Download and Install MCCE

Download and Install MCCE

MCCE runs on Linux and Mac OSX natively.

On Windows, you will need a Linux environment. It could be a virtual box instance, Cygwin, or Linux subsystem that is included in Windows. Here is a short guide of installing Windows Subsystem Linux (to be done):

Prerequisites

Compilers:

C, gfortran

MCCE comes with two parts:

MCCE main code in c/c++

Poisson Boltzmann equation solver delphi in c/fortran

You need basic Linux program tools like make and ar utility. They usually some with the operating system. If not, install them. On Ubuntu, run

sudo apt install build-essential

It is recommended to use the compilers under conda. Conda provides compilers and other programming tools under user space. If you don't have conda, you can follow instructions here https://docs.conda.io/en/latest/miniconda.html to install miniconda.

Python and modules

We need Python3 and optionally these modules: numpy, scipy, matplotlib, pygraphviz, pandas, xlrd, and openpyxl

Install Miniconda Python3: https://docs.conda.io/en/latest/miniconda.html

After installing Miniconda, install these optional modules for data analysis:

conda install requests numpy scipy matplotlib pygraphviz pandas xlrd openpyxl multiprocess

To install gfortran compiler that is compatible for delphi:

Create mcce environment

conda create -n mcce conda activate mcce

Install compilers

conda install -c conda-forge gcc gfortran

Now roll back gfortran to 9.5.0 (delphi requires an old compiler)

conda install -c conda-forge gfortran=9.5.0

Install MCCE

Download from github

Under a terminal window, run:

git clone https://github.com/GunnerLab/MCCE4-Alpha.git

Compile the code

The above command creates a directory named MCCE4-Alpha, enter the directory and compile:

$ cd MCCE4-Alpha

$ make clean

$ make

Configure environment

Find the path of Stable-MCCE installation directory:

(base) jmao@pc:~/projects/MCCE4-Alpha$ pwd

/home/jmao/projects/MCCE4-Alpha

In my case the installation directory is /home/jmao/projects/MCCE4-Alpha/

Add the executable to your path:

export PATH=/home/jmao/projects/MCCE4-Alpha/bin:$PATH

export PATH=/home/jmao/projects/MCCE4-Alpha/MCCE_bin:$PATH

Remember to replace the installation directory /home/jmao/projects/MCCE4-Alpha/ with your own installation path.

Also put this line at the end of .bashrc file under your home directory so that the environment is properly set every time you open a terminal window.