Essential Linux Commands¶

Interacting with the CoSTAR cluster happens mostly via a text-based Linux terminal. If you are new to this environment, we suggest you review the Surrey Unix Tutorial for Beginners.

Use the tabs below to find common commands categorised by workflow, along with specific examples of how they apply to cluster tasks.

📁 Navigation & Files

Command	What it does	HPC Example / Context
`pwd`	Print Working Directory. Shows where you are.	Check if you are in `/users/your_name` or a parallel path.
`ls -lh`	Lists directory contents with human-readable file sizes.	`ls -lh` reveals if a dataset or model weight file downloaded completely.
`cd <path>`	Change Directory. Moves you to a new folder.	`cd /parallel_scratch/project_name` jumps to shared storage.
`mkdir -p <name>`	Creates a new directory (and parent folders if missing).	`mkdir -p checks/run_01` sets up clean output spaces.
`cp -r <src> <dst>`	Copies files or directories recursively.	Copy a template batch script into your working workspace.
`mv <src> <dst>`	Moves or renames files and directories.	Rename a generic checkpoint file to a specific iteration name.
`rm -rf <target>`	Forcefully and recursively deletes files/folders.	Use with extreme caution. Erases directories without prompting.

🔍 Viewing & Searching

Command	What it does	HPC Example / Context
`cat <file>`	Dumps the entire contents of a file directly into the terminal.	Good for quickly verifying a short, 10-line Slurm batch script.
`less <file>`	Opens a scrollable reader. Press `q` to exit.	Use this to inspect large execution logs without crashing your terminal.
`tail -n 20 <file>`	Displays the final 20 lines of a file.	Quickly check if a completed job threw an error at the very end.
`tail -f <file>`	Displays the end of a file and updates in real-time as lines are added.	Run `tail -f slurm-12345.out` to watch live script printouts as your AI model trains.
`grep "pattern" <file>`	Searches inside text files for specific strings or phrases.	`grep "Loss:" slurm-*.out` instantly extracts training loss metrics.
`nano <file>`	A simple, straightforward command-line text editor.	Great for quick, live modifications to your Slurm option flags.

🛠️ Permissions & Diagnostics

Command	What it does	HPC Example / Context
`chmod +x <file>`	Marks a file as executable.	Run `chmod +x script.sh` before executing a file via `./script.sh`, or it will fail to launch.
`du -sh <target>`	Summarises the total disk space used by a file or folder.	`du -sh *` identifies which hidden directory is filling up your 30GB home space.
`watch -n 2 <cmd>`	Runs a command repeatedly every `n` seconds, showing changes live.	`watch -n 5 squeue -u $USER` monitors your queue position automatically without re-typing.
`<cmd> --help`	Appending help flags lists usage manuals for custom tools.	Useful for investigating deep tools like `apptainer --help` or `sacctmgr --help`.

Next Steps¶

1.5 Self-Check Quiz

Test your understanding of the introductory material before moving to Module 2.

Quiz