mcell/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.