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mkdocs.yml
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site_name: Research Computing Documentation
repo_url: https://github.com/uabrc/uabrc.github.io/
edit_uri: edit/main/docs/
theme:
name: material
search_index_only: true
custom_dir: theme
language: en
features:
- navigation.indexes
- navigation.instant
- content.code.copy
favicon: images/favicon.png
logo: images/logo.png
extra_css:
- stylesheets/extra.css
extra_javascript:
- javascripts/mathjax.js
- https://polyfill.io/v3/polyfill.min.js?features=es6
- https://cdn.jsdelivr.net/npm/mathjax@3/es5/tex-mml-chtml.js
copyright: Copyright © 2021-2024 The University of Alabama at Birmingham.<br /><b>Still stuck after reading?</b> Email us at <a href="mailto:support@listserv.uab.edu" class="supportemail">support@listserv.uab.edu</a>
markdown_extensions:
- admonition
- attr_list
- md_in_html
- pymdownx.arithmatex:
generic: true
- pymdownx.details
- pymdownx.highlight:
anchor_linenums: true
- pymdownx.keys
- pymdownx.superfences
- tables
- toc:
permalink: true
plugins:
- search
- table-reader:
data_path: docs
- gen-files:
scripts:
- scripts/pandoc_generator.py
- git-revision-date-localized:
type: date
strict: false
- glightbox:
# auto_caption: true
- redirects:
redirect_maps:
account_management/gitlab_researcher.md: account_management/gitlab_account.md
account_management/uab_researcher.md: account_management/cheaha_account.md
account_management/xias_guest.md: account_management/xias/guest_instructions.md
account_management/xias_sites.md: account_management/xias/pi_site_management.md
account_management/xias_users.md: account_management/xias/pi_guest_management.md
cheaha/conda.md: cheaha/software/software.md#anaconda-on-cheaha
cheaha/lmod.md: cheaha/software/modules.md
cheaha/open_ondemand/ood_files.md: cheaha/open_ondemand/ood_layout.md
cheaha/open_ondemand/ood_interactive.md: cheaha/open_ondemand/index.md
cheaha/open_ondemand/ood_jobs.md: cheaha/open_ondemand/ood_layout.md
cheaha/open_ondemand/ood_main.md: cheaha/open_ondemand/ood_layout.md
cheaha/slurm/sbatch_usage.md: cheaha/slurm/submitting_jobs.md
contributor_guide.md: contributing/contributor_guide.md
data_management/LTS/lts.md: data_management/lts/index.md
data_management/LTS/sharing.md: data_management/lts/iam_and_policies.md
data_management/lts/lts.md: data_management/lts/index.md
data_management/lts/policies.md: data_management/lts/iam_and_policies.md
data_management/lts/sharing.md: data_management/lts/iam_and_policies.md
environment_management/anaconda_environments.md: workflow_solutions/using_anaconda.md
environment_management/containers.md: workflow_solutions/getting_containers.md
environment_management/git.md: workflow_solutions/git_collaboration.md
uab_cloud/cloud_remote_access.md: uab_cloud/remote_access.md
uab_cloud/instance_setup_basic.md: uab_cloud/tutorial/instances.md
uab_cloud/introduction.md: uab_cloud/index.md
uab_cloud/network_setup_basic.md: uab_cloud/tutorial/networks.md
uab_cloud/security_setup_basic.md: uab_cloud/tutorial/security.md
uab_cloud/volume_setup_basic.md: uab_cloud/tutorial/volumes.md
welcome/rc_days.md: education/research_computing_days/index.md
welcome/welcome.md: index.md
workflow_solutions/getting_software_with_git.md: workflow_solutions/git_collaboration.md
exclude_docs: |
/**/res/*.md
not_in_nav: |
/**/res/*.md
nav:
- Home: index.md
- Account Management:
- account_management/index.md
- Cheaha Account: account_management/cheaha_account.md
- External Collaborator Accounts (XIAS):
- account_management/xias/index.md
- "For PIs - (1) Managing Projects & Sites": account_management/xias/pi_site_management.md
- "For PIs - (2) Managing Guests": account_management/xias/pi_guest_management.md
- "For Guests - Account Creation": account_management/xias/guest_instructions.md
- Gitlab Account: account_management/gitlab_account.md
- Data Management:
- Cheaha Storage: data_management/storage.md
- Storage Alternatives: data_management/alternate_storage.md
- Long Term Storage:
- data_management/lts/index.md
- Tutorial:
- data_management/lts/tutorial/index.md
- LTS and s3cmd Workflow: data_management/lts/tutorial/individual_lts_tutorial.md
- Interfacing with LTS: data_management/lts/interfaces.md
- Identity and Access Management: data_management/lts/iam_and_policies.md
- UAB Core Accounts: data_management/lts/lts_cores.md
- FAQ: data_management/lts/lts_faq.md
- Transfer:
- Tutorial:
- data_management/transfer/tutorial/index.md
- Globus for Individuals: data_management/transfer/tutorial/globus_individual_tutorial.md
- Globus for Organizations: data_management/transfer/tutorial/globus_organization_tutorial.md
- Globus Group Management: data_management/transfer/tutorial/globus_group_management.md
- Globus: data_management/transfer/globus.md
- RClone: data_management/transfer/rclone.md
- FileZilla: data_management/transfer/filezilla.md
- Code Storage: data_management/code_storage.md
- Workflow Solutions:
- Using the Shell: workflow_solutions/shell.md
- Using Anaconda: workflow_solutions/using_anaconda.md
- Using Workflow Managers: workflow_solutions/using_workflow_managers.md
- Using Git: workflow_solutions/git.md
- R Projects and Environments: workflow_solutions/r_environments.md
- Software Containers: workflow_solutions/getting_containers.md
- Software Collaboration with GitHub and GitLab: workflow_solutions/git_collaboration.md
- Creating Sandbox Apps: workflow_solutions/creating_sandbox_apps.md
- Cheaha Guide:
- Getting Started: cheaha/getting_started.md
- Tutorials:
- cheaha/tutorial/index.md
- Anaconda Environment Tutorial: cheaha/tutorial/pytorch_tensorflow.md
- Cheaha Web Portal:
- cheaha/open_ondemand/index.md
- Using the Web Portal: cheaha/open_ondemand/ood_layout.md
- HPC Desktop: cheaha/open_ondemand/hpc_desktop.md
- Jupyter: cheaha/open_ondemand/ood_jupyter.md
- RStudio: cheaha/open_ondemand/ood_rstudio.md
- MATLAB: cheaha/open_ondemand/ood_matlab.md
- Hardware: cheaha/hardware.md
- Software:
- Pre-installed Modules: cheaha/software/modules.md
- Self-Installed Software: cheaha/software/software.md
- SLURM:
- Introduction: cheaha/slurm/introduction.md
- Slurm Tutorial: cheaha/slurm/slurm_tutorial.md
- Submitting Jobs: cheaha/slurm/submitting_jobs.md
- Practical Batch Array Jobs: cheaha/slurm/practical_sbatch.md
- Managing Jobs: cheaha/slurm/job_management.md
- GPUs: cheaha/slurm/gpu.md
- Job Efficiency: cheaha/job_efficiency.md
- UAB Cloud (cloud.rc) Guide:
- uab_cloud/index.md
- Tutorial:
- uab_cloud/tutorial/index.md
- (1) Networks: uab_cloud/tutorial/networks.md
- (2) Security Policies: uab_cloud/tutorial/security.md
- (3) Instances: uab_cloud/tutorial/instances.md
- (4) Volumes (optional): uab_cloud/tutorial/volumes.md
- Remote Access: uab_cloud/remote_access.md
- Installing Software: uab_cloud/installing_software.md
- Snapshots and Images: uab_cloud/snapshots.md
- Sharing Cloud Environment: uab_cloud/sharing_cloud_environment.md
- UAB Kubernetes Guide:
- Startup: kubernetes/startup.md
- National Research Computing Cyberinfrastructure:
- national_ci/index.md
- The Open Science Grid: national_ci/osg.md
- NSF Cyberinfrastructure: national_ci/nsf_access.md
- NIH Cyberinfrastructure: national_ci/nih.md
- Grants & Contracts:
- RC Facilities Description: grants/facilities.md
- Acknowlding Us in Publications: grants/publications.md
- Funding Opportunities: grants/opportunities.md
- Outreach & Training:
- Case Studies: education/case_studies.md
- Research Computing Days:
- education/research_computing_days/index.md
- Offered Courses: education/courses.md
- Training Resources: education/training_resources.md
- Policies: policies.md
- Reporting Documentation Errors: contributing/reporting_errors.md
- Contributing Content: contributing/contributor_guide.md
- Help:
- Support: help/support.md
- FAQ - Frequently Asked Questions: help/faq.md
validation:
nav:
omitted_files: warn
not_found: warn
absolute_links: warn
links:
not_found: warn
anchors: warn
absolute_links: warn
unrecognized_links: warn
watch:
- scripts