Added conda section

config/templates/hpc.template

@@ -31,6 +31,7 @@ nav:
       - Best Practices: best_practices.md
       - Graphical applications with VNC: VNC.md
       - Graphical applications with X2Go: x2go.md
+      - Conda: conda.md
 {%- if site == 'Gent' %}
       - GPU clusters: gpu.md
       - Cron scripts: crontab.md

mkdocs/docs/HPC/conda.md

@@ -0,0 +1,36 @@
+# Conda
+
+We do not recommend the use of conda environments on the HPC clusters. 
+This section explains why and highlights some common issues.
+
+## Performance and Optimization
+
+Conda's packages are pre-compiled binaries that are designed to work on a wide range of systems. 
+This means they are not optimized for the specific architecture of HPC clusters, 
+leading to potential performance drawbacks compared to modules compiled specifically for the HPC environment.
+
+HPC modules on the other hand, are compiled for the specific architecture of the cluster,
+and are optimized for performance.
+
+## Compatibility and Dependency
+
+Using Conda in conjunction with centrally installed modules can lead to conflicts and unexpected errors, 
+making it difficult to debug and manage dependencies.
+
+## Package Availability
+
+Conda has a smaller repository of available packages compared to PyPI, the repository used by pip. 
+This can limit the availability of specific tools or libraries needed for certain workflows.
+
+## Environment and Installation Issues
+
+### Home Directory Usage
+
+Conda installs packages and environments in the user's home directory, 
+which can quickly fill up disk quotas due to the large number of files and directories it creates. 
+This is particularly problematic in HPC environments where home directory quotas are often limited.
+
+### Modification of Configuration Files
+
+Conda modifies the .bashrc file in the user's home directory, 
+which can lead to conflicts and unintended side effects in the user's environment setup.