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mkdocs.yml
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site_name: Docs CSC
repo_url: "https://github.com/CSCfi/csc-user-guide/"
repo_name: "CSCfi/csc-user-guide"
site_url: "https://docs.csc.fi/"
site_description: Instructions and user guides for the CSC supercomputers, cloud services, storage and software, including FAQ and tutorials
extra:
environment: !ENV [MKDOCS_ENV, "preview"]
announcement_visible: true # Controls the visibility of the announcement bar
breadcrumbs_debug: !ENV DEBUG # Renders a debug view for breadcrumbs navigation
analytics:
provider: custom
matomo_site_id: !ENV [MATOMO_SITE_ID, ""]
matomo_url: !ENV [MATOMO_URL, ""]
feedback:
title: Do you find this page useful?
ratings:
- name: "Yes"
type: Positive
description: Yes! I do find this page useful.
note: >-
Thank you for your feedback!
- name: "No"
type: Negative
description: No! This page needs to be improved.
note: >-
Thank you! Your feedback is appreciated.
exclude:
- ref.md
hooks:
- hooks/archives.py
plugins:
- tags:
tags_file: apps/by_license.md
- search
- git-revision-date-localized:
enabled: !ENV [ENABLED_GIT_REVISION_DATE, true]
fallback_to_build_date: true
type: date
custom_format: "%Y-%m-%dT%H:%M:%S%z" # Used with feedback buttons
locale: en
timezone: Europe/Helsinki
exclude:
- index.md
- support/archives/*.md
- support/glossary.md
- support/whats-new.md
- apps/index.md
- apps/by_discipline.md
- apps/by_system.md
- apps/by_license.md
- section-index
- redirects:
redirect_maps:
# deprecation:
'support/tutorials/nomachine-usage.md': 'apps/nomachine.md'
'support/faq/cannot-login-from-nomachine.md': 'apps/nomachine.md'
'support/tutorials/puhti_quick.md': 'support/tutorials/hpc-quick.md'
'support/tutorials/mahti_quick.md': 'support/tutorials/hpc-quick.md'
# renamed files:
'cloud/csc_notebooks/what_is_new.md': 'support/whats-new.md#cloud-services'
'cloud/csc_notebooks/concepts.md': 'cloud/noppe/concepts.md'
'cloud/csc_notebooks/data_persistence.md': 'cloud/noppe/data_persistence.md'
'cloud/csc_notebooks/guide_for_students.md': 'cloud/noppe/guide_for_students.md'
'cloud/csc_notebooks/guide_for_teachers.md': 'cloud/noppe/guide_for_teachers.md'
'cloud/csc_notebooks/index.md': 'cloud/noppe/index.md'
'computing/overview.md': 'computing/index.md'
'cloud/concepts.md': 'cloud/index.md'
'apps/alpha.md': 'apps/index.md'
'support/tutorials/env-guide/overview.md': 'support/tutorials/env-guide/index.md'
# for URL consistency:
'sensitive-data.md': 'data/sensitive-data/index.md'
'applications.md': 'apps/index.md'
'faq.md': 'support/faq/index.md'
'tutorials.md': 'support/tutorials/index.md'
'training-material.md': 'support/training-material.md'
'contact.md': 'support/contact.md'
'whats-new.md': 'support/whats-new.md'
# for convenience:
'glossary.md': 'support/glossary.md'
'archives.md': 'support/contact.md#archives'
markdown_extensions:
- footnotes
- admonition
- abbr
- attr_list
- def_list
- pymdownx.details
- pymdownx.tabbed:
alternate_style: true
- pymdownx.snippets:
base_path: csc-overrides/assets/snippets
auto_append:
- glossaries/hpc.md
- pymdownx.superfences:
custom_fences:
- name: mermaid
class: mermaid
format: !!python/name:pymdownx.superfences.fence_code_format
theme:
name: material
language: en
custom_dir: csc-overrides
logo: assets/images/logo.png
favicon: assets/images/logo.png
icon:
repo: material/github
palette:
scheme: csc
font: false # No loading fonts from G****e
# features:
# - announce.dismiss
extra_css:
- assets/stylesheets/extra.css
extra_javascript:
- assets/javascripts/constants.js # Constants need to be loaded first since the other scripts depend on them
- assets/javascripts/dropdown.js
- assets/javascripts/layout.js
- assets/javascripts/extra.js
- assets/javascripts/feedback.js
nav:
- Home: index.md
- Accounts:
- accounts/index.md
- Creating a new user account: accounts/how-to-create-new-user-account.md
- Changing your password: accounts/how-to-change-password.md
- Managing user information: accounts/how-to-manage-user-information.md
- Creating a new project: accounts/how-to-create-new-project.md
- When your project handles personal data: accounts/when-your-project-handles-personal-data.md
- Adding members to your project: accounts/how-to-add-members-to-project.md
- Adding service access for your project: accounts/how-to-add-service-access-for-project.md
- Managing your project: accounts/how-to-manage-your-project.md
- Applying for billing units: accounts/how-to-apply-for-billing-units.md
- Increasing disk quotas: accounts/how-to-increase-disk-quotas.md
- Accessing Mahti large partition: accounts/how-to-access-mahti-large-partition.md
- Reviewing billing unit usage: accounts/how-to-view-billing-unit-usage.md
- Billing: accounts/billing.md
- Multi-factor Authentication: accounts/mfa.md
- Strong identification: accounts/strong-identification.md
- FMI: accounts/fmi.md
- Computing:
- computing/index.md
- Usage policy: computing/usage-policy.md
- Billing: computing/hpc-billing.md
- Systems:
- computing/available-systems.md
- Puhti: computing/systems-puhti.md
- Mahti: computing/systems-mahti.md
- LUMI: "https://docs.lumi-supercomputer.eu/hardware/"
- Connecting:
- computing/connecting/index.md
- SSH client on macOS and Linux: computing/connecting/ssh-unix.md
- SSH client on Windows: computing/connecting/ssh-windows.md
- Setting up SSH keys: computing/connecting/ssh-keys.md
- Supercomputer storage:
- computing/disk.md
- Lustre filesystem: computing/lustre.md
- Allas object storage: computing/allas.md
- Module environment: computing/modules.md
- Running jobs:
- computing/running/getting-started.md
- Create Puhti batch jobs: computing/running/creating-job-scripts-puhti.md
- Puhti example scripts: computing/running/example-job-scripts-puhti.md
- Create Mahti batch jobs: computing/running/creating-job-scripts-mahti.md
- Mahti example scripts: computing/running/example-job-scripts-mahti.md
- Submitting a job: computing/running/submitting-jobs.md
- Available batch job partitions: computing/running/batch-job-partitions.md
- High throughput: computing/running/throughput.md
- Interactive usage: computing/running/interactive-usage.md
- Performance checklist: computing/running/performance-checklist.md
- Installing software:
- computing/installing.md
- Compiling on Puhti: computing/compiling-puhti.md
- Compiling on Mahti: computing/compiling-mahti.md
- Compiling on LUMI: computing/compiling-lumi.md
- High performance libraries: computing/hpc-libraries.md
- Debugging: computing/debugging.md
- Performance analysis: computing/performance.md
- Containers:
- computing/containers/overview.md
- Running containers: computing/containers/run-existing.md
- Creating containers: computing/containers/creating.md
- Container wrapper (Tykky): computing/containers/tykky.md
- Web interface:
- computing/webinterface/index.md
- Connecting: computing/webinterface/connecting.md
- Shell: computing/webinterface/shell.md
- Files and storage services: computing/webinterface/file-browser.md
- Project view: computing/webinterface/project-view.md
- Interactive apps:
- computing/webinterface/apps.md
- Accelerated visualization: computing/webinterface/accelerated-visualization.md
- Desktop: computing/webinterface/desktop.md
- Jupyter: computing/webinterface/jupyter.md
- Julia on Jupyter: computing/webinterface/julia-on-jupyter.md
- Jupyter for courses: computing/webinterface/jupyter-for-courses.md
- MATLAB: computing/webinterface/matlab.md
- MLflow: computing/webinterface/mlflow.md
- RStudio: computing/webinterface/rstudio.md
- TensorBoard: computing/webinterface/tensorboard.md
- Visual Studio Code: computing/webinterface/vscode.md
- Quantum computing:
- computing/quantum-computing/overview.md
- Kvasi QLM:
- Accessing Kvasi: computing/quantum-computing/kvasi/kvasi.md
- Kvasi Billing: computing/quantum-computing/kvasi/kvasi-billing.md
- Helmi:
- Helmi projects: computing/quantum-computing/helmi/helmi-projects.md
- Access Helmi through LUMI: computing/quantum-computing/helmi/helmi-from-lumi.md
- First quantum job: computing/quantum-computing/helmi/first-quantum-job.md
- Technical details: computing/quantum-computing/helmi/helmi-specs.md
- FiQCI partition: computing/quantum-computing/helmi/fiqci-partition.md
- Running on Helmi: computing/quantum-computing/helmi/running-on-helmi.md
- Cloud Services:
- cloud/index.md
- Pouta:
- cloud/pouta/index.md
# - What is Pouta: cloud/pouta/pouta-what-is.md
# - Security Guidelines for Pouta: cloud/pouta/security.md
# - Pouta Accounting Principles and Quotas: cloud/pouta/accounting.md
# - Virtual machine flavors and Billing Unit rates: cloud/pouta/vm-flavors-and-billing.md
- Getting started:
- cloud/pouta/getting-started.md
- Creating a virtual machine: cloud/pouta/launch-vm-from-web-gui.md
- Connecting the virtual machine: cloud/pouta/connecting-to-vm.md
- Configuration:
- cloud/pouta/configuration.md
- VM lifecycle & saving BUs: cloud/pouta/vm-lifecycle.md
- Virtual machine flavors and Billing Unit rates: cloud/pouta/vm-flavors-and-billing.md
- Networking:
- cloud/pouta/networking.md
- Storage:
- cloud/pouta/storage.md
- Ephemeral storage: cloud/pouta/ephemeral-storage.md
- Persistent volumes: cloud/pouta/persistent-volumes.md
- Snapshots: cloud/pouta/snapshots.md
- Snapshot using QEMU: cloud/pouta/qemu-vm.md
- Multi-attach Cinder storage: cloud/pouta/multiattach.md
- Advanced:
- cloud/pouta/advanced.md
- Security Guidelines for Pouta: cloud/pouta/security.md
- Command line:
- cloud/pouta/command-line-tools.md
- Install: cloud/pouta/install-client.md
- Images:
- cloud/pouta/images.md
- Creating, Converting, Uploading and Sharing virtual machine images: cloud/pouta/adding-images.md
- Additional services (email, dns): cloud/pouta/additional-services.md
- API Access: cloud/pouta/api-access.md
- Application credentials: cloud/pouta/application-credentials.md
- Application Development Practises: cloud/pouta/application-dev.md
- Orchestration with Heat: cloud/pouta/heat-orchestration.md
# - Self study and troubleshooting:
# - Pouta videos: cloud/pouta/pouta-videos.md
- Known problems and limitations: cloud/pouta/known-problems.md
- Pukki:
- cloud/dbaas/index.md
- What is DBaaS: cloud/dbaas/what-is-dbaas.md
- Security Guides: cloud/dbaas/security-guides.md
- Getting started with DBaaS:
- cloud/dbaas/getting-started.md
- Web interface: cloud/dbaas/web-interface.md
- Command Line tools: cloud/dbaas/cli.md
- Firewalls: cloud/dbaas/firewalls.md
- Database Operations: cloud/dbaas/operations.md
- Application Credentials: cloud/dbaas/application-credentials.md
- Database sizes and prices: cloud/dbaas/flavors.md
- Backups: cloud/dbaas/backups.md
- Databases:
- cloud/dbaas/databases.md
- PostgreSQL:
- cloud/dbaas/postgresql.md
- Accessing your database: cloud/dbaas/postgres-accessing.md
- PostgreSQL version differences: cloud/dbaas/postgres-versions.md
- Extensions and parameters: cloud/dbaas/postgres-extensions.md
- Permissions: cloud/dbaas/postgres-permissions.md
- More advanced features: cloud/dbaas/advanced.md
- Resizing database instance volume: cloud/dbaas/resize-volume.md
- Rahti 2:
- cloud/rahti2/index.md
- What is Rahti: cloud/rahti2/rahti-what-is.md
- Moving into Rahti: cloud/rahti2/moving-into.md
- Containers & their Orchestration: cloud/rahti2/containers.md
- Kubernetes and OpenShift concepts: cloud/rahti2/concepts.md
- Networking: cloud/rahti2/networking.md
- Security guide: cloud/rahti2/security-guide.md
- Getting Started:
- Getting access: cloud/rahti2/access.md
- Using the web interface: cloud/rahti2/usage/getting_started.md
- Command line tool installation and usage: cloud/rahti2/usage/cli.md
- Migration to Rahti 2: cloud/rahti/rahti-migration.md
- Storage in Rahti:
- cloud/rahti2/storage/index.md
- Persistent volumes: cloud/rahti2/storage/persistent.md
- Ephemeral storage: cloud/rahti2/storage/ephemeral.md
- Object storage: cloud/rahti2/storage/objectstorage.md
- Expand a volume: cloud/rahti2/storage/expand-volumes.md
- Volume snapshot: cloud/rahti2/storage/volume-snapshot.md
- Images:
- cloud/rahti2/images/overview.md
- Creating an image: cloud/rahti2/images/creating.md
- Keeping docker images small: cloud/rahti2/images/keeping_docker_images_small.md
- Using Rahti 2 integrated registry: cloud/rahti2/images/Using_Rahti_2_integrated_registry.md
- Rahti Catalog: cloud/rahti2/catalog-docs.md
- Projects and quota: cloud/rahti2/usage/projects_and_quota.md
- Billing: cloud/rahti2/billing.md
- External documentation: cloud/rahti2/ext_docs.md
- Rahti:
- cloud/rahti/index.md
- What is Rahti: cloud/rahti/rahti-what-is.md
- Containers & their Orchestration: cloud/rahti/containers.md
- Kubernetes and OpenShift concepts: cloud/rahti/concepts.md
- Networking: cloud/rahti/networking.md
- Security guide: cloud/rahti/security-guide.md
- Getting Started:
- Getting access: cloud/rahti/access.md
- Using the web interface: cloud/rahti/usage/getting_started.md
- Command line tool installation and usage: cloud/rahti/usage/cli.md
- Migration to Rahti 2: cloud/rahti/rahti-migration.md
- Storage in Rahti:
- cloud/rahti/storage/index.md
- Persistent volumes: cloud/rahti/storage/persistent.md
- Ephemeral storage: cloud/rahti/storage/ephemeral.md
- Expand a volume: cloud/rahti/storage/expand-volumes.md
- Images:
- cloud/rahti/images/overview.md
- Creating an image: cloud/rahti/images/creating.md
- Pushing to external repository: cloud/rahti/images/pushing-external.md
- Keeping docker images small: cloud/rahti/images/keeping_docker_images_small.md
- GPU in Rahti: cloud/rahti/gpu.md
- Rahti Templates: cloud/rahti/template-docs.md
- Projects and quota: cloud/rahti/usage/projects_and_quota.md
- Billing: cloud/rahti/billing.md
- External documentation: cloud/rahti/ext_docs.md
- Noppe:
- cloud/noppe/index.md
- Guide for students: cloud/noppe/guide_for_students.md
- Guide for teachers: cloud/noppe/guide_for_teachers.md
- Concepts: cloud/noppe/concepts.md
- Data persistence: cloud/noppe/data_persistence.md
- Cloud Tutorials: cloud/tutorials/index.md
- Data:
- data/index.md
# - Datasets: data/datasets.md
- Working with data:
- data/datasets/dataset-sources.md
- Tips for data management: data/datasets/datamanagement.md
- Metadata and data documentation: data/datasets/metadata-and-documentation.md
- Dataset sources: data/datasets/sourcing-datasets.md
- Storing data at CSC: data/datasets/hosting-datasets-at-CSC.md
- Publishing datasets: data/datasets/publishing-datasets.md
- Moving data:
- data/moving/index.md
- Copying files using scp: data/moving/scp.md
- Moving files using the HPC web interfaces: data/moving/web-interface.md
- Graphical file transfer tools: data/moving/graphical_transfer.md
- Using rsync for data transfer and synchronization: data/moving/rsync.md
- Using tar and SSH to transfer many small files efficiently: data/moving/tar_ssh.md
- Using wget to download data from web sites to CSC: data/moving/wget.md
- Sharing and transporting files using Funet FileSender: data/moving/funet.md
- Moving data between IDA and CSC computing environment: data/ida/using_ida.md
- Remote disk mounts: data/moving/disk_mount.md
- Copying data between Allas and IDA via Puhti: data/moving/copy_allas_ida.md
- Allas object storage:
- data/Allas/index.md
- Introduction to Allas Storage service: data/Allas/introduction.md
- Accessing Allas: data/Allas/accessing_allas.md
- Common Use Cases: data/Allas/using_allas/common_use_cases.md
- Common Error Messages: data/Allas/using_allas/error_messages.md
- Allas object storage related terms and concepts: data/Allas/terms_and_concepts.md
- Allas clients:
- a-command: data/Allas/using_allas/a_commands.md
- a-backup: data/Allas/using_allas/a_backup.md
- Cyberduck: data/Allas/using_allas/cyberduck.md
- Python with S3: data/Allas/using_allas/python_boto3.md
- Python with SWIFT: data/Allas/using_allas/python_swift.md
- Rclone from Computing environment: data/Allas/using_allas/rclone.md
- Rclone form Workstation: data/Allas/using_allas/rclone_local.md
- Swift: data/Allas/using_allas/swift_client.md
- S3cmd: data/Allas/using_allas/s3_client.md
- Web GUI: data/Allas/using_allas/web_client.md
# data/Allas/using_allas/directory_object_error.md is not linked in this structure
- Kaivos database service:
- data/kaivos/overview.md
- Getting a database account: data/kaivos/kaivos-account.md
- MySQL client programs at CSC: data/kaivos/kaivos_client_in_puhti.md
- Data import and export: data/kaivos/kaivos_import.md
- Using MySQL client through batch job system: data/kaivos/kaivos_batch_job.md
- Using kaivos.csc.fi directly from your local computer: data/kaivos/kaivos_remote.md
- Using Perl MySQL API at CSC: data/kaivos/kaivos_perl.md
# Python MySQL API at CSC:
- Sensitive data:
- data/sensitive-data/index.md
- Choose service: data/sensitive-data/choose-a-service.md
- Store and analyse:
- Start here:
- data/sensitive-data/sd-access.md
- Access as project manager: data/sensitive-data/sd-use-case-new-user-project-manager.md
- Access as project member: data/sensitive-data/sd-use-case-new-user-project-member.md
- Manage CSC project: data/sensitive-data/sd-csc-project.md
- Store with SD Connect:
- data/sensitive-data/sd_connect.md
- Login to SD Connect: data/sensitive-data/sd-connect-login.md
- Upload: data/sensitive-data/sd-connect-upload.md
- Share: data/sensitive-data/sd-connect-share.md
- Download: data/sensitive-data/sd-connect-download.md
- Download files uploaded with previous version: data/sensitive-data/sd-connect-download-old-version.md
- Delete: data/sensitive-data/sd-connect-delete.md
- Command line interface: data/sensitive-data/sd-connect-command-line-interface.md
- Troubleshooting: data/sensitive-data/sd-connect-troubleshooting.md
- Analyse with SD Desktop:
- data/sensitive-data/sd_desktop.md
- Login to SD Desktop: data/sensitive-data/sd-desktop-login.md
- Create virtual desktop: data/sensitive-data/sd-desktop-create.md
- Manage virtual desktop: data/sensitive-data/sd-desktop-manage.md
- Access virtual desktop and data: data/sensitive-data/sd-desktop-access.md
- Software in virtual desktop: data/sensitive-data/sd-desktop-software.md
- Export data: data/sensitive-data/sd-desktop-export.md
- Troubleshooting: data/sensitive-data/sd-desktop-troubleshooting.md
- Publish and reuse:
- Federated EGA:
- data/sensitive-data/federatedega.md
- Data access application: data/sensitive-data/fega-application.md
- Data access approval for DAC: data/sensitive-data/fega-dac.md
- Data submission: data/sensitive-data/fega-submission.md
- SD Apply:
- data/sensitive-data/sd-apply.md
- Data access for Data Applicant: data/sensitive-data/sd-apply-access.md
- Data approval for DAC: data/sensitive-data/sd-apply-approval.md
- Secondary use of health and social data:
- Start here:
- Access with Findata permit: data/sensitive-data/findata-permit.md
- Access with register permit: data/sensitive-data/single-register-permit.md
- Analyse with SD Desktop for secondary use:
- data/sensitive-data/sd-desktop-audited.md
- Create virtual desktop: data/sensitive-data/sd-desktop-secondary-create.md
- Manage virtual desktop: data/sensitive-data/sd-desktop-secondary-manage.md
- Access virtual desktop and data: data/sensitive-data/sd-desktop-secondary-access.md
- Export data: data/sensitive-data/sd-desktop-secondary-export.md
- Troubleshooting: data/sensitive-data/sd-desktop-secondary-troubleshooting.md
- Instructions for registers: data/sensitive-data/single-register-submission.md
- Terminology: data/sensitive-data/sd-terminology.md
- Applications:
- apps/index.md
- By discipline: apps/by_discipline.md
- By availability: apps/by_system.md
- By license: apps/by_license.md
- FAQ: support/faq/index.md
- Tutorials: support/tutorials/index.md
- Training material: support/training-material.md
- Contact: support/contact.md
- What's new: support/whats-new.md