Complete MacOS install of AToM with MacPorts

This guide will provide step-by-step instructions for installing AToM Tier 1 on a fresh MacOS system.

Prerequisites

Adminstrator access on your Mac is required for an install with this method.

Most instructions require the mac Terminal app to be open so commands can be input.

In addition, for a full install, a github account is required along with access to the following git repositories:

1. https://github.com/gafusion/OMFIT-source

2. https://github.com/ORNL-Fusion/ips-atom

3. https://github.com/gafusion/gacode

4. https://github.com/gafusion/gacode_add

5. https://github.com/gafusion/EPED

6. https://github.com/boutproject/BOUT-dev

7. https://github.com/gafusion/harvest_client

8. https://github.com/libfann/fann

9. https://github.com/gafusion/omas

10. https://github.com/gafusion/neural

Any steps you have completed previously can be skipped.

Install

1. Install Developer command line tools type

   xcode-select --install
   

   Then click the “Install” button in the dialog box that appears.

   Then agree to the license agreement.

2. Generate SSH keys if you do not currently have them. This is used to authenticate with github later.

   To check if you have existing ssh keys

   ls ~/.ssh/id_rsa.pub
   

   This will return “No such file or directory” if it does NOT exist. If it exists, skip to step 3, if not, generate your ssh keys

   ssh-keygen -t rsa -b 4096
   

   Keep the default location to save the key by pressing enter.

   Enter a passphrase. You will need this passphrase every time you access a github repo. If you do not enter a passphrase anyone who has access to your private key will be able to impersonate your computer.

3. Add public ssh key to github. Instructions found here

4. Setup git email and name

   git config --global user.name "Your Name"
   git config --global user.email "your_email@example.com"
   

5. Install Mac Ports. Instructions found here

6. In order to use any X11 enabled tools, install X-Quartz. It can be found here . After installing, it will require logging out of your computer and logging back in before it can be used. (Apple menu -> Log Out)

7. In the terminal, navigate to where you would like AToM installed and clone the git repository.

   git clone git@github.com:scidac/atom.git
   

   If it asks if you want to continue connecting, say yes.

8. Install and configure the prerequisites with Mac Ports. Enter your computer’s password (not the SSH key passphrase) when promped and enter ‘Y’ when prompted to confirm installs. Some of these installs (like openmpi) may take a while.

   sudo port install cmake
   sudo port install openmpi
   sudo port select --set mpi openmpi-mp-fortran
   sudo port install fftw-3
   sudo port install fann
   sudo port install netcdf
   sudo port install netcdf-fortran
   sudo port install netcdf-cxx
   sudo port install doxygen
   

9. Export compiler locations for cmake (Exact names may vary. If you close your terminal, you may have to do this step again)

   export FC=/opt/local/bin/gfortran-mp-7
   export CC=/opt/local/bin/gcc-mp-7
   export CXX=/opt/local/bin/g++-mp-7
   

10. Configure and make AToM. Enter your ssh key passphrase when prompted (Not your computer password)

    cd atom make set plat=GFORTRAN_OSX_MACPORTS make all ATOM_PLATFORM=GFORTRAN_OSX_MACPORTS

11. Add environment variables to your .profile so tools are available in your next terminal session

12. Install OMFIT prerequisites. Answer ‘Y’ to any prompts asking if you want to install and enter computer’s password when prompted. Assuming you are still in the atom directory, type :: cd OMFIT-source/install/ports ./install.sh

If you run into problems with Mac Ports here, you may need to switch to the unstable branch. (From within the OMFIT-source directory)

git checkout unstable
cd OMFIT-source/install/ports
./install.sh