Changes for page Co-Simulation The Virtual Brain Multiscale
Last modified by ldomide on 2024/04/08 12:55
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... ... @@ -5,7 +5,7 @@ 5 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 7 8 -(% style="color:inherit" %)Multiscale: TVB, NEST, (%%)ANNarchy, N etPyNE , Elephant, PySpike8 +(% style="color:inherit" %)Multiscale: TVB, NEST, (%%)ANNarchy, NETPYNE , Elephant, PySpike 9 9 10 10 (% style="color:inherit" %)Authors: (%%)D. Perdikis, A. Blickensdörfer, V. Bragin, L. Domide, J. Mersmann, M. Schirner, P. Ritter(% style="color:inherit" %) 11 11 ))) ... ... @@ -20,35 +20,30 @@ 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 - ==RunningTVB-MULTISCALEatEBRAINSJupyterLab==25 +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-nest.apps.hbp.eu/>>url:https://tvb-nest.apps.hbp.eu/]] 26 26 27 -T VB-multiscale ismade available at[[EBRAINS JupyterLab>>https://lab.ebrains.eu/]].27 +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. 28 28 29 - All the user has to dois login withheir EBRAINS credentials, and start a Python consoleor a Jupyternotebook usingthekernel "EBRAINS-23.09" (or a more recent version), where TVB-multiscalean be imported(e.g., via "import tvb_multiscale"). All necessaryTVB-multiscale dependencies (NEST, ANNarchy, NetPyNE (NEURON), Elephant,Pyspike) are alsoinstalledand available.29 +**[[image:https://lh6.googleusercontent.com/ytx9eYpMcL3cCScX2_Sxm4CeBW0xbKW3xKsfO2zSId10bW0gw1kiN2_SkexyYBCsF-sKsu0MaJC4cZvGVfQPjMoPBLiePbkvXOZd8BgY3Q0kFzSkRCqQ183lgDQv_6PYoqS3s7uJ||height="149" width="614"]]** 30 30 31 - This collab contains variousexamples of using TVB-Multiscalewithall threesupportedspiking simulators.We suggestcopyingthecontentsof thiscollabtoyour Library or to any collab ownedby you, and running them there(note that theuser'sdriveoffers persistentstorage,i.e.users will findheir files after loggingout and in again), asfollows:31 +Currently, the users can access 2 folders: //TVB-*-Examples// and //Contributed-Notebooks//. 32 32 33 - ~1.Select`Drive`on theleft ofthe current page(oruse[[thislink>>https://wiki.ebrains.eu/bin/view/Collabs/the-virtual-brain-multiscale/Drive||rel="noopener noreferrer"target="_blank"]]).33 +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]]) 34 34 35 - 2. Check the `tvb-multiscale-collab` folderheckbox, andcopyito your `MyLibrary` ("copy"iconwill appear abovethefiles/folderslist).35 +**[[image:https://lh6.googleusercontent.com/nnsM0mhXQinmQsJwZwwwe5Sx7f-tZc8t4ELnCh9DwksyVEPUE-jixJTkhoP4l25VKwlDGoXACWtnuxQM9NMOCYbQOzDesgMDlT3sntow___vsEqRVd4OwqMY4BPyBiLJ32BnUbmM||height="267" width="614"]]** 36 36 37 - 3. Select`Lab` (on theleft), andnavigateto the destinationwhereyoujust copiedthefolder.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). 38 38 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) 40 - 41 - 42 42 == Running TVB-MULTISCALE locally == 43 43 44 -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]] 45 45 46 - Documentednotebooksand other exampleswill 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-nest>>url:https://hub.docker.com/r/thevirtualbrain/tvb-nest]] 47 47 48 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 49 50 -== == 51 - 52 52 == Running TVB-MULTISCALE jobs on CSCS infrastructure from HBP collab == 53 53 54 54 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]]