Unix CheatSheet

Navigation

Navigation
Command	Function	Syntax/example usage
ls	list contents	ls [OPTIONS] DIRECTORY
pwd	print working directory	pwd
cd	change directory	cd ~ or cd #home directory
		cd .. #”up” a directory (parent directory)
		cd - # previous directory

File/Directory operations

File/Directory operations
Command	Function	Syntax/example usage
mkdir	make directory	mkdir DIRECTORY
cp	copy files/directories	cp SOURCE DESTINATION
man	manual page (help)	man COMMAND
mv	move files/directories	mv SOURCE DESTINATION
touch	create file	touch FILE
nano	edit file	nano FILE
less	view file (with more options)	less FILE
more	view file (with less options)	more FILE
cat	catalog file contents	cat FILE
head	show first few lines of a file	head FILE
tail	show last few lines of a file	tail FILE
rmdir	remove empty directory	rmdir DIRECTORY
rm	remove file(s)	rm FILE

File manipulations

File manipulations
Command	Function	Syntax/example usage
grep	search a pattern	grep [OPTIONS] “PATTERN” FILENAME
sed	stream edit a file	sed 's/search/replace/g' FILENAME
awk	multi-purpose command	awk 'PATTERN {ACTION}' FILENAME
tr	translate or transliterate a file	tr [OPTIONS] “STRING1” “STRING2” < INFILE
wc	word count	wc FILENAME
sort	sort files	sort FILE1 > SORTED_FILE1
uniq	display unique lines	uniq [OPTIONS] INFILE > OUTFILE
diff	display difference	diff [OPTIONS] FILE1 FILE2
comm	display common lines among files	comm [OPTIONS] FILE1 FILE2
cut	break files vertically based on fields	cut –d “DELIMITER” –f NUMBER FILE
split	break files horizontally	split [OPTIONS] FILENAME
paste	combine files side by side	paste FILE1 FILE2 > FILE3
join	join files based on common field	join -t ‘DELIMITER’ -1 N -2 N FILE1 FILE2

Compression/archiving

Compression/archiving
Command	Function	Syntax/example usage
zip	zip compress	zip OUTFILE.zip INFILE.txt
		zip -r OUTDIR.zip DIRECTORY
unzip	decompress zipped file	unzip ANYTHING.zip
tar	archive and compress files/directories	tar -czvf OUTFILE.tar.gz DIRECTORY #compress
		tar -xzvf OUTFILE.tar.gz # extract
gzip	gzip files	gzip SOMEFILE
gunzip	decompress gzipped files	gunzip SOMEFILE.gz

File permissions

File permissions
Command	Function	Syntax/example usage
chmod	change permissions for files/directories	chmod [OPTIONS] RELATIONS[+/-]PERMISSIONS FILE

ADDITIONAL COMMANDS

ADDITIONAL COMMANDS
Command	Function
du –sh	DIR show directory size
whoami	display username
date	system date/time
cal	calendar
find . –name FILE	find a file/directory
which CMD	display default cmd path
whereis CMD	show possible locations of cmd
locate FILE	find instances of a file
clear	clear screen
sleep 5	pause 5 (any) seconds
top	current running processes
ps	current running processes
wget	URL download specified URL

SHORTCUTS

SHORTCUTS
Command	Function
TAB	autocomplete names
UP/DOWN	browse previous commands
ctrl+c	interrupt/kill anything
ctrl+l	clear screen
ctrl+d	quit, exit
ctrl+z	suspend (use fg to restore)
!!	repeat last command
alt+.	last argument of previous cmd
ctrl+insert	copy selection
shift+insert	paste copied text
ctrl+a	go to start of the line
ctrl+e	go to end of the line
ctrl+r	reverse search history
cd ~	go to home

NANO SHORTCUTS

NANO SHORTCUTS
Command	Function
ctrl+r	read/insert file
ctrl+o	save file
ctrl+x	close file
alt+a	start selecting text
ctrl+k	cut selection
ctrl+u	uncut (paste) selection
alt+/	go to end of the file
ctrl+a	go to start of the line
ctrl+e	go to end of the line
ctrl+c	show line number
ctrl+_	go to line number
ctrl+w	find matching word
alt+w	find next match
ctrl+\	find and replace

PIPES, REDIRECTS

PIPES, REDIRECTS
Command	Function
cmd < file	use file as input
cmd > file	write output to file
cmd >> file	append output to file
cmd 2> stderr	error output to file
cmd 1>&2 file	send output and error to file
cmd1 \| cmd2	send output of cmd1 to cmd2

PRE-DECLARED VARIABLES

PRE-DECLARED VARIABLES
Variables*	Description
$USER	username
$HOME	home path
$PWD	working directory path
$PATH	path for executables
$HOSTNAME	machine name
$SHELL	current shell
$SSH_CLIENT	local client’s IP address
$TERM	type of terminal

• env command lists all the assigned variables

HPC-CLUSTER Commands for SLURM

HPC-CLUSTER Commands		TORQUE
Command	Function	Syntax/example usage
sinfo -a	list all queues	sinfo -a
squeue	list all jobs	squeue
squeue -u userid	list jobs for userid	squeue -u userid
squeue -t R	list running jobs	squeue -t R
smap	show jobs, partitions and nodes in a graphical network topology	smap
sbatch	submit a slurm job	sbatch [script]
scancel	delete slurm batch job	scancel [job_id]
scontrol hold	hold slurm batch jobs	scontrol hold [job_id]
scontrol release	release hold on slurm batch jobs	scontrol release [job_id]

• Tutorial on SLURM commands

HPC-CLUSTER Commands for TORQUE

HPC-CLUSTER Commands		TORQUE
Command	Function	Syntax/example usage
squeue	show state of jobs	squeue –a # current jobs on cluster
squeue –u username		# current jobs by the user
squeue –j jobid		# information about the job (id#)
squeue -l –u username		# current jobs by the user
scancel	delete job from the queue	scancel jobid
sbatch	submit job to the queue	sbatch submissionfile.sub
scontrol	control jobs	scontrol hold jobid jobid # hold the job
		scontrol release jobid jobid # release the job
		scontrol show jobid jobid # info on the job
srun	run a job command	srun -N 1 -n 16 -t 4:00:00 --pty bash # start a interactive job session
sinfo	show state of nodes and partitions	sinfo
		sinfo -p tiny # show info on tiny partition
smap	show state of jobs, nodes and partitions (colored)	smap
module	use preinstalled programs	module load PROGRAM # loads program for use
		module list # lists all loaded modules
		module avail # lists available modules
		module unload PROGRAM # unloads module

PS: An A-Z Index of the Bash command line for Linux can be found here