Changes for page Using JupyterHub in HDC

Last modified by Dennis Segebarth on 2024/10/02 18:14
From version 18.1
edited by Dennis Segebarth
on 2024/10/02 18:13
Change comment: There is no comment for this version
To version 3.1
edited by Susan Evans
on 2023/07/11 14:11
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1 -XWiki.dsegebarth
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5 5  
6 6  JupyterHub is an open-source, multi-user version of Jupyter Notebook for performing analysis of Project files in the Core. More information can be found in the application documentation [[https:~~/~~/jupyter.org/>>https://jupyter.org/]].
7 7  
8 -[[image:1723798240534-407.png||height="189" width="291"]]
9 -
10 -
11 11  = How it Works =
12 12  
13 13  JupyterHub allows Project members to create or import Jupyter Notebooks into the Project Workspace environment, retrieve Project files from the Core, perform computational workflows on the data, and write the outputs back to the Core where they can be accessed by other Project members. JupyterHub spins up a new JupyterLab instance for each Project member.
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25 25  
26 26  JupyterHub is configured at the time of Project Setup. If you launch JupyterHub and receive a notice that it hasn’t been deployed for your project, please contact your Platform Administrator.
27 27  
28 -{{info}}
29 -If you access JupyterHub of the HealthDataCloud Test Project, please be aware that the resources are limited for each user to: 2 GB of persistent storage volume, 4 GB memory, and a single CPU. These limitations can easily be adjusted for new Projects.
30 -{{/info}}
31 -
32 32  = Launching JupyterHub =
33 33  
34 -[[image:1723798257792-201.png||height="121" width="349"]]
27 +[[image:HDC Project Workspace tool navigation Jupyterhub v1.0.0 2023-05-25.png||height="9%" width="25%"]]
35 35  
36 36  1. Launch your Project and click the **JupyterHub icon** in the left menu bar.
37 37  1. Click **Sign in with Keycloak** to initiate your session. JupyterHub automatically authenticates with your existing username and password and launches your session - no additional sign-in is required.
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46 46  1. In the Launcher, click the **Python 3 Notebook **icon, or click **File > New > Notebook**.
47 47  1. Create your Notebook.
48 48  
49 -[[image:1723798278604-114.png||height="376" width="865"]]
42 +[[image:Project Workspace Jupyter Create Python Notebook v2.1.6 2023-02-07.png||height="22%" width="50%"]]
50 50  
51 51  = Launching the Terminal =
52 52  
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55 55  1. In the Launcher, click the **Terminal **icon, or click **File > New > Terminal**.
56 56  1. The terminal window opens.
57 57  
58 -[[image:1723798293872-992.png||height="162" width="863"]]
51 +[[image:Project Workspace Jupyter Launch Terminal v2.1.6 2023-02-07.png||height="9%" width="50%"]]
59 59  
60 60  Ubuntu is used to host Jupyter Notebook. Use the command cat /etc/os-release to determine to current version of Ubuntu:
61 61  
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192 192  
193 193  Afterwards, the environment will be listed when you open the Launcher to open a new Jupyter Notebook:
194 194  
195 -[[image:1723798325144-485.png||height="436" width="867"]]
188 +[[image:Project Workspace Jupyter view new Kernel 2023-07-11.png||height="25%" width="50%"]]
196 196  
197 197  
198 198  and also from each opened Notebook, e.g., via **Kernel > Change Kernel…** :
199 199  
200 -[[image:1723798338447-469.png||height="317" width="247"]]
193 +[[image:Project Workspace Jupyter Kernel change Kernel dropdown 2023-07-11.png||height="32%" width="25%"]]
201 201  
202 202  = Installing New Python Packages =
203 203  
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287 287  * Open the login window and enter your HDC username and password (i.e. your EBRAINS account credentials).
288 288  * Grant access by clicking **Yes**.
289 289  
290 -[[image:1723798355215-434.png||height="352" width="379"]]
283 +[[image:Pilotcli Jupyter user login Grant Access window v2.4.0 2023-05-25.png||height="28%" width="30%"]]
291 291  
292 -[[image:1723798365454-527.png||height="123" width="376"]]
285 +[[image:Pilotcli Jupyter user login Device Login Successful v2.4.0 2023-05-25.png||height="10%" width="30%"]]
293 293  
294 294  * After successful confirmation, return to the terminal in your JupyterHub browser tab.
295 295  
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372 372  
373 373  The file “Chemical Tracking Data.csv” can be viewed in the JupyterHub graphical user interface:
374 374  
375 -[[image:1723798383409-873.png||height="267" width="874"]]
368 +[[image:Jupyter downloaded file in Home folder v2.4.11 2023-05-25 1850.png||height="15%" width="50%"]]
376 376  
377 377  
378 378  == Uploading Project Data from JupyterHub using the Pilot Command Line Interface ==
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413 413  Chemical Tracking Data rev.csv Chemical Tracking Data.csv
414 414  {{/code}}
415 415  
416 -[[image:1723798397694-530.png||height="217" width="863"]]
409 +[[image:Jupyterhub file upload back to core v2.4.11 2023-05-25 1926.png||height="13%" width="50%"]]
417 417  
418 418  ----
419 419  
420 -Copyright © 2023-2024 [[Indoc Systems>>url:https://www.indocsystems.com]].
413 +Copyright © 2023 [[Indoc Research>>url:https://www.indocresearch.org/]].
421 421  
422 -HealthDataCloud is powered by Pilot technology, a product of [[Indoc Systems>>url:https://www.indocsystems.com]].
415 +HealthDataCloud is powered by Pilot technology, a product of [[Indoc Research>>url:https://www.indocresearch.org/]].
416 +
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