apptainer update by CallumWalley · Pull Request #1262 · nesi/support-docs

CallumWalley · 2026-05-10T22:55:06Z

Fix formatting

update examples

github-actions · 2026-05-10T22:55:16Z

Test deployment successful!! (2026-05-12T01:09:01Z)
Preview available at https://callumwalley.github.io/mkdocs-demo-deploy/nesi/support-docs/apptainer-update

Seems the following pages differ;

See all deployed demo sites

gemini-code-assist

Code Review

Avast! Ye've overhauled the Apptainer charts, swapping those nested containers for proper headers and dragging in some boilerplate macros. While the new structure is a sight better than a barnacle-covered hull, yer Slurm scripts are a disaster. Ye've ignored the code of the sea by using spaces instead of tabs for headers, forgetting to purge yer modules like a scurvy dog, and leaving code blocks as naked as a castaway. Also, stop hardcoding yer project bounty unless ye want every pirate in the archipelago raiding yer allocation. Fix those typos before the crew mutinies over yer sloppy penmanship.

gemini-code-assist · 2026-05-10T22:56:49Z


-    We recommend adding those environment variables to your `~/.bashrc` to make the future use cases of Apptainer. Please make sure to replace `/nesi/nobackup/nesi12345/apptainer-cache` with your nobackup directory. 
+```bash
+export APPTAINER_CACHEDIR="/nesi/nobackup/nesi12345/apptainer-cache"


Hardcoding nesi12345? I suppose ye want every sailor on the Seven Seas to be using yer project's bounty. Use a placeholder or a variable, ye landlubber!

Suggested change

export APPTAINER_CACHEDIR="/nesi/nobackup/nesi12345/apptainer-cache"

export APPTAINER_CACHEDIR="/nesi/nobackup/nesi99991/apptainer-cache"

gemini-code-assist · 2026-05-10T22:56:49Z

-    echo 'export APPTAINER_CACHEDIR="/nesi/nobackup/nesi12345/apptainer-cache"' >> ~/.bashrc
-    echo 'export APPTAINER_TMPDIR=${APPTAINER_CACHEDIR}' >> ~/.bashrc
-    ```
+To make these changed permanent, add them to your `~/.bashrc`:


Blimey, matey! Ye've written 'changed' when ye meant 'changes'. I suppose the sea spray is getting in yer eyes.

Suggested change

To make these changed permanent, add them to your `~/.bashrc`:

To make these changes permanent, add them to your ~/.bashrc:

gemini-code-assist · 2026-05-10T22:56:49Z

+#SBATCH --job-name      apptainer-build
+#SBATCH --time          00:30:00
+#SBATCH --mem           4GB
+#SBATCH --cpus-per-task 2
+#SBATCH --account       nesi12345


Avast! Those be spaces I see? The charts (Style Guide line 402) clearly state ye must use a tab to separate yer Slurm keywords from their values. Don't make me walk the plank for yer sloppy spacing!

Suggested change

#SBATCH --job-name apptainer-build

#SBATCH --time 00:30:00

#SBATCH --mem 4GB

#SBATCH --cpus-per-task 2

#SBATCH --account nesi12345

#SBATCH --job-name apptainer-build

#SBATCH --time 00:30:00

#SBATCH --mem 4GB

#SBATCH --cpus-per-task 2

#SBATCH --account nesi99991

References

Use tab for your Slurm header delimiter. ^(link)

gemini-code-assist · 2026-05-10T22:56:49Z

-    #SBATCH --time=0-00:30:00
-    #SBATCH --mem=4GB
-    #SBATCH --cpus-per-task=2
+module load Apptainer/{{app.default}}


I see ye've decided that module purge is beneath ye. How very brave of ye to risk a mutiny of conflicting software versions. (Style Guide line 406).

Suggested change

module load Apptainer/{{app.default}}

module purge

module load Apptainer/{{app.default}}

References

Always module purge before module load. ^(link)

gemini-code-assist · 2026-05-10T22:56:49Z

+    The `fakeroot` build method does not work for all container types. If you encounter issues, contact [support@nesi.org.nz](mailto:support@nesi.org.nz).
+
+    If you see the following error, it is likely caused by a bad upstream image on Docker Hub. Try an older version or a different base image:
    ```


Arrr, ye've left this code block naked! Give it a class like txt or stderr so the crew knows what they're looking at. (Style Guide line 355).

Suggested change

```

```txt

References

For plain text code blocks, still good to use a class as descriptor (e.g. txt, stdout, stderr). ^(link)

gemini-code-assist · 2026-05-10T22:56:49Z

+#SBATCH --job-name      container-job
+#SBATCH --time          01:00:00
+#SBATCH --mem           4G
+#SBATCH --cpus-per-task 4
+#SBATCH --account       nesi12345


More spaces where tabs should be! Are ye trying to confuse the sea monsters? Use tabs for yer Slurm headers as the law (Style Guide line 402) dictates.

Suggested change

#SBATCH --job-name container-job

#SBATCH --time 01:00:00

#SBATCH --mem 4G

#SBATCH --cpus-per-task 4

#SBATCH --account nesi12345

#SBATCH --job-name container-job

#SBATCH --time 01:00:00

#SBATCH --mem 4G

#SBATCH --cpus-per-task 4

#SBATCH --account nesi99991

References

Use tab for your Slurm header delimiter. ^(link)

gemini-code-assist · 2026-05-10T22:56:49Z

-        # Run container %runscript
-        apptainer run tensorflow-latest-gpu.sif my_tensorflow.py some_argument
-        ```
+module load Apptainer/{{app.default}}


Ye be repeating yer sins! Purge the deck before ye load the Apptainer, or ye'll find no treasure in this script. (Style Guide line 406).

Suggested change

module load Apptainer/{{app.default}}

module purge

module load Apptainer/{{app.default}}

References

Always module purge before module load. ^(link)

gemini-code-assist · 2026-05-10T22:56:49Z

+#SBATCH --job-name      gpu-container-job
+#SBATCH --time          01:00:00
+#SBATCH --mem           8G
+#SBATCH --cpus-per-task 4
+#SBATCH --gpus-per-node 1
+#SBATCH --account       nesi12345


Tabs, man! Tabs! (Style Guide line 402).

Suggested change

#SBATCH --job-name gpu-container-job

#SBATCH --time 01:00:00

#SBATCH --mem 8G

#SBATCH --cpus-per-task 4

#SBATCH --gpus-per-node 1

#SBATCH --account nesi12345

#SBATCH --job-name gpu-container-job

#SBATCH --time 01:00:00

#SBATCH --mem 8G

#SBATCH --cpus-per-task 4

#SBATCH --gpus-per-node 1

#SBATCH --account nesi99991

References

Use tab for your Slurm header delimiter. ^(link)

gemini-code-assist · 2026-05-10T22:56:49Z

+#SBATCH --gpus-per-node 1
+#SBATCH --account       nesi12345

+module load Apptainer/{{app.default}}


Ye'd think ye'd learn by now. Purge the modules! (Style Guide line 406).

Suggested change

module load Apptainer/{{app.default}}

module purge

module load Apptainer/{{app.default}}

References

Always module purge before module load. ^(link)

CallumWalley · 2026-05-10T22:58:32Z

Might be worth adding --no-xattrs to suprress build warning about acls

CallumWalley · 2026-05-11T01:59:32Z

A lot of this is no longer correct.

For example fakeroot is not enabled on the login nodes.

apptainer update

c2ea4e4

gemini-code-assist Bot reviewed May 10, 2026

View reviewed changes

nesi-mkdocs-bot added 5 commits May 11, 2026 15:50

oops no mopdules

4b6dac8

make louder

b56faeb

fix to wanring

b19cff6

mention unset bindpath first

c69dd0b

merged apptainer pages. Made link under container section.

fe92a3b

	export APPTAINER_CACHEDIR="/nesi/nobackup/nesi12345/apptainer-cache"
	export APPTAINER_CACHEDIR="/nesi/nobackup/nesi99991/apptainer-cache"

	To make these changed permanent, add them to your `~/.bashrc`:
	To make these changes permanent, add them to your ~/.bashrc:

	module load Apptainer/{{app.default}}
	module purge
	module load Apptainer/{{app.default}}

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CallumWalley commented May 10, 2026

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CallumWalley commented May 11, 2026

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github-actions Bot commented May 10, 2026 •

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