HPC Linux Tutorial - Revision history

Admin at 12:54, 29 May 2024

2024-05-29T12:54:10Z

← Older revision		Revision as of 12:54, 29 May 2024
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	'''Sudo''' stands for "super user do" and is a command to elevate your privileges to the mighty '''root''' user who has full access to the entire system. The '''root''' user is needed to install software and make system-wide changes. Unfortunately (or fortunately for the HPC administrator) you don't have access to do this, hence the incident message.		'''Sudo''' stands for "super user do" and is a command to elevate your privileges to the mighty '''root''' user who has full access to the entire system. The '''root''' user is needed to install software and make system-wide changes. Unfortunately (or fortunately for the HPC administrator) you don't have access to do this, hence the incident message.

	On a side note, even without using '''sudo''', you won't be able to use the command '''apt-get''' since it is a tool for installing packages on Debian Linux variants like Ubuntu. The ELSA cluster uses ~~CentOS~~ Linux which does not use '''apt-get''' but instead uses '''~~yum~~''' which is another package manager. But don't worry, you don't have permissions to run either of these with or without '''sudo'''. If you need software installed system-wide, contact the HPC administrator for some helpful, friendly assistance.		On a side note, even without using '''sudo''', you won't be able to use the command '''apt-get''' since it is a tool for installing packages on Debian Linux variants like Ubuntu. The ELSA cluster uses Rocky Linux which does not use '''apt-get''' but instead uses '''dnf''' which is another package manager. But don't worry, you don't have permissions to run either of these with or without '''sudo'''. If you need software installed system-wide, contact the HPC administrator for some helpful, friendly assistance.

	==Software Carpentry's Unix Shell Lesson==		==Software Carpentry's Unix Shell Lesson==

Admin: /* On-line Manual Pages */

2019-06-06T18:53:39Z

On-line Manual Pages

← Older revision		Revision as of 18:53, 6 June 2019
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	To search all man pages for a certain keyword, try using the '''-k''' option like the example below.		To search all man pages for a certain keyword, try using the '''-k''' option like the example below.

	<code>$ man -k concatenate</code>		<code>$ man -k concatenate</code>
	<pre>		<pre>

Admin: /* On-line Manual Pages */

2019-06-06T18:53:17Z

On-line Manual Pages

← Older revision		Revision as of 18:53, 6 June 2019
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	</pre>		</pre>

			To search all man pages for a certain keyword, try using the '''-k''' option like the example below.
	<code>$ man -k concatenate</code>		<code>$ man -k concatenate</code>
	<pre>		<pre>

Admin at 18:51, 6 June 2019

2019-06-06T18:51:47Z

← Older revision		Revision as of 18:51, 6 June 2019
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	~~''This content is under construction. Check back often for updates.''~~

	==Emergency Linux Procedures==		==Emergency Linux Procedures==
	''HELP!'' I'm stuck and can't get out!		''HELP!'' I'm stuck and can't get out!
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	Linux consists of thousands of commands. While the <code>command options arguments</code> syntax is common among most of them, it can be daunting to remember the various options for each command. Options don't necessary have the same meaning between different commands. For example, the <code>-i</code> option has a different meaning when used with <code>ls</code> than with <code>grep</code>. To eliminate the need to keep a thick Linux command "bible" next to you at all times (or more likely a browser window open to your favorite search engine), the system provides "manual pages" built into Linux that can be called up as needed. These are called '''man pages''' in Linux lingo. You use the <code>man</code> command to display the manual pages for a command, e.g. <code>man cat</code> will display the manual page for the '''cat''' command.		Linux consists of thousands of commands. While the <code>command options arguments</code> syntax is common among most of them, it can be daunting to remember the various options for each command. Options don't necessary have the same meaning between different commands. For example, the <code>-i</code> option has a different meaning when used with <code>ls</code> than with <code>grep</code>. To eliminate the need to keep a thick Linux command "bible" next to you at all times (or more likely a browser window open to your favorite search engine), the system provides "manual pages" built into Linux that can be called up as needed. These are called '''man pages''' in Linux lingo. You use the <code>man</code> command to display the manual pages for a command, e.g. <code>man cat</code> will display the manual page for the '''cat''' command.

	Let's review an example '''man page'''.		Let's review an example '''man page'''. The command <code>man</code> followed by most Linux commands will display a helpful screen with its syntax, description of what the it does, all of the available options, and a few examples. For more help using '''man''' try running <code>man man</code>.

	<code>$ man cat</code>		<code>$ man cat</code>
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	zcat (1p) - expand and concatenate data		zcat (1p) - expand and concatenate data
	</pre>		</pre>
	~~<!--~~
	~~===Orthogonality===~~

	~~==Manipulating Files==~~
	~~-->~~

Admin: /* But the Internet told me to do it */

2019-06-05T12:44:42Z

But the Internet told me to do it

← Older revision		Revision as of 12:44, 5 June 2019
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	===But the Internet told me to do it===		===But the Internet told me to do it===
	So you've been using the Internet to figure out how to get some piece of software working that you need for your research. It probably told you to run <code>sudo apt-get ''blahblahblah''</code> so you did that. Now the system is telling you that "This incident will be reported." Don't panic. Everything is okay. '''Sudo''' stands for "super user do" and is a command to elevate your privileges to the mighty '''root''' user who has full access to the entire system. The '''root''' user is needed to install software and make system-wide changes. Unfortunately (or fortunately for the HPC administrator) you don't have access to do this, hence the incident message.		So you've been using the Internet to figure out how to get some piece of software working that you need for your research. It probably told you to run <code>sudo apt-get ''blahblahblah''</code> so you did that. Now the system is telling you that "This incident will be reported." Don't panic. Everything is okay.

			'''Sudo''' stands for "super user do" and is a command to elevate your privileges to the mighty '''root''' user who has full access to the entire system. The '''root''' user is needed to install software and make system-wide changes. Unfortunately (or fortunately for the HPC administrator) you don't have access to do this, hence the incident message.

	On a side note, even without using '''sudo''', you won't be able to use the command '''apt-get''' since it is a tool for installing packages on Debian Linux variants like Ubuntu. The ELSA cluster uses CentOS Linux which does not use '''apt-get''' but instead uses '''yum''' which is another package manager. But don't worry, you don't have permissions to run either of these with or without '''sudo'''. If you need software installed system-wide, contact the HPC administrator for some helpful, friendly assistance.		On a side note, even without using '''sudo''', you won't be able to use the command '''apt-get''' since it is a tool for installing packages on Debian Linux variants like Ubuntu. The ELSA cluster uses CentOS Linux which does not use '''apt-get''' but instead uses '''yum''' which is another package manager. But don't worry, you don't have permissions to run either of these with or without '''sudo'''. If you need software installed system-wide, contact the HPC administrator for some helpful, friendly assistance.

Admin: /* Emergency Linux Procedures */

2019-06-05T12:43:53Z

Emergency Linux Procedures

← Older revision		Revision as of 12:43, 5 June 2019
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	* Type <code>:q!</code>		* Type <code>:q!</code>
	* Press the <code>RETURN</code> or <code>ENTER</code> key (depending on what it is called on your keyboard)		* Press the <code>RETURN</code> or <code>ENTER</code> key (depending on what it is called on your keyboard)
	You should now be back at a terminal prompt. ~~Your~~ welcome.		You should now be back at a terminal prompt. You're welcome.

	===But the Internet told me to do it===		===But the Internet told me to do it===

Admin at 12:43, 5 June 2019

2019-06-05T12:43:01Z

← Older revision		Revision as of 12:43, 5 June 2019
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	''This content is under construction. Check back often for updates.''		''This content is under construction. Check back often for updates.''

	===Software Carpentry's Unix Shell Lesson===		==Emergency Linux Procedures==
			''HELP!'' I'm stuck and can't get out!

			===How do I logout?===
			You can logout of Linux using one, or a combination, of these methods.

			* Type <code>exit</code> at the terminal prompt.
			* Type <code>logout</code> at the terminal prompt. This sometimes doesn't work, and you must use <code>exit</code> instead because of ... reasons.
			* Hold down the <code>CTRL</code> key and press <code>d</code>. CTRL-d in the universal Unix/Linux end-of-input key sequence.

			===Oh no, VI===
			Somehow you managed to stumble into the '''vi''' text editor. VI comes with with every Linux distribution and is a good editor learn, but right now you just want to get out of it. Follow these steps.
			* Press the <code>ESC</code> key. It doesn't hurt to press it 2 or 3 times.
			* Type <code>:q!</code>
			* Press the <code>RETURN</code> or <code>ENTER</code> key (depending on what it is called on your keyboard)
			You should now be back at a terminal prompt. Your welcome.

			===But the Internet told me to do it===
			So you've been using the Internet to figure out how to get some piece of software working that you need for your research. It probably told you to run <code>sudo apt-get ''blahblahblah''</code> so you did that. Now the system is telling you that "This incident will be reported." Don't panic. Everything is okay. '''Sudo''' stands for "super user do" and is a command to elevate your privileges to the mighty '''root''' user who has full access to the entire system. The '''root''' user is needed to install software and make system-wide changes. Unfortunately (or fortunately for the HPC administrator) you don't have access to do this, hence the incident message.

			On a side note, even without using '''sudo''', you won't be able to use the command '''apt-get''' since it is a tool for installing packages on Debian Linux variants like Ubuntu. The ELSA cluster uses CentOS Linux which does not use '''apt-get''' but instead uses '''yum''' which is another package manager. But don't worry, you don't have permissions to run either of these with or without '''sudo'''. If you need software installed system-wide, contact the HPC administrator for some helpful, friendly assistance.

			==Software Carpentry's Unix Shell Lesson==
	[https://software-carpentry.org/ Software Carpentry] focuses on teaching researchers the computing skills they need to get more done in less time and with less pain. Their lesson on the Unix Shell is listed below. Note that while they refer to it as Unix, the lesson also applies to its younger cousin Linux.		[https://software-carpentry.org/ Software Carpentry] focuses on teaching researchers the computing skills they need to get more done in less time and with less pain. Their lesson on the Unix Shell is listed below. Note that while they refer to it as Unix, the lesson also applies to its younger cousin Linux.

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	* [http://swcarpentry.github.io/shell-novice/reference The Unix Shell Summary of Basic Commands] Reference		* [http://swcarpentry.github.io/shell-novice/reference The Unix Shell Summary of Basic Commands] Reference

	===Ryan's Tutorials===		==Ryan's Tutorials==
	[https://ryanstutorials.net/ Ryan's Tutorials] are also excellent. Two relevant tutorials are linked below.		[https://ryanstutorials.net/ Ryan's Tutorials] are also excellent. Two relevant tutorials are linked below.

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	* [https://ryanstutorials.net/bash-scripting-tutorial/ Bash Scripting Tutorial]		* [https://ryanstutorials.net/bash-scripting-tutorial/ Bash Scripting Tutorial]

	===On-line Manual Pages===		==On-line Manual Pages==
	Linux consists of thousands of commands. While the <code>command options arguments</code> syntax is common among most of them, it can be daunting to remember the various options for each command. Options don't necessary have the same meaning between different commands. For example, the <code>-i</code> option has a different meaning when used with <code>ls</code> than with <code>grep</code>. To eliminate the need to keep a thick Linux command "bible" next to you at all times (or more likely a browser window open to your favorite search engine), the system provides "manual pages" built into Linux that can be called up as needed. These are called '''man pages''' in Linux lingo. You use the <code>man</code> command to display the manual pages for a command, e.g. <code>man cat</code> will display the manual page for the '''cat''' command.		Linux consists of thousands of commands. While the <code>command options arguments</code> syntax is common among most of them, it can be daunting to remember the various options for each command. Options don't necessary have the same meaning between different commands. For example, the <code>-i</code> option has a different meaning when used with <code>ls</code> than with <code>grep</code>. To eliminate the need to keep a thick Linux command "bible" next to you at all times (or more likely a browser window open to your favorite search engine), the system provides "manual pages" built into Linux that can be called up as needed. These are called '''man pages''' in Linux lingo. You use the <code>man</code> command to display the manual pages for a command, e.g. <code>man cat</code> will display the manual page for the '''cat''' command.

Admin at 19:32, 4 June 2019

2019-06-04T19:32:04Z

← Older revision		Revision as of 19:32, 4 June 2019
Line 5:		Line 5:

	* [http://swcarpentry.github.io/shell-novice/ The Unix Shell] Lesson		* [http://swcarpentry.github.io/shell-novice/ The Unix Shell] Lesson
	* [http://swcarpentry.github.io/shell-novice/reference/The Unix Shell Summary of Basic Commands] Reference		* [http://swcarpentry.github.io/shell-novice/reference The Unix Shell Summary of Basic Commands] Reference

	===Ryan's Tutorials===		===Ryan's Tutorials===

Admin at 18:56, 22 May 2019

2019-05-22T18:56:05Z

← Older revision		Revision as of 18:56, 22 May 2019
Line 1:		Line 1:
			''This content is under construction. Check back often for updates.''

	===Software Carpentry's Unix Shell Lesson===		===Software Carpentry's Unix Shell Lesson===
	[https://software-carpentry.org/ Software Carpentry] focuses on teaching researchers the computing skills they need to get more done in less time and with less pain. Their lesson on the Unix Shell is listed below. Note that while they refer to it as Unix, the lesson also applies to its younger cousin Linux.		[https://software-carpentry.org/ Software Carpentry] focuses on teaching researchers the computing skills they need to get more done in less time and with less pain. Their lesson on the Unix Shell is listed below. Note that while they refer to it as Unix, the lesson also applies to its younger cousin Linux.

Admin at 15:43, 16 May 2019

2019-05-16T15:43:25Z

← Older revision		Revision as of 15:43, 16 May 2019
Line 12:		Line 12:

	===On-line Manual Pages===		===On-line Manual Pages===
	Linux consists of thousands of commands. While the <code>command options arguments</code> syntax is common among most of them, it ~~may seem~~ daunting to remember the various options for each command. Options don't necessary have the same meaning between different commands. For example, the <code>-i</code> option has a different meaning when used with <code>ls</code> than with <code>grep</code>. To eliminate the need to keep a thick Linux command "bible" next to you at all times (or more likely a browser window open to your favorite search engine), the system provides "manual pages" built into Linux that can be called up as needed. These are called '''man pages''' in Linux lingo. You use the <code>man</code> command to display the manual pages for a command, e.g. <code>man cat</code> will display the manual page for the '''cat''' command.		Linux consists of thousands of commands. While the <code>command options arguments</code> syntax is common among most of them, it can be daunting to remember the various options for each command. Options don't necessary have the same meaning between different commands. For example, the <code>-i</code> option has a different meaning when used with <code>ls</code> than with <code>grep</code>. To eliminate the need to keep a thick Linux command "bible" next to you at all times (or more likely a browser window open to your favorite search engine), the system provides "manual pages" built into Linux that can be called up as needed. These are called '''man pages''' in Linux lingo. You use the <code>man</code> command to display the manual pages for a command, e.g. <code>man cat</code> will display the manual page for the '''cat''' command.

	Let's review an example '''man page'''.		Let's review an example '''man page'''.