CompuCell 3D
Parallel CompuCell 3D
We are currently able to support Windows, Mac OS X and Linux for the parallel CompCell3D. Compilation of parallel CompuCell 3D looks identical as compilation of serial code.
Version 3.6.1
Binaries:
Windows
Mac OS X
CompuCell 3.6.1 - Mac OS X 10.6 (Snow Leopard) (64bit intel) Download and Instructions
Linux (COMING SOON)
If the above packages are not suitable, building and installing 3.6.1 from source on Unix/Linux is easily done by following our Linux step-by-step tutorial .
Version 3.6.0
Binaries:
Windows
Mac OS X
CompuCell 3.6.0 - Mac OS X 10.6 (Snow Leopard) (64bit intel) Download and Instructions
Required dependencies and third-party libraries are included in the binary distribution for Mac OS X, such as Qt, PyQt, VTK, etc. CompuCell 3D relies on Python 2.6.1 as installed by default on all Mac OS X 10.6 systems. * Note: the CompuCell 3D 3.6.0 binary distribution for Mac includes dynamic libraries from the gcc 4.6 package made available by the HPC for Mac site on SourceForge: libgomp.1.dylib and its related libgcc_s.1.dylib. These two libraries are contained in the CC3D_3.5.0_MacOSX106 binary distribution as runtime replacement of the default OpenMP library included with Mac OS X 10.6. The CompuCell 3D 3.6.0 binary distribution for Mac OS X 10.6 can be successfully compiled using current XCode tools (gcc 4.2.1 etc); however, when running multithreaded scripts in CC3D 3.5.0, the default OpenMP dynamic library (libgomp) included in standard Mac OS X 10.6 systems has a bug causing CC3D to crash at runtime. Therefore, to run multithreaded scripts either recompile the OpenMP library from source, or use the precompiled OpenMP included in gcc 4.6 from the HPC sourceforge website: these can be found in /usr/local/lib/libgomp.1.dylib and /usr/local/lib/libgcc_s.1.dylib in the gcc-snwleo-intel-bin.tar.gz package. Newer CompuCell 3D binary distributions for Mac are compiled using gcc 4.6.0.
Linux
We provide binaries for several distributions:
If the above packages are not suitable, building and installing 3.6.0 from source on Unix/Linux is easily done by following our step-by-step tutorial.
Source Code SVN Access (All Platforms):
http://code.compucell3d.org/svn/cc3d/branch/3.6.0
Version 3.5.0
Binaries:
Windows
CompuCell 3.5.0 - Windows Download
You need Python 2.5 to run CompuCell 3D - Download
To get scientific plots working under CC3D you need to download numpy-1.3 Download
Mac OS X
CompuCell 3.5.0 - Mac OS X 10.6 (Snow Leopard) (64bit intel) Download and Instructions
Required dependencies and third-party libraries are included in the binary distribution for Mac OS X, such as Qt, PyQt, VTK, etc. CompuCell 3D relies on Python 2.6.1 as installed by default on all Mac OS X 10.6 systems. * Note: the CompuCell 3D 3.5.0 binary distribution for Mac includes dynamic libraries from the gcc 4.6 package made available by the HPC for Mac site on SourceForge: libgomp.1.dylib and its related libgcc_s.1.dylib. These two libraries are contained in the CC3D_3.5.0_MacOSX106 binary distribution as runtime replacement of the default OpenMP library included with Mac OS X 10.6. The CompuCell 3D 3.5.0 binary distribution for Mac OS X 10.6 is compiled using current XCode tools (gcc 4.2.1 etc); however, when running multithreaded scripts in CC3D 3.5.0, the default OpenMP dynamic library (libgomp) included in standard Mac OS X 10.6 systems has a bug causing CC3D to crash at runtime. Therefore, to run multithreaded scripts either recompile the OpenMP library from source, or use the precompiled OpenMP included in gcc 4.6 from the HPC sourceforge website: these can be found in /usr/local/lib/libgomp.1.dylib and /usr/local/lib/libgcc_s.1.dylib in the gcc-snwleo-intel-bin.tar.gz package. Newer CompuCell 3D binary distributions for Mac are compiled using gcc 4.6.0.
Linux
At the moment you need to compile 3.5.0 version of CC3D from source. We are working on supplying binaries for select distributions. For compilation instructions (compilation on Linux is quite straightforward as most of dependencies are supplied in the form of easy-to-install packages) please see the 3.6.0 compilation instructions
Source Code SVN Access (All Platforms):
http://code.compucell3d.org/svn/cc3d/branch/3.5.0
Serial CompuCell 3D
Binaries:
Mac OS X
CompuCell 3D Version 3.4.2 for Mac OS X 10.6 (Snow Leopard)
Download CompuCell 3D version 3.4.2 (32bit/64bit intel) for Mac OS X 10.6
Instructions: how to run CompuCell 3D Version 3.4.2 on Mac OS X 10.6 (Snow Leopard)
CompuCell 3D Version 3.4.2 for Mac OS X 10.5 (Leopard)
Download CompuCell 3D version 3.4.2 (32bit/64bit intel) for Mac OS X 10.5
Instructions: how to run CompuCell 3D Version 3.4.2 on Mac OS X 10.5 (Leopard)
Windows
CompuCell 3D 3.4.2 Download
You need Python 2.5 to run CompuCell 3D - Download
To get scientific plots working under CC3D you need to download numpy-1.3 Download
Linux
- Linux Distros (Version 3.4.1)
Source Code SVN Access (All Platforms):
http://code.compucell3d.org/svn/cc3d/branch/3.4.2
SBW/CompuCell 3D Integration
Instructions: Before installing soslib-setup make sure you have installed latest version of CompuCell 3D. To install soslib run soslib-setup.exe and install it to the directory where CompuCell 3D is installed. For example if CompuCell 3D is in C:\Program Files\COMPUCELL3D directory make sure that installation path of soslib is also C:\Program Files\COMPUCELL3D
Source Code and ChangeLog
CompuCell Version 3.4.1 Download tar.gz
CompuCell Version 3.4.1 Download zip
Known Issues and Requirements
- Python 2.5
- Ubuntu users must install python-qt4
CellDraw
CellDraw (formerly known as PIF Generator) is an editing and conversion software tool for PIF files, as used in CompuCell 3D simulations. It can be useful for creating PIF files containing a high number of cells and cell types, either by drawing a scene containing cell regions in a paint program, and then discretize the drawing into a PIF file, or by drawing the cell scenario directly in CellDraw.
CellDraw 1.5.0 and newer releases are included in recent CC3D installation packages (CC3D 3.6.0 or newer). The release for Mac OS X systems is also available as a stand-alone application download.
PIF Generator 1.4.0 screenshot:
Older Tools
PIFTracer
PIFTracer helps with PIF file creation. Mac OS X only.
PIFTracer download original version
PIFTracer 1.1 download with cell cluster support
PIFTracer screenshot:
Dorsal surface of a fruit fly embryo at Bowne's stage 13 (early dorsal closure). The large cells are known as amnioserosa. The labeling is with a GFP-cadherin construct.
(image courtesy of Prof. Shane Hutson)