November 2022 - NEST Users - NEST Initiative Mail

Fastest way to transfer dense connectivity data in a parallel simulation?
by Robin Gilbert De Schepper 01 Feb '23

01 Feb '23

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>

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About Polling Algorithm
by 1538356357＠qq.com 22 Nov '22

22 Nov '22

Dear NEST community： We all know that distributed computing is carried out in Nest, and neurons are distributed to each neuron through polling. However, considering the load balancing and sparsity of communication, this is a NP hard problem. Should we adopt some other methods, such as directed graph segmentation technology. Whether this will be considered in Nest, or whether graph segmentation is helpful in SNN simulation. If you can spare time to reply, thank you very much

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Open NEST Developer Video Conference Monday Nov 21 2022 11:30 CET (UTC+1)
by Dennis Terhorst 21 Nov '22

21 Nov '22

Dear NEST Users & Developers! I would like to invite you to our next fortnightly Open NEST Developer Video Conference, today Monday November 21, 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 mechanisms around /Tsodyks-style synapses/ 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/2022-11-21-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

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errors when using command"d1_pop.set({"V_m":nest.random.uniform(-80.0, -55.0)})"
by 王梓瑞 15 Nov '22

15 Nov '22

Dear NEST community, Thank you so much for your previous suggestions on writing my own neuron model with NESTML. I constructed a multiple synapses version of simple integrate-and-fire ("iaf_cond_beta_multisynapse") neuron based on the existing "iaf_cond_beta" neuron model. And I did this by simply adding two synaptic channels (AMPA and NMDA) without changing the structure of the neuron model. But when I called this model on NEST to set the initial membrane potentials from a uniform distribution (from 280 to 255 mV), for example:"d1_pop.set({"V_m":nest.random.uniform(-80.0, -55.0)})", an error reporting NESTErrors.TypeMismatch: "TypeMismatch in SLI function SetStatus_id: Expected datatype: doubletype Provided datatype: parametertype" appeared. So I wonder is there any coding errors in my own neuron model, since it worked just fine when I set the initial membrane potentials to a number like -80, and how can I fix this error. Best, Zirui

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Re: weight_recorder with large number of synapses
by Hans Ekkehard Plesser 14 Nov '22

14 Nov '22

Hello Alice, Setting repeated recording windows is currently not possible (but maybe create a feature request on Github). What you can do is the following n1 = nest.Create('iaf_psc_delta', params={'I_e': 1000.}) n2 = nest.Create('iaf_psc_delta') wr = nest.Create('weight_recorder', params={'origin': 0., 'start': 0, 'stop': 1000}) nest.CopyModel('stdp_synapse', 'stdp_synapse_rec', {'weight_recorder': wr}) nest.Connect(n1, n2, syn_spec={'synapse_model': 'stdp_synapse_rec', 'weight': 20}) nest.Connect(n2, sr) t_block = 5000 for k in range(10): wr.origin = k * t_block nest.Simulate(t_block) This will simulate in 5s blocks and record weights only during the first 1s of each block. The actual recording windows are given by (origin+start, origin+stop]. You need to do this with Simulate() calls since you need to change the origin parameter; therefore RunManager + run() does not work. You could also record to file if that is an option for your workflow, by setting wr.record_to = 'ascii'. If you want to combine that with a loop, you need to set wr.label to a different value for each loop iteration, otherwise data will be overwritten for each round through the loop. Best, Hans Ekkehard -- Prof. Dr. Hans Ekkehard Plesser Head, Department of Data Science Faculty of Science and Technology Norwegian University of Life Sciences PO Box 5003, 1432 Aas, Norway Phone +47 6723 1560 Email hans.ekkehard.plesser(a)nmbu.no<mailto:hans.ekkehard.plesser@nmbu.no> Home http://arken.nmbu.no/~plesser From: Alice Geminiani <alice.geminiani(a)polimi.it> Reply to: NEST User Mailing List <users(a)nest-simulator.org> Date: Friday, 11 November 2022 at 18:47 To: "users(a)nest-simulator.org" <users(a)nest-simulator.org> Subject: [NEST Users] weight_recorder with large number of synapses Some people who received this message don't often get email from alice.geminiani(a)polimi.it. Learn why this is important<https://aka.ms/LearnAboutSenderIdentification> Dear NEST users, I am trying to record weights from a network with about 1.5 million synapses, for simulations of a 30-minute protocol, and using the weight_recorder causes memory errors. Is there a way to record only in specific time instants of the simulation (e.g. every 5 minutes)? Thanks a lot! Cheers, Alice ---------------------------- Alice Geminiani, PhD PostDoctoral Researcher NeuroEngineering And medical Robotics Laboratory - NEARLab Department of Electronics, Information and Bioengineering - DEIB Politecnico di Milano Neurocomputational laboratory Department of Brain and Behavioral Sciences University of Pavia

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weight_recorder with large number of synapses
by Alice Geminiani 11 Nov '22

11 Nov '22

Dear NEST users, I am trying to record weights from a network with about 1.5 million synapses, for simulations of a 30-minute protocol, and using the weight_recorder causes memory errors. Is there a way to record only in specific time instants of the simulation (e.g. every 5 minutes)? Thanks a lot! Cheers, Alice ---------------------------- Alice Geminiani, PhD PostDoctoral Researcher NeuroEngineering And medical Robotics Laboratory - NEARLab Department of Electronics, Information and Bioengineering - DEIB Politecnico di Milano Neurocomputational laboratory Department of Brain and Behavioral Sciences University of Pavia

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how to construct multiple synapse simple integrate-and-fire model
by 王梓瑞 07 Nov '22

07 Nov '22

Hi, I planned to use simple integrate-and-fire model (iaf_cond_beta) to construct the cortico-striatal network, but then it appeared some issues. Since striatum neurons have multiple synapses (AMPA and NMDA for example), ‘iaf_cond_beta’ seemed not to support multiple synapse input. I searched the whole Model directory and found multiple synapse neuron models like “aeif_cond_beta_multisynapse”, “aeif_cond_alpha_multisynapse” and “aeif_psc_alpha_multisynaps”. So I wondered if there’s a multiple synapse version of simple integrate-and-fire model (iaf_cond_beta), or can I construct a multiple synapse simple integrate-and-fire model through nestml. Thank you Best, Zirui

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Open NEST Developer Video Conference Monday Nov 7 2022 11:30 CET (UTC+1)
by Dennis Terhorst 07 Nov '22

07 Nov '22

Dear NEST Users & Developers! I would like to invite you to our next fortnightly Open NEST Developer Video Conference, today Monday November 7, 11.30-12.30 CET (UTC+1). (note the changed timezone!) 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 is /Eligibility Propagation/ 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/2022-11-07-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

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