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--- pandoc:introduction-to-vsc:03_linux_primer:linuxprimer [2018/01/31 13:17] – Pandoc Auto-commit pandoc
+++ pandoc:introduction-to-vsc:03_linux_primer:linuxprimer [2020/10/20 09:13] (current) – Pandoc Auto-commit pandoc
@@ Line 1: / Line 1: @@
 ====== Linux Primer ======
@@ Line 7: / Line 6: @@
 ==== Note ====
-Please use the ''%%Table of Contents%%'' or your browsers ''%%quick search%%'' to find what you’re looking for, as this document is auto-generated from a presentation and context may not always be recognisable without the corresponding talk.
+Please use the ''%%Table of Contents%%'' or your browsers ''%%quick search%%'' to find what you’re looking for, as this document is auto-generated from a presentation and context may not always be recognizable without the corresponding talk.
+----
@@ Line 19: / Line 21: @@
 ==== Filesystem 101 ====
-The job of filesystems is to keep data in a structured way. Every filesystem has a filesystem root, directories and files. The filesystem root is a special object which acts as an entrypoint for using that filesystem. All other objects (directories and files) are structured below the root.
+The job of filesystems is to keep data in a structured way. Every filesystem has a filesystem root, directories and files. The filesystem root is a special object which acts as an entry-point for using that filesystem. All other objects (directories and files) are structured below the root.
 Two main concepts emerged for using more than one filesystem on a single machine:
@@ Line 49: / Line 51: @@
     * relative: ''%%dir2/object%%''
   - special objects in directories:
-    * ''%%.%%'' — is a reference to the directory itself
+    * “''%%.%%''” is a reference to the directory itself
-    * ''%%..%%'' — is a reference to the parent directory
+    * “''%%..%%''” is a reference to the parent directory
   - the system may consist of multiple filesystems
     * filesystems may be mounted at any (empty) directory
@@ Line 58: / Line 60: @@
 Next to basic storage and organization of data filesystems have different properties and functionality. Most filesystems provide a way to store and access attributes, different kinds of special files and some filesystems provide various advanced features:
   * Attributes
@@ Line 76: / Line 77: @@
   * Advanced FS features
     * data integrity
-    * device managment
+    * device management
-    * subvolume support
+    * sub-volume support
@@ Line 83: / Line 85: @@
 ==== Filesystem tree ====
-{{:pandoc:introduction-to-vsc:03_linux_primer:linuxprimer:linux_directories.jpg}}
+{{.:linux_directories.jpg}}
-<HTML>
-<!--
-### Mountpoints
-> Linux presents only one tree for file access - but every filesystems has its own tree!
-#### Attaching a filesystem to the current tree: {.incremental}
-> - takes a filesystem
->     - **`FS`** usually a device file or a network address
-> - takes an empty directory in the current tree
->     - usually `/mnt/XXX` or `/mnt`
-> - makes the root of the new filesystem available in place of the empty directory
->     - **`FS`** `-> /mnt/`
-<div class=incremental>
-> This process is called mounting.
-</div>
--->
-</HTML>
 ==== Special filesystems used on VSC ====
@@ Line 133: / Line 115: @@
 > This is how the prompt looks by default:
+<HTML>
+<!-- ![](pictures/tango_terminal.svg){height=100px style="float: left; padding-left: 2em;" .slidy}-->
+</HTML>
 <code bash>
 [myname@l3_ ~]$
@@ Line 154: / Line 137: @@
   * Think about why the program failed - maybe you (un-)intentionally tried to force the program to do something it’s not intended for?
-  * Just copy that message into your favourite search engine and don’t forget to remove the parts that are specific to your environment (e.g. directory and user names).
+  * Just copy that message into your favorite search engine and don’t forget to remove the parts that are specific to your environment (e.g. directory and user names).
   * Most programs supports a ''%%-h%%''/''%%--help%%'' flag
   * ''%%man <COMMAND>%%'' will be available for most programs too, if not ''%%man -K <KEYWORD>%%'' will search all man-pages that contain the keyword. (FYI: press ‘q’ to quit)
@@ Line 169: / Line 152: @@
 gcc FizzBuzz.c -o FizzBuzz
 ./FizzBuzz
-module load non-existent-module
+false
 echo $?
 </code>
@@ Line 178: / Line 161: @@
   * ''%%gcc%%'' is a program that is in a directory specified by the ''%%$PATH%%'' variable and will be found without specifying its exact location.
   * ''%%./FizzBuzz%%'' is a newly compiled executable, which is not found by looking at ''%%$PATH%%'', so we explicitly add ''%%./%%'', to show that we want to execute it from the current directory
-  * ''%%module load non-existent-module%%'' fails, as the module command can’t find ''%%non-existent-module%%''. Whenever a command fails, its ''%%return value%%'' is set to a value other than zero. The manual for some commands has a map from return-value to error-description to aid the user debuging.
+  * ''%%module load non-existent-module%%'' fails, as the module command can’t find ''%%non-existent-module%%''. Whenever a command fails, its ''%%return value%%'' is set to a value other than zero. The manual for some commands has a map from return-value to error-description to aid the user debugging.
   * ''%%echo $?%%'' is a command that prints the return value of the previous command.
@@ Line 223: / Line 206: @@
 COMMAND -j auto --color 2   # PROBABLY WRONG
 </code>
-== Escapes & Quotes ==
+==== Escapes & Quotes ====
 Whenever a parameter has to contain a character that is either unprintable or reserved for the shell, you can use:
@@ Line 240: / Line 223: @@
 COMMAND 'This is a single parameter'
 </code>
@@ Line 248: / Line 233: @@
-<code bash>
+<code>
 alias ll='ls -alh'
 alias rm='rm -i'
 alias myProject='cd $ProjectDir; testSuite; compile && testSuite; cd -'
 </code>
 After that, you can use the aliases synonymously.
@@ Line 323: / Line 309: @@
 === Chaining Commands ===
-The simplest mechanism for control flow is to chain commands together in a simple ''%%if COMMAND then NEXTCOMMAND else ERRORCOMMAND%%''. Since this would be cumbersome to write, most shells provide simple syntax for this: ''%%COMMAND && NEXTCOMMAND || ERRORCOMMAND%%'' and if a command should be run without relying on the return velue of its predecessor it’s written: ''%%COMMAND; NEXTCOMMAND%%''. And if you only want to execute further commands in one case (but not the other), you don’t even have to specify both branches.
+The simplest mechanism for control flow is to chain commands together in a simple ''%%if COMMAND then NEXTCOMMAND else ERRORCOMMAND%%''. Since this would be cumbersome to write, most shells provide simple syntax for this: ''%%COMMAND && NEXTCOMMAND || ERRORCOMMAND%%'' and if a command should be run without relying on the return value of its predecessor it’s written: ''%%COMMAND; NEXTCOMMAND%%''. And if you only want to execute further commands in one case (but not the other), you don’t even have to specify both branches.
@@ Line 472: / Line 458: @@
 </div>
 </div>
-</HTML>
-===== Basic command line programs =====
-==== Looking around ====
-> Looking through files is done with the ''%%ls%%'' command under Linux, which is an abreviation for ''%%list%%''.
-By default (meaning without parameters) the ''%%ls%%'' command shows the content in the current directory. It does hide elements starting with a dot though. These hidden elements can be shown by adding the ''%%-a%%'' parameter, which stands for ''%%all%%''. If you want detailed information about the elements, add the ''%%-l%%'' parameter for ''%%long listing%%''. You can also specify a file/directory which you want to examine, by just appending the path to the command.
-<code>
-$ ls      # shows files and directories
-testdir  test
-$ ls -a   # includes hidden ones
-.  ..  testdir  test
-$ ls -l   # detailed view
-drwxr-xr-x 1 myuser p12345 0 Apr 13  2017 testdir
--rw-r--r-- 1 myuser p12345 4 Apr 13 11:55 test
-$ ls /tmp/
-allinea-USERNAME
-ssh-6E553lWZCM
-ssh-C6a754pJ1d
-systemd-private-a4214393983d448fbdc689791806519c-ntpd.service-LrAgBP
-tmp7CJZRA
-yum_save_tx.2017-04-03.12-07.VCUowf.yumtx
-$ ls -alh ~
-drwxr-xr-x  5 myuser mygroup   45 Jan 30  2017 .allinea
--rw-------  1 myuser mygroup  21K May  3 17:14 .bash_history
--rw-r-----  1 myuser mygroup  231 Dec  2  2016 .bashrc
-drwx------  1 myuser mygroup   76 Aug 22  2017 Simulation
-drwx------  2 myuser mygroup   76 Dec 12  2016 .ssh
-</code>
-==== Moving around ====
-> Moving through directories is done with the ''%%cd%%'' command, which stands for ''%%change directory%%''.
-The ''%%cd%%'' command can be called without any arguments, in which case it just switches to the home directory. Otherwise it takes a absolute (starting with a dash) or relative path as an argument and switches to that directory. The argument ''%%-%%'' (just a single dash) will cause cd to switch to the previous directory. This can be used to alternate between two directories without typing their path’s every time.
-<code>
-$ cd /bin   # go to an absolute directory
-$ cd [~]    # go home
-$ cd -      # go to previous directory
-</code>
-==== Copying & moving files around ====
-> Copying and moving files and directories is done with the ''%%cp%%'' and ''%%mv%%'' commands, which stand for ''%%copy%%'' and ''%%move%%'' respectively.
-Both commands take at least two parameters, which correspond to the ''%%<SOURCE>%%'' and ''%%<DESTINATION>%%'' files or directories. For ''%%cp%%'' to work with directories as a source, it needs the ''%%-r%%'' (recursive) or ''%%-a%%'' (archive) flag.
-> Beware of the pitfalls! you can overwrite data and therefor lose it, without getting any confirmation prompt! If in doubt use ''%%-i%%'' (interactive) flag.
-<code>
-$ mv old   new     # rename old to new
-$ mv old   dir/    # move old into dir
-$ mv file1 file2   # overwrite file2 with file1
-                   # (BEWARE)
-</code>
-<code>
-$ cp -i input input.bak   # input to input.bak
-$ cp -i input backup/     # input into backup
-$ cp -a dir1/ dir2        # exact copy of dir1
-</code>
-==== Creating and deleting ====
-=== directories ===
-> creating directories is done with the ''%%mkdir%%'' command, which stands for ''%%make directory%%''.
-The ''%%mkdir%%'' command takes an optional ''%%-p%%'' (parents) parameter and a path. When optional parameter is given, it will create all the ancestors of the specified directory aswell. Otherwise the command fails if the directory either exists already or its parent doesn’t exist either.
-> deleting directories is done with the ''%%rmdir%%'' command, which stands for ''%%remove directory%%''.
-This command removes the specified directory, but only if it’s already empty. it can also take an optional ''%%-p%%'' parameter, in which case it removes the specified directory and all the ancestors you included.
-==== Finding stuff ====
-> To look at everything
-  - in your home directory
-  - and nested up to three levels deep inside it
-  - that ends in ''%%.txt%%''
-  - or starts with ''%%log_%%''
-  - and is an ordinary file
-  - concatenated as one stream:
-<code bash>
-find \
-  ~ \
-  -maxdepth 3 \
-  -iname "*.txt" \
-  -or -iname "log_*" \
-  -type f \
-  -exec cat '{}' \; | less
-</code>
-<code bash>
-find \
-  ~ \
-  -maxdepth 3 \
-  -iname "*.txt" \
-  -or -iname "log_*" \
-  -type f \
-  -exec cat '{}' +  | less
-</code>
-==== Contents of files ====
-> **viewing** is done by the **''%%less%%''** command:
-> **concatenating** is done by the **''%%cat%%''** command:
-<code>
-$ less file.txt      # exit with 'q'
-$ less -R file.txt   # keep colors
-$ cat file1 file2 | less
-</code>
-<code>
-$ cat file
-$ cat -A printable
-$ cat -n numbered
-</code>
-<code>
-$ echo "VSC is great" > file
-$ cat file
-VSC is great
-</code>
-<code>
-$ echo "VSC is awesome" >> file
-$ cat file
-VSC is great
-VSC is awesome
-</code>
-<code>
-$ cat file | grep awesome
-VSC is awesome
-</code>
-<code>
-$ grep awesome file
-VSC is awesome
-</code>
-==== Space accounting ====
-> viewing **used space** is done by the **''%%du%%''** (disk usage) command:
-> viewing **free space** is done by the **''%%df%%''** (disk free) command:
-<code>
-$ du -h file1 file2   # human readable output
-$ du -s dir           # summarize
-</code>
-<code>
-$ df -h       # human readable output
-$ df -t nfs   # only list filesystems of a type
-</code>
-{{:pandoc:introduction-to-vsc:03_linux_primer:linuxprimer:screenshot_df.png?0x440}}
-==== Recap ====
-<code>
-$ mv space.log space.log.bak
-</code>
-<code>
-$ df -h | grep "lv12345\|lv54321" > space.log
-</code>
-<code>
-$ cat space.log
-</code>
-<code>
-nfs05.ib.cluster:/e/lv12345    200G  185G   16G  93% /home/lv12345
-nfs04.ib.cluster:/e/lv54321   1000G  979G   22G  98% /home/lv54321
-</code>
-> we do this often, let’s wrap it up!
-==== Recap++ ====
-<code>
-$ mv space.log space.log.bak
-</code>
-<code>
-$ df -h | grep "lv12345\|lv54321" > space.log
-</code>
-<code>
-$ cat space.log
-</code>
-<code>
-nfs05.ib.cluster:/e/lv12345    200G  185G   16G  93% /home/lv12345
-nfs04.ib.cluster:/e/lv54321   1000G  979G   22G  98% /home/lv54321
-</code>
-> we do this often, let’s wrap it up!
-<code>
-$ echo '#!/bin/bash' > spacelog.sh
-$ echo 'mv space.log space.log.bak' >> spacelog.sh
-$ echo 'df -h | grep "lv12345\|lv54321" > space.log' >> spacelog.sh
-$ echo 'cat space.log' >> spacelog.sh
-</code>
-<code>
-$ chmod +x spacelog.sh
-</code>
-<code>
-$ ./spacelog.sh
-</code>
-==== Sed and awk ====
-> **sed** (stream editor) and **awk** are powerful tools when working with the command line
-<code>
-$ mycommand | sed "..."
-</code>
-<code>
-$ mycommand | awk '{...}'
-</code>
-> Using sed and awk in action
-^program  ^             command              ^description                                                                ^
-|sed      |        ''%%s/old/new/%%''        |replace ''%%old%%'' with ''%%new%%''                                       |
-|sed      |  ''%%/from/,/to/ s/old/new/%%''  |replace ''%%old%%'' with ''%%new%%'', between ''%%from%%'' and ''%%to%%''  |
-|awk      |      ''%%'print $5 $3'%%''       |print columns 5 and 3 of every line                                        |
-Example script:
-<code bash>
-#!/bin/bash
-mv space.log space.log.bak
-df -h | grep "lv12345\|lv54321" > space.log
-cat space.log
-</code>
-<code bash>
-#!/bin/bash
-mv space.log space.log.bak
-df -h | grep "lv12345\|lv54321" > space.log
-cat space.log | sed "s|/home/lv12345|ProjectA|" \
-              | awk '{print $6, "free:", $4}' \
-              | column -t
-</code>
-<HTML>
 <!--
-### Sort and uniq
+## Pause Please?<br><br> &#8594; Get Coffee<br> &#8594; Get Cookies {.slidy}
-> **sort** and **uniq** (unique) are used to sort and uniquify adjacent lines
 -->
 </HTML>
@@ Line 767: / Line 473: @@
 <code bash>
+# only works with root privileges
+chown user file
 chown -R user:group dirs files
-# only works with root privilages
 </code>
 === chmod ===
@@ Line 780: / Line 488: @@
 chmod 750                executables
 </code>
+  * there are three bits for:
+    * read (4)
+    * write (2)
+    * execute (1)
+  * three times for:
+    * user
+    * group
+    * other
 ==== Shebang ====
@@ Line 798: / Line 517: @@
 </code>
-> Don’t we have an OS, capable of executing everything it recognises as an executable?
+> Don’t we have an OS, capable of executing everything it recognizes as an executable?
 > Yes, we do!
@@ Line 852: / Line 571: @@
 allNumbersFromTo 1 10
 </code>
-===== Editors =====
-==== General ====
-  * Many different editors
-    * Unique (dis-)advantages
-    * Different look and feel
-  * Editors should provide us with
-    - Simple text editing
-    - Copy and paste
-    - Search and replace
-    - Saving changes
-    - Wide availability
-=== Two editors that satisfy our needs: ===
-  * nano
-  * vim
-=== Common starting point ===
-<code bash>
-nano filename
-</code>
-<code bash>
-vim filename
-</code>
-==== Nano ====
-{{:pandoc:introduction-to-vsc:03_linux_primer:linuxprimer:screenshot_nano.png}}
-==== Nano explained ====
-> This editor is focused on being easy to use, but still providing every feature a user might need.
-=== Interface ===
-> The interface consists of four parts, namely from top to bottom:
-  * Title bar
-  * Text area
-  * Command line
-  * Key bindings
-=== Usage ===
-> Nothing special, key-bindings visible while editing
-^Feature       ^                 Usage                 ^
-|Navigation    |              Arrow keys               |
-|Actual editing|         Typing text, as usual         |
-|Cut/Paste line|  ''%%<CTRL>%%''+k / ''%%<CTRL>%%''+u  |
-|…             |    explained in key bindings field    |
-=== Short ===
-> Use this editor if you are new to the command line.\\
-> It is straight forward, but can be extended on the way.
-  * Auto-indentation
-  * Syntax highlighting
-  * Multi-buffer
-{{:pandoc:introduction-to-vsc:03_linux_primer:linuxprimer:screenshot_nano.png?0x300}}
-==== Vi(m) ====
-{{:pandoc:introduction-to-vsc:03_linux_primer:linuxprimer:screenshot_vim.png}}
-==== Vi(m) explained ====
-> This editor is focused on productivity and efficiency, providing everything a user might need.
-=== Interface ===
-> The simple interface consists of two parts:
-  * Text area
-  * Command line
-> Since this editor is very easy to extend, after setting up a few plugins, it will probably look quite different!
-=== Usage ===
-> This is a multimode editor, you’ll have to switch modes whenever you change what you want to do.
-^Feature   ^                    Usage                    ^
-|Navigation|                 Arrow keys                  |
-|Writing   |  change to input mode, then write as usual  |
-|Commands  |     exit current mode, press ''%%:%%''      |
-|…         |           explained on next slide           |
-=== Short ===
-> Use this editor if you like a challenge.\\
-> It is fast and very nice — but you’ll sometimes get hurt on the way.
-  * Auto-indentation, Syntax highlighting, Multi-buffer – just like nano
-  * File/Project Management
-  * Use a plugin manager
-{{:pandoc:introduction-to-vsc:03_linux_primer:linuxprimer:screenshot_vim.png?0x300}}
-==== Vi(m) modes and keys ====
-  * any mode:
-    * back to the **default mode**: **''%%<ESC>%%''**
-  * command mode (followed by ''%%<RETURN>%%''):
-    * **save** current file: **''%%w [filename]%%''**
-    * **quit** the editor
-      * after saving: **''%%q%%''**
-      * without confirmation: **''%%q!%%''**
-    * **help**: **''%%h [topic]%%''**, e.g. **''%%h tutorial%%''**
-    * **search and replace**: **''%%%s/old/new/gc%%''**
-  * //default mode//:
-    * enter **input mode**: **''%%i%%''**
-    * enter **command mode**: **''%%:%%''** //(colon)//
-    * **mark**
-      * **character**-wise: **''%%v%%''**
-      * **line**-wise: **''%%<SHIFT>-v%%''**
-    * **delete**
-      * **character**-wise: **''%%x%%''**
-      * **line**-wise: **''%%dd%%''**
-      * **marked content**: **''%%d%%''**
-    * **search**: **''%%/abc%%''**
-[[http://www.ks.uiuc.edu/Training/Tutorials/Reference/virefcard.pdf|VI Reference]]
 ===== .bashrc =====