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mkdocs.yml
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# ------------------------------------
# -------- Project Information -------
# ------------------------------------
site_name: NCAR HPC Documentation
site_description: NCAR HPC Docs website
repo_url: https://github.com/NCAR/HPC-Docs/
site_url: https://ncar-hpc-docs.readthedocs.io/en/latest/
site_author: CISL CSG (Consulting Services Group)
edit_uri: edit/main/docs/
# directories to watch for automatic rebuilding when running "mkdocs serve"
watch:
- mkdocs.yml
- themes/
- docs/
# ------------------------------------
# -------- validation config ---------
# ------------------------------------
validation:
nav:
not_found: warn # check if stubs exist or not!
omitted_files: ignore # check for files that exist without any links to them in nav
absolute_links : warn # check for absolute links -- pointers to outside htmls in nav
links:
not_found: ignore # check for broken links inside mds. (to be activated later!)
absolute_links : ignore # check for absolute links -- pointers to outside htmls in files (to be activated later!)
unrecognized_links: ignore # unrecognized relative links (to be activated later!)
# ------------------------------------
# ----------- content ----------------
# ------------------------------------
nav:
- Home : index.md
- Getting Started:
- getting-started/index.md
- User Responsibilities: getting-started/user-responsibilities.md
- Accounts:
- getting-started/accounts/index.md
- CIT Passwords: getting-started/accounts/cit-passwords.md
- Duo Two-Factor Authentication:
- getting-started/accounts/duo/index.md
- Enrolling with Duo: getting-started/accounts/duo/enrolling.md
- SAM: getting-started/accounts/systems-accounting-manager.md
- Allocations:
- allocations/index.md # -- https://arc.ucar.edu/knowledge_base/74317835
- Managing Your Allocation: getting-started/managing-your-allocation.md
- NCAR Allocations:
- allocations/ncar-allocations/index.md
- NCAR Strategic Capability (NSC) projects: allocations/ncar-allocations/ncar-strategic-capability-nsc-projects.md
- University Allocations:
- allocations/university-allocations/index.md
- University Large Allocation Request Preparation Instructions : allocations/university-allocations/university-large-allocation-request-preparation-instructions.md
- Determining computational resource needs: allocations/determining-computational-resource-needs.md
- CISL HPC Allocations Panel:
- allocations/chap/index.md
- Allocation Review Criteria: allocations/chap/chap-allocation-review-criteria.md
- Conflict of Interest Policy: allocations/chap/chap-conflict-of-interest-policy.md
- VPN access : getting-started/vpn-access.md
- System Usage Policies: getting-started/system-usage-policies.md
- Data Retention Policies: getting-started/data-retention-policies.md
- Best Practices for Supercomputer Users: getting-started/best-practices-for-supercomputer-users.md
- Acknowledging NCAR and CISL: getting-started/acknowledging-ncar-and-cisl.md
- Storage Systems and Data Transfer:
- storage-systems/index.md
- GLADE (POSIX File Systems):
- storage-systems/glade/index.md
- Campaign storage file system: storage-systems/glade/campaign.md
- Scratch Lustre file system: storage-systems/glade/lustre.md
- Setting File and Directory Permissions: storage-systems/glade/setting-file-directory-permissions.md
- Using Access Control Lists : storage-systems/glade/using-access-control-lists.md
- Recovering files from snapshots : storage-systems/glade/recovering-files-from-snapshots.md
- Removing large number of files : storage-systems/glade/removing-large-number-of-files.md
- Quasar (Tape Storgae):
- storage-systems/quasar/index.md
- Quasar system specifications : storage-systems/quasar/quasar+system+specifications.md
- Stratus (Object Storage): storage-systems/stratus/index.md
- Data Access Nodes: storage-systems/data-access-nodes.md
- Transferring Data:
- storage-systems/data-transfer/index.md
- Globus:
- storage-systems/data-transfer/globus/index.md
- Sharing data and making unattended transfers: storage-systems/data-transfer/globus/Sharing+data+and+making+unattended+transfers.md
- SCP, SFTP and other tools: storage-systems/data-transfer/scp-and-sftp.md
- CMIP Analysis Platform: storage-systems/cmip-analysis-platform.md
- User Environment and HPC Software:
- environment-and-software/index.md
- User Environment:
- environment-and-software/user-environment/index.md
- Modules: environment-and-software/user-environment/modules.md
- Conda: environment-and-software/user-environment/conda.md
- Containers:
- environment-and-software/user-environment/containers/index.md
- Working with Containers: environment-and-software/user-environment/containers/working_with_containers.md
- Example Workflows: environment-and-software/user-environment/containers/examples.md
- Utilities: environment-and-software/user-environment/utilities.md
- Customizing User Environment: environment-and-software/user-environment/customizing.md
- Spack: environment-and-software/user-environment/spack/index.md
- HPC Software:
- environment-and-software/hpc-software/index.md
- Community Models: environment-and-software/community-models.md
- Data Analysis and Visualization : environment-and-software/data-analysis-and-visualization.md
- NCL : environment-and-software/ncl.md
- MATLAB Parallel Computing Toolbox: environment-and-software/matlab-parallel-computing-toolbox.md
- Numerical Libraries: environment-and-software/numerical-libraries.md
- Machine Learning and Deep Learning : environment-and-software/machine-learning-and-deep-learning.md
- NCAR Classic Libraries for Geophysics: environment-and-software/ncar-classic-libraries-for-geophysics.md
- Profiling & Debuggers: # -- tentative placement
- Debugging and Profiling with Forge Tools: environment-and-software/hpc-software/profiling-and-debuggers/running-ddt-map-and-pr-jobs.md
- Intel Parallel Studio XE: environment-and-software/hpc-software/profiling-and-debuggers/intel-parallel-studio-xe.md
- Benchmarks:
- environment-and-software/benchmarks/index.md
- NCAR Benchmarking applications - 2015 release: environment-and-software/benchmarks/ncar-benchmarking-2015.md
- NCAR Benchmarking applications - 2019-2020 release: environment-and-software/benchmarks/ncar-benchmarking-2019-2020.md
- Compute Systems and Services:
- Derecho:
- compute-systems/derecho/index.md
- Derecho Use Policies: compute-systems/derecho/derecho-use-policies.md
- Compiling Code on Derecho: compute-systems/derecho/compiling-code-on-derecho/index.md
- Starting Derecho Jobs:
- compute-systems/derecho/starting-derecho-jobs/index.md
- Derecho Job Script Examples:
- compute-systems/derecho/starting-derecho-jobs/derecho-job-script-examples.md
- Process Binding : compute-systems/derecho/starting-derecho-jobs/process-binding.md
- Derecho Software: compute-systems/derecho/derecho-modules.md
- Moving to Derecho from Cheyenne: compute-systems/derecho/moving-from-cheyenne.md
- Casper:
- compute-systems/casper/index.md
- Casper Use Policies: compute-systems/casper/casper-use-policies.md
- Compiling Code on Casper: compute-systems/casper/compiling-code-on-casper/index.md
- Starting Casper Jobs:
- compute-systems/casper/starting-casper-jobs/index.md
- Casper job Script Examples: compute-systems/casper/starting-casper-jobs/casper-job-script-examples.md
- Using Remote Desktops: compute-systems/casper/remote-desktops.md
- Casper Software: compute-systems/casper/casper-modules.md
- JupyterHub:
- compute-systems/jupyterhub/index.md
- Jupyter and IPython: compute-systems/jupyter-and-ipython.md
- Additional Resources:
- Cron services: compute-systems/additional-resources/cron.md
- Thunder test system: compute-systems/additional-resources/thunder-test-system.md
- Running Jobs (PBS):
- pbs/index.md
- Job Scripts:
- pbs/job-scripts/index.md
- Queues and Charging: pbs/charging.md
- Using Preemption: pbs/preemption.md
- Common Causes of Job Failures:
- pbs/common-causes-of-job-failures/index.md
- Checking Memory Use:
- pbs/checking-memory-use/index.md
- Storing temporary files: pbs/storing-temporary-files.md
- Tutorials:
- tutorials/index.md
- New User Training: tutorials/new-user-training.md
- Derecho Overview: tutorials/derecho-overview.md
- Dask Tutorial: tutorials/dask-tutorial.md
- Profiling and Debugging: tutorials/profiling-and-debugging.md
- Advanced PBS: tutorials/advanced-pbs.md
- Using Globus v5: tutorials/globus.md
- NCAR Storage Spaces: tutorials/storage.md
- JupyterHub: tutorials/jupyterhub.md
- Remote Desktop Services: tutorials/remote-desktops.md
# - Containers: tutorials/containers.md
# - GPU Workshop: tutorials/gpu-workshop.md
- User Support:
- user-support/index.md
# - Troubleshooting Tips:
# - Killed processes on login nodes: user-support/troubleshooting-tips/killed-processes-on-login-nodes.md
# - Common causes of job failures: user-support/troubleshooting-tips/common-causes-of-job-failures.md
# - Batch jobs crashing: user-support/troubleshooting-tips/batch-job-crashing.md
- NCAR User Group (NHUG):
- nhug/index.md
- Contributing to the Documentation: contributing.md
# ------------------------------------
# -- configuration - themes
# (note theme.yml should be a symbolic link to one of several options'
# ------------------------------------
INHERIT: theme.yml
extra_javascript:
- https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.0/MathJax.js?config=TeX-MML-AM_CHTML
copyright: '© 2023-2024 UCAR, Licensed under the <a href="https://creativecommons.org/licenses/by-sa/4.0/">Creative Commons CC-BY-SA 4.0</a>.'
# ------------------------------------
# -- configuration - extensions
# ------------------------------------
markdown_extensions:
- meta
- attr_list
- footnotes
- admonition
- md_in_html
- def_list
- toc:
permalink: true
title: "Page Outline"
# https://squidfunk.github.io/mkdocs-material/reference/code-blocks/
- pymdownx.highlight:
anchor_linenums: true
line_spans: __span
pygments_lang_class: true
- pymdownx.inlinehilite
- pymdownx.snippets:
url_download: true
- pymdownx.superfences:
custom_fences:
- name: mermaid
class: mermaid
format: !!python/name:pymdownx.superfences.fence_code_format
- codehilite:
guess_lang: true
- pymdownx.arithmatex
- pymdownx.betterem:
smart_enable: all
- pymdownx.caret
- pymdownx.critic
- pymdownx.emoji:
emoji_generator: !!python/name:pymdownx.emoji.to_svg
- pymdownx.magiclink
- pymdownx.mark
- pymdownx.smartsymbols:
fractions: false
- pymdownx.superfences
- pymdownx.details
- pymdownx.tasklist:
custom_checkbox: true
- pymdownx.tilde
- pymdownx.arithmatex:
generic: true
- pymdownx.betterem:
smart_enable: all
- pymdownx.caret
- pymdownx.details
- pymdownx.emoji:
emoji_generator: !!python/name:materialx.emoji.to_svg
- pymdownx.keys
- pymdownx.magiclink:
repo_url_shorthand: true
user: squidfunk
repo: mkdocs-material
- pymdownx.mark
- pymdownx.smartsymbols
- pymdownx.tabbed:
alternate_style: true
- pymdownx.tasklist:
custom_checkbox: true
- pymdownx.tilde
# ------------------------------------
# -- configuration - extensions
# ------------------------------------
plugins:
- search:
enabled: true
- git-revision-date-localized:
enable_creation_date: true
type: timeago
- glightbox:
touchNavigation: true
loop: false
effect: zoom
slide_effect: slide
width: 100%
height: auto
zoomable: true
draggable: true
skip_classes:
- custom-skip-class-name
auto_caption: false
caption_position: bottom
- minify:
minify_html: true
- open-in-new-tab
- redirects:
redirect_maps:
'nhug/index.md': 'https://nhug.readthedocs.io/en/latest/'
# ------------------------------------
# -- configuration - extras
# ------------------------------------
extra:
analytics:
provider: google
property: G-RZLJ37D0K6
social:
- icon: material/home-circle
link: https://arc.ucar.edu/
- icon: material/help-circle
link: https://ithelp.ucar.edu/plugins/servlet/desk/site/rc
- icon: fontawesome/brands/github
link: https://github.com/NCAR
- icon: fontawesome/brands/slack
link: https://join.slack.com/t/ncarhpcusergroup/shared_invite/zt-1z00napom-SU0X8CzJWVY90C2GzRvUCg