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Last modified by ldomide on 2024/04/08 12:55
From version 33.1
edited by dionperd
on 2023/09/26 19:31
Change comment: There is no comment for this version
To version 30.1
edited by dionperd
on 2023/03/22 15:45
Change comment: There is no comment for this version

Summary

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20 20  * TVB Dedicated Wiki [[https:~~/~~/wiki.ebrains.eu/bin/view/Collabs/the-virtual-brain/>>url:https://wiki.ebrains.eu/bin/view/Collabs/the-virtual-brain/]]
21 21  * TVB in HBP User Story [[https:~~/~~/wiki.ebrains.eu/bin/view/Collabs/user-story-tvb/>>url:https://wiki.ebrains.eu/bin/view/Collabs/user-story-tvb/]]
22 22  
23 -== ==
23 +== Use our Jupyter Hub setup online ==
24 24  
25 -== Running TVB-MULTISCALE at EBRAINS JupyterLab ==
26 -
27 -TVB-multiscale is made available at [[EBRAINS JupyterLab>>https://lab.ebrains.eu/]].
28 -
29 -All the user has to do is login with the EBRAINS credentials, and start a Python console or a Jupyter notebook, TVB-multiscale being available for importing (e.g., via "import tvb_multiscale").
30 -
31 -All necessary TVB-multiscale dependencies (NEST, ANNarchy, NetPyNE (NEURON), Elephant, Pyspike) are also installed and available.
32 -
33 -We suggest the users to upload [[documented notebooks>>https://github.com/the-virtual-brain/tvb-multiscale/tree/master/docs/notebooks]] and/or [[examples' scripts and notebooks >>https://github.com/the-virtual-brain/tvb-multiscale/tree/master/examples]]from TVB-multiscale Github repository and run them there.
34 -
35 -Alternatively, users can sparse checkout the docs and examples folders of TVB-multiscale Github repo, via the following sequence of commands in a terminal or in Jupyter notebook's cells (for notebooks you need to use "!" before each command!):
36 -
37 -~1. Get into the user's My Libraries folder:
38 -
39 -{{{cd /mnt/user/drive/My Libraries}}}
40 -
41 -2. Create a folder, e.g., "tvb-multiscale-examples"
42 -
43 -{{{mkdir tvb-multiscale-examples}}}
44 -
45 -3. Create an empty git repository:
46 -
47 -{{{git init
48 -
49 -3. Add tvb-multiscale remote:
50 -git remote add -f origin }}}
51 -
52 -This fetches all objects but doesn't check them out.
53 -
54 -4. Allow for sparse checkout in git config:
55 -
56 -{{{git config core.sparseCheckout true
57 -}}}
58 -
59 -5. Add the docs and examples folders to the ones to be checked out:
60 -
61 -{{{echo "docs" >> .git/info/sparse-checkout
62 -
63 -echo "examples" >> .git/info/sparse-checkout}}}
64 -
65 -6. Finally, pull the master from the remote:
66 -
67 -{{{git pull origin master}}}
68 -
69 -which will download the specified folders.
70 -
71 -All these steps can of course be made from any user fork of the TVB-multiscale repository.
72 -
73 -Last but not least, users will also have to modify the attribute config.DEFAULT_CONNECTIVITY_ZIP of the base configuration class Config in all cases of examples and notebooks, to be able to load a default TVB connectivity for the simulations to run.  For instance, in the case of the above folder structure after sparse checkout, and assuming that the user runs the [[documented TVB-NEST_WilsonCowan.ipynb notebook>>https://github.com/the-virtual-brain/tvb-multiscale/blob/master/docs/notebooks/TVB-NEST_WilsonCowan.ipynb]], the correct path would be:
74 -
75 -config.DEFAULT_CONNECTIVITY_ZIP = "/mnt/user/drive/My Libraries/tvb-multiscale-examples/examples/data/tvb_data/berlinSubjects/QL_20120814/QL_20120814_Connectivity.zip"
76 -
77 -
78 -
79 -== Use our Jupyter Hub setup online ((% style="color:#c0392b" %)DEPRECATED(%%)) ==
80 -
81 -(% style="color:#c0392b" %)**TVB-multiscale app is deprecated and will stop being available after the end of 2023!**
82 -
83 83  We have setup a Jupyter Hub service with tvb-multiscale as backed already prepared. You will only need an HBP account for accessing this: [[https:~~/~~/tvb-multiscale.apps.hbp.eu/>>https://tvb-multiscale.apps.hbp.eu/]]
84 84  
85 85  This JupyterHub installation works smoothly with HBP Collab user credentials (login only once at HBP and get access here too). We use a custom Docker Hub tvb-multiscale image as a backend, and thus a ready to use environment is available immediately, without the need of any local installation or download. This should be the ideal env for demos, presentations or even workshops with tvb-multiscale.
... ... @@ -92,19 +92,16 @@
92 92  
93 93  **[[image:https://lh6.googleusercontent.com/nnsM0mhXQinmQsJwZwwwe5Sx7f-tZc8t4ELnCh9DwksyVEPUE-jixJTkhoP4l25VKwlDGoXACWtnuxQM9NMOCYbQOzDesgMDlT3sntow___vsEqRVd4OwqMY4BPyBiLJ32BnUbmM||height="267" width="614"]]**
94 94  
95 -Folder **Contributed-Notebooks** is not shared. Here, users can experiment with their own private examples. This folder is persisted on restarts in the user HBP Collab personal space. Thus, users will be able to access their work even after a redeploy. (e.g. during a workshop every participant could have in here his own exercise solution)
37 +Folder **Contributed-Notebooks** is not shared. Here, users can experiment with their own private examples. This folder is persisted on restarts in the user HBP Collab personal space. Thus, users will be able to access their work even after a redeploy. (e.g. during a workshop every participant could have in here his own exercise solution).
96 96  
97 -
98 98  == Running TVB-MULTISCALE locally ==
99 99  
100 -See more on Github [[https:~~/~~/github.com/the-virtual-brain/tvb-multiscale>>url:https://github.com/the-virtual-brain/tvb-multiscale]] .
41 +See more on Github [[https:~~/~~/github.com/the-virtual-brain/tvb-multiscale>>url:https://github.com/the-virtual-brain/tvb-multiscale]]  and check this notebook example: [[https:~~/~~/drive.ebrains.eu/f/b3ea5740fcc34f12af7a/?dl=1>>url:https://drive.ebrains.eu/f/b3ea5740fcc34f12af7a/?dl=1]]
101 101  
102 -Documented notebooks and other examples will be ok to download and try yourself locally, after you have also prepared and launched locally a Docker env: [[https:~~/~~/hub.docker.com/r/thevirtualbrain/tvb-multiscale>>https://hub.docker.com/r/thevirtualbrain/tvb-multiscale]]
43 +This notebook will be ok to download and try yourself locally, after you have also prepared and launched locally a Docker env: [[https:~~/~~/hub.docker.com/r/thevirtualbrain/tvb-multiscale>>https://hub.docker.com/r/thevirtualbrain/tvb-multiscale]]
103 103  
104 104  This is the path recommended for people working closely with tvb-multiscale. They are able to download it in their local work env and code freely and fast with it.
105 105  
106 -== ==
107 -
108 108  == Running TVB-MULTISCALE jobs on CSCS infrastructure from HBP collab ==
109 109  
110 110  The CSCS and HBP Collab deployment of tvb-multiscale is a good example to show how tvb-multiscale can run with an HPC backend. This will be efficient when the simulation jobs are very large. From our experience, with small jobs, the stage-in/out time is considerable, and then the user might be better with just a local run. Also, this deployment requires that **the user have an active CSCS personal account**. More details on how to use this deployment can be found in this movie: [[https:~~/~~/drive.google.com/open?id=1osF263FK_NjhZcBJfpSy-F7qkbYs3Q-E>>url:https://drive.google.com/open?id=1osF263FK_NjhZcBJfpSy-F7qkbYs3Q-E]]