Quick Reference Guide

Linux

Below are the minimum Linux definitions, commands, and shortcuts that you should know to do work on an HPC cluster.

Definitions

1. Command - Word or letters typed into a terminal to make a computer do something. Executed by pressing enter after typing the command.

2. Command line - Literally, the line on which your cursor is on in the terminal. Sometimes used to describe the whole experience of not a graphical user interface, i.e. "Command Line Interface" or "CLI".

3. Command prompt - The text at the beginning of the command line, before your cursor. Typically [username@computername].

4. Directory - Another word for "Folder" (just like a folder in Windows or Mac). Often shortened to "dir" in commands, documentation, conversation, etc...

5. Terminal - Category of software that allows you to interact with your computer via commands, and can allow you to connect to a remote computer (via a CLI).

6. Path - The location of a file or directory. A series of subsequent directories to get to some file or directory. e.g., /home/john/file.txt

7. First / (in a path) - The root directory, where everything starts in the Linux file system.

8. Absolute path - a path that is written beginning with / (root)

9. Relative path - a path that is written relative to some other directory (does not begin with /)

10. (Command) Option - extra letter or word (-SomeLetter or --SomeWord) put after a command to modify its behavior.

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Commands

Getting Help (most important)

Command	Description	Examples
command --help	Print a commands help output to the terminal	ls --help
man command	Read a command's manual (press q to exit)	man ls

Directories

Command	Description	Examples
ls	List the contents of a particular directory (current dir if no path specified)	ls /scratch/MyID
mkdir	Make a new directory at the specified path	mkdir /scratch/MyID/workdir
cd	Change directory to a particular directory (personal /home dir if no path specified)	cd /scratch/MyID/workdir
rmdir	Remove an empty directory	rmdir tmpdir

Files

Command	Description	Examples
nano	Create or edit a file with nano (to save and exit: ctrl + x, y, enter)	nano sub.sh
cat	Print the contents of a file to the terminal (better for shorter files)	cat slurm-42342.out
less	View the contents of a file (better for longer files)	less slurm-42342.out
cp	Copy a file or files (cp sourcepath(s) destinationpath)	cp /scratch/MyID/workdir/sub.sh /work/labgroup
mv	Move a file or files (mv sourcepath(s) destinationpath)	mv /scratch/MyID/workdir/sub.sh /work/labgroup
rm	Remove a file or files	rm oldfile.txt
rm -r	Remove a directory and all of its contents, recursively (starting with the last dir in the path)	rm -r /home/MyID/olddir
dos2unix	Removes DOS/Windows line endings in file	dos2unix file.txt
mac2unix	Removes Mac line endings in file.	mac2unix file.txt

Software

Command	Description	Examples
ml spider <software name>	See if a software is available, will also show you which versions are available	ml spider Blast+
ml <software name>	Load a software module	ml BLAST+/2.12.0-gompi-2020b

Also see the Software page and Software section of our FAQ.

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Shortcuts

Linux

Shortcut	Description
ctrl + l (lowercase L)	Clear your terminal screen (scroll up to see previous output)
up/down arrow keys	Cycle through previously entered commands
tab	auto-complete a file or directory name when typing a path (tab tab if more than one file begins with the letters you've typed)
esc, . (escape, then period)	Cycle through previous arguments to commands
ctrl + w	Backspace typed text on the command line, one word at a time
ctrl + c	Cancel typed text on the command line

less

Shortcut	Description
shift + g	Go to the end of file
gg	Go to the beginning of file
-N then enter	Display/hide line numbers
/SomePattern	Search forward through a file for SomePattern (/ then enter to keep searching forward for the same pattern)
?SomePattern	Search backwards through a file for SomePattern (? then enter to keep searching forward for the same pattern)
q	Exit less

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Slurm

Below are the minimum Slurm commands that you should know to do work on an HPC cluster. The first table are default Slurm commands. The next table are GACRC pre-formatted wrapper scripts of the Slurm commands to provide more information and flexibility.

Default Slurm Commands

Command	Description	Examples
sbatch	Submit a submission script to the cluster	sbatch sub.sh
squeue	Check status currently running jobs (--me for only your jobs)	squeue --me
sacct -X	Check status of your jobs started since midnight of current day (-X for one line per job)	sacct -X
sacct -X -S yyyy-mm-dd	Check status of your jobs since yyyy-mm-dd	sacct -X -S 2021-10-20
sacct -j jobID	Check status of a particular job	sacct -j 234213
scancel jobID	Cancel one of your running jobs	scancel 456781
sinfo	Check the status of partitions	sinfo -p batch

GACRC Slurm Commands

Command	Description/Slurm Equivalent	Examples
interact	Start an interactive job. (Same as qlogin but with more flexibility)	interact -c 4 --mem 10gb --time 01:00:00
sq	squeue	sq --me
sacct-gacrc -X	sacct	sacct-gacrc -X