add TODO

materials/csc.md

@@ -12,8 +12,10 @@
 
 Geoportti Research Infrastructure (RI) is a shared service for researchers, teachers and students using geospatial data and geocomputing tools. Geoportti RI helps the researchers in Finland to use, to refine, to preserve and to share their geospatial resources.
 
+TODO: text fix, logo
 
 ## [Location Innovation Hub](https://locationinnovationhub.eu)
 
 The Location Innovation Hub (LIH) is a centre of excellence in location information coordinated by the Finnish Geospatial Research Institute. Our services are produced in conjunction with a partner network. We help companies to grow their business with location information. We also serve the public sector.
 
+TODO: text fix, logo

materials/exercise_basics.md

@@ -1,7 +1,8 @@
 # Exercise - basics
 
-## Interactive
+TODO: update to fit here; current texts from env eff course
 
+## Interactive
 
 # Batch job tutorial - Interactive jobs
 

materials/fair_share.md

@@ -1,5 +1,6 @@
 # Fair share of use
 
+TODO: fix texts and reorder
 TODO: restaurant analogy?
 
 

materials/htc.md

@@ -1,5 +1,7 @@
 # High Throughput Computing (HTC) and parallelization
 
+TODO: fix texts and reorder
+
 ## Running things at same time
 
 * within batch script 

materials/jobs.md

@@ -2,6 +2,8 @@
 
 # Jobs 
 
+TODO: fix texts and reorder
+
 ![](./images/puhti_overview.png)
 
 ## Jobs and queueing 
@@ -41,17 +43,14 @@ srun hostname                    # Print compute node name that has been allocat
 * `scancel <jobid>`
 
 
-# What if your job fails? Troubleshooting checklist 1/2
+# What if your job fails? Troubleshooting checklist
 
 1. Did the job run out of time?
 2. Did the job run out of memory?
 3. Did the job actually use the resources you specified?
    - Problems in the batch job script can cause parameters to be ignored and default values are used instead
 4. Did it fail immediately or did it run for some time?
    - Jobs failing immediately are often due to something simple like typos, missing inputs, bad parameters, _etc_.
-
-# What if your job fails? Troubleshooting checklist 2/2
-
 5. Check the error file captured by the batch job script
 6. Check any other error files and logs the your program may have produced
 7. Error messaged can sometimes be long, cryptic and a bit intimidating, but ...

materials/own_project.md

@@ -1,5 +1,7 @@
 # Own project hints
 
+TODO: fix texts and reorder
+
 * keep scripts under version control (also simplifies collaboration and synchronising different computers, e.g. git(hub))
 * on Puhti: 
     * scripts in `/projappl/project_200xxxx/your_groupname/`

materials/support.md

@@ -1,5 +1,6 @@
 # CSC support
 
+TODO: clean up
 
 [`docs.csc.fi`](https://docs.csc.fi)
 

materials/teachers_guide.md

@@ -1,3 +1,5 @@
 # Teachers guide
 
+TODO: write
+
 Work in progress.

materials/terminal.md

@@ -1,5 +1,138 @@
 # Terminal
 
+TODO: Shorten and share with prerequisites
+TODO: Check advanced
+
+## Why use?
+
+TODO: fill
+
+## 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).
+
+## Navigating folders
+
+1. Now that you have logged in to Puhti, check which folder you are in by typing `pwd` and hitting `Enter`:
+
+```bash
+pwd
+```
+
+{:start="2"}
+2. Check if there are any files:
+
+```bash
+ls
+```
+
+{:start="3"}
+3. Make a directory and see if it appears:
+
+```bash
+mkdir YourNameTestFolder    # replace YourName
+ls
+```
+
+{:start="4"}
+4. Go to that folder.
+
+```bash
+cd YourNameTestFolder       # replace YourName
+```
+
+💡 Note: if you just type `cd` and the first letter of the folder name, then hit `tab` key, the terminal completes the name. Handy!
+
+## Exploring files
+
+1. Download a file into this new folder. Use the command `wget` for downloading from a URL:
+
+```bash
+wget https://github.com/csc-training/csc-env-eff/raw/master/_hands-on/linux_prerequisites/my-first-file.txt
+```
+
+{:start="2"}
+2. Check what kind of file you got and what size it is using the `ls` command with some extra options:
+
+```bash
+ls -lth         # options are l for long format, t for sorting by time and h for convenient size units. Anything that starts with a hashtag is a comment and is not executed
+```
+
+{:start="3"}
+3. Use the `less` command to check out what the file looks like:
+
+```bash
+less my-first-file.txt
+```
+
+{:start="4"}
+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) straight into the command line. For long texts `less` is recommended.
+
+{:start="5"}
+5. Make a copy of this file:
+
+```bash
+cp my-first-file.txt YourName-first-file.txt    # replace YourName
+ls -lth
+less YourName-first-file.txt                    # replace YourName
+```
+
+{:start="6"}
+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 'move/rename' the file. Syntax is the same: `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!
+
+💡 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).
+
+## Basic file editing
+
+> ‼️ 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).
+
+> ☝🏻 Note: For graphical output to work you need to log in with `ssh -X [email protected]`. On Windows/macOS you also need to have an X server installed and running. [See details in the previous tutorial](https://csc-training.github.io/csc-env-eff/hands-on/connecting/ssh-puhti.html#remote-graphics). Another option is to use the Puhti web interface.
+
+In the [previous tutorial](https://csc-training.github.io/csc-env-eff/hands-on/linux_prerequisites/basic-linux-commands.html) we downloaded a file called `my-first-file.txt`, made a copy of it named `YourName-first-file.txt`, and now we practice how to edit it!
+
+💬 These exercises are done with the `nano` editor, but you can use your favorite editor too.
+
+💡 Here's a [nano cheat sheet](https://www.nano-editor.org/dist/latest/cheatsheet.html)
+
+## Processing text files
+
+1. Open the file with `nano`:
+
+```bash
+nano YourName-first-file.txt      # replace YourName
+```
+
+{:start="2"}
+2. Edit the file. Type something there!
+3. Exit `nano` with `Ctrl+X`, type `Y` to confirm saving and press enter to accept the filename.
+4. Check that the modifications are actually there:
+
+```bash
+less YourName-first-file.txt      # replace YourName
+```
+
+{:start="5"}
+5. Exit the preview with `q`.
+
 ## Login with SSH
 
 - SSH is a terminal program that gives you command-line access on the CSC supercomputer
@@ -25,4 +158,3 @@
 - Follow these [detailed instructions to set them up](https://docs.csc.fi/support/tutorials/remote-dev/)
 - Note that [Visual Studio Code](https://docs.csc.fi/computing/webinterface/vscode/) and [Jupyter Notebooks](https://docs.csc.fi/computing/webinterface/jupyter/) are also available through the Puhti web interface
 
-## File editing

materials/terminology.md

@@ -1,5 +1,7 @@
 # Terminology
 
+TODO: clean up and texts
+
 - You can roughly think that one **node** is a single computer
 - A node on a supercomputer contains:
   - One or more central processing units (**CPUs**) with many **cores**