Setting the Stage

Installation Option A: Quick Installation with Scripts

Scripts:

These scripts automate many steps & download a generic NGPB image:

• MCCE_bin/quick_install.sh (Linux, bash shell)
• MCCE_bin/quick_install_zsh.sh (MacOS)

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

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

2. Run the “Quick Install” script:

i. Go to your MCCE4-Alpha clone:

 cd ~/clone_dir/MCCE4-Alpha

ii. Run the approriate script:

• On MacOS, run:

   sh ./MCCE_bin/quick_install_zsh.sh
  

• On Linux, run:

   bash ./MCCE_bin/quick_install.sh
  

  Note: Creating ‘install.log’ is not required but is recommended as you could copy its contents if your created an “installation issue”, which could help us fix an unexpected problem.

3. Follow the instructions displayed by the script to test your installation.

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Installation Option B: Installation with NGPB Optimized Image Creation:

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 \your [clone_dir]/MCCE4-Alpha/MCCE_bin/p_info

2. Compile Executables

MCCE4 contains C and C++ libraries that must be compiled prior to use. Two compilations are required: for the mcce executable and for NGPB, the default PBE solver.

• NOTE: We also provide the DelPhi PBE solver executable file (delphi), without guarantying its runnability on all systems.

• To compile mcce and ngpb:
  • Ensure you have sudo access as it is necessary for the installation of the NGPB container (~15min+)
  • cd into your MCCE4-Alpha clone directory
  • Run these commands:
    1. First and fast compilation command:

         make clean
       

    2. Second and slow compilation (& container setup) command:
       • IMPORTANT: In case this is not the first time the command is run, make sure to delete its target file, i.e.:

          rm bin/NextGenPB_MCCE4.sif
         

         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:

       • Run make command, without logging:

          make
         

       • Run make command, with redirection to a log file:

          make > make.log 2>&1
         

• NOTE: To use the Openeye Zap solver, see “Zap Installation” below.

3. Test Installation

• Create and activate a conda environment using MCCE4-Alpha environment file mca.yml. Choose either Command 1 or 2 below to create the environment:
  1. Command 1: To use the default environment name of ‘mca’:

      conda env create -f mca.yml
     

  2. Command 2: If you want something else, e.g. ‘new_env’ to be the environment name instead of ‘mca’:

      conda env create -f mca.yml -n new_env
     

• Activate the mca env:

   conda activate mca
  

• Check that a tool is functional; Its usage message should display:

   p_info
  

• Display a command’s help, e.g:

   step1.py -h