= Index = * [[#OnlineTest|Do you want to test CompuCell3D before installing?]] * [[#Issue|Installation Issue, Bugs, sudden crashes?]] * [[#AWS|Running CC3D 4.2.5 Amazon Web Services (AWS)]] * [[#MostRecent|Most Recent Release 4.5.0 (Jan 09, 2024)]] * [[#MostRecentWindows|Windows]] * [[#MostRecentMac|Mac]] * [[#MostRecentLinux|Linux]] * [[#OldVersions|Older Releases]] * [[#441|CC3D 4.4.1 (Jul 08 2023)]] * [[#440|CC3D 4.4.0 (Apr 06 2023)]] * [[#432|CC3D 4.3.2 (Nov 06 2022)]] * [[#431|CC3D 4.3.1 (July 22 2022)]] * [[#430|CC3D 4.3.0 (April 14 2022)]] * [[#425|CC3D 4.2.5 (June 12 2021)]] * [[#424|CC3D 4.2.4 (January 18 2021)]] * [[#EvenOlder|Even Older Releases]] * [[#Migrating34|Migrating old CC3D 3.x to 4.x]] ---- <> = Do you want to test CompuCell3D before installing? = We have several CompuCell3D demos deployed for online testing, visit: [[https://compucell3d.org/Models-nanoHub|Repository of nanoHub CompuCell3D Tools|target=_blannk]]. ---- <> = Installation Issues, Bugs, sudden crashes? = If you encounter any problems with CompuCell3D or Twedit++ please [[Problems_and_bugs|visit this page|target=_blank]]. ---- <> = 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: === * Added Polygon Initializer with extensions to 3D * Added Tube Initializer 3D * Added support for generating simulation movies * Added on-demand snapshots to Python API === Changes === * All Gillespie solvers are now initialized with random seed. You can still fix the seed using {{{ self.set_gillespie_integrator_seed }}} === Bug fixes: === * Fixed !DeveloperZone on Windows * Fixing issue with attaching Python dictionary to Link objects * Fixed restart capability * Multiple minor bug fixes == Known Issues == * GPU solvers on OSX 10.14 or higher may not work properly. Windows GPU solvers may not work on all machines * If you move the Player window across multiple monitors you may see errors on the axes. You may need to delete the _settings.sqlite files (described [[https://compucell3d.org/Problems_and_bugs#crashes|here|target=_blank]]). * You may knock out libRoadRunner (the SBML tools) when you install other Python packages, e.g. if you install PyTorch. CC3D displays an uninformative error in the console. Reinstalling CC3D is the only solution to this issue. <> == Binary distribution packages == === Windows - 64-bit === * CompuCell3D 4.5.0 - Windows (select one of the '''exe''' files) [[http://www.sourceforge.net/projects/cc3d/files/4.5.0/windows/|Download]] '''We have a step-by-step installation guide in [[attachment:Installing_CC3D_430v2_on_Windows_10.pdf|pdf|&do=get]] and [[attachment:Installing_CC3D_430v2_on_Windows_10.docx|docx|&do=get]] 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//CompuCell3D''' ==== For M1-M3 processors (newer Macs) ==== Download the installer: * CompuCell3D 4.5.0 - MacOS arm64 processors (M1, M2) [[https://sourceforge.net/projects/cc3d/files/4.5.0/mac/arm64_M1/cc3d-installer-osx-4.5.0-arm64.sh/download|Download]] Run the following commands: {{{ chmod +x cc3d-installer-osx-4.5.0-arm64.sh ./cc3d-installer-osx-4.5.0-arm64.sh }}} CompuCell3D installer will install packages in '''/Users//CompuCell3D''' ==== For older Macs with Intel processors: ==== Download the installer: * CompuCell3D 4.5.0 - MacOS x86 Intel processors [[https://sourceforge.net/projects/cc3d/files/4.5.0/mac/x86/cc3d-installer-osx-4.5.0-x86.sh/download|Download]] Run the following commands {{{ chmod +x cc3d-installer-osx-4.5.0-x86.sh ./cc3d-installer-osx-4.5.0-x86.sh }}} CompuCell3D installer will install packages in '''/Users//CompuCell3D''' ==== Handling antimony-related error on older OSX system ==== 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) * CompuCell3D 4.5.0 - Linux (Ubuntu/RedHat) [[http://sourceforge.net/projects/cc3d/files/4.5.0/linux/|Download]] Before installing, make sure to remove previous installation of CompuCell3D - simply delete'''/home//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-4.5.0-x86-64bit.sh ./cc3d-installer-linux-4.5.0-x86-64bit.sh }}} CompuCell3D installer will install packages in '''/home//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 4.5.0 directly type: Install miniconda - use latest miniconda package from https://docs.conda.io/en/latest/miniconda.html . Install '''mamba''' to speed up package resolution: {{{ conda install -c conda-forge mamba }}} Create separate environment for CC3D - we will call this environment '''cc3d_450_310''' - to remind us that we will be installing !CompuCell3D version 4.5.0 working with Python 3.10 but you can cally anything you want: {{{ conda create -n cc3d_450_310 python=3.10 }}} Activate the new environment {{{ conda activate cc3d_450_310 }}} Finally, install compucell3d - notice that we are using mamba to install packages because package resolution is way faster when using mamba compared to native conda: {{{ mamba install -c conda-forge -c compucell3d compucell3d=4.5.0 }}} 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 }}} 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 [[https://github.com/CompuCell3D/cc3d_build_scripts/blob/master/linux/aws/aws_notes.rst#using-existing-ami-image-to-launch-aws-instance-with-cc3d-installed|Running CC3D on AWS cloud]]. Make sure to replace CC3D version described in this manual with the current version. ---- <> = Older Releases = <> = CC3D Version 4.4.1 (Jul 08, 2023) = == Improvements and new features == === New features: === * Added support for all Python versions >= 3.7 * Updated muParser to the latest version * Changed the way updates are handled: we are now redirecting users to sourceforge to download the new package * Improved package resolution - results in much faster download and installation times === Bug fixes: === * Fixed integration between Twedit and Player * Fixed cc3d.__init__ to run with python versions > 3.7 * Fixed Python bindings and Python scripts to behave properly when working with Python> 3.7 and newer versions of numpy * Minor fixes to C++ code to compile properly with the latest versions of C++ compilers and use a newer versions of OpenMP on linux/OSX == Known Issues == * GPU solvers on OSX 10.14 or higher may not work properly. Windows GPU solvers may not work on all machines * If you move the Player window across multiple monitors you may see errors on the axes. You may need to delete the _settings.sqlite files (described [[https://compucell3d.org/Problems_and_bugs#crashes|here|target=_blank]]). * You may knock out libRoadRunner (the SBML tools) when you install other Python packages, e.g. if you install PyTorch. CC3D displays an uninformative error in the console. Reinstalling CC3D is the only solution to this issue. <> = 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: === * Added all-Python frontend * Implemented interactive execution and visualization in pure Python * Added support for Jupyter Notebook * Added select Jupyter Notebook widgets for interactive execution and visualization * Added finite volume reaction diffusion solver * Improved glyphs rendering * Added backend logging * Upgraded VTK to 9.x * Upgraded SWIG to 4.x * Improved conda builds === Bug fixes: === * Fixed 3D concentration visualization * Fixed ordering of cell type ID generation * Fixed python-based rendering * Fixed random number generator * Fixed randomization of cleavage plane during random orientation mitosis <> = 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 == * Fixing crashes during rendering of scalar fields on non-square lattices == Known Issues == * GPU solvers on OSX 10.14 or higher may not work properly. Windows GPU solvers may not work on all machines == Binary distribution packages == === Windows - 32-bit and 64-bit === * CompuCell3D 4.3.2 - Windows (select one of the '''exe''' files) [[http://www.sourceforge.net/projects/cc3d/files/4.3.2/windows/|Download]] '''We have a step-by-step installation guide in [[attachment:Installing_CC3D_430v2_on_Windows_10.pdf|pdf|&do=get]] and [[attachment:Installing_CC3D_430v2_on_Windows_10.docx|docx|&do=get]] 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 === * CompuCell3D 4.3.2 - Mac OS X [[https://sourceforge.net/projects/cc3d/files/4.3.2/mac/|Download]] 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//CompuCell3D''' === Linux === We are providing binaries for 64 bit Ubuntu and !RedHat (you should not need to compile anything) * CompuCell3D 4.3.2 - Linux (Ubuntu/RedHat) [[http://sourceforge.net/projects/cc3d/files/4.3.2/linux/|Download]] 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 == * New, conda-based packaging * Integrated miniconda - gives users access to the entire Python ecosystem * One-click configuration for !DeveloperZone - enables users to quickly develop C++ plugins and steppables (updated Developers Manual coming soon) * Integrated C/C++ compilers (Linux, OSX) * Much easier future upgrades * Added support for cell link inventory lists in Python * Added support for relocatability and builds with cc3d as a dependency * Split code into 3 separate packages - cc3d-core, Player, Twedit * cc3d core code released under MIT license * Multiple bug fixes == Known Issues == * GPU solvers on OSX 10.14 or higher may not work properly. Windows GPU solvers may not work on all machines == Binary distribution packages == === Windows - 32-bit and 64-bit === * CompuCell3D 4.3.0 - Windows (select one of the '''exe''' files) [[http://www.sourceforge.net/projects/cc3d/files/4.3.0/windows/|Download]] '''We have a step-by-step installation guide in [[attachment:Installing_CC3D_430v2_on_Windows_10.pdf|pdf|&do=get]] and [[attachment:Installing_CC3D_430v2_on_Windows_10.docx|docx|&do=get]] 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 === * CompuCell3D 4.3.0 - Mac OS X [[https://sourceforge.net/projects/cc3d/files/4.3.0/mac/|Download]] 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//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) * CompuCell3D 4.3.0 - Linux (Ubuntu/RedHat) [[http://sourceforge.net/projects/cc3d/files/4.3.0/linux/|Download]] 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//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 === * Added Boolean Network solver (MaBoSS) * Added selection of !RoadRunner integrator to API * Added Reciprocated algorithm to Chemotaxis plugin * Added log-scaled chemotaxis by cell center of mass concentration * Added multiple vertical axes in Player plots * Added python dictionary to all Link classes * Added support for attaching Antimony, SBML and CellML models to individual links * Optimization of cell shell made optional in Player * First rendering now occurs after start in Player * Added cell velocity to CellG derived properties * Added a cell type color map to Player * Added display of parameter scan iteration in Player * Minor updates to Twedit code snippets === Multiple bug fixes including === * Disabled problematic plot menu items in Player * Fixed memory leaks associated with Player plot windows * Better handling of output folder location by parameter scans * Fixed static font size show concentration ranges in Player * Fixed automatic scaling in diffusion solver !ConstantConcentration * Fixed eccentricity calculations in moment of inertia plugin === Known Issues === * GPU solvers on OSX 10.14 or higher may not work properly === Binary distribution packages === ==== Windows - 32-bit and 64-bit ==== * CompuCell3D 4.2.5 - Windows (select one of the '''exe''' files) [[http://www.sourceforge.net/projects/cc3d/files/4.2.5/windows/|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 4.2.5 - Mac OS X [[https://sourceforge.net/projects/cc3d/files/4.2.5/mac/|Download]] <
> (Note: Don't download the version using the green box, scroll down to the directory listing and download the .zip file for your version of OSX.) [[SrcBin/OSXInstallBinaries|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 4.2.5 - Linux (Ubuntu/RedHat) [[http://sourceforge.net/projects/cc3d/files/4.2.5/linux/|Download]] <> == 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 === * Added regression test suite * Major overhaul of !FocalPointPlasticity Plugin including * Added regular, internal and anchor link objects * Revised plugin throughout on the basis of link objects * Added link attributes and methods for link-specific manipulations * Added link inventory management methods to !SteppableBasePy * Added Callable CC3D renderer * Added !DerivedProperty for read-only attributes in python calculated on-demand in C++ * Added derived properties for cells: pressure, surface tension, * Added derived properties to regular and internal links: length, tension, linked cells * Added derived properties to anchor links: length, tension, linked cell === Multiple bug fixes including === * Minor bug fixes === Known Issues === * GPU solvers on OSX 10.14 or higher may not work properly <> === Binary distribution packages === ==== Windows - 32-bit and 64-bit ==== * CompuCell3D 4.2.4 - Windows (select one of the '''exe''' files) [[http://www.sourceforge.net/projects/cc3d/files/4.2.4/windows/|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 4.2.4 - Mac OS X [[https://sourceforge.net/projects/cc3d/files/4.2.4/mac/|Download]] <
> (Note: Don't download the version using the green box, scroll down to the directory listing and download the .zip file for your version of OSX.) [[SrcBin/OSXInstallBinaries|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 4.2.4 - Linux (Ubuntu/RedHat) [[http://sourceforge.net/projects/cc3d/files/4.2.4/linux/|Download]] ---- <> == Need older releases? == [[SrcBinOldReleases|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.