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on 2020/06/26 12:28
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Summary

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Title
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1 -Co-Simulation The Virtual Brain Multiscale
1 +Co-Simulation The Virtual Brain-multiscale
Author
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1 -XWiki.dionperd
1 +XWiki.ldomide
Content
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2 2  (((
3 3  (% class="container" %)
4 4  (((
5 -= (% style="color:inherit" %)TVB Co-Simulation {{html}}<iframe width="302" height="170" src="https://www.youtube.com/embed/6hEuvxD7IDk?list=PLVtblERyzDeLcVv4BbW3BvmO8D-qVZxKf" frameborder="0" allow="accelerometer; autoplay; encrypted-media; gyroscope; picture-in-picture" allowfullscreen></iframe>{{/html}}  (%%) =
5 += My Collab's Extended Title =
6 6  
7 -
8 -(% style="color:inherit" %)Multiscale: TVB, NEST, (%%)ANNarchy, NetPyNE , Elephant, PySpike
9 -
10 -(% style="color:inherit" %)Authors: (%%)D. Perdikis, A. Blickensdörfer, V. Bragin, L. Domide, J. Mersmann, M. Schirner, P. Ritter(% style="color:inherit" %)
7 +My collab's subtitle
11 11  )))
12 12  )))
13 13  
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15 15  (((
16 16  (% class="col-xs-12 col-sm-8" %)
17 17  (((
18 -For more details on TVB see:
15 += What can I find here? =
19 19  
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 -* 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/]]
17 +* Notice how the table of contents on the right
18 +* is automatically updated
19 +* to hold this page's headers
22 22  
23 -(% class="wikigeneratedid" %)
24 -== ==
21 += Who has access? =
25 25  
26 -(% class="wikigeneratedid" %)
27 -== Running TVB-MULTISCALE at EBRAINS JupyterLab ==
28 -
29 -TVB-multiscale is made available at [[EBRAINS JupyterLab>>https://lab.ebrains.eu/]]. 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"). All necessary TVB-multiscale dependencies (NEST, ANNarchy, NetPyNE (NEURON), Elephant, Pyspike) are also installed and available. 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.
30 -
31 -
32 -== Use our Jupyter Hub setup online ((% style="color:#c0392b" %)DEPRECATED(%%)) ==
33 -
34 -(% style="color:#c0392b" %)**TVB-multiscale app is deprecated and will stop being available after the end of 2023!**
35 -
36 -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/]]
37 -
38 -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.
39 -
40 -**[[image:https://lh6.googleusercontent.com/ytx9eYpMcL3cCScX2_Sxm4CeBW0xbKW3xKsfO2zSId10bW0gw1kiN2_SkexyYBCsF-sKsu0MaJC4cZvGVfQPjMoPBLiePbkvXOZd8BgY3Q0kFzSkRCqQ183lgDQv_6PYoqS3s7uJ||height="149" width="614"]]**
41 -
42 -Currently, the users can access 2 folders: //TVB-*-Examples// and //Contributed-Notebooks//.
43 -
44 -The notebooks under **TVB-*-Examples** are public, shared by everyone accessing the instance. Periodically, we will clean all changes under TVB-*-Examples folder (by redeploying the pod image), and show the original example notebooks submitted on our Github repo. If users intend to contribute here, they are encouraged to submit changes through Pull Requests ([[https:~~/~~/github.com/the-virtual-brain/tvb-multiscale>>url:https://github.com/the-virtual-brain/tvb-multiscale]])
45 -
46 -**[[image:https://lh6.googleusercontent.com/nnsM0mhXQinmQsJwZwwwe5Sx7f-tZc8t4ELnCh9DwksyVEPUE-jixJTkhoP4l25VKwlDGoXACWtnuxQM9NMOCYbQOzDesgMDlT3sntow___vsEqRVd4OwqMY4BPyBiLJ32BnUbmM||height="267" width="614"]]**
47 -
48 -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)
49 -
50 -
51 -== Running TVB-MULTISCALE locally ==
52 -
53 -See more on Github [[https:~~/~~/github.com/the-virtual-brain/tvb-multiscale>>url:https://github.com/the-virtual-brain/tvb-multiscale]] .
54 -
55 -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]]
56 -
57 -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.
58 -
59 -(% class="wikigeneratedid" %)
60 -== ==
61 -
62 -== Running TVB-MULTISCALE jobs on CSCS infrastructure from HBP collab ==
63 -
64 -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]]
65 -
66 -* Create a collab space of your own
67 -* Clone and run in your HBP Collab Hub ([[https:~~/~~/lab.ebrains.eu/>>url:https://lab.ebrains.eu/]]) the notebooks from here: [[https:~~/~~/drive.ebrains.eu/d/245e6c13082f45bcacfa/>>url:https://drive.ebrains.eu/d/245e6c13082f45bcacfa/]]
68 -** test_tvb-nest_installation.ipynb  Run the cosimulate_tvb_nest.sh script on the CSCS Daint supercomputer. In this example, basically we are running the //installation_test.py// file which is in the docker folder.
69 -** run_custom_cosimulation.ipynb For this example we are using the //cosimulate_with_staging.sh// script in order to pull the tvb-multiscale docker image and we are using a custom simulation script (from Github page) which will be uploaded in the staging in phase
70 -** run_custom_cosimulation_from_notebook.ipynb  This example is running the same simulation as the example above but instead of using an external file with the simulation code we will build a simulation file from a few notebook cells and we will pass this file to the CSCS server.
71 -
72 -Few technical details about what we do in these notebooks:
73 -
74 -1. Prepare UNICORE client api.
75 -
76 -PYUNICORE client library is available on PYPI. In order to use it you have to install it using:
77 -
78 ->pip install pyunicore
79 -
80 -Next step is to configure client registry and what supercomputer to use
81 -
82 ->tr = unicore_client.Transport(oauth.get_token())
83 ->r = unicore_client.Registry(tr, unicore_client._HBP_REGISTRY_URL)
84 -># use "DAINT-CSCS" change if another supercomputer is prepared for usage
85 ->client = r.site('DAINT-CSCS')
86 -
87 -1. Prepare job submission
88 -
89 -In this step we have to prepare a JSON object which will be used in the job submission process.
90 -
91 -># What job will execute (command/executable)
92 ->my_job['Executable'] = 'job.sh'
93 ->
94 -># To import files from remote sites to the job’s working directory
95 ->my_job['Imports'] = [{
96 -> "From": "https:~/~/raw.githubusercontent.com/the-virtual-brain/tvb-multiscale/update-collab-examples/docker/cosimulate_tvb_nest.sh",
97 -> "To" : job.sh
98 ->}]
99 ->
100 -># Specify the resources to request on the remote system
101 ->my_job['Resources'] = { 
102 -> "CPUs": "1"}
103 -
104 -1. Actual job submission
105 -
106 -In order to submit a job we have to use the JSON built in the previous step and also if we have some local files, we have to give their paths as a list of strings (inputs argument) so the UNICORE library will upload them in the job's working directory in the staging in phase, before launching the job.
107 -
108 ->job = site_client.new_job(job_description=my_job, inputs=['/path1', '/path2'])
109 ->job.properties
110 -
111 -1. Wait until job is completed and check the results
112 -
113 -Wait until the job is completed using the following command
114 -
115 -># TRUE or FALSE
116 ->job.is_running()
117 -
118 -Check job's working directory for the output files/directories using
119 -
120 ->wd = job.working_dir
121 ->wd.listdir()
122 -
123 -From working job you can preview files content and download files
124 -
125 -># Read 'stdout' file
126 ->out = wd.stat("stdout")
127 ->f = out.raw()
128 ->all_lines = f.read().splitlines()
129 ->all_lines[-20:]
130 ->
131 -># Download 'outputs/res/results.npy' file
132 ->wd.stat("outputs/res/results.npy").download("results.npy")
23 +Describe the audience of this collab.
133 133  )))
134 134  
135 135  
Collaboratory.Apps.Collab.Code.CollabClass[0]
Description
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1 -Multiscale Co-Simulation with The Virtual Brain (TVB) and NEST.
2 -This space contains tutorials for configuring and running in HBP Collab simulations with TVB simulator in combination with the NEST simulator, and do co-simulations.
1 +This space contains tutorials for configuring and running in HBP Collab simulations with TVB simulator in combination with the NEST simulator, and do a co-simulation. Full Brain Modeling. Human. Animal. EEG, MEG, SEEG, iEEG, BOLD. Large Scale Connectivity. Surface Simulations. TVB-multiscale co-simulation
owner
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1 -ldomide
XWiki.XWikiComments[0]
Author
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1 -XWiki.ldomide
Comment
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1 -Check this movie on tvb-multiscale https://www.youtube.com/watch?v=6hEuvxD7IDk&feature=youtu.be
Date
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1 -2020-07-27 21:56:05.0
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