Manage Files and Storage

Overview

Manage files and directories on the HPC system during your workflow.

---

Before you begin

Make sure:

• you can log into the HPC system
  (see: Log into HPC)
• you know where your data is stored (home, project, or other locations)
• you have appropriate permissions for the files you are working with

---

Steps

1. Log into HPC

ssh <username>@hpc.uct.ac.za

---

2. Check your current location

pwd

This shows your current directory.

---

3. List files and directories

ls

For more detail:

ls -lh

---

4. Change directories

cd <directory-name>

Example:

cd data

To move up one level:

cd ..

---

5. Create directories

mkdir <directory-name>

Example:

mkdir results

---

6. Copy files

cp <source> <destination>

Example:

cp input.txt results/

---

7. Move or rename files

mv <source> <destination>

Example:

mv input.txt data/

Rename a file:

mv old.txt new.txt

---

8. Remove files or directories

Remove a file:

rm <file-name>

Remove a directory:

rm -r <directory-name>

Use with caution. This action cannot be undone.

---

9. Check disk usage

du -sh *

Check total usage of current directory:

du -sh .

---

10. Check available space

df -h

---

Verify

Check that:

• files are present in expected locations (ls)
• file sizes are as expected (ls -lh)
• directories contain the correct contents

---

Troubleshooting

Permission denied

Possible causes:

• insufficient permissions
• attempting to modify protected files or directories

---

File not found

Possible causes:

• incorrect path
• file does not exist in current directory

Check location:

pwd
ls

---

Disk quota exceeded

Possible causes:

• storage limit reached
• too many files or large datasets

Check usage:

du -sh .

---

Related pages

• Log into HPC
• Submit a job
• Use software modules