Latest revision as of 12:48, 6 March 2023

Linux

Below are the minimum Linux definitions, commands, and shortcuts that you should know to do work on an HPC cluster. Some videos covering introductory Linux commands are available here.

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.

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`

@@ Line 1: / Line 1: @@
 =Linux=
-Below are the minimum Linux commands and shortcuts that you should know to do work on an HPC cluster.
+Below are the minimum Linux definitions, commands, and shortcuts that you should know to do work on an HPC cluster. Some videos covering introductory Linux commands are available '''[https://kaltura.uga.edu/playlist/dedicated/176125031/1_uwkiealj/1_81u2kfi2  here]'''.
+==Definitions==
+. '''Command''' - Word or letters typed into a terminal to make a computer do something.  Executed by pressing enter after typing the command.
+. '''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".
+. '''Command prompt''' - The text at the beginning of the command line, before your cursor.  Typically [''username''@''computername''].
+. '''Directory''' - Another word for "Folder" (just like a folder in Windows or Mac).  Often shortened to "dir" in commands, documentation, conversation, etc...
+. '''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).
+. '''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
+. '''First /''' (in a path) - The root directory, where everything starts in the Linux file system.
+. '''Absolute path''' - a path that is written beginning with / (root)
+. '''Relative path''' - a path that is written relative to some other directory (does not begin with /)
+. (Command) '''Option''' - extra letter or word (-''SomeLetter'' or --''SomeWord'') put after a command to modify its behavior.
+----
 ==Commands==
+<big>'''Getting Help'''</big> (most important)
+{| class="wikitable"
+! Command !! Description !! Examples
+|-
+| <code>''command'' --help</code> || Print a commands help output to the terminal || <code>ls --help</code>
+|-
+| <code>man ''command''</code> || Read a command's manual (press q to exit) || <code>man ls</code>
+|-
+|}
 <big>'''Directories'''</big>
 {| class="wikitable"
@@ Line 19: / Line 50: @@
 ! Command !! Description !! Examples
 |-
-| <code>nano</code> || Create or edit a file with nano(To save and exit: ctrl + x, y, enter)|| <code>nano sub.sh</code>
+| <code>nano</code> || Create or edit a file with nano (to save and exit: ctrl + x, y, enter)|| <code>nano sub.sh</code>
 |-
 | <code>cat</code> || Print the contents of a file to the terminal (better for shorter files) || <code>cat slurm-42342.out</code>
@@ Line 25: / Line 56: @@
 | <code>less</code> || View the contents of a file (better for longer files) || <code>less slurm-42342.out</code>
 |-
-| <code>cp</code> || Copy a file or files (<code>cp ''sourcepath(s) destinationpath</code>) || <code>cp /scratch/'''MyID'''/workdir/sub.sh /work/'''labgroup'''</code>
+| <code>cp</code> || Copy a file or files (<code>cp ''sourcepath(s) destinationpath''</code>) || <code>cp /scratch/'''MyID'''/workdir/sub.sh /work/'''labgroup'''</code>
+|-
+| <code>mv</code> || Move a file or files (<code>mv ''sourcepath(s) destinationpath''</code>) || <code>mv /scratch/'''MyID'''/workdir/sub.sh /work/'''labgroup'''</code>
 |-
 | <code>rm</code> || Remove a file or files || <code>rm oldfile.txt</code>
 |-
 | <code>rm -r</code> || Remove a directory and '''all''' of its contents, recursively (starting with the last dir in the path)|| <code>rm -r /home/'''MyID'''/olddir</code>
+|-
+| <code>dos2unix</code> || Removes DOS/Windows line endings in file || <code>dos2unix file.txt</code>
+|-
+| <code>mac2unix</code> || Removes Mac line endings in file. || <code>mac2unix file.txt</code>
+|-
 |}
+<big>'''Software'''</big>
+{| class="wikitable"
+|-
+!Command!!Description!!Examples
+|-
+|<code>ml spider <software name></code>||See if a software is available, will also show you which versions are available||<code>ml spider Blast+</code>
+|-
+|<code>ml <software name></code>||Load a software module||<code>ml BLAST+/2.12.0-gompi-2020b</code>
+|-
+|}
+Also see the [[Software]] page and [[Frequently Asked Questions#Software|Software]] section of our FAQ.
 ----
 [[#top|Back to Top]]
-==Shortcuts==
+==Shortcuts ==
+'''Linux'''
+{| class="wikitable"
+|-
+!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'''
 {| class="wikitable"
 |-
-! Shortcut !! Description
+!Shortcut!!Description
 |-
-| ctrl + l (lowercase L)|| Clear your terminal screen (scroll up to see previous output)
+| shift + g ||Go to the end of file
 |-
-| up/down arrow keys || Cycle through previously entered commands
+|gg||Go to the beginning of file
 |-
-| esc, . (escape, then period)|| Cycle through previous arguments to commands
+| -N then enter ||Display/hide line numbers
 |-
-| ctrl + w || Backspace typed text on the command line, one word at a time
+|/''SomePattern''||Search forward through a file for ''SomePattern'' (/ then enter to keep searching forward for the same pattern)
 |-
-| ctrl + c || Cancel typed text on the command line
+|?''SomePattern''||Search backwards through a file for ''SomePattern'' (? then enter to keep searching forward for the same pattern)
+|-
+|q ||Exit less
 |-
 |}
 ----
 [[#top|Back to Top]]
 =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.
@@ Line 57: / Line 133: @@
 '''Default Slurm Commands'''
 {| class="wikitable"
-! Command !! Description !! Examples
+!Command!!Description!!Examples
 |-
-| <code>sbatch</code> || Submit a submission script to the cluster|| <code>sbatch sub.sh</code>
+|<code>sbatch</code>|| Submit a submission script to the cluster||<code>sbatch sub.sh</code>
 |-
-| <code>squeue</code> || Check status currently running jobs (--me for only your jobs) || <code>squeue --me</code>
+|<code>squeue</code>||Check status currently running jobs (--me for only your jobs)||<code>squeue --me</code>
 |-
-| <code>sacct -X</code> || Check status of your jobs started since midnight of current day (-X for one line per job)|| <code>sacct -X</code>
+|<code>sacct -X</code>||Check status of your jobs started since midnight of current day (-X for one line per job)||<code>sacct -X</code>
 |-
-| <code>sacct -X -S yyyy-mm-dd</code> || Check status of your jobs since yyyy-mm-dd || <code>sacct -X -S 2021-10-20</code>
+|<code>sacct -X -S yyyy-mm-dd</code>||Check status of your jobs since yyyy-mm-dd||<code>sacct -X -S 2021-10-20</code>
 |-
-| <code>sacct -j ''jobID'' || Check status of a particular job || <code>sacct -j 234213</code>
+|<code>sacct -j ''jobID'' ||Check status of a particular job||<code>sacct -j 234213</code>
 |-
-| <code>scancel ''jobID'' || Cancel one of your running jobs || <code>scancel 456781</code>
+|<code>scancel ''jobID'' ||Cancel one of your running jobs ||<code>scancel 456781</code>
 |-
-| <code>sinfo</code> || Check the status of partitions || <code>sinfo -p batch</code>
+|<code>sinfo</code>||Check the status of partitions||<code>sinfo -p batch</code>
 |-
 |}
 '''GACRC Slurm Commands'''
 {| class="wikitable"
-! Command !! Slurm Equivalent !! Examples
+!Command!!Description/Slurm Equivalent!!Examples
 |-
-| <code>interact</code> || Same as <code>qlogin</code> but with more flexibility || <code>interact -c 4 --mem 10gb --time 01:00:00</code>
+|<code>interact</code>||Start an interactive job.  (Same as <code>qlogin</code> but with more flexibility)||<code>interact -c 4 --mem 10gb --time 01:00:00</code>
 |-
-| <code>sq</code> || <code>squeue</code> || <code>sq --me</code>
+|<code>sq</code>||<code>squeue</code>||<code>sq --me</code>
 |-
-| <code>sacct-gacrc -X</code> || <code>sacct</code>|| <code>sacct-gacrc -X</code>
+|<code>sacct-gacrc -X</code>||<code>sacct</code>||<code>sacct-gacrc -X</code>
 |-
 |}

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