The UPPMAX filesystem

Learning outcomes

• Can find the UPPMAX project folder of this course
• Can find out which folders have a backup

For teachers

Teaching goals are:

• Learners have found the UPPMAX project folder of this course
• Learners have found find out which folders have a backup

Prior questions:

• How do you think the folder structure looks on the UPPMAX HPC clusters?
• What is the purpose of a home folder?
• What is the purpose of a project folder?
• What is the purpose of a nobackup folder?

Why?

You want to know where to put your files. You want to know if/how your lost files can be retrieved.

Exercises

Need a video?

Here is a video that shows the solution of these exercises

Exercise 1: important folders

• Read the UPPMAX documentation on the backup service
• What is the name of the folder that contains all projects?

Answer

It is called /proj.

The initial slash indicates it is in the root folder.

• Navigate to that folder (in your favorite way!). Estimate the number of projects in that folder

Answer

Using the terminal:

Here we navigate to the /proj folder:

cd /proj

Counting the number of folders in that folder:

ls | wc --lines

Gives us around 7000 projects

• Guess which of these folders has a backup:

  • /proj/uppmax2025-2-262
  • /proj/uppmax2025-2-262/nobackup
  • /proj/uppmax2025-2-262/nobackup/backup
  • /home/sven
  • /home/sven/nobackup
  • /home/sven/nobackup/backup

Answer

Folder name	Has backup?
/proj/uppmax2025-2-262	Yes, folders have a backup by default
/proj/uppmax2025-2-262/nobackup	No, because it has nobackup in the name
/proj/uppmax2025-2-262/nobackup/backup	No, because it has nobackup in the name
/home/sven	Yes, folders have a backup by default
/home/sven/nobackup	No, because it has nobackup in the name
/home/sven/nobackup/backup	No, because it has nobackup in the name

Isn't that obvious?

No.

We at UPPMAX do get complaints from users that (1) place their raw data in a nobackup folder, then (2) delete that folder, (3) ask us for a backup, (4) complain that we did not have a backup.

• Give an example of which kind of files you would store in these folders:

  • /proj/uppmax2025-2-262
  • /proj/uppmax2025-2-262/nobackup
  • /home/sven
  • /home/sven/nobackup

Answer

Folder name	Example file
/proj/uppmax2025-2-262	The raw data, your scripts
/proj/uppmax2025-2-262/nobackup	Intermediate files of your analyses
/home/sven	Your personal scripts
/home/sven/nobackup	Intermediate files of your personal analyses