Let rumdl fix the fixable errors it found

Oa8choo2 · Oa8choo2 · commit a33a84beff71 · 2025-11-17T12:53:47.000+01:00
$ rumdl check getting_started.md
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Issues: Found 91 issues in 1 file (69ms)
Run `rumdl fmt` to automatically fix 45 of the 91 issues

$ rumdl check --fix getting_started.md
Fixed: Fixed 45/91 issues in 1 file (116ms)

$ rumdl check getting_started.md
...
Issues: Found 61 issues in 1 file (69ms)
Run `rumdl fmt` to automatically fix 16 of the 61 issues

$ rumdl check --fix getting_started.md
Fixed: Fixed 16/61 issues in 1 file (103ms)

$ rumdl check getting_started.md
Issues: Found 45 issues in 1 file (68ms)

$ rumdl check getting_started.md | grep 'Line length' -c
45

=&gt; rumdl can not fix the line length errors automatically
diff --git a/mkdocs/docs/HPC/getting_started.md b/mkdocs/docs/HPC/getting_started.md
@@ -1,4 +1,7 @@
+# Title
+
 {% set exampleloc="mkdocs/docs/HPC/examples/Getting_Started/tensorflow_mnist" %}
+
 # Getting Started
 
 Welcome to the "Getting Started" guide. This chapter will lead you through the initial steps of logging into the {{hpcinfra}} and submitting your very first job. We'll also walk you through the process step by step using a practical example.
@@ -7,25 +10,25 @@ In addition to this chapter, you might find the [recording of the *Introduction
 
 Before proceeding, read [the introduction to HPC](introduction.md) to gain an understanding of the {{ hpcinfra }} and related terminology.
 
-### Getting Access
+## Getting Access
 
 To get access to the {{hpcinfra}}, visit [Getting an HPC Account](account.md).
 
-If you have not used Linux before, 
+If you have not used Linux before,  
 {%- if site == 'Gent' %}
 now would be a good time to follow our [Linux Tutorial](linux-tutorial/index.md).
 {%- else %}
 please learn some basics first before continuing. (see [Appendix C - Useful Linux Commands](useful_linux_commands.md))
 {%- endif %}
 
-#### A typical workflow looks like this:
+### A typical workflow looks like this
 
-1.  Connect to the login nodes 
-2.  Transfer your files to the {{hpcinfra}}
-3.  Optional: compile your code and test it 
-4.  Create a job script and submit your job
-5.  Wait for job to be executed
-6.  Study the results generated by your jobs, either on the cluster or
+1. Connect to the login nodes  
+2. Transfer your files to the {{hpcinfra}}
+3. Optional: compile your code and test it  
+4. Create a job script and submit your job
+5. Wait for job to be executed
+6. Study the results generated by your jobs, either on the cluster or
     after downloading them locally.
 
 We will walk through an illustrative workload to get you started. In this example, our objective is to train a deep learning model for recognizing hand-written digits (MNIST dataset) using [TensorFlow](https://www.tensorflow.org/);
@@ -38,10 +41,10 @@ There are two options to connect
 - Using a terminal to connect via SSH (for power users) (see [First Time connection to the {{ hpcinfra}}](connecting.md#first-time-connection-to-the-hpc-infrastructure))
 - [Using the web portal](web_portal.md)
 
-Considering your operating system is **{{OS}}**, 
+Considering your operating system is **{{OS}}**,  
 
 {%- if OS == linux %}
-it is recommended to make use of the `ssh` command in a terminal to get the most flexibility. 
+it is recommended to make use of the `ssh` command in a terminal to get the most flexibility.  
 
 Assuming you have already generated SSH keys in the previous step ([Getting Access](#getting-access)), and that they are in a default location, you should now be able to login by running the following command:
 
@@ -50,12 +53,16 @@ ssh {{userid}}@{{loginnode}}
 ```
 
 !!! Warning "User your own VSC account id"
-    
-    Replace **{{userid}}** with your VSC account id (see <https://account.vscentrum.be>)
+
+```text
+Replace **{{userid}}** with your VSC account id (see <https://account.vscentrum.be>)
+```
 
 !!! Tip
 
-    You can also still use the web portal (see [shell access on web portal](web_portal.md#shell-access))
+```text
+You can also still use the web portal (see [shell access on web portal](web_portal.md#shell-access))
+```
 
 {%- else %}
 {%- if OS == windows %} it is recommended to use the web portal.
@@ -72,16 +79,17 @@ Make sure you can get to a shell access to the {{hpcinfra}} before proceeding wi
 
 !!! Info
 
-    When having problems see the [connection issues section on the troubleshooting page](troubleshooting.md#sec:connecting-issues).
-
+```text
+When having problems see the [connection issues section on the troubleshooting page](troubleshooting.md#sec:connecting-issues).
+```
 
 ### Transfer your files
 
 Now that you can login, it is time to transfer files from your local computer to your **home directory** on the {{hpcinfra}}.
 
 Download following the example scripts to your computer:
 
-- [tensorflow_mnist.py](https://raw.githubusercontent.com/hpcugent/vsc_user_docs/main/{{exampleloc}}/tensorflow_mnist.py) 
+- [tensorflow_mnist.py](https://raw.githubusercontent.com/hpcugent/vsc_user_docs/main/{{exampleloc}}/tensorflow_mnist.py)  
 - [run.sh](https://raw.githubusercontent.com/hpcugent/vsc_user_docs/main/{{exampleloc}}/run.sh)
 
 You can also find the example scripts in our git repo: [https://github.com/hpcugent/vsc_user_docs/](https://github.com/hpcugent/vsc_user_docs/tree/main/mkdocs/docs/HPC/examples/Getting_Started/tensorflow_mnist).
@@ -95,17 +103,21 @@ Upload both files (`run.sh` and `tensorflow-mnist.py`) to your **home directory*
 
 !!! Info
 
-    As an alternative, you can use WinSCP (see [our section](connecting.md#winscp))
+```text
+As an alternative, you can use WinSCP (see [our section](connecting.md#winscp))
+```
 
 {%- else %}
 
 On your local machine you can run:
+
 ```shell
 curl -OL https://raw.githubusercontent.com/hpcugent/vsc_user_docs/main/{{exampleloc}}/tensorflow_mnist.py
 curl -OL https://raw.githubusercontent.com/hpcugent/vsc_user_docs/main/{{exampleloc}}/run.sh
 ```
 
 Using the `scp` command, the files can be copied from your local host to your *home directory* (`~`) on the remote host (HPC).
+
 ```shell
 scp tensorflow_mnist.py run.sh {{userid}}{{ loginnode }}:~
 ```
@@ -115,18 +127,22 @@ ssh  {{userid}}@{{ loginnode }}
 ```
 
 !!! Warning "User your own VSC account id"
-    
-    Replace **{{userid}}** with your VSC account id (see <https://account.vscentrum.be>)
+
+```text
+Replace **{{userid}}** with your VSC account id (see <https://account.vscentrum.be>)
+```
 
 !!! Info
 
-    For more information about transfering files or `scp`, see [tranfer files from/to hpc](connecting.md#transfer-files-tofrom-the-hpc).
+```text
+For more information about transfering files or `scp`, see [tranfer files from/to hpc](connecting.md#transfer-files-tofrom-the-hpc).
+```
 
 {%- endif %}
 
 When running `ls` in your session on the {{hpcinfra}}, you should see the two files listed in your home directory (`~`):
 
-```
+```text
 $ ls ~
 run.sh tensorflow_mnist.py
 ```
@@ -137,8 +153,8 @@ When you do not see these files, make sure you uploaded the files to your **home
 
 Jobs are submitted and executed using job scripts. In our case **run.sh** can be used as a (very minimal) job script.
 
-A job script is a shell script, a text file that specifies the resources, 
-the software that is used (via `module load` statements), 
+A job script is a shell script, a text file that specifies the resources,  
+the software that is used (via `module load` statements),  
 and the steps that should be executed to run the calculation.
 
 Our job script looks like this:
@@ -150,8 +166,8 @@ module load TensorFlow/2.15.1-foss-2023a
 
 python tensorflow_mnist.py
 ```
-As you can see this job script will run the Python script named **tensorflow_mnist.py**.
 
+As you can see this job script will run the Python script named **tensorflow_mnist.py**.
 
 The jobs you submit are per default executed on **cluser/{{defaultcluster}}**, you can swap to another cluster by issuing the following command.
 
@@ -160,32 +176,42 @@ module swap cluster/{{othercluster}}
 ```
 
 !!! Tip
-    
-    When submitting jobs with limited amount of resources, it is recommended to use the [debug/interactive cluster](interactive_debug.md#interactive-and-debug-cluster): `donphan`. 
+
+```text
+When submitting jobs with limited amount of resources, it is recommended to use the [debug/interactive cluster](interactive_debug.md#interactive-and-debug-cluster): `donphan`. 
+```
 
 {%- if site == 'Gent' %}
 
-    To get a list of all clusters and their hardware, see <https://www.ugent.be/hpc/en/infrastructure>.
+```text
+To get a list of all clusters and their hardware, see <https://www.ugent.be/hpc/en/infrastructure>.
+```
 
 {%- endif %}
 
 This job script can now be submitted to the cluster's job system for execution, using the qsub (**q**ueue **sub**mit) command:
 
-```
+```text
 $ qsub run.sh
 {{jobid}}
 ```
 
 This command returns a job identifier (*{{jobid}}*) on the HPC cluster. This is a unique identifier for the job which can be used to monitor and manage your job.
 
 !!! Warning "Make sure you understand what the `module` command does"
- 
-    Note that the module commands only modify environment variables. For instance, running `module swap cluster/{{othercluster}}` will update your shell environment so that `qsub` submits a job to the `{{othercluster}}` cluster, 
-    but our active shell session is still running on the login node.
-    
-    It is important to understand that while `module` commands affect your session environment, they do ***not*** change where the commands your are running are being executed: they will still be run on the login node you are on.
-    
-    When you submit a job script however, the commands ***in*** the job script will be run on a workernode of the cluster the job was submitted to (like `{{othercluster}}`).
+
+```text
+Note that the module commands only modify environment variables. For instance, running `module swap cluster/{{othercluster}}` will update your shell environment so that `qsub` submits a job to the `{{othercluster}}` cluster, 
+but our active shell session is still running on the login node.
+```
+
+```text
+It is important to understand that while `module` commands affect your session environment, they do ***not*** change where the commands your are running are being executed: they will still be run on the login node you are on.
+```
+
+```text
+When you submit a job script however, the commands ***in*** the job script will be run on a workernode of the cluster the job was submitted to (like `{{othercluster}}`).
+```
 
 For detailed information about `module` commands, read the [running batch jobs](running_batch_jobs.md) chapter.
 
@@ -195,15 +221,17 @@ Your job is put into a queue before being executed, so it may take a while befor
 (see [when will my job start?](running_batch_jobs.md#when-will-my-job-start) for scheduling policy).
 
 You can get an overview of the active jobs using the `qstat` command:
-```
+
+```text
 $ qstat
 Job ID     Name             User            Time Use S Queue
 ---------- ---------------- --------------- -------- - -------
 {{jobid}}     run.sh           {{userid}}        0:00:00  Q {{othercluster}}
 ```
 
 Eventually, after entering `qstat` again you should see that your job has started running:
-```
+
+```text
 $ qstat
 Job ID     Name             User            Time Use S Queue
 ---------- ---------------- --------------- -------- - -------
@@ -227,25 +255,30 @@ By default located in the directory where you issued `qsub`.
 
 !!! Info
 
-    For more information about the stdout and stderr output channels, see this [section](linux-tutorial/beyond_the_basics.md#inputoutput).
+```text
+For more information about the stdout and stderr output channels, see this [section](linux-tutorial/beyond_the_basics.md#inputoutput).
+```
 
 {%- endif %}
 
 In our example when running `ls` in the current directory you should see 2 new files:
- 
+
 - **run.sh.o{{jobid}}**, containing *normal output messages* produced by job {{jobid}};
 - **run.sh.e{{jobid}}**, containing *errors and warnings* produced by job {{jobid}}.
 
 !!! Info
-    
+
     run.sh.e{{jobid}} should be empty (no errors or warnings).
 
 !!! Warning "Use your own job ID"
 
-    Replace **{{jobid}}** with the jobid you got from the `qstat` command (see above) or simply look for added files in your current directory by running `ls`.
+```text
+Replace **{{jobid}}** with the jobid you got from the `qstat` command (see above) or simply look for added files in your current directory by running `ls`.
+```
 
 When examining the contents of ``run.sh.o{{jobid}}`` you will see something like this:
-```
+
+```text
 Downloading data from https://storage.googleapis.com/tensorflow/tf-keras-datasets/mnist.npz
 11493376/11490434 [==============================] - 1s 0us/step
 Epoch 1/5
@@ -265,9 +298,13 @@ Hurray 🎉, we trained a deep learning model and achieved 97,64 percent accurac
 
 !!! Warning
 
-    When using TensorFlow specifically, you should actually submit jobs to a GPU cluster for better performance, see [GPU clusters](gpu.md).
+```text
+When using TensorFlow specifically, you should actually submit jobs to a GPU cluster for better performance, see [GPU clusters](gpu.md).
+```
 
-    For the purpose of this example, we are running a very small TensorFlow workload on a CPU-only cluster.
+```text
+For the purpose of this example, we are running a very small TensorFlow workload on a CPU-only cluster.
+```
 
 ### Next steps
 
