Indentation is 4, fix #73

docs/cluster_guides/bianca.md

@@ -11,13 +11,13 @@ suitable for working with sensitive data.
 - [Submitting jobs, using Slurm](slurm.md)
 - [Starting an interactive node](start_interactive_node_on_bianca.md)
 - [File transfer](transfer_bianca.md)
-  - [File transfer using a graphical program](bianca_file_transfer_using_gui.md)
+    - [File transfer using a graphical program](bianca_file_transfer_using_gui.md)
 - [The module system](bianca_modules.md)
 - [IDEs](ides_on_bianca.md)
-  - [Jupyter](../software/jupyter.md)
-  - [RStudio](rstudio_on_bianca.md)
-  - :no_entry: [VSCode](vscode_on_bianca.md)
-  - [VSCodium](vscodium_on_bianca.md)
+    - [Jupyter](../software/jupyter.md)
+    - [RStudio](rstudio_on_bianca.md)
+    - :no_entry: [VSCode](vscode_on_bianca.md)
+    - [VSCodium](vscodium_on_bianca.md)
 - [Workshops and courses](../workshops_courses/workshops_courses.md)
 - NAISS-sens
 - Best practices

docs/cluster_guides/dardel_migration.md

@@ -37,7 +37,6 @@ The really short description is:
 See the rest of this guide for more information about these steps.
 
 
-
 ## Long version
 
 ???- question "Prefer a video?"
@@ -411,5 +410,3 @@ rm ~/id_ed25519_pdc*
 
     You can do nothing, except wait until Dardel is up again.
 
-
-

docs/cluster_guides/darsync.md

@@ -162,16 +162,16 @@ Once you have mitigated any warnings you got you are ready to generate the Slurm
 To generate a transfer script you will need to supply Darsync with some information. Make sure to have this readily available:
 
 - **ID of the UPPMAX project** that will run the transfer job, e.g. `naiss2099-23-99`
-  - If you don't remember if, find the name of the project you want to transfer by looking in [the list of active project in SUPR](https://supr.naiss.se/project/).
+    - If you don't remember if, find the name of the project you want to transfer by looking in [the list of active project in SUPR](https://supr.naiss.se/project/).
 - **Path to the folder you want to transfer**, .e.g. `/proj/naiss2099-23-999`
-  - Either transfer your whole project, or put the files and folder your want to transfer into a new folder in your project folder and transfer that folder.
-  - The project's folder on UPPMAX will be located in the `/proj/` folder, most likely a folder with the same name as the project's ID, `/proj/<project id>`, e.g. `/proj/naiss2024-23-999`. If your project has picked a custom *directory name* when it was created it will have that name instead of the project ID, e.g. `/proj/directory_name`. Check which directory name your project has by looking at the project's page in [SUPR](https://supr.naiss.se/project/) and look at the field called `Directory name:`
+    - Either transfer your whole project, or put the files and folder your want to transfer into a new folder in your project folder and transfer that folder.
+    - The project's folder on UPPMAX will be located in the `/proj/` folder, most likely a folder with the same name as the project's ID, `/proj/<project id>`, e.g. `/proj/naiss2024-23-999`. If your project has picked a custom *directory name* when it was created it will have that name instead of the project ID, e.g. `/proj/directory_name`. Check which directory name your project has by looking at the project's page in [SUPR](https://supr.naiss.se/project/) and look at the field called `Directory name:`
 - **Your Dardel username**.
-  - You can see your Dardel username in [SUPR](https://supr.naiss.se/account/)
+    - You can see your Dardel username in [SUPR](https://supr.naiss.se/account/)
 - **The path on Dardel** where you want to put your data, e.g. `/cfs/klemming/projects/snic/naiss2099-23-999`
-  - Check which project ID you have for your project on Dardel in [the list of active project in SUPR](https://supr.naiss.se/project/).
+    - Check which project ID you have for your project on Dardel in [the list of active project in SUPR](https://supr.naiss.se/project/).
 - The **path to the SSH key** you have prepared to be used to login from Rackham to Dardel, e.g. `~/.ssh/id_rsa`
-  - Check
+    - Check
 - The path to where you want to **save the generated transfer script**.
 
 To initiate the gen mode you run Darsync with the `gen` argument. If you run it without any other arguments it will ask you interactive questions to get the information it needs.

docs/cluster_guides/debuggers.md

@@ -62,4 +62,3 @@ Then you can use the gdb commands, like run, break, step, help, ...
 
 Exit with `Ctrl+D`.
 
-

docs/cluster_guides/install.md

@@ -9,7 +9,7 @@
 - check with: ``$ ml avail gcc`` and ``$ ml avail intel``
 - [Guide for compiling **serial** programs](compiling_serial.md)
 - [Guide for compiling **parallel** programs](compiling_parallel.md)
-  - [Available **combinations** of compilers and parallel libraries](compiling_parallel.md#overview-of-available-compilers-from-gcc-and-intel-and-compatible-mpi-libraries)
+    - [Available **combinations** of compilers and parallel libraries](compiling_parallel.md#overview-of-available-compilers-from-gcc-and-intel-and-compatible-mpi-libraries)
 
 
 ## Packages and libraries to scripting programs
@@ -54,8 +54,8 @@
 
 - On UPPMAX the module ``R_packages`` is an omnibus package library containing almost all packages in the CRAN and BioConductor repositories.
 - As of 2023-05-31, there were a total of 23100 R packages installed in ``R_packages/4.2.1``.
-  - A total of 23109 packages were available in CRAN and BioConductor, and 23000 of these were installed in ``R_packages/4.2.1``
-  - The additional 100 R packages available in this module were installed from the CRAN/BioConductor archives, or were hosted on github, gitlab or elsewhere.
+    - A total of 23109 packages were available in CRAN and BioConductor, and 23000 of these were installed in ``R_packages/4.2.1``
+    - The additional 100 R packages available in this module were installed from the CRAN/BioConductor archives, or were hosted on github, gitlab or elsewhere.
 
 - [Installing R packages](../software/r.md)
 
@@ -112,7 +112,7 @@ Docker will unfortunately not work on the clusters, since it requires root permi
 - You may have your own code that you want to run on UPPMAX.
 - [Guide for compiling **serial** programs](compiling_serial.md)
 - [Guide for compiling **parallel** programs](compiling_parallel.md)
-  - [Available **combinations** of compilers and parallel libraries](compiling_parallel.md#overview-of-available-compilers-from-gcc-and-intel-and-compatible-mpi-libraries)
+    - [Available **combinations** of compilers and parallel libraries](compiling_parallel.md#overview-of-available-compilers-from-gcc-and-intel-and-compatible-mpi-libraries)
 - [User guide for debuggers](../cluster_guides/debuggers.md)
 - [User guide for profilers](../cluster_guides/profilers.md)
 

docs/cluster_guides/rackham.md

@@ -17,17 +17,17 @@ Rackham is one of the [UPPMAX clusters](uppmax_cluster.md).
 - [Log in](../getting_started/login_rackham.md)
 - [Starting an interactive node](start_interactive_node_on_rackham.md)
 - [File transfer](transfer_rackham.md)
-  - [using a graphical program](rackham_file_transfer_using_gui.md)
-  - [using SCP](rackham_file_transfer_using_scp.md)
-  - [using SFTP](rackham_file_transfer_using_sftp.md)
+    - [using a graphical program](rackham_file_transfer_using_gui.md)
+    - [using SCP](rackham_file_transfer_using_scp.md)
+    - [using SFTP](rackham_file_transfer_using_sftp.md)
 - [The module system](rackham_modules.md)
 - [IDEs](ides_on_rackham.md)
-  - [Jupyter](../software/jupyter.md)
-  - [RStudio](rstudio_on_rackham.md)
-  - [VSCode](vscode_on_rackham.md)
-  - :no_entry: [VSCodium](vscodium_on_rackham.md)
+    - [Jupyter](../software/jupyter.md)
+    - [RStudio](rstudio_on_rackham.md)
+    - [VSCode](vscode_on_rackham.md)
+    - :no_entry: [VSCodium](vscodium_on_rackham.md)
 - Isolated environments
-  - [venv](venv_on_rackham.md)
+    - [venv](venv_on_rackham.md)
 - Best practices
 - Rackham installation guides
 - Rackham workshops

docs/cluster_guides/rackham_file_transfer_using_gui.md

@@ -50,9 +50,9 @@ To transfer files to/from Rackham using FileZilla, do:
 
 - Create a name for the site, e.g. `rackham`.
 - For that site, use all standards, except:
-  - Set protocol to 'SFTP - SSH File Transfer Protocol'
-  - Set host to `rackham.uppmax.uu.se`
-  - Set user to `[username]`, e.g. `richel`
+    - Set protocol to 'SFTP - SSH File Transfer Protocol'
+    - Set host to `rackham.uppmax.uu.se`
+    - Set user to `[username]`, e.g. `richel`
 
 ???- tip "How does that look like?"
 
@@ -103,9 +103,9 @@ To transfer files to/from Rackham using WinSCP, do:
 - Start WinSCP
 - Create a new site
 - For that site, use all standards, except:
-  - Set file protocol to 'SFTP'
-  - Set host name to `rackham.uppmax.uu.se`
-  - Set user name to `[username]`, e.g. `richel`
+    - Set file protocol to 'SFTP'
+    - Set host name to `rackham.uppmax.uu.se`
+    - Set user name to `[username]`, e.g. `richel`
 
 ### File transfer overview
 

docs/cluster_guides/running_jobs/runtime_tips.md

@@ -120,7 +120,6 @@
     - [More about interactive](interactive_more.md)
 
 
-
 ## Related to Batch jobs
 
 
@@ -202,7 +201,6 @@
         - And then there's also the PSS figure which tries to calculate a proportional memory usage per user for all shared memory buffers and caches (i.e. the figure will fall between USS and RSS).
 
 
-
 ???- question "My job has very low priority! What can be wrong?"
 
 

docs/cluster_guides/slurm.md

@@ -153,8 +153,6 @@ Here, two cores are used.
     ```
 
 
-
-
 This is especially important if you might adjust core usage
 of the job to be something less than a full node.
 
@@ -172,7 +170,6 @@ to ensure that only 8 cores (less than a single node) are allocated for such a j
 ### The `devcore` partition
 
 
-
 ### Specifying job parameters
 
 Whether you use the UPPMAX clusters interactively or in batch mode, you always

docs/cluster_guides/transfer_bianca.md

@@ -72,7 +72,7 @@ See [the UPPMAX documentation on the Transit server](transit.md).
 * Note that your home directory is mounted _read-only_, any changes you do to your "local" home directory (on transit) will be lost upon logging out.
 
 * You can use commands like ``rsync``, ``scp`` to fetch data and transfer it to your bianca wharf.
-  * You can use cp to copy from Rackham to the wharf
+    * You can use cp to copy from Rackham to the wharf
 * Remember that you cannot make lasting changes to anything except for mounted wharf directories. Therefore you have to use rsync and scp to transfer from the ``wharf`` to Rackham.
 * The mounted directory will be kept for later sessions.
 

docs/cluster_guides/transit_file_transfer_using_gui.md

@@ -136,9 +136,9 @@ To transfer files to/from Transit using WinSCP, do:
 - Start WinSCP
 - Create a new site
 - For that site, use all standards, except:
-  - Set file protocol to 'SFTP'
-  - Set host name to `transit.uppmax.uu.se`
-  - Set user name to `[username]`, e.g. `richel`
+    - Set file protocol to 'SFTP'
+    - Set host name to `transit.uppmax.uu.se`
+    - Set user name to `[username]`, e.g. `richel`
 
 ### File transfer overview
 

docs/cluster_guides/uppmax_systems.md

@@ -206,7 +206,6 @@ Each node contains several CPU/GPU cores, RAM and local storage space.
 A user logs in to a login node via the Internet.
 
 
-
 ## Summary
 
 !!! abstract "keypoints"

docs/getting_started/linux.md

@@ -30,7 +30,7 @@
 ![Content](./img/images.jfif)
 
 - Actually, for it to be an OS, it is supplied with GNU software and other additions giving us the name **GNU/Linux**.
-  - [Linux naming controversy](https://en.wikipedia.org/wiki/GNU/Linux_naming_controversy)
+    - [Linux naming controversy](https://en.wikipedia.org/wiki/GNU/Linux_naming_controversy)
 
 ![Content](./img/gnu.png)
 
@@ -58,7 +58,7 @@ is how to use the command-line on the UPPMAX Bianca cluster.
 - The command-line interface: the bash prompt $
 - bash can be seen as a program that finds and runs other programs
 - bash is scripting language that is referred to as a shell
-  - (because it sits around the kernel making it easy to interact with)
+    - (because it sits around the kernel making it easy to interact with)
 
 ![Content](./img/unix_architecture.jpg)
 
@@ -71,16 +71,16 @@ is how to use the command-line on the UPPMAX Bianca cluster.
 
 - [info] is configurable, and usually tells you who you are, on what system, and where in the file system.
 
-  - Example:
+    - Example:
 
     ```bash
     [bjornc@rackham3 linux_tutorial]$
     ```
 
-  - For changing info (only for advanced users!)  Does not matter for this course!:
-    - <https://www.cyberciti.biz/tips/howto-linux-unix-bash-shell-setup-prompt.html>
-  - The program to run is the first word
-  - All words are separated by spaces
+    - For changing info (only for advanced users!)  Does not matter for this course!:
+        - <https://www.cyberciti.biz/tips/howto-linux-unix-bash-shell-setup-prompt.html>
+    - The program to run is the first word
+    - All words are separated by spaces
 
 ![folders](./img/folders.png)
 
@@ -184,7 +184,6 @@ which are described at the UPPMAX 'Text editors' page [here](../software/text_ed
           - Solution: ``alias rm='rm -i' ``
 
 
-
 ## Links
 
 - A free online book about Linux: ['The Linux Command Line'](https://linuxcommand.org/tlcl.php).