Quick Reference Guide access

Quick Reference Guide

Overview

This page provides a quick reference for basic Linux and Slurm concepts commonly used on a high-performance computing (HPC) cluster.

It is intended as a starting point for new users. The Linux section introduces basic terms, commands, and keyboard shortcuts. The Slurm section lists common job submission and job monitoring commands.

For introductory Linux training videos, see the Linux command videos.

How to use this page

Use the following sections based on what you need:

• Go to Linux definitions for basic terminology.
• Go to Linux commands for common file system and software commands.
• Go to Linux shortcuts for useful keyboard shortcuts.
• Go to Slurm commands for batch and interactive job commands.

Linux

Below are the minimum Linux definitions, commands, and shortcuts that are useful for working on an HPC cluster.

Linux definitions

Definitions of common Linux terms

Term	Definition
Command	A word or set of letters typed into a terminal to make the computer do something. A command is executed by pressing Enter after typing it.
Command line	The line in the terminal where your cursor appears. This term is also used more generally to describe working without a graphical user interface, also called a command-line interface (CLI).
Command prompt	The text at the beginning of the command line, before your cursor. It often looks like [username@computername].
Directory	Another word for a folder. The term is often shortened to dir in commands, documentation, and conversation.
Terminal	A type of software that lets you interact with a computer by typing commands. A terminal can also be used to connect to a remote computer through a command-line interface.
Path	The location of a file or directory. A path is a series of directories that leads to a file or directory, for example /home/john/file.txt.
First slash in a path	The first / in a path represents the root directory, which is the starting point of the Linux file system.
Absolute path	A path that begins with /, meaning it starts from the root directory.
Relative path	A path written relative to the current directory. It does not begin with /.
Option	An extra letter or word placed after a command to modify its behavior, such as -x or --help.

Linux commands

Getting help

Commands for getting help

Command	Description	Example
command --help	Print a command's help output in the terminal.	ls --help
man command	Open a command's manual page. Press q to exit the manual.	man ls

Directories

Commands for working with directories

Command	Description	Example
ls	List the contents of a directory. If no path is given, it lists the current directory.	ls /scratch/MyID
mkdir	Create a new directory at the specified path.	mkdir /scratch/MyID/workdir
cd	Change to a different directory. If no path is given, it changes to your home directory.	cd /scratch/MyID/workdir
rmdir	Remove an empty directory.	rmdir tmpdir

Files

Commands for working with files

Command	Description	Example
nano	Create or edit a file with the nano text editor. To save and exit, press Ctrl + X, then Y, then Enter.	nano sub.sh
cat	Print the contents of a file to the terminal. This is usually best for short files.	cat slurm-42342.out
less	View the contents of a file in a pager. This is usually better for longer files.	less slurm-42342.out
cp	Copy one or more files from a source path to a destination path.	cp /scratch/MyID/workdir/sub.sh /work/labgroup
mv	Move one or more files from a source path to a destination path.	mv /scratch/MyID/workdir/sub.sh /work/labgroup
rm	Remove a file.	rm oldfile.txt
rm -r	Remove a directory and all of its contents recursively.	rm -r /home/MyID/olddir
dos2unix	Remove DOS or Windows line endings from a file.	dos2unix file.txt
mac2unix	Remove older Mac-style line endings from a file.	mac2unix file.txt

Software

Commands for finding and loading software

Command	Description	Example
ml spider <software name>	Check whether software is available and see which versions are installed.	ml spider Blast+
ml <software name>	Load a software module.	ml BLAST+/2.16.0-gompi-2024a

For more information, see the Software page and the software section of the FAQ.

Linux shortcuts

Terminal shortcuts

Keyboard shortcuts for the Linux terminal

Shortcut	Description
Ctrl + l (lowercase L)	Clear the terminal screen. You can still scroll up to see previous output.
Up and down arrow keys	Cycle through previously entered commands.
Tab	Auto-complete a file or directory name while typing a path. Press Tab twice to see multiple matches.
Esc, then .	Cycle through arguments used in previous commands.
Ctrl + w	Delete typed text on the command line one word at a time.
Ctrl + c	Cancel typed text on the command line.

less shortcuts

Keyboard shortcuts for the less command

Shortcut	Description
Shift + g	Go to the end of the file.
gg	Go to the beginning of the file.
-N, then Enter	Show or hide line numbers.
/SomePattern	Search forward through a file for text matching SomePattern. Press Enter again to continue searching for the same pattern.
?SomePattern	Search backward through a file for text matching SomePattern. Press Enter again to continue searching for the same pattern.
q	Exit less.

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Slurm commands

Below are the minimum Slurm commands that are useful for working on an HPC cluster.

The first table lists standard Slurm commands. The second table lists GACRC wrapper commands that provide additional convenience or formatting.

Default Slurm commands

Standard Slurm commands

Command	Description	Example
sbatch	Submit a batch submission script to the cluster.	sbatch sub.sh
squeue	Check the status of currently running or queued jobs. Use --me to show only your jobs.	squeue --me
sacct -X	Check the status of your jobs started since midnight of the current day. The -X option shows one line per job.	sacct -X
sacct -X -S yyyy-mm-dd	Check the status of your jobs starting from a specified date.	sacct -X -S 2021-10-20
sacct -j jobID	Check the status of a particular job by job ID.	sacct -j 234213
scancel jobID	Cancel one of your running or queued jobs by job ID.	scancel 456781
sinfo	Check the status of partitions.	sinfo -p batch

GACRC Slurm commands

GACRC wrapper commands for Slurm

Command	Description or equivalent	Example
interact	Start an interactive job. This is similar to qlogin and provides additional flexibility.	interact -c 4 --mem 10gb --time 01:00:00
sq	Wrapper for squeue.	sq --me
sacct-gacrc -X	Wrapper for sacct.	sacct-gacrc -X

Related resources

• Software
• FAQ: Software section

Notes

This guide is intended as a quick reference. For fuller documentation, consult the related wiki pages and command help output.