bit

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

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)

CC3D Version 4.2.4 (Jan 18 2021)

NOTE: The original release version of 4.2.4 had a bug in Twedit++ that omitted the CC3DML menu. Please make sure your installed version is 4.2.4 with the time stamp of 20210123 (Jan. 23, 2021) or later.

We are pleased to announce new version 4.2.4 of our software CompuCell3D. This a bug-fix release that includes the following features and bug-fixes:

Improvements and new features

Multiple bug fixes including

Known Issues

Binary distribution packages

Windows - 32-bit and 64-bit

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

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)

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

Multiple bug fixes including

Known Issues

Binary distribution packages

Windows - 32-bit and 64-bit

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

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)

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

Multiple bug fixes including

Known Issues

Binary distribution packages

Windows - 32-bit and 64-bit

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

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)

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

Multiple bug fixes including

Known Issues

Binary distribution packages

Windows - 32-bit and 64-bit

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

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)

Need older releases?

Old releases

Updating from CC3D 3.x to 4.x

Because we switched from Python 2 to Python 3 your old simulations will require minor modifications Please see https://pythonscriptingmanual.readthedocs.io/en/4.0.0/transition_to_cc3d_4.html for instructions on how to port your simulations.