MCCE4 default PBE solver is NextGenPB (NGPB).

There are two ways you can install MCCE4-Alpha, which differ on whether a script is used:

Option A:
- Keep the provided mcce and delphi (alternate PBE solver) executables compiled for Linux OS;
- Use the semi-automated setup using provided script that download a generic NGPB image.
Option B: Manual setup that includes: the compilation of mcce with or without that of delphi, and the creation of a NGPB image optimized for your platform.

Option A: Quick Installation with Scripts

1. Clone the repository to a desired place on your computer (referred to as “clone_dir”):

Git clone MCCE4-Alpha to a desired place on your computer:

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

2. Run each of the following scripts (POSIX compliant):

First script to run: ./MCCE_bin/check_environment.sh This script determines if you’re missing apptainer, the container application used by NGPB, or conda and provides you with useful links to install them if necessary. Run:
```
 sh ./MCCE_bin/check_environment.sh
```
Second script to run: ./MCCE_bin/quick_install.sh This script automates the conda environment creation, shows how to setup references in your .bashrc (.bash_profile) file, and download a generic NGPB image. Run:
```
 sh ./MCCE_bin/quick_install.sh
```
The quick installation is completed by following the instructions displayed on the screen.

Option B: Installation with Executable Compilation and Creation of a NGPB Image Optimized for your System:

1. Clone the repository to a desired place on your computer (referred to as “clone_dir”):

Git clone MCCE4-Alpha to a desired place on your computer:

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

Add the clone’s bin paths to your .bashrc (.bash_profile) file then save it.

   export PATH="clone_dir/MCCE4-Alpha/bin:$PATH"
   export PATH="clone_dir/MCCE4-Alpha/MCCE_bin:$PATH"

Then apply the changes to your PATH variable by sourcing your .bashrc (.bash_profile) file, depending on your system.
Check a tool’s command correct path location (tools do not require compiling):
```
which p_info
```
The command should return ~/clone_dir/MCCE4-Alpha/MCCE_bin/p_info

2. Executables and NGPB Container Image

MCCE4 contains C and C++ libraries that must be compiled prior to use. These consist of two executable files and a container image for the PBE solver, NGPB

mcce : Main simulation executable
delphi : Legacy PBE solver (support not guaranteed on all systems)
NextGenPB_MCCE4.sif : Container image for NGPB, the default MCCE4 PBE solver

Currently, the MCCE4-Alpha Repository provides both the mcce and delphi compiled executables for Linux OS but the NGPB container requires sudo access to compile. Therefore, we also provide a Linux OS–compiled NGPB container (NextGenPB_MCCE4_LinuxCompiled.sif) at the Dropbox link below. Please place this in your MCCE4/bin as NextGenPB_MCCE4.sif

👉 Download NextGenPB_MCCE4_LinuxCompiled.sif

⚠️ Warning: We cannot guarantee that the DelPhi PBE solver executable (delphi) will run on your system. This is one of the reasons NextGenPB is now the default PBE solver in MCCE4.

Compile Executables and NGPDB Container Image

If the provided executables and NGPB container do not work for your system, they must be compiled via the MakeFile. To proceed with compiling, please do the following:

⚠️ Warning: Ensure you have sudo access as it is necessary for the installation of the NGPB container (~15 min+).

cd into your MCCE4-Alpha clone directory:
```
cd ~/clone_dir/MCCE4-Alpha
```

Clean up previous versions, if any:

make clean                  # remove bin/mcce and bin/delphi if present
rm bin/NextGenPB_MCCE4.sif  # remove existing container image

Re-create the three objects: The screen output of this long compilation is extensive and not recoverable if not directed to a file, so there are two way to run the command:

a. Run make all command, without logging:
```
make all
```
Or compile each individually:
```
make mcce
make delphi
make ngpb
```
b. Run make all command, with redirection to a log file:
```
  make all > make.log 2>&1
```
Or redirect logs for each target individually:
```
make mcce   > make_mcce.log   2>&1
make delphi > make_delphi.log 2>&1
make ngpb   > make_ngpb.log   2>&1
```

NOTE: To use the Openeye Zap solver, see the “PBE Solvers” section.

3. Test Installation

Create and activate a conda environment using MCCE4-Alpha environment file mc4.yml. Choose either Command 1 or 2 below to create the environment:
1. Command 1: To use the default environment name of ‘mc4’:
```
 conda env create -f mc4.yml
 conda activate mc4
```
2. Command 2: If you want something else, e.g. ‘new_env’ to be the environment name instead of ‘mc4’:
```
 conda env create -f mc4.yml -n new_env
 conda activate new_env
```

Alternate way with pyenv (conda is not abolutely necessary):

  pyenv virtualenv 3.10 mc4
  pyenv activate mc4
  pip install -r ../requirements.txt

Check that a tool is functional; Its usage message should display:
```
 p_info
```
Display a command’s help, e.g:
```
 p_info -h
 step1.py -h
```