# Project information site_name: HPCE User Documentation site_url: https://hpce.pages.psi.ch # Repository repo_name: "User Documentation Repository" repo_url: https://gitea.psi.ch/hpce/gitea-pages # TODO unsure if this works, branch needs to be changed from `mkdocs` to `main` edit_uri: _edit/master/docs/ # Copyright copyright: Copyright © 2025 — 2026 HPC and Emerging Technologies Group/CSD @ Paul Scherrer Institut # CSS extra_css: - css/custom-nav.css # Configuration theme: name: material favicon: images/favicon.ico logo: images/hpce_logo.png custom_dir: overrides features: - navigation.instant - navigation.tabs - navigation.tabs.sticky - navigation.sections - navigation.indexes - toc.follow - content.action.edit # doesn't work with Gitea as the URL is based upon `edit_uri` which has an # explcit '_' underline prefixed for edit but not raw?! #- content.action.view palette: - media: "(prefers-color-scheme)" toggle: icon: material/link name: Switch to light mode - media: "(prefers-color-scheme: light)" scheme: default toggle: icon: material/toggle-switch name: Switch to dark mode - media: "(prefers-color-scheme: dark)" scheme: slate toggle: icon: material/toggle-switch-off name: Switch to system preference # plugins plugins: - search - exclude-search: exclude: - 'merlin6/*' - 'gmerlin6/*' - 'merlin5/*' - optimize - blog: blog_dir: news - glightbox - include-markdown - llmstxt: markdown_description: HPCE User documentation for the Merlin Clusters sections: Cluster Docs: - 'merlin*/*.md' - 'meg*/*.md' CSCS Userlab Docs: - 'cscs*/*.md' Support: - 'support/*.md' News: - 'news/*.md' # Extensions markdown_extensions: - admonition - attr_list - footnotes - md_in_html - meta - tables - toc: permalink: true - pymdownx.caret - pymdownx.critic - pymdownx.blocks.caption - pymdownx.details - pymdownx.highlight: anchor_linenums: true line_spans: __span pygments_lang_class: true auto_title: true - pymdownx.inlinehilite - pymdownx.keys - pymdownx.mark - pymdownx.snippets - pymdownx.superfences: custom_fences: - name: mermaid class: mermaid format: !!python/name:pymdownx.superfences.fence_code_format - pymdownx.tilde # Page tree nav: - Home: index.md - News: - news/index.md - Merlin 7: - Quick Start Guide: - merlin7/01-quick-start-guide/introduction.md - merlin7/01-quick-start-guide/code-of-conduct.md - merlin7/01-quick-start-guide/requesting-accounts.md - merlin7/01-quick-start-guide/requesting-projects.md - merlin7/01-quick-start-guide/accessing-interactive-nodes.md - merlin7/01-quick-start-guide/accessing-slurm.md - Connecting to Merlin7: - merlin7/02-connecting-to-merlin/host-keys.md - SSH: - merlin7/02-connecting-to-merlin/connect-from-linux.md - merlin7/02-connecting-to-merlin/connect-from-windows.md - merlin7/02-connecting-to-merlin/connect-from-macos.md - SSH Key-pairs: merlin7/02-connecting-to-merlin/ssh-keys.md - Remote Desktop: merlin7/02-connecting-to-merlin/nomachine.md - Other Clients: - merlin7/02-connecting-to-merlin/connecting-with-vscode-remote.md - merlin7/02-connecting-to-merlin/agentic-tools-bridges.md - How To Use Merlin7: - merlin7/03-how-to-use-merlin/storage.md - merlin7/03-how-to-use-merlin/transfer-data.md - merlin7/03-how-to-use-merlin/archive.md - merlin7/03-how-to-use-merlin/merlin-rmount.md - merlin7/03-how-to-use-merlin/merlin_tools.md - merlin7/03-how-to-use-merlin/kerberos.md - merlin7/03-how-to-use-merlin/software-repositories.md - Slurm General Documentation: - merlin7/04-slurm-general-documentation/merlin7-configuration.md - merlin7/04-slurm-general-documentation/slurm-configuration.md - merlin7/04-slurm-general-documentation/interactive-sessions.md - merlin7/04-slurm-general-documentation/interactive-jobs.md - merlin7/04-slurm-general-documentation/slurm-examples.md - merlin7/04-slurm-general-documentation/slurm-mail.md - Jupyterhub: - merlin7/05-jupyterhub/jupyterhub.md - Open OnDemand: - Introduction: merlin7/06-open-ondemand/open-ondemand.md - Software Support: - merlin7/07-software-support/pmodules.md - merlin7/07-software-support/openmpi.md - merlin7/07-software-support/mpich.md - merlin7/07-software-support/cray-module.env.md - merlin7/07-software-support/ansys.md - merlin7/07-software-support/ansys-rsm.md - merlin7/07-software-support/cp2k.md - merlin7/07-software-support/dirac.md - merlin7/07-software-support/gromacs.md - merlin7/07-software-support/ippl.md - merlin7/07-software-support/lammps.md - merlin7/07-software-support/matlab.md - merlin7/07-software-support/opal-x.md - merlin7/07-software-support/quantum-espresso.md - merlin7/07-software-support/spack.md - merlin7/07-software-support/vscode.md - Merlin 6: - Quick Start Guide: - merlin6/introduction.md - merlin6/quick-start-guide/code-of-conduct.md - merlin6/quick-start-guide/requesting-accounts.md - merlin6/quick-start-guide/requesting-projects.md - merlin6/quick-start-guide/accessing-interactive-nodes.md - merlin6/quick-start-guide/accessing-slurm.md - How To Use Merlin: - merlin6/how-to-use-merlin/connect-from-linux.md - merlin6/how-to-use-merlin/connect-from-windows.md - merlin6/how-to-use-merlin/connect-from-macos.md - merlin6/how-to-use-merlin/storage.md - merlin6/how-to-use-merlin/transfer-data.md - merlin6/how-to-use-merlin/archive.md - merlin6/how-to-use-merlin/ssh-keys.md - merlin6/how-to-use-merlin/kerberos.md - merlin6/how-to-use-merlin/using-modules.md - Slurm General Documentation: - merlin6/slurm-general-docs/slurm-accounts.md - merlin6/slurm-general-docs/slurm-basic-commands.md - merlin6/slurm-general-docs/running-jobs.md - merlin6/slurm-general-docs/interactive-jobs.md - merlin6/slurm-general-docs/slurm-examples.md - merlin6/slurm-general-docs/monitoring.md - GPU Cluster: - gmerlin6/cluster-introduction.md - gmerlin6/hardware-and-software-description.md - gmerlin6/slurm-configuration.md - Jupyterhub: - merlin6/jupyterhub/jupyterhub.md - merlin6/jupyterhub/jupyter-examples.md - merlin6/jupyterhub/jupytext.md - merlin6/jupyterhub/jupyter-extensions.md - merlin6/jupyterhub/jupyterlab.md - merlin6/jupyterhub/jupyterhub-trouble.md - Software Support: - merlin6/software-support/ansys.md - merlin6/software-support/ansys-rsm.md - merlin6/software-support/ansys-cfx.md - merlin6/software-support/ansys-fluent.md - merlin6/software-support/ansys-mapdl.md - merlin6/software-support/ansys-hfss.md - merlin6/software-support/gothic.md - merlin6/software-support/merlin-rmount.md - merlin6/software-support/impi.md - merlin6/software-support/openmpi.md - merlin6/software-support/paraview.md - merlin6/software-support/python.md - MeG: - meg/introduction.md - meg/contact.md - meg/migration-to-merlin7.md - CLS: # - Archiving: - Data Transfer: - cls/data_transfer/emf.md - cls/data_transfer/scopem.md - cls/data_transfer/unil_s3_bucket.md - cls/data_transfer/uni_basel.md - Software: - cls/software/modules.md - Electron Microscopy: - cls/software/EM/relion.md - CryoSPARC: - cls/software/EM/cryosparc/installation.md - cls/software/EM/cryosparc/usage.md - cls/software/EM/cryosparc/lanes.md - cls/software/EM/cryosparc/update.md - cls/software/EM/cryosparc/patch.md - cls/software/EM/cryosparc/issues.md - cls/software/EM/cryosparc/benchmarks.md - Protein Structure Prediction and Design: - cls/software/protein_structure_prediction/alphafold3.md # - Molecular and Volumetric Visualization: # - Molecular Dynamics: # - Bioinformatics: - PSI@CSCS: - cscs-userlab/introduction.md - cscs-userlab/transfer-data.md - Support: - support/introduction.md - support/faq.md - support/known-problems.md - support/troubleshooting.md