hpcugent · Oa8choo2 · Oct 23, 2025 · Oct 21, 2025 · Oct 21, 2025 · Oct 21, 2025
diff --git a/mkdocs/docs/HPC/FAQ.md b/mkdocs/docs/HPC/FAQ.md
@@ -319,8 +319,8 @@ Please send an e-mail to {{hpcinfo}} that includes:
 
 {% endif %}
 
-If the software is a Python package, you can manually install it in a virtual environment. 
-More information can be found [here](./setting_up_python_virtual_environments.md).
+If the software is a Python package, you can manually
+[install it in a virtual environment](./setting_up_python_virtual_environments.md).
 Note that it is still preferred to submit a software installation request, 
 as the software installed by the HPC team will be optimized for the HPC environment.
 This can lead to dramatic performance improvements.

diff --git a/mkdocs/docs/HPC/alphafold.md b/mkdocs/docs/HPC/alphafold.md
@@ -20,8 +20,8 @@ It is therefore recommended to first familiarize yourself with AlphaFold. The fo
 - VSC webpage about AlphaFold: <https://www.vscentrum.be/alphafold>
 - Introductory course on AlphaFold by VIB: <https://elearning.vib.be/courses/alphafold>
 - "Getting Started with AlphaFold" presentation by Kenneth Hoste (HPC-UGent)
-    - recording available [on YouTube](https://www.youtube.com/watch?v=jP9Qg1yBGcs)
-    - slides available [here (PDF)](https://www.vscentrum.be/_files/ugd/5446c2_f19a8723f7f7460ebe990c28a53e56a2.pdf?index=true)
+    - [recording available](https://www.youtube.com/watch?v=jP9Qg1yBGcs) (on YouTube)
+    - [slides available](https://www.vscentrum.be/_files/ugd/5446c2_f19a8723f7f7460ebe990c28a53e56a2.pdf?index=true) (PDF)
     - see also <https://www.vscentrum.be/alphafold>
 
 
@@ -130,8 +130,8 @@ Likewise for `jackhmmer`, the core count can be controlled via `$ALPHAFOLD_JACKH
 
 ### CPU/GPU comparison
 
-The provided timings were obtained by executing the `T1050.fasta` example, as outlined in the Alphafold [README]({{readme}}). 
-For the corresponding jobscripts, they are available [here](./example-jobscripts).
+The provided timings were obtained by executing the `T1050.fasta` example, as outlined in the [Alphafold README]({{readme}}). 
+The [corresponding jobscripts](#example-jobscripts) are available.
 
 Using `--db_preset=full_dbs`, the following runtime data was collected:
 

diff --git a/mkdocs/docs/HPC/getting_started.md b/mkdocs/docs/HPC/getting_started.md
@@ -79,8 +79,12 @@ Make sure you can get to a shell access to the {{hpcinfra}} before proceeding wi
 
 Now that you can login, it is time to transfer files from your local computer to your **home directory** on the {{hpcinfra}}.
 
-Download [tensorflow_mnist.py](https://raw.githubusercontent.com/hpcugent/vsc_user_docs/main/{{exampleloc}}/tensorflow_mnist.py) 
-and [run.sh](https://raw.githubusercontent.com/hpcugent/vsc_user_docs/main/{{exampleloc}}/run.sh) example scripts to your computer (from [here](https://github.com/hpcugent/vsc_user_docs/tree/main/{{exampleloc}})).
+Download following the example scripts to your computer:
+
+- [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).
 
 {%- if OS == windows %}
 

diff --git a/mkdocs/docs/HPC/infrastructure.md b/mkdocs/docs/HPC/infrastructure.md
@@ -13,8 +13,8 @@ Science and Innovation (EWI).
 Log in to the HPC-UGent Tier-2 infrastructure via [https://login.hpc.ugent.be](https://login.hpc.ugent.be)
 or using SSH via `login.hpc.ugent.be`.
 
-More info on using the web portal you can find [here](web_portal.md),
-and about connection with SSH [here](connecting.md).
+Read more info on [using the web portal](web_portal.md),
+and [about making a connection with SSH](connecting.md).
 
 ## Tier-2 compute clusters
 

diff --git a/mkdocs/docs/HPC/jupyter.md b/mkdocs/docs/HPC/jupyter.md
@@ -89,7 +89,9 @@ $ module load SciPy-bundle/2023.11-gfbf-2023b
 ```
 This throws no errors, since this module uses a toolchain that is compatible with the toolchain used by the notebook
 
-If we use a different SciPy module that uses an incompatible toolchain, we will get a module load conflict when trying to load it (For more info on these errors, see [here](troubleshooting.md#module-conflicts)).
+If we use a different SciPy module that uses an incompatible toolchain, 
+we will get a module load conflict when trying to load it 
+(for more info on these errors, consult the [troubleshooting page](troubleshooting.md#module-conflicts)).
 
 ```shell
 $ module load JupyterNotebook/7.2.0-GCCcore-13.2.0

diff --git a/mkdocs/docs/HPC/multi_core_jobs.md b/mkdocs/docs/HPC/multi_core_jobs.md
@@ -47,7 +47,7 @@ MPI.
 
 !!! warning
     Just requesting more nodes and/or cores does not mean that your job will automatically run faster.
-    You can find more about this [here](troubleshooting.md#job_does_not_run_faster).
+    This is explained on the [troubleshooting page](troubleshooting.md#job_does_not_run_faster).
 
 ## Parallel Computing with threads
 

diff --git a/mkdocs/docs/HPC/multi_job_submission.md b/mkdocs/docs/HPC/multi_job_submission.md
@@ -159,7 +159,11 @@ a parameter instance is called a work item in Worker parlance.
     ```
     module swap cluster/donphan
     ```
-    We recommend using a `module swap cluster` command after submitting the jobs. Additional information about this as well as more comprehensive details concerning the 'Illegal instruction' error can be accessed [here](troubleshooting.md#multi-job-submissions-on-a-non-default-cluster).
+
+    We recommend using a `module swap cluster` command after submitting the jobs.
+    Additional information about this as well as more comprehensive details
+    concerning the 'Illegal instruction' error can be found
+    on [the troubleshooting page](troubleshooting.md#multi-job-submissions-on-a-non-default-cluster).
 
 ## The Worker framework: Job arrays
 [//]: # (sec:worker-framework-job-arrays)

diff --git a/mkdocs/docs/HPC/only/gent/2023/donphan-gallade.md b/mkdocs/docs/HPC/only/gent/2023/donphan-gallade.md
@@ -15,7 +15,7 @@ For software installation requests, please use the [request form](https://www.ug
 
 `donphan` is the new debug/interactive cluster.
 
-It replaces `slaking`, which will be retired on **Monday 22 May 2023**.
+It replaces `slaking`, which was retired on **Monday 22 May 2023**.
 
 It is primarily intended for interactive use: interactive shell sessions, using GUI applications through the
 [HPC-UGent web portal](../../../web_portal.md), etc.
@@ -135,4 +135,6 @@ a `gallade` workernode has 128 cores (so ~7.3 GiB per core on average), while a
 (so ~20.5 GiB per core on average).
 
 It is important to take this aspect into account when submitting jobs to `gallade`, especially when requesting
-all cores via `ppn=all`. You may need to explictly request more memory (see also [here](../../../fine_tuning_job_specifications#pbs_mem)).
+all cores via `ppn=all`.
+You may need to explictly request more memory by
+[setting the memory parameter](../../../fine_tuning_job_specifications#pbs_mem).
diff --git a/mkdocs/docs/HPC/running_batch_jobs.md b/mkdocs/docs/HPC/running_batch_jobs.md
@@ -833,7 +833,9 @@ The output of the various commands interacting with jobs (`qsub`,
 It is possible to submit jobs from a job to a cluster different than the one your job is running on.
 This could come in handy if, for example, the tool used to submit jobs only works on a particular cluster 
 (or only on the login nodes), but the jobs can be run on several clusters.
-An example of this is the `wsub` command of `worker`, see also [here](troubleshooting.md#multi-job-submissions-on-a-non-default-cluster).
+An example of this is the `wsub` command of `worker`.
+More info on these commands is in the document on [multi job submission](multi_job_submission.md)
+or on the [troubleshooting page](troubleshooting.md#multi-job-submissions-on-a-non-default-cluster).
 
 To submit jobs to the `{{othercluster}}` cluster, you can change only what is needed in your session environment 
 to submit jobs to that particular cluster by using `module swap env/slurm/{{othercluster}}` instead of using 

diff --git a/mkdocs/docs/HPC/setting_up_python_virtual_environments.md b/mkdocs/docs/HPC/setting_up_python_virtual_environments.md
@@ -363,7 +363,8 @@ $ python
 Illegal instruction (core dumped)
 ```
 
-we are presented with the illegal instruction error. More info on this [here](troubleshooting.md#illegal-instruction-error)
+we are presented with the illegal instruction error.
+More info on this on the [troubleshooting page](troubleshooting.md#illegal-instruction-error)
 
 ### Error: GLIBC not found
 

diff --git a/mkdocs/docs/HPC/troubleshooting.md b/mkdocs/docs/HPC/troubleshooting.md
@@ -60,7 +60,7 @@ or because the pinning is done incorrectly and several threads/processes are bei
 - **Lack of sufficient memory**: When there is not enough memory available, or not enough memory bandwidth, 
 it is likely that you will not see a significant speedup when using more cores (since each thread or process most likely requires additional memory).
 
-More info on running multi-core workloads on the {{ hpcinfra }} can be found [here](multi_core_jobs.md).
+There is more info on [running multi-core workloads](multi_core_jobs.md) on the {{ hpcinfra }}.
 
 ### Using multiple nodes
 When trying to use multiple (worker)nodes to improve the performance of your workloads, you may not see (significant) speedup.
@@ -74,7 +74,7 @@ Actually using additional nodes is not as straightforward as merely asking for m
 Using the resources of multiple nodes is often done using a [Message Passing Interface (MPI)](https://en.wikipedia.org/wiki/Message_Passing_Interface) library.
 MPI allows nodes to communicate and coordinate, but it also introduces additional complexity.
 
-An example of how you can make beneficial use of multiple nodes can be found [here](multi_core_jobs.md#parallel-computing-with-mpi).
+We have an example of [how you can make beneficial use of multiple nodes](multi_core_jobs.md#parallel-computing-with-mpi).
 
 You can also use MPI in Python, some useful packages that are also available on the HPC are:
 

diff --git a/mkdocs/docs/HPC/web_portal.md b/mkdocs/docs/HPC/web_portal.md
@@ -32,11 +32,9 @@ Through this web portal, you can:
 
 -   open a terminal session directly in your web browser;
 
-More detailed information is available below, as well as in the [Open
-OnDemand
-documentation](https://osc.github.io/ood-documentation/latest/). A
-walkthrough video is available on YouTube
-[here](https://www.youtube.com/watch?v=4-w-4wjlnPk).
+More detailed information is available below, as well as in the
+[Open OnDemand documentation](https://osc.github.io/ood-documentation/latest/).  
+A [walkthrough video](https://www.youtube.com/watch?v=4-w-4wjlnPk) is available on YouTube.
 
 ## Pilot access