Merge pull request #673 from lbarraga/venv-docs

Add tip and warning to venv docs, add link in FAQ

mkdocs/docs/HPC/FAQ.md

@@ -319,6 +319,12 @@ 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).
+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.
+
 ### Is my connection compromised? Remote host identification has changed
 
 On Monday 25 April 2022, the login nodes received an update to RHEL8.

mkdocs/docs/HPC/setting_up_python_virtual_environments.md

@@ -25,6 +25,14 @@ python -m venv myenv      # Create a new virtual environment named 'myenv'
 This command creates a new subdirectory named `myenv` in the current working directory. 
 This directory will contain the packages, scripts, and binaries that are needed to manage the virtual environment.
 
+!!! warning
+    When you create a virtual environment on top of a loaded Python module, 
+    the environment becomes specific to the cluster you're working on. 
+    This is because modules are built and optimized for the operating system and CPUs of the cluster.
+    This means that you should create a new virtual environment for each cluster you work on. 
+    See [Creating a virtual environment for a specific cluster](#creating-a-virtual-environment-for-a-specific-cluster) for more information.
+
+
 ### Activating a virtual environment
 
 To use the virtual environment, you need to *activate* it. 
@@ -49,10 +57,18 @@ No administrator privileges are required to install packages in a virtual enviro
 
 It is now possible to run Python scripts that use the installed packages in the virtual environment.
 
-!!! note
-    Always prefer to use Python packages that are centrally installed, which are available via the environment modules interface.
-    Software installations available via the modules interface are compiled and optimized for the HPC cluster, while packages installed with `pip` are not.
-    To check if a package is available as a module, you can use the following command:
+!!! tip
+    When creating a virtual environment, it's best to install only *pure* Python 
+    packages. Pure Python packages consist solely of Python code and don't require compilation. 
+    The installation method of these packages doesn't impact performance since they're not compiled.
+
+    Compiled libraries with a Python wrapper (*non-pure* Python packages) are better loaded as modules 
+    rather than installed in the virtual environment. 
+    This is because modules are optimized for the HPC cluster’s specific hardware and operating system. 
+    If a non-pure Python package isn't available as a module, you can 
+    [submit a software installation request](https://www.ugent.be/hpc/en/support/software-installation-request).
+
+    To check if a package is available as a module, use:
 
     ```bash
     module av package_name