01 - UA HPC Tutorial

Logging into the UA HPC

Using your computer’s command line prompt

Find your terminal

• On a Mac, you can open the Launchpad and search for “Terminal”; alternatively, you can press Command+Space Bar, and then search for “Terminal”
• On a PC, you will need to install a separate program to access a shell prompt. You can find more information on the options on the UA HPC documentation website

In the terminal, type ssh netid@hpc.arizona.edu and press enter, then enter your password and confirm your dual authentication when prompted. This lands you on the gatekeeper/bastion host. Now, type shell and press enter. This moves you to one of the login nodes (junonia/wentletrap).

Using the UA’s Open OnDemand interface

Go to ood.hpc.arizona.edu, then select Clusters -> Shell access from the top menu bar. This will open a terminal window within your browser. When it opens, you’ll see that you’re automatically logged into a login node (junonia/wentletrap).

Using the UA HPC

Now that you’re logged into the UA HPC and on a login node (either junonia or wentletrap), we can practice some basic Linux commands.

• pwd to print the directory you currently are in (you should land in your home directory when you first login)
• ls to see what files are in your current directory
• hostname (to find out which node you’re currently on)
• Moving around: cd (to move to a different directory), e.g. cd /xdisk/jrick/consbioinf to move into our shared class directory
• If we wanted make a new directory, we can use mkdir new_directory
• To check permissions, ls -l
• To look preview the contents of a file, we can use less filename, where filename is the file we want to look at
• To copy files, we use cp
• To request an interactive session, interactive -a consbioinf -t 2:00:00, where the -t flag indicates how long you want your interactive session to be good for (e.g., 2:00:00 indicates 2 hours, 0 minutes, 0 seconds)

Modules!

• module list
• module avail
• module spider

Moving files to/from the HPC

There are several options: ssh or Globus or file transfer in Open OnDemand