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mkdocs.yml
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site_name: ULHPC Technical Documentation
nav:
##########
# - General:
- Home: 'index.md'
- Getting Started: 'getting-started.md'
- HPC Trainings and Tutorials: 'hpc-schools.md'
- Accounts:
- Get an Account: 'accounts/index.md'
- Password Policy: 'policies/passwords.md'
- Collaboration Accounts: 'accounts/collaboration_accounts.md'
- Projects Accounts: 'accounts/projects.md'
- Identity Management Portal: 'connect/ipa.md'
- Slurm Account Hierarchy: 'slurm/accounts.md'
- Teaching with the ULHPC: 'teaching-with-the-ulhpc.md'
##############
- Data Center:
- Centre de Calcul (CDC): 'data-center/index.md'
#######################
- ULHPC Supercomputers:
- Overview: 'systems/index.md'
- Aion:
- Aion System: 'systems/aion/index.md'
- Compute Nodes: 'systems/aion/compute.md'
- Fast Local Interconnect: 'systems/aion/interconnect.md'
# - Storage: 'filesystems/index.md'
- Timeline: 'systems/aion/timeline.md'
- Iris:
- Iris System: 'systems/iris/index.md'
- Compute Nodes: 'systems/iris/compute.md'
- Fast Local Interconnect: 'systems/iris/interconnect.md'
# - Storage: 'filesystems/index.md'
- Timeline: 'systems/iris/timeline.md'
- Live status: https://hpc.uni.lu/live-status/motd
#######################
- Interconnect:
# - Overview: 'interconnect/index.md'
- Fast Infiniband Interconnect: 'interconnect/ib.md'
- Ethernet Interconnect: 'interconnect/ethernet.md'
#######################
- Storage Systems:
- Overview: 'filesystems/index.md'
- GPFS/SpectrumScale: 'filesystems/gpfs.md'
- Lustre: 'filesystems/lustre.md'
- OneFS Isilon: 'filesystems/isilon.md'
- Live status: https://hpc.uni.lu/live-status/motd
#################
- Access/Connect:
- Access/Login Servers: 'connect/access.md'
- SSH: 'connect/ssh.md'
- Identity Management (IdM/IPA): 'connect/ipa.md'
- Open On Demand Portal: 'connect/ood.md'
- Troubleshooting: 'connect/troubleshooting.md'
# - Multi-Factor Authentication: 'connect/mfa.md'
##################
- Data Management:
- Global Directory Structure: 'data/layout.md'
- Data Sharing: 'data/sharing.md'
- Data Transfer: 'data/transfer.md'
- GDPR Compliance: 'data/gdpr.md'
- Quotas: 'filesystems/quotas.md'
- Project Data Management: 'data/project.md'
- Scratch Data Management: 'filesystems/lfs.md'
- Backups: 'data/backups.md'
# - Archiving: 'data/archiving.md'
- Unix File Permissions: 'filesystems/unix-file-permissions.md'
# - Version Control with Git: 'workflow/git.md'
- Sensitive Data Protection: 'data/encryption.md'
##############
- Environment:
- Overview: 'environment/index.md'
- Modules: 'environment/modules.md'
- Easybuild: 'environment/easybuild.md'
- Conda: 'environment/conda.md'
###########
- Policies:
- Acceptable Use Policy (AUP): 'policies/aup.md'
- Downtime and Maintenance: 'policies/maintenance.md'
# - Software Update Policy: 'policies/software.md'
- Usage Charging Policy: 'policies/usage-charging.md'
- HPC Resource Allocations for Research Project: 'policies/usage-charging.md#hpc-resource-allocations-for-research-project'
- HPC Service Agreement for Externals: 'policies/usage-charging.md#hpc-service-contract-for-external-and-private-partners'
- Expert-level HPC services: 'support/professional-services.md'
# - Data Policy: 'policies/data.md
###############
- Running Jobs:
- Slurm Overview: 'slurm/index.md'
- Convenient Slurm Commands: 'slurm/commands.md'
- Partition/Queues: 'slurm/partitions.md'
- Quality of Service (QOS): 'slurm/qos.md'
- Account Hierarchy: 'slurm/accounts.md'
- Job State and Reason Code: 'jobs/reason-codes.md'
- Fairsharing: 'slurm/fairsharing.md'
- Job Priority and Backfilling: 'jobs/priority.md'
- Job Accounting and Billing: 'jobs/billing.md'
# - Limits: 'jobs/limits.md'
- Interactive Job: 'jobs/interactive.md'
- Passive/Batch Job: 'jobs/submit.md'
- GPU Jobs: 'jobs/gpu.md'
- Long Jobs: 'jobs/long.md'
- Best-effort Jobs: 'jobs/best-effort.md'
- Launcher Scripts Examples: 'slurm/launchers.md'
# - Affinity: 'jobs/affinity.md'
# - (Multi-)GPU Jobs: 'jobs/gpu.md'
# - Memory Management: 'jobs/memory.md'
# - Best Practices: 'jobs/best-practices.md'
# - Reservations: 'jobs/reservations.md'
# - Monitoring: 'jobs/monitoring.md'
# - Licenses Management: 'slurm/licenses.md'
# - FAQs: 'jobs/faq.md'
# - Workflow Tools:
# - Overview: 'jobs/workflow/index.md'
# - GNU Parallel: 'jobs/workflow/gnuparallel.md'
# - Parsl: 'jobs/workflow/parsl.md'
# - Snakemake: 'jobs/workflow/snakemake.md'
# - Spark Cluster: 'bigdata/spark.md'
- Jupyter Notebook: 'services/jupyter.md'
# - Checkpoint/Restart: 'jobs/checkpoint-restart.md'
###########
- Software:
### BEGIN GENERATED CONTENT
- Supported Software List:
- Overview: 'software/swsets/index.md'
- Full List (alphabetical order): 'software/swsets/all_softwares.md'
- Biology: 'software/swsets/bio.md'
- CFD/Finite element modelling: 'software/swsets/cae.md'
- Chemistry: 'software/swsets/chem.md'
- Compilers: 'software/swsets/compiler.md'
- Data processing: 'software/swsets/data.md'
- Debugging: 'software/swsets/debugger.md'
- Development: 'software/swsets/devel.md'
# - Weather modelling: 'software/swsets/geo.md'
- Programming Languages: 'software/swsets/lang.md'
- Libraries: 'software/swsets/lib.md'
- Mathematics: 'software/swsets/math.md'
- MPI: 'software/swsets/mpi.md'
- Numerical libraries: 'software/swsets/numlib.md'
- Performance measurements: 'software/swsets/perf.md'
- Physics: 'software/swsets/phys.md'
- System-level software: 'software/swsets/system.md'
- Toolchains (software stacks): 'software/swsets/toolchain.md'
- Utilities: 'software/swsets/tools.md'
- Visualisation: 'software/swsets/vis.md'
- Software Sets:
- 2019b: 'software/swsets/2019b.md'
- 2020a: 'software/swsets/2020b.md'
### END GENERATED CONTENT
# - Software Set Versioning: 'software/swsets.md'
- Compiling/building your own software: 'software/build.md'
- EESSI software stack: 'software/eessi.md'
# - Management: 'software/management.md'
# - Contributing: 'software/contributing.md'
# - BigData Analytics: 'software/bigdata/index.md'
# - Bioinformatics/Life Science: 'software/bio/index.md'
- Containers: 'containers/index.md'
- Computer Aided Eng. (CAE):
- FEniCS : 'software/cae/fenics.md'
- ANSYS : 'software/cae/ansys.md'
- OpenFOAM : 'software/cae/openfoam.md'
- Abaqus : 'software/cae/abaqus.md'
- FDS : 'software/cae/fds.md'
- Meshing-Tools : 'software/cae/meshing-tools.md'
- Physics:
- WRF: 'software/physics/wrf.md'
- Computational Chemistry:
- Electronics:
- ABINIT: 'software/computational-chemistry/electronics/abinit.md'
- ASE: 'software/computational-chemistry/electronics/ase.md'
- MEEP: 'software/computational-chemistry/electronics/meep.md'
- Quantum Espresso: 'software/computational-chemistry/electronics/quantum-espresso.md'
- VASP: 'software/computational-chemistry/electronics/vasp.md'
- Molecular Dynamics:
- CP2K: 'software/computational-chemistry/molecular-dynamics/cp2k.md'
- GROMACS: 'software/computational-chemistry/molecular-dynamics/gromacs.md'
- NAMD: 'software/computational-chemistry/molecular-dynamics/namd.md'
- NWCHEM: 'software/computational-chemistry/molecular-dynamics/nwchem.md'
- Helping Libraries: 'software/computational-chemistry/molecular-dynamics/helping-libraries.md'
# - Deep and Machine Learning: 'software/ml/index.md'
# - Earth Sciences: 'software/geo/index.md'
- Mathematics & Statistics:
- MATLAB: 'software/maths/matlab.md'
- MATHEMATICA: 'software/maths/mathematica.md'
- Stata: 'software/maths/stata.md'
- Julia: 'software/maths/julia.md'
- Optimizers: 'software/optim/index.md'
# - Performance/Debugging: 'development/performance-debugging-tools/index.md'
# - Physics: 'software/phys/index.md'
# - Toolchains/Compilers: 'development/toolchains/index.md'
- Visualization:
- ParaView: 'software/visu/paraview.md'
##############
- Development:
# - Toolchains and Compilers:
# - Overview: 'development/toolchains/index.md'
# - FOSS: 'development/toolchains/foss.md'
# - Intel: 'development/toolchains/intel.md'
# - LLVM: 'development/compilers/llvm.md'
# - PGI: 'development/compilers/pgi.md'
# - Build Tools:
# - Autoconf and Make: 'development/build-tools/autoconf-make.md'
# - CMake: 'development/build-tools/cmake.md'
# - EasyBuild: 'development/build-tools/easybuild.md'
# - Spack: 'https://spack-tutorial.readthedocs.io/en/latest/'
# - Programming Models:
# - Overview: 'development/programming-models/index.md'
# - MPI Stack:
# - About: 'development/programming-models/mpi/index.md'
# - OpenMPI: 'development/programming-models/mpi/openmpi.md'
# - OpenMP: 'development/programming-models/openmp/openmp.md'
# - CUDA: 'development/programming-models/cuda.md'
# - Kokkos : 'development/programming-models/kokkos.md'
# - UPC : 'development/programming-models/upc.md'
# - Languages:
# - Go: 'development/languages/go.md'
# - Java: 'development/languages/java.md'
# - Julia: 'development/languages/julia.md'
# - Python:
# - About: 'development/languages/python/index.md'
# - Virtual Env.: 'development/languages/python/venv.md'
# - Best Practices: 'development/languages/python/best-practices.md'
# - Python on GPU: 'development/languages/python/python-on-gpu.md'
# - Scaling Up: 'development/languages/python/scaling-up.md'
# - Multiprocessing: 'development/languages/python/multiprocessing.md'
# - mpi4py: 'development/languages/python/mpi4py.md'
# - Notebook: 'development/languages/python/notebook.md'
# - Python Profiling: 'development/languages/python/profiling.md'
# - Python FAQ: 'development/languages/python/faq.md'
# - R: 'development/languages/r.md'
# - Ruby: 'development/languages/ruby.md'
# - Rust: 'development/languages/rust.md'
# - Libraries:
# - About: 'development/libraries/index.md'
# - Boost C++: 'development/libraries/boost.md'
# - FFTW : 'development/libraries/fftw.md'
# - HDF5 : 'development/libraries/hdf5.md'
# - LAPACK : 'development/libraries/lapack.md'
# - MKL : 'development/libraries/mkl.md'
# - NetCDF : 'development/libraries/netcdf.md'
- Performance/Debugging:
# - About: 'development/performance-debugging-tools/index.md'
- Arm Forge: 'development/performance-debugging-tools/arm-forge.md'
# - GDB: 'development/performance-debugging-tools/gdb.md'
- Intel VTune: 'development/performance-debugging-tools/vtune.md'
- Intel Advisor: 'development/performance-debugging-tools/advisor.md'
- Intel Inspector: 'development/performance-debugging-tools/inspector.md'
- Intel Trace Analyzer and Collector: 'development/performance-debugging-tools/itac.md'
# - LIKWID: 'development/performance-debugging-tools/likwid.md'
# - Nvidia Nsight: 'development/performance-debugging-tools/nsight.md'
# - Roofline Performance Model: 'development/performance-debugging-tools/roofline.md'
# - PAPI: 'development/performance-debugging-tools/papi.md'
- Scalasca: 'development/performance-debugging-tools/scalasca.md'
- Valgrind: 'development/performance-debugging-tools/valgrind.md'
- APS: 'development/performance-debugging-tools/aps.md'
- Containers:
- About: 'containers/index.md'
# - Singularity: 'containers/singularity.md'
###############
# - Applications:
# - Overview: 'software/index.md'
#########################
- Services: 'services/index.md'
# - Gitlab: 'services/gitlab.md'
# - Gforge: 'service/gforge.md'
# - Jupyter : 'services/jupyter.md'
# - EtherPad: 'services/etherpad.md'
# - PrivateBin: 'services/privatebin.md'
# - Databases: 'services/databases.md'
#########################
- Help and Support:
# - FAQ: 'support/faq.md'
- Overview: 'support/index.md'
- Helpdesk / Ticket Portal: https://hpc.uni.lu/support
#########################
# - DevOps Management:
# - Collaborative Development:
# - SSH: 'tools/ssh.md'
# - DSH: 'tools/dsh.md'
# - ClusterShell: 'tools/clustershell.md'
# - GPG: 'tools/gpg.md'
# - Git:
# - Basics: 'git/index.md'
# - Workflow: 'git/workflow.md'
# - Password Management: 'tools/password-manager.md'
# - Configuration Management:
# - Puppet: 'infra/management/puppet.md'
# - Ansible: 'infra/management/ansible.md'
# - Compute Node Provisioning:
# - FAI: 'infra/deployment/fai.md'
# - Bright Computing: 'infra/deployment/bright.md'
# - KickStart: 'infra/deployment/kickstart.md'
# - Identity Management: 'infra/idm.md'
# - Resource and Job Management Systems: 'infra/slurm.md'
# - Monitoring: 'infra/monitoring.md'
# - Virtualization:
# - KVM: 'virtualization/kvm/index.md'
- Contributing:
- Overview: 'contributing/index.md'
- Semantic Versioning: 'contributing/versioning.md'
##############
- Web Portals:
- ULHPC Website: https://hpc.uni.lu
- Technical Documentation: https://hpc-docs.uni.lu
# - OpenOn Demand: https://hpc.uni.lu/ood
# - Live Platform status: https://hpc.uni.lu/live-status/motd
- ULHPC Tutorials: https://ulhpc-tutorials.readthedocs.io/
- Helpdesk / Ticket Portal: https://hpc.uni.lu/support
##############
# - Acronyms: 'help/acronyms.md'
##############
# - AWS cluster:
# - Overview: aws/overview.md
# - Connect to cluster: aws/connection.md
# - Environment Setup: aws/setup.md
# tab Clusters:
# - Organization: 'layout.md'
# - Pre-Requisites and Repository Setup: 'setup.md'
# - Contributing:
# - Overview: 'contributing/index.md'
# - Directory Layout: 'layout.md'
# - Repository Setup and Git Developments: 'contributing/setup.md'
# - Semantic Versioning: 'contributing/versioning.md'
# Project Information
site_name: ULHPC Technical Documentation
site_description: ULHPC Technical Documentation
site_author: S. Varrette and Uni.lu HPC (ULHPC) Team
site_dir: public
site_url: "https://hpc-docs.uni.lu/"
# Repository
repo_name: ULHPC/ulhpc-docs
repo_url: https://github.com/ULHPC/ulhpc-docs
edit_uri: blob/master/docs/
# Copyright
copyright: Copyright © 2007-2022 S. Varrette and Uni.lu HPC (ULHPC) Team
# Configuration
# strict: true
theme:
name: material
logo: images/logo_ULHPC_square.jpg
language: en
palette:
primary: blue
accent: light blue
features:
- navigation.instant
# # - tabs
plugins:
- search # necessary for search to work
- git-revision-date-localized:
type: date
- progress
- include-markdown
- exclude:
glob:
- software/swsets/base/*.md
- software/swsets/bio/*.md
- software/swsets/cae/*.md
- software/swsets/chem/*.md
- software/swsets/compiler/*.md
- software/swsets/data/*.md
- software/swsets/debugger/*.md
- software/swsets/devel/*.md
- software/swsets/lang/*.md
- software/swsets/lib/*.md
- software/swsets/math/*.md
- software/swsets/mpi/*.md
- software/swsets/numlib/*.md
- software/swsets/perf/*.md
- software/swsets/phys/*.md
- software/swsets/system/*.md
- software/swsets/toolchain/*.md
- software/swsets/tools/*.md
- software/swsets/vis/*.md
# Extras
extra:
social:
- icon: fontawesome/brands/github-alt
link: https://github.com/ULHPC
- icon: fontawesome/brands/twitter
link: https://twitter.com/ULHPC
# Extra stylesheets (incl. Twitter Bootstrap)
extra_css:
- stylesheets/extra.css
# - stylesheets/bootstrap.min.css
# Extra javascript
extra_javascript:
- javascripts/extra.js
- javascripts/bootstrap.min.js
- https://cdn.jsdelivr.net/npm/mathjax@3/es5/tex-svg.js
# https://squidfunk.github.io/mkdocs-material/reference/data-tables/#sortable-tables
- https://cdnjs.cloudflare.com/ajax/libs/tablesort/5.2.1/tablesort.min.js
- javascripts/tables.js
# Extensions
markdown_extensions:
- attr_list
# notes, warnings, hints, ...
- admonition
- codehilite:
guess_lang: false
- footnotes
- markdown_include.include:
base_path: docs
- markdown.extensions.admonition
- meta
- pymdownx.arithmatex
- pymdownx.details
# Icons from Emoji extensions, giving access to following icon sets:
# - Material Design: https://materialdesignicons.com/
# - FontAwesome: https://fontawesome.com/icons?d=gallery&m=free
# – Octicons: https://octicons.github.com/
- pymdownx.emoji:
emoji_index: !!python/name:materialx.emoji.twemoji
emoji_generator: !!python/name:materialx.emoji.to_svg
# auto-link HTML, FTP, and email links
- pymdownx.magiclink:
repo_url_shorthand: true
social_url_shorthand: true
- pymdownx.snippets:
base_path: snippets
- pymdownx.tabbed
- pymdownx.smartsymbols
# code blocks with syntax highlighting, graphs
- pymdownx.superfences
- toc:
permalink: true