NEST Users December 2022

users@nest-simulator.org

7 participants
5 discussions

Fastest way to transfer dense connectivity data in a parallel simulation?

by Robin Gilbert De Schepper

Hi all! In the world of biophysical detail, it's commonplace that the connectome is generated with algorithms that specify connections as dense tabular data, with each row specifying a synaptic location on a cell pair (SONATA for example). A) In NEST I can't really find the opportunity to fit this data into any of the connection rules: I want to specify pairwise connections from the multiset A to multiset B. - Is this possible with `pairwise bernoulli`, or do the inputs have to be strict sets? - The probability step is superfluous, can it be skipped? B) Then there's the fact that NEST parallelizes transparently, but since this data was generated in parallel by tiling the biological volume, I have neatly fragmented data already available on each node in the distributed cluster. It would be such a waste to communicate all the data to each node, for NEST to communicate and distribute them back another way. The data is too big to allgather and fit into memory of any single node. Not only is this a lot of overhead to implement, but NEST will throw away all but `1 / Nnodes` of the data on each node again, leaving me with a reshuffled version of my starting data. Is there a way to bypass the transparency and to imperatively declare the cells and connections on each machine? -- Robin De Schepper, MSc (they/them) Department of Brain and Behavioral Sciences Unit of Neurophysiology University of Pavia, Italy Via Forlanini 6, 27100 Pavia - Italy Tel: (+39) 038298-7607 http://www-5.unipv.it/dangelo/ Interested in large scale network modelling? Discover our framework <https://bsb.readthedocs.io/en/latest/>: <https://github.com/dbbs-lab/bsb>

1 month, 3 weeks

Open NEST Developer Video Conference Monday Dec 19 2022 11:30 CET (UTC+1)

by Dennis Terhorst

Dear NEST Users & Developers! I would like to invite you to our next fortnightly Open NEST Developer Video Conference, today Monday December 19, 11.30-12.30 CET (UTC+1). Feel free to join the meeting also if it's just to bring your own questions for direct discussion in the in-depth section. As usual, in the Project team round, a contact person of each team will give a short statement summarizing ongoing work in the team and cross-cutting points that need discussion among the teams. The remainder of the meeting we would go into a more in-depth discussion of topics that came up on the mailing list or that are suggested by the teams. Agenda * Welcome * Review of NEST User Mailing List * Project team round * In-depth discussion The agenda for this meeting is also available online, see https://github.com/nest/nest-simulator/wiki/2022-12-19-Open-NEST-Developer-… As I will not be joining today, I delegated chairing the meeting. Looking forward to seeing you again next year! Merry Christmas and a happy new year! Cheers, Dennis Terhorst :*) ------------------ Log-in information ------------------ We use a virtual conference room provided by DFN (Deutsches Forschungsnetz). You can use the web client to connect. We however encourage everyone to use a headset for better audio quality or even a proper video conferencing system (see below) or software when available. Web client * Visit https://conf.dfn.de/webapp/conference/97938800 * Enter your name and allow your browser to use camera and microphone * The conference does not need a PIN to join, just click join and you're in. In case you see a dfnconf logo and the phrase "Auf den Meetingveranstalter warten", just be patient, the meeting host needs to join first (a voice will tell you). VC system/software How to log in with a video conferencing system, depends on you VC system or software. - Using the H.323 protocol (eg Polycom): vc.dfn.net##97938800 or 194.95.240.2##97938800 - Using the SIP protocol:97938800@vc.dfn.de - By telephone: +49-30-200-97938800 For those who do not have a video conference system or suitable software, Polycom provides a pretty good free app for iOS and Android, so you can join from your tablet (Polycom RealPresence Mobile, available from AppStore/PlayStore). Note that firewalls may interfere with videoconferencing in various and sometimes confusing ways. For more technical information on logging in from various VC systems, please see http://vcc.zih.tu-dresden.de/index.php?linkid=1.1.3.4

3 months, 1 week

how to customize Ion channels and receptor types of "cm_default" neuron model through nestml

by 王梓瑞

Dear nest community, I wonder if any of you know how to customize Ion channels and receptor types of "cm_default" neuron model through nestml. I noticed some information on Extending NESTML- Running NESTML with custom templates, but I still found myself confused due to my poor understanding. Is there any way to acquire the .nestml file of the cm_default neuron model? Thank you. Best, Zirui

3 months, 3 weeks

Open NEST Developer Video Conference Monday Dec 5 2022 11:30 CET (UTC+1)

by Dennis Terhorst

Dear NEST Users & Developers! I would like to invite you to our next fortnightly Open NEST Developer Video Conference, today Monday December 5, 11.30-12.30 CET (UTC+1). Feel free to join the meeting also if it's just to bring your own questions for direct discussion in the in-depth section. Special topic for the in-depth discussion for today are / Hackathon Results / As usual, in the Project team round, a contact person of each team will give a short statement summarizing ongoing work in the team and cross-cutting points that need discussion among the teams. The remainder of the meeting we would go into a more in-depth discussion of topics that came up on the mailing list or that are suggested by the teams. Agenda * Welcome * Review of NEST User Mailing List * Project team round * In-depth discussion The agenda for this meeting is also available online, see https://github.com/nest/nest-simulator/wiki/2022-12-05-Open-NEST-Developer-… Looking forward to seeing you again soon! Cheers, Dennis Terhorst ------------------ Log-in information ------------------ We use a virtual conference room provided by DFN (Deutsches Forschungsnetz). You can use the web client to connect. We however encourage everyone to use a headset for better audio quality or even a proper video conferencing system (see below) or software when available. Web client * Visit https://conf.dfn.de/webapp/conference/97938800 * Enter your name and allow your browser to use camera and microphone * The conference does not need a PIN to join, just click join and you're in. In case you see a dfnconf logo and the phrase "Auf den Meetingveranstalter warten", just be patient, the meeting host needs to join first (a voice will tell you). VC system/software How to log in with a video conferencing system, depends on you VC system or software. - Using the H.323 protocol (eg Polycom): vc.dfn.net##97938800 or 194.95.240.2##97938800 - Using the SIP protocol:97938800@vc.dfn.de - By telephone: +49-30-200-97938800 For those who do not have a video conference system or suitable software, Polycom provides a pretty good free app for iOS and Android, so you can join from your tablet (Polycom RealPresence Mobile, available from AppStore/PlayStore). Note that firewalls may interfere with videoconferencing in various and sometimes confusing ways. For more technical information on logging in from various VC systems, please see http://vcc.zih.tu-dresden.de/index.php?linkid=1.1.3.4

3 months, 3 weeks

docker questions

by 1538356357＠qq.com

I use Docker to create a nest environment. The version is v2.16.0 But when I execute the code as follows，vt_dummy = nest.Create("global_volume_transmitter", 1, {'deliver_interval': 10})， , I encounter an error, the error is pynestkernel.NESTError: UnknownModelName in GetDefaults_l: /global_volume_transmitter is not a known model name. Please check the modeldict for a list of available models . but after I use the nest2.16 source code to install, the same code executes successfully. I don't know why

3 months, 3 weeks

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NEST Users December 2022