Quick Reference Guide - Revision history

Shtsai at 00:09, 1 August 2025

2025-08-01T00:09:55Z

← Older revision		Revision as of 20:09, 31 July 2025
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	\|<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 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>		\|<code>ml <software name></code>\|\|Load a software module\|\|<code>ml BLAST+/2.16.0-gompi-2024a</code>
	\|-		\|-
	\|}		\|}

Shtsai: /* Linux */

2023-03-06T17:48:49Z

Linux

← Older revision		Revision as of 13:48, 6 March 2023
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	=Linux=		=Linux=
	Below are the minimum Linux definitions, 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==		==Definitions==
	1. '''Command''' - Word or letters typed into a terminal to make a computer do something. Executed by pressing enter after typing the command.		1. '''Command''' - Word or letters typed into a terminal to make a computer do something. Executed by pressing enter after typing the command.

Karen: Software section

2022-11-09T13:25:03Z

Software section

← Older revision		Revision as of 09:25, 9 November 2022
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	\|-		\|-
	\|}		\|}

			<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]]		[[#top\|Back to Top]]
	==Shortcuts==		==Shortcuts ==

	'''Linux'''		'''Linux'''
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	{\| class="wikitable"		{\| class="wikitable"
	\|-		\|-
	! Shortcut !! Description		!Shortcut!! Description
	\|-		\|-
	\| ctrl + l (lowercase L)\|\| Clear your terminal screen (scroll up to see previous output)		\| ctrl + l (lowercase L)\|\|Clear your terminal screen (scroll up to see previous output)
	\|-		\|-
	\| up/down arrow keys \|\| Cycle through previously entered commands		\|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)		\|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		\|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 + w\|\|Backspace typed text on the command line, one word at a time
	\|-		\|-
	\| ctrl + c \|\| Cancel typed text on the command line		\|ctrl + c\|\| Cancel typed text on the command line
	\|-		\|-
	\|}		\|}
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	{\| class="wikitable"		{\| class="wikitable"
	\|-		\|-
	! Shortcut !! Description		!Shortcut!!Description
	\|-		\|-
	\| shift + g \|\| Go to the end of file		\| shift + g \|\|Go to the end of file
	\|-		\|-
	\| gg \|\| Go to the beginning of file		\|gg\|\|Go to the beginning of file
	\|-		\|-
	\| -N then enter \|\| Display/hide line numbers		\| -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 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)		\|?''SomePattern''\|\|Search backwards through a file for ''SomePattern'' (? then enter to keep searching forward for the same pattern)
	\|-		\|-
	\| q \|\| Exit less		\|q \|\|Exit less
	\|-		\|-
	\|}		\|}
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	'''Default Slurm Commands'''		'''Default Slurm Commands'''
	{\| class="wikitable"		{\| 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'''		'''GACRC Slurm Commands'''
	{\| class="wikitable"		{\| class="wikitable"
	! Command !! Description/Slurm Equivalent !! Examples		!Command!!Description/Slurm Equivalent!!Examples
	\|-		\|-
	\| <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>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>
	\|-		\|-
	\|}		\|}

Ben at 13:26, 9 November 2021

2021-11-09T13:26:02Z

← Older revision		Revision as of 09:26, 9 November 2021
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	\| <code>less</code> \|\| View the contents of a file (better for longer files) \|\| <code>less slurm-42342.out</code>		\| <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</code> \|\| Remove a file or files \|\| <code>rm oldfile.txt</code>
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	\|-		\|-
	\| up/down arrow keys \|\| Cycle through previously entered commands		\| 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		\| esc, . (escape, then period)\|\| Cycle through previous arguments to commands

Ben at 17:10, 8 November 2021

2021-11-08T17:10:56Z

← Older revision		Revision as of 13:10, 8 November 2021
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	\|-		\|-
	\| <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>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>
			\|-
	\|}		\|}
	----		----

Ben at 16:33, 8 November 2021

2021-11-08T16:33:26Z

@@ 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.
 ==Commands==
 <big>'''Getting Help'''</big> (most important)
@@ Line 81: / Line 102: @@
 |-
 |}
 ----
 [[#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.

Ben at 16:16, 8 November 2021

2021-11-08T16:16:05Z

← Older revision		Revision as of 12:16, 8 November 2021
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	\|-		\|-
	\| ?''SomePattern'' \|\| Search backwards 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
	\|-		\|-
	\|}		\|}

Ben at 16:14, 8 November 2021

2021-11-08T16:14:59Z

@@ Line 43: / Line 43: @@
 [[#top|Back to Top]]
 ==Shortcuts==
 {| class="wikitable"
 |-
@@ Line 58: / Line 61: @@
 |-
 |}
 ----
 [[#top|Back to Top]]

Ben at 12:33, 13 October 2021

2021-10-13T12:33:08Z

← Older revision		Revision as of 08:33, 13 October 2021
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	'''GACRC Slurm Commands'''		'''GACRC Slurm Commands'''
	{\| class="wikitable"		{\| 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>

Ben at 23:00, 12 October 2021

2021-10-12T23:00:47Z

← Older revision		Revision as of 19:00, 12 October 2021
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	! Command !! Description !! Examples		! 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>		\| <code>cat</code> \|\| Print the contents of a file to the terminal (better for shorter files) \|\| <code>cat slurm-42342.out</code>