Self Guided Practice: Getting Started on the Great Lakes cluster [Phase 1/3]

Summary

Wanting to work on Great Lakes, but don't know where to start, or learn some Linux commands to create a work flow and batch scripts for jobs. You've come to the right place, and this is Phase 1/3 of the self-guided practice. 

As always, if you have questions or concerns while going through the learning material, please don't hesitate to stop by Office Hours (Monday's 2-3pm and Thursday's 3-4pm), our HPC related workshops will be linked below or submit a ticket to arc-support@umich.edu.

"Go forth and compute!" - Dr. Charles Antonelli

Environment

High Performance Computing (HPC) on the Great Lakes cluster  (non-sensitive data)

Directions 

• Request a User Login
  • You can request a User Login for Great Lakes on the following page by clicking the Request an HPC User Login Button - User Login Request
    Note: If you are on campus, you will need to be connected to MWireless or on the UMVPN to connect to the cluster.
    • Getting started with the Great Lakes Cluster
    • Install VPN software on your computer

• Log into the Cluster via ssh and through Open OnDemand
  Note: The cluster can be accessed in several different ways. As a user, there are charge free methods to prep and create batch scripts. Running batch scripts will charge the account specified in the Slurm preamble. Open OnDemand interactive sessions are GUI equivalent to batch scripts. 
  • Mac or Linux via a Terminal window or Windows 11 or later in a Command Prompt or Powershell window
    • Open Terminal/Command Prompt/Powershell and type:
      ssh uniqname@greatlakes.arc-ts.umich.edu (replace "uniqname" with your own uniqname)
  • Windows 10 and Earlier (using PuTTY)
    • Download and install PuTTY here
      Launch PuTTY and enter the below host name, and open
      greatlakes.arc-ts.umich.edu
  • Accessing the Cluster via Open OnDemand with Clusters or an Interactive Session
    • Open a web browser and follow this link: Great Lakes, log in and authenticate with Duo
      • With Open OnDemand, you can access the cluster free of charge by selecting Clusters > and selecting “Great Lakes Shell Access”
      • You can charge an account by selecting “Interactive Sessions” > clicking which Interactive App you would like to use and with the drop down menus you are creating a batch script for an Interactive Job.

• Learn basic Linux commands
  • Command Line Basics: (~22 mins)
    • What is the command line
    • Understand how commands are structured
    • Write commands in a shell at the prompt
    • Finding help for commands
    • Challenge: Find command information
    • Solution: Find command information
  • Files, Directories, and Permissions: (~ 28 mins)
    • Understanding file paths
    • Navigating the file system
    • Exploring the output of the ls command
    • Create and remove directories
    • Copy, move, and delete files and directories
    • Find Files from the command line
    • Challenge: Practice working with files
    • Solution: Practice working with files
  • Common Command Line tools: (~13 mins)
    • View text files with cat, head, tail, and less
    • Edit text with Vim
    • Edit text with nano

• TTC workshops: All upcoming workshops:
  • Workshops we recommend for learning HPC and assist with:
    • Linux command line
    • Introduction to Research Computing on the Great Lakes Cluster
    • Advanced Research Computing on the Great Lakes Cluster
    • Transferring files with Globus