forked from CSCfi/csc-user-guide
-
Notifications
You must be signed in to change notification settings - Fork 0
/
mkdocs.yml
419 lines (403 loc) · 20.4 KB
/
mkdocs.yml
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
263
264
265
266
267
268
269
270
271
272
273
274
275
276
277
278
279
280
281
282
283
284
285
286
287
288
289
290
291
292
293
294
295
296
297
298
299
300
301
302
303
304
305
306
307
308
309
310
311
312
313
314
315
316
317
318
319
320
321
322
323
324
325
326
327
328
329
330
331
332
333
334
335
336
337
338
339
340
341
342
343
344
345
346
347
348
349
350
351
352
353
354
355
356
357
358
359
360
361
362
363
364
365
366
367
368
369
370
371
372
373
374
375
376
377
378
379
380
381
382
383
384
385
386
387
388
389
390
391
392
393
394
395
396
397
398
399
400
401
402
403
404
405
406
407
408
409
410
411
412
413
414
415
416
417
418
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:
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'
# renamed files:
'cloud/csc_notebooks/what_is_new.md': 'support/whats-new.md#cloud-services'
'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
- 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.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
- 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:
- cloud/index.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
- Rahti Tutorials:
- Deploying a static web server using the web interface: cloud/rahti/tutorials/basic-console.md
- Deploying a static web server using the command line: cloud/rahti/tutorials/elemental_tutorial.md
- Custom domain names and secure transport: cloud/rahti/tutorials/custom-domain.md
- Configuration, ConfigMaps and Secrets: cloud/rahti/tutorials/configuration.md
- Webhooks: cloud/rahti/tutorials/webhooks.md
- Reverse proxy authentication using a sidecar container: cloud/rahti/tutorials/sidecar_proxy_authentication.md
- Short introduction to YAML: cloud/rahti/tutorials/yaml_introduction.md
- How to transfer data to Rahti?: cloud/rahti/tutorials/transfer_data_rahti.md
- How to add docker hub credentials to a project: cloud/rahti/tutorials/docker_hub_login.md
- How to manually cache images in Rahti's registry: cloud/rahti/tutorials/docker_hub_manual_caching.md
- How to package a Kubernetes application with Helm?: cloud/rahti/tutorials/helm.md
- Kustomize: cloud/rahti/tutorials/kustomize.md
- CI/CD on Rahti: cloud/rahti/tutorials/ci_cd_introduction.md
- How to run an ad-hoc interactive container: cloud/rahti/tutorials/oc-run.md
- How backup a Postgres DB into Allas: cloud/rahti/tutorials/backup-postgres-allas.md
- Annotations: cloud/rahti/tutorials/annotations.md
- Sending e-mail from Rahti: cloud/rahti/tutorials/email.md
- Accessing databases on Rahti from CSC supercomputers: cloud/rahti/tutorials/connect-database-hpc.md
- Multi stage builds: cloud/rahti/tutorials/multi-stage-builds.md
- Storage in Rahti:
- cloud/rahti/storage/index.md
- Persistent volumes: cloud/rahti/storage/persistent.md
- Ephemeral storage: cloud/rahti/storage/ephemeral.md
- Object storage: cloud/rahti/storage/objectstorage.md
- Expand a volume: cloud/rahti/storage/expand-volumes.md
- Images:
- cloud/rahti/images/overview.md
- Creating an image: cloud/rahti/images/creating.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
- 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 with Pouta:
- Creating a virtual machine in Pouta: cloud/pouta/launch-vm-from-web-gui.md
- Connecting to your virtual machine: cloud/pouta/connecting-to-vm.md
- Install command line tools: cloud/pouta/install-client.md
- Command line client tools: cloud/pouta/command-line-tools.md
- Application credentials: cloud/pouta/application-credentials.md
- API Access to Pouta: cloud/pouta/api-access.md
- Virtual machine lifecycle & saving billing units: cloud/pouta/vm-lifecycle.md
- Storage in Pouta:
- 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
- Images:
- cloud/pouta/images.md
- Creating, Converting, Uploading and Sharing virtual machine images: cloud/pouta/adding-images.md
- Networking:
- cloud/pouta/networking.md
- Application Development Practises in Pouta: cloud/pouta/application-dev.md
- Orchestration with Heat: cloud/pouta/heat-orchestration.md
- Jumphost in cPouta: cloud/pouta/create-jumphost.md
- Additional services in Pouta (email, dns): cloud/pouta/additional-services.md
- Self study and troubleshooting:
- Pouta videos: cloud/pouta/pouta-videos.md
- Known problems and limitations: cloud/pouta/known-problems.md
- Pukki (DBaaS):
- 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
- More advanced features: cloud/dbaas/advanced.md
- Resizing database instance volume: cloud/dbaas/resize-volume.md
- Grid computing:
- The Grid Monitor: cloud/grid/grid-monitor.md
- CSC Notebooks:
- cloud/csc_notebooks/index.md
- Guide for students: cloud/csc_notebooks/guide_for_students.md
- Guide for teachers: cloud/csc_notebooks/guide_for_teachers.md
- Concepts: cloud/csc_notebooks/concepts.md
- Data persistence: cloud/csc_notebooks/data_persistence.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 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 Library: data/Allas/using_allas/python_library.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
- Store with SD Connect:
- data/sensitive-data/sd_connect.md
- Login to SD Connect: data/sensitive-data/sd-connect-login.md
- Data upload for analysis: data/sensitive-data/sd-connect-upload-for-analysis.md
- Data upload for storage and sharing: data/sensitive-data/sd-connect-upload-for-storage-and-sharing.md
- Command line interface: data/sensitive-data/sd-connect-command-line-interface.md
- Information about data encryption: data/sensitive-data/sd-connect-introduction-to-data-encryption.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