For each new student joining the group, we ask them to onboard by completing each of the following items in the order given:

(1) Go to osc.edu and request an account

• https://www.osc.edu/supercomputing/portals/client_portal/self_signup_for_accounts
• Fill out the info and for the Project Code put PAS1960 (and PAS0654 if you're able to do both).

(2) Complete the following tutorials and reading. Note that the order of these does not matter, however, I would suggest "how to use Git" comes last, as it is the lease important for you to start. Finally, I advise you work on a tutorial concurrently with reading the pages assigned below from my Dissertation. 

• OSC tutorials
  • Because this project uses a lot of computation power, we run on the Ohio Super Computing Center's clusters. Please utilize these tutorials to learn more. 
• Read Julie's Dissertation pages 1-9, 12-20 (starting at section 1.5.2), 28-37 (starting at section 2.3)
  • Feel free to read chapter 3, as it has the history of this project and goes into details of our most up-to-date endeavors. This is optional and not mandatory. 
• Complete the introduction to Bash project
• Complete the introduction to Python Project
• How to use Git (optional)
  • Git is a resource used for version control when writing software. See more for an introduction here: https://www.simplilearn.com/tutorials/git-tutorial/what-is-git
  • BEFORE reviewing this power point, I highly advise you take the code academy class https://www.codecademy.com/learn/learn-git. We use Git and GitHub to keep records and versions of the changes we make, so reverting back to other versions is doable. 
• Make sure to get an XFdtd license on OSC
  • See instructions here 

(3) Finally, review the full manual and complete the bullets below. The full manual is Appendix A of Julie's Dissertation.

• Appendix A of my dissertation is our manual and acts as the holy grail of our research. Anything you need can be found here (from where our info exists on the web, to how to run the code). 
• Once you have read this through entirely, we advise you log on to OSC and explore the code for PAEA in PAS1960. Once you have done so, complete this homework by making a copy of this google doc and filling it out on your own. 

Once these are completed, the students are ready to start helping. This is all of the coding information and basic background information on evolutionary algorithms students must know to be proficient in assisting. 

Other useful materials we have may include:

1. Our old GENETIS manual 
   1. This is somewhat out of date; however, it does have information on the general working on the loop. 
2. Julie's candidacy paper 
3. Complete the writing a genetic algorithm in C++ project
   1. This is still a work in progress! I'll complete it shortly!
4. Read chapter 3 of this book (more if you have time) by Eiben and Smith, "Introduction to Evolutionary Computation" for a quick introduction. The book should be available electronically from a university library.  Let us know if you can't find it there.
5. Get to know XFdtd
   1. XFdtd manual is also attached; however, the link above (in 5) is more useful for coding a .xmacro.
       

Important notes:

MAC USERS: Using a GUI when connecting to OSC via SSH from your terminal.

You will need to set up X11 forwarding. Otherwise, when you go to plot via SSH, they will not display (they don't forward from OSC to your machine). If you are unable to run GUI's on OSC through your computer's terminal, follow these instructions:

1. In your own system's terminal, type: sudo vi /etc/ssh/sshd_config
2. Search for the following line: X11Forwarding no
3. Change it to: X11 Forwarding yes. Save the file and exit.
4. In your own system's terminal, type: sudo systemctl restart sshd
5. For a Mac, download and install XQuartz.
6. Connect to OSC using ssh -XY username@hostname.
7. You can test that this works by typing 'xeye' or 'xclock' in the terminal when logged into OSC. 

Now you should be able to use OSC's GUIs.

PC USERS: 

As a PC user, there are a few things you need to do:

(1) Enable the Windows Subsystem for Linux on your device (https://developerinsider.co/stepwise-guide-to-enable-windows-10-subsystem-for-linux/#:~:text=To%20enable%20the%20Windows%20Subsystem,list%20here%20and%20click%20OK.)

(2) Get Bash on Ubuntu installed on your machine. You are going to need to have Bash on Ubuntu installed prior to starting these trainings; otherwise Bash commands will not be recognized.

•  https://ubuntu.com/tutorials/install-ubuntu-on-wsl2-on-windows-10#1-overview

(3) Get X11 forwarding working. Otherwise, when you go to plot via SSH, they will not display (they don't forward from OSC to your machine).

• Follow these steps here.  
  • http://courses.cms.caltech.edu/cs11/misc/xwindows.html
• Change your config file. To do so, in terminal (with Bash on Ubuntu open) 
  • type: sudo vi /etc/ssh/sshd_config
  • Then change '#X11Forwarding no' to '#X11Forwarding yes' and save it.
    • https://www.businessnewsdaily.com/11035-how-to-use-x11-forwarding.html
• Make sure Putty and Xming are running every time before you ssh in. Use Xlaunch application to run Xming and press yes to everyrthing.
  • Xming should now be running as a background task.
  • Open PuTTY and open the pre-saved like you saved in PuTTY. (This will open a Bash terminal that asks for your OSC login password.)