Separate prerequisites

index.md

@@ -7,22 +7,28 @@ nav_order: 1
 # CSC Computing Environment
 {: .fs-9 }
 
-Welcome! This website contains materials for the *CSC Computing Environment* -course.
+Welcome! This website contains materials for the *CSC Computing Environment*
+-course.
 {: .fs-6 .fw-300 }
 
+[Part 1 -- Get started with the basics!](part-1){: .btn .btn-primary .fs-5 .mb-4 .mb-md-0 .mr-2 }
+[Part 2 -- Dig deeper into HPC workflows!](part-2){: .btn .btn-primary .fs-5 .mb-4 .mb-md-0 .mr-2 }
+
 ## Guidelines
 
-1. The course is divided into two parts and the material is organized by topics of increasing complexity -- Feel free to jump to Part 2 if you know the basics already!
-2. In each topic, first read the slides / watch the video.
-3. Complete the tutorial(s) to make sure you’ve got the steps right.
-4. Try out the exercises to verify your new skills.
-5. If you get stuck, consult [Docs CSC](https://docs.csc.fi) linked in the slides and the tutorials.
-6. If the documentation does not provide a sufficient answer, please contact support by emailing <mailto:[email protected]> or by filling in the contact form at <https://research.csc.fi/support>.
-   * You may also [join our weekly user support coffees](https://ssl.eventilla.com/usersupportcoffee/EN) if you'd like to discuss your issue in person with our specialists!
-7. Press and hold ctrl/cmd and click to open links in a new window or tab.
-8. Left-click the slides to enable navigation with the arrow keys (or use the arrow icons in the bottom-right corner on each slide).
-9. Click the home icon in the bottom-right corner on any slide to return to this page.
-10.  [A video with study tips](https://video.csc.fi/media/t/0_d7trmsru).
+1.  The course is divided into two parts and the material is organized by topics of increasing complexity -- Feel free to jump to Part 2 if you know the basics already!
+2.  If you're completely new to CSC and working on a command-line, start by going through the Prerequisites.
+3.  In each topic, first read the slides / watch the video.
+4.  Complete the tutorial(s) to make sure you’ve got the steps right.
+5.  Try out the exercises to verify your new skills.
+6.  If you get stuck, consult [Docs CSC](https://docs.csc.fi) linked in the slides and the tutorials.
+7.  If the documentation does not provide a sufficient answer, please contact support by emailing <mailto:[email protected]> or by filling in the contact form at <https://research.csc.fi/support>.
+    * You may also [join our weekly user support coffees](https://ssl.eventilla.com/usersupportcoffee/EN) to discuss your issue in person with our specialists!
+8.  Navigate the slides by using the arrow keys or click the arrow icons in the bottom-right corner of each slide.
+9.  Press and hold ctrl/cmd and click to open links in a new window or tab.
+10. Click the home icon in the bottom-right corner of any slide to return to this page.
+11. [A video with study tips](https://video.csc.fi/media/t/0_d7trmsru).
 
-[Part 1 -- Get started with the basics!](part-1){: .btn .btn-primary .fs-5 .mb-4 .mb-md-0 .mr-2 }
-[Part 2 -- Dig deeper into HPC workflows!](part-2){: .btn .btn-primary .fs-5 .mb-4 .mb-md-0 .mr-2 }
+{: .highlight}
+Don't have a CSC account yet? Never used a Linux command-line interface?
+[Get acquainted with the prerequisites!](prereq){: .btn .btn-outline .mt-2 }

part-1/index.md

@@ -1,13 +1,13 @@
 ---
 layout: default
 title: Part 1
-nav_order: 2
+nav_order: 3
 has_children: true
 ---
 
 # Part 1 -- Basics
 
-Start here to learn the basics of working efficiently in CSC's computing environment! This part
-walks you through the prerequisites and introduces essential concepts such as disk areas, the
+Start here to learn the basics of working efficiently in CSC's computing
+environment! This part introduces essential concepts such as disk areas, the
 module system, batch jobs and the object storage service Allas.
 {: .fs-6 .fw-300 }

part-2/index.md

@@ -1,7 +1,7 @@
 ---
 layout: default
 title: Part 2
-nav_order: 3
+nav_order: 4
 has_children: true
 ---
 

part-1/prerequisites/basic-file-editing.md → prereq/cli/basic-file-editing.md

@@ -1,9 +1,9 @@
 ---
 layout: default
 title: Basic file editing
-parent: 1. Prerequisites
-grand_parent: Part 1
-nav_order: 4
+parent: 2. Command-line basics
+grand_parent: Prerequisites
+nav_order: 2
 permalink: /hands-on/linux_prerequisites/basic-file-editing.html
 ---
 

prereq/cli/basic-linux-commands.md

@@ -0,0 +1,184 @@
+---
+layout: default
+title: Basic Linux commands
+parent: 2. Command-line basics
+grand_parent: Prerequisites
+nav_order: 1
+permalink: /hands-on/linux_prerequisites/basic-linux-commands.html
+---
+
+# Basic Linux commands
+
+> ‼️ To begin make sure you have a
+> [user account at CSC](https://docs.csc.fi/accounts/how-to-create-new-user-account/)
+> that is a member of a project which
+> [has access to the Puhti service](https://docs.csc.fi/accounts/how-to-add-service-access-for-project/).
+
+> ☝🏻 You should also have already
+> [logged in to Puhti with SSH](https://csc-training.github.io/csc-env-eff/hands-on/connecting/ssh-puhti.html)
+> or via the Puhti web interface (and opened a login node shell).
+
+## Briefly about Linux commands
+
+CSC supercomputers use Linux operating systems. The traditional, and typically
+most efficient, way of interacting with a Linux operating system is through a
+text-based command-line interface (CLI), also called a *shell*. The user inputs
+lines of text (commands), which are interpreted by the shell as directives for
+the computer to execute a specific task.
+
+The general syntax of Linux commands is:
+
+```bash
+command parameter1 parameter2 ... parameterN
+```
+
+The parameters correspond to options or input arguments provided by the user
+that alter the behavior of the command. They may be optional or mandatory.
+Options are usually denoted by a single hyphen and a single character (e.g.
+`command -o`). Some options may also have a longer, more descriptive
+alternative prefixed by two hyphens (e.g. `command --option`).
+
+Some commands allow single-character options to be combined. For example,
+`command -o -p` could be written more succinctly as `command -op`. Otherwise,
+any letter following an option would be interpreted as an argument for it.
+
+Most Linux commands have their own manual page. If you at any point need help
+with using a certain command, you can study its reference manual on the
+command-line using `man`:
+
+```bash
+man command
+```
+
+## Navigating folders
+
+1. Now that you have logged in to Puhti, check which folder (a.k.a. directory)
+   you are in by typing `pwd` (**p**rint **w**orking **d**irectory) and
+   hitting `Enter`:
+
+   ```bash
+   pwd
+   ```
+
+2. Probably you got `/users/<username>` as the result (with `<username>`
+   replaced by your actual CSC username). This is your *home* directory.
+   Different levels in the hierarchical directory tree are distinguished by the
+   forward-slash character `/`. The first `/` denotes the *root directory* --
+   all other files and directories are located in subdirectories of this
+   directory so that each file has a unique combination of a name and a
+   directory path.
+
+3. Check if there are any files or subdirectories in your home directory by
+   typing the `ls` command (**l**i**s**t):
+
+   ```bash
+   ls
+   ```
+
+4. Create a new directory using the `mkdir` command (**m**a**k**e
+   **dir**ectory) and see if it appears:
+
+   ```bash
+   mkdir my-test-folder
+   ls
+   ```
+
+5. Go to that folder using the `cd` command (**c**hange **d**irectory).
+
+   ```bash
+   cd my-test-folder
+   ```
+
+   💡 Note: if you just type `cd` and the first few letters of the folder name,
+   then hit `Tab` key, the terminal completes the name. Handy!
+
+6. Various shorthand arguments are available for navigating directories. Return
+   to the *parent directory* (i.e. move one level up in the hierarchy) by using
+   the shorthand `../`:
+
+   ```bash
+   cd ../
+   ```
+
+   💡 To move multiple directories up, you would just repeat the pattern, e.g.
+   `cd ../../` to move two levels up. Note that a single dot `./` is used to
+   represent the current directory.
+
+7. Another useful shorthand is `~/` which denotes your home directory. Move
+   again into your new directory `my-test-folder` with:
+
+   ```bash
+   cd ~/my-test-folder
+   ```
+
+   💡 The previous command would work from any directory as it is essentially a
+   shorthand for giving the full path, `/users/<username>/my-test-folder`.
+
+## Exploring files
+
+1. Download a file into the `my-test-folder` directory. The command `wget` is a
+   convenient tool for downloading from a URL:
+
+   ```bash
+   wget https://a3s.fi/CSC_training/my-first-file.txt
+   ```
+
+2. Check what kind of file you got and what size it is using the `ls` command
+   with some extra options:
+
+   ```bash
+   ls -lth
+   ```
+
+   - `-l` is for long listing format
+   - `-t` is for sorting by time (most recently edited file first)
+   - `-h` is for convenient human-readable size units (also `--human-readable`)
+
+3. Use the `less` command to check out what the file looks like:
+
+   ```bash
+   less my-first-file.txt
+   ```
+
+4. To exit the `less` preview of the file, hit `q`.
+
+   💡 Tip: Instead of `less` you can use `cat` which prints the content of the
+   file(s) directly on the command-line. For long texts `less` is recommended.
+
+5. Make a copy of this file:
+
+   ```bash
+   cp my-first-file.txt my-second-file.txt
+   ls -lth
+   less my-second-file.txt
+   ```
+
+6. Remove the file we originally downloaded (leave your own copy).
+
+   ```bash
+   rm my-first-file.txt
+   ls
+   ```
+
+   💡 Tip: If you don't want to have duplicate files you can use `mv` to
+   **m**o**v**e and, optionally, rename files. The syntax is similar:
+
+   ```bash
+   mv /path/to/source/oldname /path/to/destination/newname
+   ```
+
+## More information
+
+* Learn
+  [how to edit that file](https://csc-training.github.io/csc-env-eff/hands-on/linux_prerequisites/basic-file-editing.html)
+  in the next tutorial!
+* [Linux guide in Docs CSC](https://docs.csc.fi/support/tutorials/env-guide/)
+
+💡 For more information of a given command-line `command`: type `man command`
+or `command --help` where `command` is replaced with the one that you need help
+with.
+
+💡 Tip: If you remember *a part of a command* that you have used recently you
+can search for it with the command `history | grep string`. This will show all
+your used commands that have included the string `string` (replace this with
+the pattern you are searching for).

prereq/cli/index.md

@@ -0,0 +1,15 @@
+---
+layout: default
+title: 2. Command-line basics
+parent: Prerequisites
+nav_order: 2
+has_children: true
+has_toc: false
+---
+
+# 2. Command-line basics
+
+## 2.1 Tutorials and exercises
+
+1. [Tutorial - Basic Linux commands]({{ site.baseurl }}{% link prereq/cli/basic-linux-commands.md %})
+2. [Tutorial - Basic file editing]({{ site.baseurl }}{% link prereq/cli/basic-file-editing.md %})