Changes for page Using JupyterHub in HDC

Last modified by Dennis Segebarth on 2024/10/02 18:14
From version 19.1
edited by Dennis Segebarth
on 2024/10/02 18:14
Change comment: There is no comment for this version
To version 6.1
edited by Dennis Segebarth
on 2024/03/01 09:14
Change comment: There is no comment for this version

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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"]]
8 +[[image:Jupyterhub-Logo-300x100px cropped.png||height="13%" width="20%"]]
9 9  
10 10  
11 11  = How it Works =
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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"]]
30 +[[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"]]
45 +[[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"]]
54 +[[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"]]
191 +[[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"]]
196 +[[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"]]
286 +[[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"]]
288 +[[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"]]
371 +[[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"]]
412 +[[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  
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420 420  Copyright © 2023-2024 [[Indoc Systems>>url:https://www.indocsystems.com]].
421 421  
422 422  HealthDataCloud is powered by Pilot technology, a product of [[Indoc Systems>>url:https://www.indocsystems.com]].
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