Skip to content
master
Go to file
Code

Latest commit

 

Git stats

Files

Permalink
Failed to load latest commit information.
Type
Name
Latest commit message
Commit time
 
 
 
 
 
 
man
 
 
src
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 

README.md

MCell

Overview

MCell (Monte Carlo Cell) development is supported by the NIGMS-funded (P41GM103712) National Center for Multiscale Modeling of Biological Systems (MMBioS).

MCell is a program that uses spatially realistic 3D cellular models and specialized Monte Carlo algorithms to simulate the movements and reactions of molecules within and between cells—cellular microphysiology.

Build Requirements:

Ubuntu 16.04:

Run the following commands:

sudo apt-get update
sudo apt-get install cmake build-essential bison flex python3-dev swig libboost-all-dev

Windows

Install the package manager chocolatey from https://chocolatey.org/install. Follow the instructions listed on that page, which will have you copy a command into PowerShell as an Administrator.

Once chocolatey is installed, open up a new PowerShell terminal as an Administrator, and run the following commands:

choco install -y git
choco install -y python3
choco install -y cmake
choco install -y ninja
choco install -y msys2
choco install -y winflexbison
choco install -y swig

Open a new PowerShell Administrator terminal and enter the following:

msys2

This will open a different MSYS2 terminal (not a PowerShell terminal). In this MSYS2 terminal, enter the following commands:

pacman -Syuu
pacman -S --needed base-devel mingw-w64-i686-toolchain mingw-w64-x86_64-toolchain \
                git subversion mercurial \
                mingw-w64-i686-cmake mingw-w64-x86_64-cmake
pacman -Sy mingw-w64-i686-boost mingw-w64-x86_64-boost

Add CMake and MinGW64 to your Windows PATH Environment Variable. If you have installed these dependencies with Chocolatey and your top level drive is named C:, you can append (or prepend) the following paths into your Windows PATH (Search "Control Panel"; View by small icons; System; Advanced System Settings; Environment Variables; User Variables; Path; Edit):

C:\tools\msys64\mingw64\bin
C:\Program Files\CMake\bin

Building MCell Executable from Source (OSX, Linux, Windows)

Open a terminal (non-Administrator PowerShell for Windows users), clone the mcell_tools repo and run:

git clone https://github.com/mcellteam/mcell_tools.git
cd mcell_tools
python3 run.py

This will clone all the required repositories and run build of all the components. Running 'python3 run.py --help' shows other options.

To build just MCell, run these commands after you ran the 'python run.py'.

cd mcell_tools/work/build_mcell
cmake ../../../mcell -DCMAKE_BUILD_TYPE=Release
make 

Testing MCell

cd mcell_tests
python3 run_tests.py

Running 'python3 run_tests.py --help' shows other options.

You can’t perform that action at this time.