Quick Reference Guide

Linux

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

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
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

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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
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)

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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