3. Navigating Gadi File Systems

Overview

Tutorial: 30 min

Objectives:

• Learn how to use the Gadi terminal.

• Learn how to navigate the filesystem.

• Learn how to manage files and directories.

• Learn how to copy files to and from Gadi.

This page introduces essential commands to get you started on Gadi. For a more detailed guide, see the Linux Command Quick Reference. If you are completely new to Linux, we recommend you to go over the The Unix Shell first.

3.1. Gadi File Systems

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Gadi File Systems Overview

Location	Purpose	Backup / Quota	Notes
/home	Personal user storage	Backed up 10 GiB per user	Store important and hard-to-reproduce files. Meant for config and critical content only.
/scratch	Temporary project storage, high performance	Not backed up Project quota 100 days expiry	Fastest storage. Temporary: files deleted after 100 days of no access. Use for raw experimental output.
/g/data	Persistent project storage	Not backed up Project quota	Long-term storage for datasets, code, and results. Allocations are set per project through stakeholder entitlements. RAID redundancy protects data integrity on disk, but no storage is guaranteed forever—projects must manage their data over the life of their allocation.
JOBFS ($PBS_JOBFS)	Fast, local scratch during a job	Not backed up Per-job limit	Local disk on the compute node, available only while the job runs. Request with #PBS -l jobfs=<size> and access paths via the $PBS_JOBFS environment variable. Contents are removed when the job ends.
/apps	NCI Third-party software catalogue	Managed by NCI Read-only	Contains installed software modules and applications for all users.

Massdata Storage System

Location	Purpose	Backup / Quota	Notes
massdata (MDSS)	Archival storage	Backed up Project quota	Massdata is an integrated system of front-end servers, disk cache, and tape archive. There is no /mdss mount path on Gadi. Use the mdss command to store and retrieve data. Best for large archives, not many small files.

Most workflows use a combination of these systems rather than relying on one alone. For example, you might stage inputs from /g/data into /scratch or JOBFS for a job, write outputs back to /g/data, and archive finished datasets to massdata. Effective job scripting is about orchestrating these resources, not picking a single filesystem and stopping there.

Knowledge Check 1: The Storage Dilemma

Scenario: You have a 500GB dataset that you need to analyze over the next three days. You plan to run 10 different jobs against this data.

Question: Which file system should you store the data in while the jobs are running, and why?

A) /home: Because it is the most secure.

B) /scratch: Because it is high-speed and designed for large-scale temporary usage.

C) /g/data: Because it is where my project is hosted.

Show answer

Answer: B) /scratch. While /g/data is great for persistent project storage, /scratch is optimized for the high-speed I/O (Input/Output) required during active job execution. For very I/O-intensive work within a single job, you might also use JOBFS via $PBS_JOBFS. When you are done, move results you want to keep back to /g/data.

3.2. Understanding your location (pwd)

Your current directory is where terminal commands run. pwd (print working directory) shows its full path.

pwd

3.3. Listing files (ls)

General syntax of a command:

ls lists files and folders in the current directory.

Detailed list view with permissions, size, and timestamps:

ls -l

Human-readable sizes (easier when checking large files):

ls -lh

Show hidden files (names starting with .):

ls -a

Hint

Use ls --help anytime you need option names and short descriptions.

3.4. Practice: Find your bearings

Exercise

• Find out what directory you are in and list the files and directories there.

• Then list contents with sizes in a human-readable form, sorted by size. Hint: check ls --help for sorting options.

See solution

pwd
ls
cd /scratch/vp91/$USER
ls -lhS

3.5. Changing directory (cd)

Move to an absolute path:

cd /path/to/directory

Go up one level:

cd ..

Jump to your home directory:

cd ~

3.6. Practice: Explore shared locations

Exercise

• Go to /scratch/vp91/$USER and see where it is.

• In separate visits (cd, ls, then cd somewhere else), look at what is under /apps, /scratch, and /g/data. These are important areas on Gadi; you don’t need to understand everything yet—just get a sense of how they’re laid out.

• Find out the latest version of python3 available in /apps. How would you sort the files to find the latest version?

See solution

cd /scratch/vp91/$USER
pwd
ls
cd /apps
ls
ls -lht /apps/python3

3.7. Managing files and directories

mkdir: create a directory

mkdir test

touch: create an empty file (or update a file’s timestamp if it exists)

touch test.txt

rm: delete files (no “rubbish bin” on the cluster — see the warning below).

Remove one file:

rm test.txt

Remove a directory and everything inside (use carefully):

rm -rf test

cp: copy files or directories

Copy file1 to file2:

touch file1.txt
cp file1.txt file2.txt

Copy a directory recursively:

mkdir dir1
cp -r dir1 dir2

mv: move or rename files and directories.

Rename file:

mv file1.txt renamed.txt

Move a directory inside another directory:

mv dir1 dir2

Delete with caution

There is no Trash folder to restore from once a file is removed. Backup tools exist, but rely on backups you made yourself — there is no guarantee of recovery here. Prefer rm on copies or test folders until you’re confident.

3.8. Viewing and editing text

cat: print whole file contents to the terminal:

cat file.txt

less: scroll through a large file interactively (press q to quit):

less file.txt

nano: simple terminal editor:

nano file.txt

vim: more powerful modal editor:

vim file.txt

Note

These are some of the options available for managing and editing files on Gadi. You can also use other tools such as Emacs or IDEs like VS Code.

3.9. Practice: Create, inspect, tidy up

Exercise

Under /scratch/vp91/$USER:

• Create a directory called hello_world.

• Create a file hello_world/hello_world.txt and put Hello, World! inside it (your editor choice, or redirect from echo if you prefer).

• Display the contents in the terminal, then delete the file and folder when you’re done.

See solution

cd /scratch/vp91/$USER
mkdir hello_world
# or using nano, vim, or another editor:
# nano hello_world/hello_world.txt
echo "Hello, World!" > hello_world/hello_world.txt
cat hello_world/hello_world.txt
rm -rf hello_world

3.10. Copying files to and from Gadi (scp)

scp copies files over SSH—useful for moving scripts or outputs between your laptop and Gadi.

Copy from your computer to Gadi:

scp local_file YOUR_USERNAME@gadi.nci.org.au:/remote/path/

Copy from Gadi to your current local folder:

scp YOUR_USERNAME@gadi.nci.org.au:/remote/path/file .

Note

Another option is to use rsync. Unlike scp, which copies files in full each time, rsync transfers only the changed portions of files, making it more efficient for large or frequently updated datasets.

3.11. Practice: Prepare the code for your first job on Gadi

Exercise

1. Create /scratch/vp91/$USER/first_job.

2. Save hello_mpi.c onto your laptop, then upload it into first_job with scp (adjust paths and username to match yours).