Last modified by ldomide on 2024/04/08 12:55
From version 14.1
edited by ldomide
on 2020/06/26 12:49
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To version 41.1
edited by ldomide
on 2024/04/08 12:55
Change comment: There is no comment for this version

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Title
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1 -The Virtual Brain Multiscale
1 +Co-Simulation The Virtual Brain Multiscale
Content
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2 2  (((
3 3  (% class="container" %)
4 4  (((
5 -= (% style="color:inherit" %)TVB Co-Simulation [[image:https://github.com/the-virtual-brain/tvb-multiscale/blob/master/docs/documented_example_notebook/ConceptGraph.png?raw=true||alt="ConceptGraph.png" height="197" width="255"]] (%%) =
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}}  (%%) =
6 6  
7 -(% style="color:inherit" %)Multiscale: TVB - NEST
8 8  
9 -(% style="color:inherit" %)Authors: (%%)D. Perdikis, L. Domide, J. Mersmann, M. Schirner, P. Ritter(% style="color:inherit" %)
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" %)
10 10  )))
11 11  )))
12 12  
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14 14  (((
15 15  (% class="col-xs-12 col-sm-8" %)
16 16  (((
17 -For more details on TVB itself, check this: [[https:~~/~~/wiki.ebrains.eu/bin/view/Collabs/the-virtual-brain/>>url:https://wiki.ebrains.eu/bin/view/Collabs/the-virtual-brain/]]
18 +For more details on TVB see:
18 18  
19 -== Use our Jupyter Hub setup online ==
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/]]
20 20  
21 -We have setup a Jupyter Hub service with tvb-nest as backed already prepared. You will only need an HBP account for accessing this: [[https:~~/~~/tvb-nest.apps.hbp.eu/>>url:https://tvb-nest.apps.hbp.eu/]]
23 +== ==
22 22  
23 -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-nest 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-nest.
25 +== Running TVB-MULTISCALE at EBRAINS JupyterLab ==
24 24  
25 -**[[image:https://lh6.googleusercontent.com/ytx9eYpMcL3cCScX2_Sxm4CeBW0xbKW3xKsfO2zSId10bW0gw1kiN2_SkexyYBCsF-sKsu0MaJC4cZvGVfQPjMoPBLiePbkvXOZd8BgY3Q0kFzSkRCqQ183lgDQv_6PYoqS3s7uJ||height="149" width="614"]]**
27 +TVB-multiscale is made available at [[EBRAINS JupyterLab>>https://lab.ebrains.eu/]].
26 26  
27 -Currently, the users can access 2 folders: //TVB-NEST-Examples// and //Contributed-Notebooks//.
29 +All the user has to do is log in with their EBRAINS credentials, and start a Python console or a Jupyter notebook using the kernel "EBRAINS-23.09" (or a more recent version), where TVB-multiscale can be imported (e.g., via "import tvb_multiscale"). All necessary TVB-multiscale dependencies (NEST, ANNarchy, NetPyNE (NEURON), Elephant, Pyspike) are also installed and available.
28 28  
29 -The notebooks under **TVB-NEST-Examples** are public, shared by everyone accessing the instance. Periodically, we will clean all changes under TVB-NEST-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]])
31 +This collab contains various examples of using TVB-Multiscale with all three supported spiking simulators. We suggest copying the contents of this collab to your Library or to any collab owned by you, and running them there (note that the user's drive offers persistent storage, i.e. users will find their files after logging out and in again), as follows:
30 30  
31 -**[[image:https://lh6.googleusercontent.com/nnsM0mhXQinmQsJwZwwwe5Sx7f-tZc8t4ELnCh9DwksyVEPUE-jixJTkhoP4l25VKwlDGoXACWtnuxQM9NMOCYbQOzDesgMDlT3sntow___vsEqRVd4OwqMY4BPyBiLJ32BnUbmM||height="267" width="614"]]**
33 +~1. Select `Drive` on the left of the current page (or use [[this link>>https://wiki.ebrains.eu/bin/view/Collabs/the-virtual-brain-multiscale/Drive||rel="noopener noreferrer" target="_blank"]]).
32 32  
33 -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).
35 +2. Check the `tvb-multiscale-collab` folder checkbox, and copy it to your `My Library` ("copy" icon will appear above the files/folders list).
34 34  
35 -== Running TVB-NEST locally ==
37 +3. Select `Lab` (on the left), and navigate to the destination where you just copied the folder.
36 36  
37 -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]]
39 +4. Enter the `tvb-multiscale-collab` folder, and open either of example notebooks. Ensure you select the appropriate ipykernel (EBRAINS-23.09 or a more recent one)
38 38  
39 -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-nest>>url:https://hub.docker.com/r/thevirtualbrain/tvb-nest]]
40 40  
41 -This is the path recommended for people working closely with tvb-nest. They are able to download it in their local work env and code freely and fast with it.
42 +== Running TVB-MULTISCALE locally ==
42 42  
43 -== Running TVB-NEST jobs on CSCS infrastructure from HBP collab ==
44 +See more on Github [[https:~~/~~/github.com/the-virtual-brain/tvb-multiscale>>url:https://github.com/the-virtual-brain/tvb-multiscale]] .
44 44  
45 -The CSCS and HBP Collab deployment of tvb-nest is a good example to show how tvb-nest 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]]
46 +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]]
46 46  
48 +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.
49 +
50 +== ==
51 +
52 +== Running TVB-MULTISCALE jobs on HPC infrastructure from HBP collab ==
53 +
54 +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, such a deployment requires that **the user have an active HPC personal account and allocation project active**. 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]]
55 +
47 47  * Create a collab space of your own
48 48  * 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/]]
49 -** 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.
50 -** run_custom_cosimulation.ipynb For this example we are using the //cosimulate_with_staging.sh// script in order to pull the tvb-nest docker image and we are using a custom simulation script (from Github page) which will be uploaded in the staging in phase
51 -** 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.
58 +** test_tvb-nest_installation.ipynb  Run the cosimulate_tvb_nest.sh script on the HPC supercomputer where you have an account active. In this example, basically we are running the //installation_test.py// file which is in the docker folder.
59 +** 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
60 +** 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 HPC.
52 52  
53 53  Few technical details about what we do in these notebooks:
54 54  
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62 62  
63 63  >tr = unicore_client.Transport(oauth.get_token())
64 64  >r = unicore_client.Registry(tr, unicore_client._HBP_REGISTRY_URL)
65 -># use "DAINT-CSCS" change if another supercomputer is prepared for usage
74 +># we used "DAINT-CSCS", but you should change it to another supercomputer where you have a project active
66 66  >client = r.site('DAINT-CSCS')
67 67  
68 -1. Prepare job submission
77 +2. Prepare job submission
69 69  
70 70  In this step we have to prepare a JSON object which will be used in the job submission process.
71 71  
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82 82  >my_job['Resources'] = { 
83 83  > "CPUs": "1"}
84 84  
85 -1. Actual job submission
94 +3. Actual job submission
86 86  
87 87  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.
88 88  
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89 89  >job = site_client.new_job(job_description=my_job, inputs=['/path1', '/path2'])
90 90  >job.properties
91 91  
92 -1. Wait until job is completed and check the results
101 +4. Wait until job is completed and check the results
93 93  
94 94  Wait until the job is completed using the following command
95 95  
Collaboratory.Apps.Collab.Code.CollabClass[0]
owner
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1 +ldomide
Description
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1 -Co-Simulation The Virtual Brain-multiscale. 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
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.
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1 +2020-07-27 21:56:05.0
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1 +XWiki.ldomide
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1 +Check this movie on tvb-multiscale https://www.youtube.com/watch?v=6hEuvxD7IDk&feature=youtu.be
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