Instructor Notes

Timing

Episode	Teaching	Exercises
Why I/O matters	15	0
The file systems	20	10
Files and directories	10	25
Permissions and quota	10	20
Space for a job	15	25

Teaching is 70 minutes and exercises are 80 minutes. The first episode is a discussion, not a typing exercise. If the room is short on time, keep that discussion, the survival challenge, chmod g-r, and iend=8 wdir=TMPDIR sbatch run.sh. Skip scratch-node when the room is on the course cluster. Skip the optional thousand-file challenge whenever disk or time is tight.

Source

The deck is course-module-snellius-fs/slides/snellius-fs.org in https://github.com/HaoZeke/introduction-to-supercomputing.

Branch: fix/slides-fs-source

Commit: 4709c85d9b7b38b1c943486bb1bf4b328fd48a6e

The hands-on notes are course-module-snellius-fs/README.md at that commit. episodes/files/ex1/print-n.c and episodes/files/ex1/run.sh are copied from course-module-snellius-fs/ex1/. episodes/files/PROVENANCE.md records the same branch and commit.

The deck’s table is the Snellius lifetime table: home 200 GiB, scratch-shared 14 days, scratch-local 6 days, scratch-node at job end, project and archive at project end. The worked $TMPDIR transcript (jobs 4401218 and 4401219 on tcn386) is from the README, not from a slide. The slide does not discuss metadata servers. That section is the reason the later file-count exercise is slow, taught here so the command is not the first time learners hear it.

What to skip

Do not run the full sbatch run.sh (10^6 through 10^9 values, default directory home) on a small cluster. The tab has iend=8 wdir=TMPDIR sbatch run.sh.

Do not ask the course cluster for --constraint=scratch-node. The tab says the constraint is absent and $TMPDIR is already on the node disk.

The published job scripts name the rome partition. Leave those lines. The course cluster is a SURF Research Cloud workspace, and the course tab requests --partition=rome.

Do not generate 1000 files of 1 MB if df -h shows little free space. The optional challenge uses 100 files on the course cluster.

Common mistakes

Creating /scratch-shared/$USER on the course cluster. The path is not there. The tab names the scratch path.
Treating $TMPDIR on the login node as the job’s $TMPDIR. They are different directories. wdir=TMPDIR is a keyword the script expands inside the job.
Leaving ex1.dat in home. The published script’s default wdir is $HOME.
rmdir on a non-empty directory, then reaching for rm -r on a path they have not printed.
chmod g-r when the group read bit is already clear, and reading that as a broken chmod. Set chmod 640 first so the change is visible.
Reading the two tcn386 paths as one directory. The job id in the name is 4401218 versus 4401219.
Assuming scratch-local and scratch-node expire the same way. The table gives scratch-local 6 days and scratch-node the end of the job.

Prep checklist

Confirm the machine. Put the scratch path from the tab on the board next to /scratch-shared.
myquota works on Snellius, or df -h and du -sh ~ work on the course cluster.
Home has room for a few small text files. It does not need room for the full print-n run.
From episodes/files/ex1, module load 2025 and module load GCC/14.2.0 succeed in a job shell. If GCC/14.2.0 is absent, stop and check module spider GCC. Do not invent a version in the script during the room.
On Snellius, only if you will run the scratch-node challenge: a node with the scratch-node feature is available. Otherwise teach the script and skip the submit.
The optional file-set challenge is a choice you announce, not a default. Check free space first.

What to collect

One ls -l mode string from chmod g-r, and one job output that prints both $TMPDIR and realpath. The job id will not be 4401218. The shape of the two paths is the point.

Why I/O matters

The file systems

Files and directories

Permissions and quota

Space for a job

Optional

This challenge is optional. Skip it when time is short or when df -h shows little free space. On the course cluster, create 100 files of 1 MB, not 1000. If home and the scratch path are the same disk, the copy is not a useful comparison. Use the job’s $TMPDIR as the destination, or skip the challenge.