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 Issues, Bugs, sudden crashes?

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

CC3D Version 4.6.0 (Jul 06, 2024)

We are pleased to announce the new version 4.6.0 of our software CompuCell3D. This release includes many new features and bug fixes.

Improvements and new features

New features:

Changes

Bug fixes:

Known Issues

Binary distribution packages

Windows - 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 the 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 the _settings.sqlite file in the Simulation subfolder of the .cc3d project folder

Mac OS X - binaries

Make sure you pick the installer package that is appropriate for your Mac Processor

Prerequisites

Before installing, make sure to remove previous installation of CompuCell3D - simply delete /Users/<your_login_name>/CompuCell3D

For M1-M3 processors (newer Macs)

Download the installer:

* CompuCell3D 4.6.0 - MacOS arm64 processors (M1, M2) Download

Run the following commands: 

chmod +x cc3d-installer-osx-4.6.0-arm64.sh
./cc3d-installer-osx-4.6.0-arm64.sh

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

For older Macs with Intel processors:

Download the installer:

* CompuCell3D 4.6.0 - MacOS x86 Intel processors Download

Run the following commands 

chmod +x cc3d-installer-osx-4.6.0-x86.sh
./cc3d-installer-osx-4.6.0-x86.sh

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

If you are getting antimony related error on OSX (typically on older Macs with x86 processors) - see below: 

OSError: dlopen(CompuCell3D/miniconda3/lib/python3.10/site-packages/antimony/libantimony.dylib, 6): no suitable image found.  Did find:

or 

OSError: dlopen(lib/python3.10/site-packages/antimony/libantimony.dylib, 6): Symbol not found: __ZNKSt3__115basic_stringbufIcNS_11char_traitsIcEENS_9allocatorIcEEE3strEv
  Referenced from: /Users/m/miniconda3/envs/cc3d-network-solvers-test/lib/python3.10/site-packages/antimony/libantimony.dylib (which was built for Mac OS X 12.0)
  Expected in: /usr/lib/libc++.1.dylib

try reinstalling antimony directly into python that is use by CompuCell3D. To do that run the following command for the terminal: 

~/CompuCell3D/miniconda3/bin/pip install antimony

Linux

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

Before installing, make sure to remove previous installation of CompuCell3D - simply delete/home/<your_login_name>/CompuCell3D

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

chmod +x cc3d-installer-linux-4.6.0-x86-64bit.sh
./cc3d-installer-linux-4.6.0-x86-64bit.sh

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

Installing directly using conda (for users comfortable with installing using Anaconda/Miniconda)

1. If you don't have Miniconda installed, you need to first install it

Install Miniconda - use the latest Miniconda package from https://docs.conda.io/en/latest/miniconda.html. Scroll down on that page and choose the install package for your platform (Windows, Mac or Linux).

2. Ready to install CC3D

First, create an environment for CC3D - we will call this environment cc3d_460_310 - to remind us that we will be installing CompuCell3D version 4.6.0 working with Python 3.10 but you can call it anything you want: 

conda create -n cc3d_460_310 python=3.10

Activate the new environment 

conda activate cc3d_460_310

3. Install mamba

Install mamba to speed up package resolution: 

conda install -c conda-forge mamba

4. Install CC3D

Finally, install CompuCell3D - notice that we are using mamba to install packages because package resolution is much faster when using mamba compared to native conda:

on Windows, you would run: 

set PYTHONIOENCODING=utf-8
mamba install -c main -c conda-forge -c compucell3d compucell3d=4.6.0

on other platforms (Linux, OSX) you can skip the first command and just run: 

mamba install -c main -c conda-forge -c compucell3d compucell3d=4.6.0

Alternatively, you can use the regular conda install command, this will be slower and may take tens of minutes to complete: 

conda install -c main -c conda-forge -c compucell3d compucell3d=4.6.0

Note that in the above commands, you need to specify two channels (code repositories) conda-forge and compucell3d in order to get all the needed packages. If you decide to use this way of installing you will need to manually install the Demos folder.

5. Install the CC3D Demos

To download the Demos from the CC3D GitHub repository navigate to https://download-directory.github.io/ and paste into the dialog box the URL below: 

https://github.com/CompuCell3D/CompuCell3D/tree/2e89970bfd51b4e7d4a7f4edb695130f70f97a46/CompuCell3D/core/Demos

then hit Enter. This will create and download a zip file containing the demos.

Create a "Demos" folder in your top level CC3D directory and unzip the zip archive into that directory.

6. Running Player (CC3D) or Twedit++

To start Player that was installed directly via Miniconda you would run: 

python -m cc3d.player5

To run Twedit++: 

python -m cc3d.twedit5

To run CC3D without any GUI: 

python -m cc3d.run_script

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 4.5.0 (Jan 09, 2024)

We are pleased to announce the new version 4.5.0 of our software CompuCell3D. This release is mostly a bug-fix release but it also provides support for all Python versions starting with Python 3.7.

Improvements and new features

New features:

Changes

Bug fixes:

Known Issues

CC3D Version 4.4.1 (Jul 08, 2023)

Improvements and new features

New features:

Bug fixes:

Known Issues

CC3D Version 4.4.0 (Apr 06, 2023)

We are pleased to announce new version 4.4.0 of our software CompuCell3D. This release includes multiple bug fixes and new features.

Improvements and new features

New features:

Bug fixes:

CC3D Version 4.3.2 (Nov 22, 2022)

We are pleased to announce new version 4.3.2 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-4.3.2.0.sh
   ./cc3d-installer-osx-4.3.2.0.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-4.3.2sh
   ./cc3d-installer-linux-4.3.2sh

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)

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.

CompuCell3D: SrcBin (last edited 2024-11-19 17:37:23 by JamesSluka)