Update and add skill to the OS branch

skill-tree.mm

@@ -192,7 +192,7 @@
 <node TEXT="4: Algorithms (BDA1.4)" ID="ID_724281420" CREATED="1549369642621" MODIFIED="1725378991818" LINK="bda/1/4/b.txt"/>
 <node TEXT="5: Ethical/Privacy (BDA1.5)" ID="ID_1871275461" CREATED="1549369810781" MODIFIED="1725378997401" LINK="bda/1/5/b.txt"/>
 </node>
-<node TEXT="2: Big Data Tools in HPC (BDA2)" POSITION="top_or_left" ID="ID_252779504" CREATED="1552388544674" MODIFIED="1744724991409" LINK="bda/2/b.txt">
+<node TEXT="2: Big Data Tools in HPC (BDA2)" FOLDED="true" POSITION="top_or_left" ID="ID_252779504" CREATED="1552388544674" MODIFIED="1744724991409" LINK="bda/2/b.txt">
 <icon BUILTIN="emoji-1F4C1"/>
 <node TEXT="1: Ophidia (BDA2.1)" ID="ID_10676718" CREATED="1592498720169" MODIFIED="1725379011880" LINK="bda/2/1/b.txt"/>
 <node TEXT="2: Jupyter Notebooks (BDA2.2)" LOCALIZED_STYLE_REF="default" ID="ID_1273880444" CREATED="1552388597638" MODIFIED="1725379017247" LINK="bda/2/2/b.txt">
@@ -312,6 +312,9 @@
 <node TEXT="2: Spack (USE1.5.2)" ID="ID_564286239" CREATED="1705399834204" MODIFIED="1725378323760" LINK="use/1/5/2/b.txt"/>
 <node TEXT="3: Conda environments (USE1.5.3)" ID="ID_1383141956" CREATED="1725614268627" MODIFIED="1725614418118" LINK="use/1/5/3/b.txt"/>
 </node>
+<node TEXT="6: CLI File editors (USE1.6)" ID="ID_249777418" CREATED="1740738976370" MODIFIED="1740739004709" LINK="use/1/6/b.txt"/>
+<node TEXT="7: Terminal Multiplexers (USE1.7)" ID="ID_1253558070" CREATED="1744634779685" MODIFIED="1744634807187" LINK="use/1/7/b.txt"/>
+<node TEXT="8: Manage background processes and signals (USE1.8)" ID="ID_1384411765" CREATED="1757602699508" MODIFIED="1757602734453" LINK="use/1/8/b.txt"/>
 </node>
 <node TEXT="2: Running of Parallel Programs (USE2)" FOLDED="true" POSITION="bottom_or_right" ID="ID_739006785" CREATED="1504024427911" MODIFIED="1744724013293" LINK="use/2/b.txt">
 <icon BUILTIN="emoji-1F4C1"/>

use/1/1/b.txt

@@ -14,11 +14,11 @@ Part of this skill is the general principles of the interaction with a shell, to
 
 ## Learning Outcomes
 
-* Utilize the bash shell to execute individual programs with arguments.
-* Describe the meaning of the exit code of a program.
-* Run multiple programs after another depending on the exit code ;, &&, ||.
+* Use the bash shell to execute individual programs with arguments.
 * List the set of basic programs and their tasks:
     * pwd
+    * ls
+    * cd
     * whoami
     * sleep
     * kill
@@ -27,23 +27,14 @@ Part of this skill is the general principles of the interaction with a shell, to
     * man
     * vi, vim, emacs, nano
     * exit
-* Utilize the available help of a program (--help argument and the man pages).
-* Interrupt or abort a program execution:
-    * CTRL-C
-    * CTRL-Z
-    * using kill -9
+    * ...
+* Demonstrate interrupting or aborting of a program execution using CTRL-C.
+* Use the available help of a program (--help argument and the man pages).
 * Use the shell history to search and execute previously executed commands.
-* Set and print shell variables.
-* Print all currently set variables
+* Demonstrate setting and printing shell variables.
+* Show all currently set variables and set as well as unset one manually.
 * Identify potential special characters that must be handled with care.
-    * List strings that could refer to files/directories
+* List strings that could refer to files/directories
 * Utilize escaping to ensure correct handling of arguments.
-* Understand wildcard characters to select a group of files/directories:
-    * *
-    * ?
-    * [-,]
-* How to close popular command line text editors with/or without saving changes:
-    * nano
-    * vi
-    * emacs
+* Understand wildcard characters to select a group of files/directories: "*", "?", "[-,]"
 

use/1/2/b.txt

@@ -15,7 +15,7 @@ This skill covers the bash shell.
 
 * Create a basic shell script that executes a sequence of programs.
 * Design a script using the bash construct "if" that handles conditional execution based on:
-    * Performing a test for the existing of a file/directory,
+    * Performing a test for the existing of a file/directory/variable,
     * Testing for the presence of certain text in a file,
 * Design a script that performs a task repeatedly using the bash "for" or "while" loop.
 * Utilize debugging options for troubleshooting of shell programs:

use/1/3/b.txt

@@ -10,6 +10,8 @@ Typically, several elementary programs are pre-installed and allow access and ma
 
 ## Requirements
 
+* [[skill-tree:use:1:1:b]]
+
 ## Learning Outcomes
 
 * Describe the organization of a hierarchical file system.

use/1/4/b.txt

@@ -5,33 +5,29 @@ Learning the ways of general interaction with the remote system and the tools in
 
 Users must connect to an HPC system typically using the Secure Shell (SSH), which then starts a shell and allows the interactive access.
 When the user disconnects, such a session is terminated.
-A server-sided session that persists after disconnection enables the user to execute long-running programs remotely and allows the continuation of a previous session seamlessly.
 Data transfer between a local user system (e.g., desktop or laptop) and a remote system requires special tools. 
 Interactive access is also allowed.
 
 The tools discussed here are generally valid for systems using Linux, Mac, Windows, and also mobile devices.
 
 ## Requirements
 
+* [[skill-tree:use:1:1:b]]
+
 ## Learning Outcomes
 
 * Describe how SSH-authentication works:
     * Password authentication.
     * Public-key authentication.
     * The role of an authentication agent and the security implications.
 * Generate an SSH public/private key under Linux.
-* Register a key for public-key authentication using ssh-copy-id.
+* Register a key for public-key authentication using ssh-copy-id or other local methods.
 * Perform a remote login from Linux using SSH.
-* Use SSH-agent or Windows equivalents.
+* Use SSH-agent or equivalents.
 * Use Agent forwarding to connect to a third HPC system from an HPC system that you logged into with ssh from your computer.
 * Know when to use and how to create a config file.
 * Utilize tools to transfer data between the local and remote system:
     * scp
     * sftp
     * rsync (-avz)
-* Describe how SSHFS allows mounting a remote directory to a local directory for interactive usage (Mac/Linux only), e.g. for copying files or to transparently use your favourite graphical text editor on the local computer for editing files on the remote cluster.
-* Utilize screen and tmux to preserve a session between logins:
-    * Creation of a session.
-    * Detaching from the current session.
-    * Resuming a previous session.
 

use/1/6/b.txt

@@ -0,0 +1,29 @@
+# USE1.6 CLI File editors
+
+Running programs using the CLI often also includes editing files without a GUI available.
+Many programs are available and are also often suggested in tutorials and by other people.
+It is of importance to being able to navigate file editing using different editors and understanding how to write files and exit the editor.
+
+Most common editors will all be included here, meaning one should be taught and the other need to be mentioned for completeness:
+    * VI/Vim
+    * Emacs
+    * Nano
+
+## Requirements
+
+* [[skill-tree:use:1:1:b]]
+* [[skill-tree:use:1:3:b]]
+
+## Learning Objectives
+
+* Define the abilities of a CLI based file editor
+* Discuss what a CLI file editor needs to be able to do and how it should behave
+* Demonstrate the usage of an editor to open a file in write mode and save the file
+* Show how to quit an editor (relevant for all editors)
+* Solve undo and redo operations to recover from changes and restore them
+* Indicate how to use the mouse pointer
+* Define how to copy and paste using the clipboard
+* Contrast differences between available editors
+    * Summarize the controversy between Emacs and Vim users
+
+

use/1/7/b.txt

@@ -0,0 +1,26 @@
+# USE1.7 Terminal multiplexer
+
+Sometimes running longer tasks or processes interactively can become error prone on a remote system.
+A loss of network breaks the SSH connection and terminates the commands a user has running on the remote system.
+
+This can be prevented by running terminal multiplexer.
+These are programs that run on a remote system and a user can attach and detach from such a session.
+All output is cached in the session and can be checked gain.
+Commands that are started run in this session and are independent of the SSH connection, breaking it will only detach from the multiplexer.
+
+Some even allow multiple users or multiple sessions of the same user to connect to them.
+
+## Requirements
+
+* [[skill-tree:use:1:1:b]]
+* [[skill-tree:use:1:4:b]]
+
+## Learning outcomes
+
+* Give examples for use cases for such a multiplexer.
+* Discuss using such a session for longer data transfers using SSH.
+* Review editing files using a terminal multiplexer
+* Utilize screen or tmux to preserve a session between logins:
+    * Creation of a session.
+    * Detaching from the current session.
+    * Resuming a previous session.

use/1/8/b.txt

@@ -0,0 +1,23 @@
+# USE1.8 Manage background processes and signals
+
+Background processes are very useful to use a single bash session and run multiple programs in it.
+They can either run in parallel in the background or are stopped and can be resumed later.
+
+Similarly, sending signals to other programs in the background can be used to change the state of the program by making it active again or move a program in to the foreground.
+In order to do this there exists a program called kill, which does not only kill by signal a kill.
+
+## Requirements
+
+* [[skill-tree:use:1:1:b]]
+
+## Learning Outcomes
+
+* Understand interrupting or aborting of a program execution using CTRL-C and CTRL-Z.
+* Describe the difference between SIGINT and SIGTSTP.
+* Demonstrate the use of CTRL-Z in combination with the commands jobs and fg.
+
+* Understand what a Process ID is and how it can be used to identify any programs.
+* Demonstrate how the command jobs can display the process id.
+* Understand the behaviour of the kill command.
+* Demonstrate the kill command and send the signals SIGKILL, SIGINT, SIGTSTP, also via the numbers instead of the names
+

use/1/b.txt

@@ -15,6 +15,13 @@ While there are many similarities to single-user Linux systems, HPC systems diff
 * Understand terminal multiplexers and use them to run longer commands without keeping a connection alive.
 * Utilize tools to transfer data between a desktop/laptop system and a remote HPC system.
 * Utilize package management tools that provide access to a wide variety of software.
+* Demonstrate the usage of an editor to open a file in write mode and save the file and define why CLI based editors are useful in an HPC environment.
+* Utilize screen or tmux to preserve a session between logins and classify usecases for these three operations:
+    * Creation of a session.
+    * Detaching from the current session.
+    * Resuming a previous session.
+* Illustrate the use of CTRL-Z and CTRL-C in combination with the commands jobs and fg to send the signals SIGINT and SIGTSTP.
+* Experiment with the kill command and send the signals SIGKILL, SIGINT, SIGTSTP, also via the numbers instead of the names to a specific process id
 
 ## Subskills
 
@@ -23,3 +30,6 @@ While there are many similarities to single-user Linux systems, HPC systems diff
 * [[skill-tree:use:1:3:b]]
 * [[skill-tree:use:1:4:b]]
 * [[skill-tree:use:1:5:b]]
+* [[skill-tree:use:1:6:b]]
+* [[skill-tree:use:1:7:b]]
+* [[skill-tree:use:1:8:b]]

use/b.txt

@@ -11,6 +11,7 @@ Various user roles are covered as part of this subtree: practitioners that aim t
 ## Learning Outcomes
 
 * Apply tools provided by the operating system to navigate and manage files and executables.
+* Explain what programs and processes are and how the CLI interacts with and manages them.
 * Use a workload manager to allocate HPC resources and run job using scripts.
 * Select the software environment to build existing OpenSource projects 
 * Develop novel parallel applications effectively.