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Re: Heaviside function in a Kernel?
by Charl Linssen 12 Mar '26

12 Mar '26

Dear Jeanne, I have taken a look at the code that Zhang et al. made available on GitHub, but I'm afraid that to really grok it I have to do a deep dive. I am not sure why the authors would take the max-value of the postsynaptic response rather than accumulating them; could it be related to a conductance based mechanism like shunting inhibition? Your grid search fit in any case looks like a promising approximation. In conversation with Prof. Markus Diesmann, he pointed me to another way in which the polynomial system could be integrated. Please see the example in this paper (Rotter et al. 1999) <https://brainworks.biologie.uni-freiburg.de/1999/journal%20papers/RotterDie…> on the bottom left of page 385. Using this method, you should be able to integrate a numerically exact (up to floating point precision) solution of the original polynomial. I made a little test script that performs this simulation and also clips the polynomial to zero (see the bottom panel in the plot below). Hopefully this will be useful to you as a basis for further work. Please don't hesitate to get/stay in touch about further steps in the implementation. With kind regards, Charl On Thu, Mar 5, 2026, at 07:04, Jeanne Barthelemy wrote: > > Dear Charl, > > Thank you very much for your follow up. > I agree that using a linear system of ODEs would be preferable. I made a proxy version that uses a beta kernel (inspired from iaf_cond_beta_neuron.nestml). The rise and decay time constants, and a modulatory parameter to scale the conductance, may be tuned to approximate the polynomials derived by Zhang and colleagues. In the attachment, my result is provided from a simple grid search, comparing the proxy with two exponentials and the polynomial from Zhang and colleagues. > > It may be interesting indeed to perform a ReScience paper comparing the beta kernel version in NESTML with the version from Zhang and colleagues (for your information, their matlab code is available on github). However, in order to do so, another part of their implementation puzzles me. Their total model takes into account the polynomial component, but also multiplied by an inhibition efficiency that relies on the firing rate of the ChI population. In their code, from my understanding, they compute the inhibition at time i + k via a multiplication (efficiency due to ChI firing at time i X inhibition along time via the value of the polynomial at time k), but keep only the maximum value along i and k, rather than actually summing the effect of spikes at distinct times. I am not sure to understand the reason between this modelling choice. Do you think it may be interesting as well to compare this with a more traditional approach in NESTML, where the efficiency is computed online at the time t of the simulation, and the beta kernel allows to integrate all past spikes? Even if we integrate a new modulatory parameter for scaling the entire inhibition response and fit better the average behavior of the model from Zhang and colleagues． > > Please do not hesitate to let me know your thoughts about this. > Thank you, > Kind regards, > Jeanne Barthelemy > > > *From:* Charl Linssen <nest-users(a)turingbirds.com> > *Sent:* Thursday, March 5, 2026 1:47 AM > *To:* users(a)nest-simulator.org <users(a)nest-simulator.org> > *Subject:* [NEST Users] Re: Heaviside function in a Kernel? > > Dear Jeanne, > > Much obliged for the link to the paper and clarification. If a postsynaptic response is well described by a polynomial, it makes total sense to use that as part of model fitting. From a simulation perspective, it may be more efficient though to describe the response in the form of a (preferably linear) system of ODEs. Therefore if you could use the alpha or beta functions for the postsynaptic response, that would indeed be an ideal solution. > > That being said, please let me know if this could create an interesting opportunity for a ReScience paper comparing the responses of the alpha versus the polynomial; we could then look into doing a precise simulation of the polynomial more deeply. > > My colleagues also kindly attended me to the possibility of using the so-called Linear Chain Trick in the context of delay differential equations, which could be an attractive alternative method for fitting and simulating postsynaptic responses. > > Cheers, with kind regards, > Charl > > > On Tue, Mar 3, 2026, at 06:04, Jeanne Barthelemy wrote: >> Dear Charl, >> >> Thank you very much for this relevant answer. >> I was trying to reproduce with NESTML the model from this paper: Zhang, Yan-Feng, et al. "An axonal brake on striatal dopamine output by cholinergic interneurons." *Nature Neuroscience* 28.4 (2025): 783-794.". Though, I am starting to think that approximating their model with an alpha kernel, without any need for an heaviside function, may be a better option in my case. >> >> Thank you very much, >> Kind regards, >> Jeanne Barthelemy >> >> >> *From:* Charl Linssen <nest-users(a)turingbirds.com> >> *Sent:* Monday, March 2, 2026 11:47 PM >> *To:* users(a)nest-simulator.org <users(a)nest-simulator.org> >> *Subject:* [NEST Users] Re: Heaviside function in a Kernel? >> >> Dear Jeanne, >> >> Thank you for writing in and thank you for this interesting question. I'm sorry that the advanced kernel shape you need is not supported by the numerical backend. The central issue with this kernel is that it cannot be described by a linear and time-invariant system. As such it makes adding contributions from different spikes much harder, because you cannot simply add the effects of different spikes together (something that only makes sense mathematically for LTI systems). >> >> Actually, there are two components that make this a tricky kernel to work with: the factor *t*^2 as well as the Heaviside function. May I ask how you obtained the shape and parameters of this kernel? Would it be possible to replace it with an LTI kernel like the “alpha” or “beta” function? (You can have a look at the neuron models in NESTML for a definition of both.) >> >> As for the Heaviside function: I tried to think of an approach to implement this behaviour. One thing you could do is to create an additional buffer in the model that corresponds to the 200 ms time interval. When a spike comes in (let's say at time *t*_sp), it would then not only trigger the kernel response (ignoring the Heaviside term), but also add an entry to the buffer, so that 200 ms later, a *negative *contribution would be added to the state, cancelling out the value at that time to reset the value back to zero. The magnitude of this negative contribution would be of equal magnitude to the kernel at time *t_*sp + 200 ms, but with an opposite sign, so that it cancels out. I believe this would work well, even with multiple spikes arriving all the time. >> >> If you can confirm that you are interested in making an implementation of this, I would be happy to look at it together. >> >> Much obliged, >> Charl >> >> >> On Fri, Feb 27, 2026, at 10:20, Jeanne Barthelemy wrote: >>> Dear all, >>> >>> This is a question about best practices for NESTML. I would like to build in the equations block a Kernel, such as for instance: >>> >>> "kernel inh_time_end = ((-0.00002*t*t)/(pow(tau,2.0)) + 0.0087*t/tau + 0.006)/tau" >>> >>> , but modulated by the heaviside function H depending on 200 - t (i.e., H(200.0 ms -t)). To sum up, I would like to get the following kernel: >>> >>> "kernel inh_time_end_modulated = H(200.0 ms -t)*((-0.00002*t*t)/(pow(tau,2.0)) + 0.0087*t/tau + 0.006)/tau" >>> >>> There does not appear to be a direct implementation of the heaviside function H in nestml. I tried to build my own function to convert booleans to 1.0 or 0.0 in my NestML model, upon the condition "200.0 ms > t", and use that instead of the heaviside, but the model is really slow to build on my laptop. I tried other versions with if conditions in the update block, or ternary operators, but they all led to bugs. So, I am unsure of the correct practice to implement an heaviside-modulated polynomial kernel. If anyone has a good and fast solution to propose I would be very happy to learn about it ! >>> >>> Thank you very much, >>> Kind regards, >>> Jeanne BARTHELEMY >>> _______________________________________________ >>> NEST Users mailing list -- users(a)nest-simulator.org >>> To unsubscribe send an email to users-leave(a)nest-simulator.org >>> >> >> >> *CAUTION:* This email originated from outside the organization. Do not click links or open attachments unless you recognize the sender and know the content is safe. >> >> >> _______________________________________________ >> NEST Users mailing list -- users(a)nest-simulator.org >> To unsubscribe send an email to users-leave(a)nest-simulator.org >> > > > *CAUTION:* This email originated from outside the organization. Do not click links or open attachments unless you recognize the sender and know the content is safe. > > > _______________________________________________ > NEST Users mailing list -- users(a)nest-simulator.org > To unsubscribe send an email to users-leave(a)nest-simulator.org > > > *Attachments:* > • inhibition_score.pdf

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Open NEST Developer Video Conference Monday March 9, at 11:30 CET (UTC+0100)
by Dennis Terhorst 09 Mar '26

09 Mar '26

Dear NEST Users & Developers! I would like to invite you to our next fortnightly Open NEST Developer Video Conference today *Monday March 9, at 11:30 CET (UTC+0100).* As usual, in the Project team round, a contact person of each team will give a short statement summarizing ongoing and planned work in the team and highlight 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. Feel free to join the meeting also if it’s just to bring your own quick questions for direct discussion in the in-depth section. Agenda * Welcome * Review of NEST User Mailing List * Project team round * In-depth discussion: /Hackathon updates/ o Recent changes to NEST o Replacing boost::any by C++20 variants The agenda for this meeting is also available online, see https://github.com/nest/nest-simulator/wiki/2026-03-09-Open-NEST-Developer-… <https://github.com/nest/nest-simulator/wiki/2026-03-09-Open-NEST-Developer-…> Looking forward to seeing you soon! Cheers, Dennis Terhorst Log-in information We use a virtual conference room provided by DFN <https://www.dfn.de/en/> (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 <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 <mailto: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 <http://vcc.zih.tu-dresden.de/index.php?linkid=1.1.3.4> -- Dipl.-Phys. Dennis Terhorst Coordinator Software Development Institute for Advanced Simulation (IAS-6) Computational and Systems Neuroscience & JARA-Institute Brain Structure-Function Relationships (INM-10) Institute of Neuroscience and Medicine Jülich Research Center, Member of the Helmholz Association 52425 Jülich, Germany http://www.csn.fz-juelich.de/ --------------------------------------------------------------------------------------------- Forschungszentrum Jülich GmbH 52425 Jülich Sitz der Gesellschaft: Jülich Eingetragen im Handelsregister des Amtsgerichts Düren Nr. HR B 3498 Vorsitzender des Aufsichtsrats: MinDir Stefan Müller Geschäftsführung: Prof. Dr. Astrid Lambrecht (Vorsitzende), Dr. Stephanie Bauer (stellvertretende Vorsitzende), Prof. Dr. Ir. Pieter Jansens, Prof. Dr. Laurens Kuipers ---------------------------------------------------------------------------------------------

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Major changes (mostly behind the scenes) in NEST Simulator
by Hans Ekkehard Plesser 05 Mar '26

05 Mar '26

Dear NEST Users and Developers, This week has brought a range of important changes of NEST Simulator, mostly behind the scenes. Building on years of work, started by Jochen Eppler and Håkon Mørk, and a huge effort to port thousands of SLI-based tests to Python, we have finally removed the SLI interpreter from NEST. The Python interface now interacts directly with the C++ backend. These changes are currently only available to those who build NEST themselves form the source code on Github. We plan to release the first SLI-free NEST versions, NEST 3.10, ahead of the NEST Conference in June. Then, you will finally be able to pip install nest. For users, this should bring only minimal changes. You will find them documented on https://nest-simulator.readthedocs.io/en/latest/whats_new/v3.10/index.html#…. Please let us know if you run into any difficulties adjusting your model scripts. Developers may need to make some adjustments to your code, but also those changes should be rather schematic. The key points are described in the "What's new in 3.10" document linked above. Again, do not hesitate to contact us if you have any questions or run into problems. Finally, we have changed the name of the central branch for NEST Simulator from "master" to "main" on Github. So if you have NEST cloned to your computer from the public NEST repository, please do the following in your local repo, assuming that nest_public is the name for the remote git@github.com:nest/nest-simulator.git: git branch -m master main git fetch nest_public git branch -u nest_public/main main # do this only if you want to set nest_public/main as upstream tracking branch git remote set-head nest_public -a On behalf of the NEST developer crowd Hans Ekkehard -- Prof. Dr. Hans Ekkehard Plesser Research Committee Chair, Faculty of Science and Technology 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

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NEST Conference 2026 Abstract Submission and Registration open
by Hans Ekkehard Plesser 05 Mar '26

05 Mar '26

Dear Colleagues, The NEST Initiative is excited to invite everyone interested in Neural Simulation Technology and the NEST Simulator to the NEST Conference 2026. The NEST Conference provides an opportunity for the NEST Community to meet, exchange success stories, swap advice, learn about current developments in and around NEST spiking network simulation and its application. Take the opportunity to advance your skills in using NEST at our hands-on workshops! We explicitly encourage young scientists to participate in the conference! This year's conference will again take place as a virtual conference on Tuesday/Wednesday 16/17 June 2026. We are delighted to welcome * Marja-Leena Linne, Tampere University * Maxime Carriere and Fynn Dobler, Freie Universität Berlin * Agnes Korcsak-Gorzo, Forschungszentrum Jülich * Pablo Martínez Cañada, University of Granada as one of our keynote speakers at this year’s conference. Registration and submission of contributions are now open! We are inviting you to submit contributions in the form of talks and "posters". Please register and submit your contribution(s) via the conference website https://nest-simulator.org/conference. Important dates: 10 April 2026 - Deadline for submission of contributions 05 May 2026 - Notification of acceptance 09 June 2026 - Registration deadline We are looking forward to seeing you all in June! Hans Ekkehard Plesser and the conference organizing committee -- Prof. Dr. Hans Ekkehard Plesser Research Committee Chair, Faculty of Science and Technology 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

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Heaviside function in a Kernel?
by Jeanne Barthelemy 05 Mar '26

05 Mar '26

Dear all, This is a question about best practices for NESTML. I would like to build in the equations block a Kernel, such as for instance: "kernel inh_time_end = ((-0.00002*t*t)/(pow(tau,2.0)) + 0.0087*t/tau + 0.006)/tau" , but modulated by the heaviside function H depending on 200 - t (i.e., H(200.0 ms -t)). To sum up, I would like to get the following kernel: "kernel inh_time_end_modulated = H(200.0 ms -t)*((-0.00002*t*t)/(pow(tau,2.0)) + 0.0087*t/tau + 0.006)/tau" There does not appear to be a direct implementation of the heaviside function H in nestml. I tried to build my own function to convert booleans to 1.0 or 0.0 in my NestML model, upon the condition "200.0 ms > t", and use that instead of the heaviside, but the model is really slow to build on my laptop. I tried other versions with if conditions in the update block, or ternary operators, but they all led to bugs. So, I am unsure of the correct practice to implement an heaviside-modulated polynomial kernel. If anyone has a good and fast solution to propose I would be very happy to learn about it ! Thank you very much, Kind regards, Jeanne BARTHELEMY

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Open NEST Developer Video Conference Monday February 23, at 11:30 CET (UTC+0100)
by Dennis Terhorst 23 Feb '26

23 Feb '26

Dear NEST Users & Developers! I would like to invite you to our next fortnightly Open NEST Developer Video Conference today *Monday February 23, at 11:30 CET (UTC+0100).* As usual, in the Project team round, a contact person of each team will give a short statement summarizing ongoing and planned work in the team and highlight 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. Feel free to join the meeting also if it’s just to bring your own quick questions for direct discussion in the in-depth section. Agenda * Welcome * Review of NEST User Mailing List * Project team round * In-depth discussion: /Support for three factor learning synapse NESTML/ The agenda for this meeting is also available online, see https://github.com/nest/nest-simulator/wiki/2026-02-23-Open-NEST-Developer-… <https://github.com/nest/nest-simulator/wiki/2026-02-23-Open-NEST-Developer-…> Looking forward to seeing you soon! Cheers, Dennis Terhorst Log-in information We use a virtual conference room provided by DFN <https://www.dfn.de/en/> (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 <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 <mailto: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 <http://vcc.zih.tu-dresden.de/index.php?linkid=1.1.3.4> -- Dipl.-Phys. Dennis Terhorst Coordinator Software Development Institute for Advanced Simulation (IAS-6) Computational and Systems Neuroscience & JARA-Institute Brain Structure-Function Relationships (INM-10) Institute of Neuroscience and Medicine Jülich Research Center, Member of the Helmholz Association 52425 Jülich, Germany http://www.csn.fz-juelich.de/ --------------------------------------------------------------------------------------------- Forschungszentrum Jülich GmbH 52425 Jülich Sitz der Gesellschaft: Jülich Eingetragen im Handelsregister des Amtsgerichts Düren Nr. HR B 3498 Vorsitzender des Aufsichtsrats: MinDir Stefan Müller Geschäftsführung: Prof. Dr. Astrid Lambrecht (Vorsitzende), Dr. Stephanie Bauer (stellvertretende Vorsitzende), Prof. Dr. Ir. Pieter Jansens, Prof. Dr. Laurens Kuipers ---------------------------------------------------------------------------------------------

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NEST 3.9 incompatible with PyGSL and libpthread.so issue
by Pedro R. Pinheiro 20 Feb '26

20 Feb '26

Hi everyone. I have a couple of questions pertaining to NESTML and would appreciate some support. I use NEST via WSL with Ubuntu 24.04.3 LTS. More specifically, I use the micromamba extension on VS Code to manage virtual environments and install python packages via conda-forge. 1) When using NEST 3.9 I get an error saying that PyGSL is incompatible and the simulator returns me a warning saying the stiffness test will be skipped. [image: image.png] WARNING:root:PyGSL is not available. The stiffness test will be skipped. WARNING:root:Error when importing: No module named 'pygsl I didn't have this problem before, when I used NEST 3.8. My installation steps currently are essentially: micromamba install -c conda-forge nest-simulator=3.9 ipython cxx-compiler cmake make swig pkg-config pip install nestml When I try to install pygsl via micromamba the only version I can attempt is 2.6.2. Installing pygsl via pip also gives an error even if I have swig and pkg-config installed. 2) When generating a target using generate_target, I get the following error message: /.micromamba/envs/default/x86_64-conda-linux-gnu/sysroot/usr/lib/libpthread.so: No such file or directory I realised that while I do not have libpthread.so under that path I do have libpthread.so.0 and creating a symlink directing the former to the latter solves the problem. Is this acceptable? ln -s /.micromamba/envs/default/x86_64-conda-linux-gnu/sysroot/usr/lib/libpthread.so.0 /.micromamba/envs/default/x86_64-conda-linux-gnu/sysroot/usr/lib/libpthread.so 3) I would like to know if using NESTCodeGeneratorUtils.generate_code_for is better or equivalent to using generate_target. That's it for now. Thank you in advance for your help. Best, Pedro.

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NEST tutorial at the EBRAINS Student Conference: invitation
by Charl Linssen 09 Feb '26

09 Feb '26

Dear all, Please join us for a hands-on NEST tutorial at the EBRAINS Student Conference on Interdisciplinary Brain Research. The EBRAINS Student Conference offers an open platform for early career researchers to exchange innovative ideas across disciplines relevant to brain research and neuroscience. You will have the opportunity to learn about the various software tools on the EBRAINS platform, get first-hand experience using NEST Simulator and tools like NESTML and NEST Desktop, and ask questions and get expert feedback about using simulation in your own research. We will create models from the single synapse, to large-scale spiking neural networks. The conference takes place March 11-13th in Nice, France. Registration is open! Please visit the website for more information: https://ebrains.eu/news-and-events/events/2026/1st-ebrains-student-conferen… Looking forward to seeing you there! _____________________________________ Charl Linssen Ir. MSc Simulation and Data Lab Neuroscience Jülich Supercomputer Centre (JSC) Institute for Advanced Simulation Forschungszentrum Jülich GmbH c.linssen(a)fz-juelich.de +49 (0)2461 61-5269 _____________________________________

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Open NEST Developer Video Conference Monday February 9, at 11:30 CET (UTC+0100)
by Dennis Terhorst 09 Feb '26

09 Feb '26

Dear NEST Users & Developers! I would like to invite you to our next fortnightly Open NEST Developer Video Conference today *Monday February 9, at 11:30 CET (UTC+0100).* As usual, in the Project team round, a contact person of each team will give a short statement summarizing ongoing and planned work in the team and highlight 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. Feel free to join the meeting also if it’s just to bring your own quick questions for direct discussion in the in-depth section. 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/2026-02-09-Open-NEST-Developer-… <https://github.com/nest/nest-simulator/wiki/2026-02-09-Open-NEST-Developer-…> Looking forward to seeing you soon! Cheers, Dennis Terhorst Log-in information We use a virtual conference room provided by DFN <https://www.dfn.de/en/> (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 <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 <mailto: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 <http://vcc.zih.tu-dresden.de/index.php?linkid=1.1.3.4> -- Dipl.-Phys. Dennis Terhorst Coordinator Software Development Institute for Advanced Simulation (IAS-6) Computational and Systems Neuroscience & JARA-Institute Brain Structure-Function Relationships (INM-10) Institute of Neuroscience and Medicine Jülich Research Center, Member of the Helmholz Association 52425 Jülich, Germany http://www.csn.fz-juelich.de/ --------------------------------------------------------------------------------------------- Forschungszentrum Jülich GmbH 52425 Jülich Sitz der Gesellschaft: Jülich Eingetragen im Handelsregister des Amtsgerichts Düren Nr. HR B 3498 Vorsitzender des Aufsichtsrats: MinDir Stefan Müller Geschäftsführung: Prof. Dr. Astrid Lambrecht (Vorsitzende), Dr. Stephanie Bauer (stellvertretende Vorsitzende), Prof. Dr. Ir. Pieter Jansens, Prof. Dr. Laurens Kuipers ---------------------------------------------------------------------------------------------

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Open NEST Developer Video Conference Monday January 26, at 11:30 CET (UTC+0100)
by Dennis Terhorst 26 Jan '26

26 Jan '26

Dear NEST Users & Developers! I would like to invite you to our next fortnightly Open NEST Developer Video Conference today *Monday January 26, at 11:30 CET (UTC+0100).* As usual, in the Project team round, a contact person of each team will give a short statement summarizing ongoing and planned work in the team and highlight 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. Feel free to join the meeting also if it’s just to bring your own quick questions for direct discussion in the in-depth section. 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/2026-01-26-Open-NEST-Developer-… <https://github.com/nest/nest-simulator/wiki/2026-01-26-Open-NEST-Developer-…> Looking forward to seeing you soon! Cheers, Dennis Terhorst Log-in information We use a virtual conference room provided by DFN <https://www.dfn.de/en/> (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 <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 <mailto: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 <http://vcc.zih.tu-dresden.de/index.php?linkid=1.1.3.4> -- Dipl.-Phys. Dennis Terhorst Coordinator Software Development Institute for Advanced Simulation (IAS-6) Computational and Systems Neuroscience & JARA-Institute Brain Structure-Function Relationships (INM-10) Institute of Neuroscience and Medicine Jülich Research Center, Member of the Helmholz Association 52425 Jülich, Germany http://www.csn.fz-juelich.de/ --------------------------------------------------------------------------------------------- Forschungszentrum Jülich GmbH 52425 Jülich Sitz der Gesellschaft: Jülich Eingetragen im Handelsregister des Amtsgerichts Düren Nr. HR B 3498 Vorsitzender des Aufsichtsrats: MinDir Stefan Müller Geschäftsführung: Prof. Dr. Astrid Lambrecht (Vorsitzende), Dr. Stephanie Bauer (stellvertretende Vorsitzende), Prof. Dr. Ir. Pieter Jansens, Prof. Dr. Laurens Kuipers ---------------------------------------------------------------------------------------------

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Open NEST Developer Video Conference Monday January 12, at 11:30 CET (UTC+0100)
by Dennis Terhorst 12 Jan '26

12 Jan '26

Dear NEST Users & Developers! I would like to invite you to our next fortnightly Open NEST Developer Video Conference today *Monday January 12, at 11:30 CET (UTC+0100).* As usual, in the Project team round, a contact person of each team will give a short statement summarizing ongoing and planned work in the team and highlight 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. Feel free to join the meeting also if it’s just to bring your own quick questions for direct discussion in the in-depth section. 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/2026-01-12-Open-NEST-Developer-… <https://github.com/nest/nest-simulator/wiki/2026-01-12-Open-NEST-Developer-…> Looking forward to seeing you soon! Cheers, Dennis Terhorst Log-in information We use a virtual conference room provided by DFN <https://www.dfn.de/en/> (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 <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 <mailto: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 <http://vcc.zih.tu-dresden.de/index.php?linkid=1.1.3.4> -- Dipl.-Phys. Dennis Terhorst Coordinator Software Development Institute for Advanced Simulation (IAS-6) Computational and Systems Neuroscience & JARA-Institute Brain Structure-Function Relationships (INM-10) Institute of Neuroscience and Medicine Jülich Research Center, Member of the Helmholz Association 52425 Jülich, Germany http://www.csn.fz-juelich.de/ --------------------------------------------------------------------------------------------- Forschungszentrum Jülich GmbH 52425 Jülich Sitz der Gesellschaft: Jülich Eingetragen im Handelsregister des Amtsgerichts Düren Nr. HR B 3498 Vorsitzender des Aufsichtsrats: MinDir Stefan Müller Geschäftsführung: Prof. Dr. Astrid Lambrecht (Vorsitzende), Dr. Stephanie Bauer (stellvertretende Vorsitzende), Prof. Dr. Ir. Pieter Jansens, Prof. Dr. Laurens Kuipers ---------------------------------------------------------------------------------------------

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Please merge master into open PRs to avoid problems with NumPy in the testsuite
by Hans Ekkehard Plesser 08 Jan '26

08 Jan '26

Hi! If you have any open PRs against NEST, please merge current master into them to benefit from the recently merged #3717 (thanks to thomaskroi1996!), which replaces a long-deprecated and now removed NumPy call with its modern counterpart. Without this, tests will currently fail under macOS and are expected to fail on Linux as well once that switches to NumPy 2.4. Best, Hans Ekkehard -- Prof. Dr. Hans Ekkehard Plesser Research Committee Chair, Faculty of Science and Technology 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

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Gap junction implementation using NESTML on aeif_cond_beta_neuron model
by Beatrice Baldi 23 Dec '25

23 Dec '25

Hello everyone, I'm writing to ask for advice on how to correctly implement electrical synapses in a custom NESTML neuron model (aeif_cond_beta_nestml). I have attached the relevant NESTML and Python files used to build and install the aeif_cond_beta neuron model with gap junctions enabled. I ran a trial using the "Gap Junctions: Inhibitory network example" script available on the nest website, changing the neuron model to my aeif_cond_beta_nestml, and it does not seem to implement the gap junctions correctly, as changing parameters like gap weight does synchronise the network or influence the output. For reference, I am using NEST version 3.9.0. If you had any advice on how to correctly implement gap junctions using NESTML, I would greatly appreciate it. Thanks. Best regards, Beatrice

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NEST Conference 2026 – Save the date: 16-17 June 2026
by Hans Ekkehard Plesser 18 Dec '25

18 Dec '25

[Image] Dear Colleagues, The NEST Initiative is excited to invite everyone interested in Neural Simulation Technology and the NEST Simulator to the NEST Conference 2026. Save the date for the virtual conference, taking place on June 16-17, 2026! The annual NEST Conference provides an opportunity for the NEST Community to meet, exchange success stories,swap advice, learn about current developments in and around NEST spiking network simulation and its application. Weparticularly encourage young scientists to participate in the conference! Registration and abstract submission will open soon. For more information on the event please visit the conference website https://nest-simulator.org/conference We are looking forward to seeing you in June! Hans Ekkehard Plesser - on behalf of the conference organizing committee - -- Prof. Dr. Hans Ekkehard Plesser Research Committee Chair, Faculty of Science and Technology Head, Department of Data Science 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

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Open NEST Developer Video Conference Monday December 15, at 11:30 CET (UTC+0100)
by Dennis Terhorst 15 Dec '25

15 Dec '25

Dear NEST Users & Developers! I would like to invite you to our next fortnightly Open NEST Developer Video Conference today *Monday December 15, at 11:30 CET (UTC+0100).* As usual, in the Project team round, a contact person of each team will give a short statement summarizing ongoing and planned work in the team and highlight 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. Feel free to join the meeting also if it’s just to bring your own quick questions for direct discussion in the in-depth section. 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/2025-12-15-Open-NEST-Developer-… <https://github.com/nest/nest-simulator/wiki/2025-12-15-Open-NEST-Developer-…> Looking forward to seeing you soon! Cheers, Dennis Terhorst Log-in information We use a virtual conference room provided by DFN <https://www.dfn.de/en/> (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 <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 <mailto: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 <http://vcc.zih.tu-dresden.de/index.php?linkid=1.1.3.4> -- Dipl.-Phys. Dennis Terhorst Coordinator Software Development Institute for Advanced Simulation (IAS-6) Computational and Systems Neuroscience & JARA-Institute Brain Structure-Function Relationships (INM-10) Institute of Neuroscience and Medicine Jülich Research Center, Member of the Helmholz Association 52425 Jülich, Germany http://www.csn.fz-juelich.de/ --------------------------------------------------------------------------------------------- Forschungszentrum Jülich GmbH 52425 Jülich Sitz der Gesellschaft: Jülich Eingetragen im Handelsregister des Amtsgerichts Düren Nr. HR B 3498 Vorsitzender des Aufsichtsrats: MinDir Stefan Müller Geschäftsführung: Prof. Dr. Astrid Lambrecht (Vorsitzende), Dr. Stephanie Bauer (stellvertretende Vorsitzende), Prof. Dr. Ir. Pieter Jansens, Prof. Dr. Laurens Kuipers ---------------------------------------------------------------------------------------------

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Open NEST Developer Video Conference Monday November 17, at 11:30 CET (UTC+0100)
by Dennis Terhorst 17 Nov '25

17 Nov '25

Dear NEST Users & Developers! I would like to invite you to our next fortnightly Open NEST Developer Video Conference today *Monday November 17, at 11:30 CET (UTC+0100).* We will have a short round on ongoing and planned work in the Focus Topics section and check for cross-cutting points that need discussion In-depth discussion. Feel free to join the meeting also if it’s just to bring your own quick questions for direct discussion in the in-depth section. Agenda * Welcome * Review of NEST User Mailing List * Focus Topics * In-depth discussion The agenda for this meeting is also available online, see https://github.com/nest/nest-simulator/wiki/2025-11-17-Open-NEST-Developer-… <https://github.com/nest/nest-simulator/wiki/2025-11-17-Open-NEST-Developer-…> Looking forward to seeing you soon! Cheers, Dennis Terhorst Log-in information We use a virtual conference room provided by DFN <https://www.dfn.de/en/> (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 <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 <mailto: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 <http://vcc.zih.tu-dresden.de/index.php?linkid=1.1.3.4> -- Dipl.-Phys. Dennis Terhorst Coordinator Software Development Institute for Advanced Simulation (IAS-6) Computational and Systems Neuroscience & JARA-Institute Brain Structure-Function Relationships (INM-10) Institute of Neuroscience and Medicine Jülich Research Center, Member of the Helmholz Association 52425 Jülich, Germany http://www.csn.fz-juelich.de/ --------------------------------------------------------------------------------------------- Forschungszentrum Jülich GmbH 52425 Jülich Sitz der Gesellschaft: Jülich Eingetragen im Handelsregister des Amtsgerichts Düren Nr. HR B 3498 Vorsitzender des Aufsichtsrats: MinDir Stefan Müller Geschäftsführung: Prof. Dr. Astrid Lambrecht (Vorsitzende), Dr. Stephanie Bauer (stellvertretende Vorsitzende), Prof. Dr. Ir. Pieter Jansens, Prof. Dr. Laurens Kuipers ---------------------------------------------------------------------------------------------

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simulation control from a gui
by Peter Mason 03 Nov '25

03 Nov '25

I have a GUI to control and analyse the data from the simulation and it's parameters which uses shared memory to manage the state of the simulation and pass the data to the recipients. It seemed like a good idea to have a simulation restart button to normalise the start position and eventually have more than a single independent simulation. This would require the simulation to run independently of the GUI which up to this point it did not. To implement this I tried running the simulation code in a separate thread having forgotten that Nest is not tread safe and it crashed. The simulation code including Nest currently runs in multiple processes. Before attempting to do it myself i asked CoPilot to produce the code attached which I do not understand in detail but this is normal because it uses python features of which I have no knowledge. Up to now. The code runs apart from some 'hopefully simple' details of the button control lost in this conversion Is this application of interest? Is there a standard way to do this?

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Open NEST Developer Video Conference Monday November 3, at 11:30 CET (UTC+0100)
by Dennis Terhorst 03 Nov '25

03 Nov '25

Dear NEST Users & Developers! I would like to invite you to our next fortnightly Open NEST Developer Video Conference today *Monday November 3, at 11:30 CET (UTC+0100).* As usual, in the Project team round, a contact person of each team will give a short statement summarizing ongoing and planned work in the team and highlight 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. Feel free to join the meeting also if it’s just to bring your own quick questions for direct discussion in the in-depth section. 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/2025-11-03-Open-NEST-Developer-… <https://github.com/nest/nest-simulator/wiki/2025-11-03-Open-NEST-Developer-…> Looking forward to seeing you soon! Cheers, Dennis Terhorst Log-in information We use a virtual conference room provided by DFN <https://www.dfn.de/en/> (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 <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 <mailto: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 <http://vcc.zih.tu-dresden.de/index.php?linkid=1.1.3.4> -- Dipl.-Phys. Dennis Terhorst Coordinator Software Development Institute for Advanced Simulation (IAS-6) Computational and Systems Neuroscience & JARA-Institute Brain Structure-Function Relationships (INM-10) Institute of Neuroscience and Medicine Jülich Research Center, Member of the Helmholz Association 52425 Jülich, Germany http://www.csn.fz-juelich.de/ --------------------------------------------------------------------------------------------- Forschungszentrum Jülich GmbH 52425 Jülich Sitz der Gesellschaft: Jülich Eingetragen im Handelsregister des Amtsgerichts Düren Nr. HR B 3498 Vorsitzender des Aufsichtsrats: MinDir Stefan Müller Geschäftsführung: Prof. Dr. Astrid Lambrecht (Vorsitzende), Dr. Stephanie Bauer (stellvertretende Vorsitzende), Prof. Dr. Ir. Pieter Jansens, Prof. Dr. Laurens Kuipers ---------------------------------------------------------------------------------------------

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Re: MPI problem with e-prop tutorials
by Xavier Otazu Porter 31 Oct '25

31 Oct '25

Hi Camilo, Thanks a lot for your help ... but problem remains. Now I get: Traceback (most recent call last): File "eprop_supervised_regression_handwriting_bsshslm_2020.py", line 545, in <module> readout_signal = readout_signal.reshape((readout_signal[0], n_iter, batch_size, steps["sequence"])) #readout_signal = readout_signal.reshape((n_out, n_iter, batch_size, steps["sequence"])) TypeError: only integer scalar arrays can be converted to a scalar index Xavier ________________________________ From: Camilo Jara Do Nascimento <C.Jara-Do-Nascimento(a)sussex.ac.uk> Sent: Wednesday, October 29, 2025 4:56 PM To: NEST User Mailing List <users(a)nest-simulator.org>; Xavier Otazu Porter <xotazu(a)cvc.uab.cat> Subject: Re: [NEST Users] MPI problem with e-prop tutorials Hi Xavier, The problem I see is that the readout first dimension is based on the n_out, and when using mpi to parallelizing it will use this first dimension to parallelize your instances. I quickly fixed it by changing the first dimension to be readout_signal.shape[0] since its already defined before by using the "idc" indexes. readout_signal = readout_signal.reshape((readout_signal.shape[0], n_iter, batch_size, steps["sequence"])) Hope this helps. Best, Camilo Jara D. ________________________________ From: Xavier Otazu <xotazu(a)cvc.uab.cat> Sent: 29 October 2025 14:03 To: users(a)nest-simulator.org <users(a)nest-simulator.org> Subject: [NEST Users] MPI problem with e-prop tutorials Hello, I have tried to execute one of the e-prop tutorials (eprop_supervised_regression_handwriting_bsshslm_2020.py) and get into problems when activating MPI. I do not know whether it is an e-prop C++ implementation problem or a Python tutorial code problem (in some cases, but not all of them, it looks like the last one). I have two files (hostfile_orig_1 and hostfile_orig_2) to define in what nodes of the cluster to execute the program. The content of these files is: hostfile_orig_1: node0 slots=1 node1 slots=1 hostfile_orig_2: node0 slots=2 node0 slots=2 The 'slots' key tells how many (mpi) processes can be executed on a particular node. Depending on the number of processes, the errors are a bit different. In all the following examples, I use "total_num_virtual_procs": 2 on line 173 of tutorial file. Below I write the execution command and the output error. Command: mpirun -np 1 -hostfile hostfile_orig_1 python3 eprop_supervised_regression_handwriting_bsshslm_2020.py Output: With a "serial" execution like this one, everything is OK: Command: mpirun -np 2 -hostfile hostfile_orig_2 python3 eprop_supervised_regression_handwriting_bsshslm_2020.py Output: Traceback (most recent call last): File "eprop_supervised_regression_handwriting_bsshslm_2020.py", line 404, in <module> nest.GetConnections(nrns_rec[0], nrns_rec[1:3]).set([params_init_optimizer] * 2) File "/home/neurobit/local/nest_3.9/lib64/python3.8/site-packages/nest/lib/hl_api_types.py", line 945, in set raise TypeError("status dict must be a dict, or a list of dicts of length {}".format(self.__len__())) TypeError: status dict must be a dict, or a list of dicts of length 1 Command: mpirun -np 2 -hostfile hostfile_orig_2 python3 eprop_supervised_regression_handwriting_bsshslm_2020.py (commenting line 404) Output: Traceback (most recent call last): File "eprop_supervised_regression_handwriting_bsshslm_2020.py", line 545, in <module> readout_signal = readout_signal.reshape((n_out, n_iter, batch_size, steps["sequence"])) ValueError: cannot reshape array of size 364800 into shape (2,200,1,1824) Command: mpirun -np 2 -hostfile hostfile_orig_1 python3 eprop_supervised_regression_handwriting_bsshslm_2020.py (commenting line 404) Output: Traceback (most recent call last): File "eprop_supervised_regression_handwriting_bsshslm_2020.py", line 545, in <module> readout_signal = readout_signal.reshape((n_out, n_iter, batch_size, steps["sequence"])) ValueError: cannot reshape array of size 364800 into shape (2,200,1,1824) Command: mpirun -np 4 -hostfile hostfile_orig_2 python3 eprop_supervised_regression_handwriting_bsshslm_2020.py (commenting line 404 and using "total_num_virtual_procs": 4 on line 173 of tutorial file.) Output: Traceback (most recent call last): File "eprop_supervised_regression_handwriting_bsshslm_2020.py", line 493, in <module> "rec_out": get_weights(nrns_rec, nrns_out), File "eprop_supervised_regression_handwriting_bsshslm_2020.py", line 482, in get_weights conns["senders"] = np.array(conns["source"]) - np.min(conns["source"]) TypeError: tuple indices must be integers or slices, not str In this last case, program stops and hungs. If you want, I could submit a bug report on github. Xavier _______________________________________________ NEST Users mailing list -- users(a)nest-simulator.org To unsubscribe send an email to users-leave(a)nest-simulator.org Computer Vision Center<http://www.cvc.uab.cat> CONFIDENTIALITY WARNING<http://www.cvc.uab.es/?page_id=7475>

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SynapseCollection.get() causes overhead
by M. Maurycy Miękus 29 Oct '25

29 Oct '25

Hello, I am trying to access the list of approx. 13 000 000 synapses in my network. However, accessing any of the values in SynapseCollection runs longer than my whole simulation and can cause out of memory issues. In the following snippet, just the `conns.get('weight')` line takes my computer 13 minutes to compute and uses over 5 GB of memory, even though the data I am interested in should not be larger than 50 MB. importnest neurons= nest.Create('iaf_psc_exp', 20000) conn_dict= {'rule': 'fixed_indegree', 'indegree': 300} nest.Connect(neurons, neurons, conn_dict, syn_spec={'weight': 1.0}) conns= nest.GetConnections() conns.get('weight') How should I efficiently access/export the `source`, `target`, `weight` and `distance` synaptic variables without unnecessary time or memory overhead? Thank you. Best regards, Maurycy Miękus

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MPI problem with e-prop tutorials
by Xavier Otazu 29 Oct '25

29 Oct '25

Hello, I have tried to execute one of the e-prop tutorials (eprop_supervised_regression_handwriting_bsshslm_2020.py) and get into problems when activating MPI. I do not know whether it is an e-prop C++ implementation problem or a Python tutorial code problem (in some cases, but not all of them, it looks like the last one). I have two files (hostfile_orig_1 and hostfile_orig_2) to define in what nodes of the cluster to execute the program. The content of these files is: hostfile_orig_1: node0 slots=1 node1 slots=1 hostfile_orig_2: node0 slots=2 node0 slots=2 The 'slots' key tells how many (mpi) processes can be executed on a particular node. Depending on the number of processes, the errors are a bit different. In all the following examples, I use "total_num_virtual_procs": 2 on line 173 of tutorial file. Below I write the execution command and the output error. Command: mpirun -np 1 -hostfile hostfile_orig_1 python3 eprop_supervised_regression_handwriting_bsshslm_2020.py Output: With a "serial" execution like this one, everything is OK: Command: mpirun -np 2 -hostfile hostfile_orig_2 python3 eprop_supervised_regression_handwriting_bsshslm_2020.py Output: Traceback (most recent call last): File "eprop_supervised_regression_handwriting_bsshslm_2020.py", line 404, in <module> nest.GetConnections(nrns_rec[0], nrns_rec[1:3]).set([params_init_optimizer] * 2) File "/home/neurobit/local/nest_3.9/lib64/python3.8/site-packages/nest/lib/hl_api_types.py", line 945, in set raise TypeError("status dict must be a dict, or a list of dicts of length {}".format(self.__len__())) TypeError: status dict must be a dict, or a list of dicts of length 1 Command: mpirun -np 2 -hostfile hostfile_orig_2 python3 eprop_supervised_regression_handwriting_bsshslm_2020.py (commenting line 404) Output: Traceback (most recent call last): File "eprop_supervised_regression_handwriting_bsshslm_2020.py", line 545, in <module> readout_signal = readout_signal.reshape((n_out, n_iter, batch_size, steps["sequence"])) ValueError: cannot reshape array of size 364800 into shape (2,200,1,1824) Command: mpirun -np 2 -hostfile hostfile_orig_1 python3 eprop_supervised_regression_handwriting_bsshslm_2020.py (commenting line 404) Output: Traceback (most recent call last): File "eprop_supervised_regression_handwriting_bsshslm_2020.py", line 545, in <module> readout_signal = readout_signal.reshape((n_out, n_iter, batch_size, steps["sequence"])) ValueError: cannot reshape array of size 364800 into shape (2,200,1,1824) Command: mpirun -np 4 -hostfile hostfile_orig_2 python3 eprop_supervised_regression_handwriting_bsshslm_2020.py (commenting line 404 and using "total_num_virtual_procs": 4 on line 173 of tutorial file.) Output: Traceback (most recent call last): File "eprop_supervised_regression_handwriting_bsshslm_2020.py", line 493, in <module> "rec_out": get_weights(nrns_rec, nrns_out), File "eprop_supervised_regression_handwriting_bsshslm_2020.py", line 482, in get_weights conns["senders"] = np.array(conns["source"]) - np.min(conns["source"]) TypeError: tuple indices must be integers or slices, not str In this last case, program stops and hungs. If you want, I could submit a bug report on github. Xavier

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Open NEST Developer Video Conference Monday October 20, at 11:30 CEST (UTC+0200)
by Dennis Terhorst 20 Oct '25

20 Oct '25

Dear NEST Users & Developers! I would like to invite you to our next fortnightly Open NEST Developer Video Conference today *Monday October 20, at 11:30 CEST (UTC+0200).* As usual, in the Project team round, a contact person of each team will give a short statement summarizing ongoing and planned work in the team and highlight 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. Feel free to join the meeting also if it’s just to bring your own quick questions for direct discussion in the in-depth section. 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/2025-10-20-Open-NEST-Developer-… <https://github.com/nest/nest-simulator/wiki/2025-10-20-Open-NEST-Developer-…> Looking forward to seeing you soon! Cheers, Dennis Terhorst Log-in information We use a virtual conference room provided by DFN <https://www.dfn.de/en/> (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 <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 <mailto: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 <http://vcc.zih.tu-dresden.de/index.php?linkid=1.1.3.4> -- Dipl.-Phys. Dennis Terhorst Coordinator Software Development Institute for Advanced Simulation (IAS-6) Computational and Systems Neuroscience & JARA-Institute Brain Structure-Function Relationships (INM-10) Institute of Neuroscience and Medicine Jülich Research Center, Member of the Helmholz Association 52425 Jülich, Germany http://www.csn.fz-juelich.de/ --------------------------------------------------------------------------------------------- Forschungszentrum Jülich GmbH 52425 Jülich Sitz der Gesellschaft: Jülich Eingetragen im Handelsregister des Amtsgerichts Düren Nr. HR B 3498 Vorsitzender des Aufsichtsrats: MinDir Stefan Müller Geschäftsführung: Prof. Dr. Astrid Lambrecht (Vorsitzende), Dr. Stephanie Bauer (stellvertretende Vorsitzende), Prof. Dr. Ir. Pieter Jansens, Prof. Dr. Laurens Kuipers ---------------------------------------------------------------------------------------------

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Re: NEST Users Digest, Vol 79, Issue 2
by M. Maurycy Miękus 16 Oct '25

16 Oct '25

Dear Hans, Thank you for your response. Yes, I could be interested in contributing. Best regards, Maurycy On 15/10/2025 14:18, users-request(a)nest-simulator.org wrote: > Send NEST Users mailing list submissions to > users(a)nest-simulator.org > > To subscribe or unsubscribe via email, send a message with subject or > body 'help' to > users-request(a)nest-simulator.org > > You can reach the person managing the list at > users-owner(a)nest-simulator.org > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of NEST Users digest..." > > Today's Topics: > > 1. Re: SynapseCollection.get() causes overhead > (Hans Ekkehard Plesser) > > _______________________________________________ > NEST Users mailing list -- users(a)nest-simulator.org > To unsubscribe send an email to users-leave(a)nest-simulator.org

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Open NEST Developer Video Conference Monday October 06 at 11:30 CEST (UTC+0200)
by Jessica Mitchell 06 Oct '25

06 Oct '25

Dear NEST Users & Developers! I would like to invite you to our next fortnightly Open NEST Developer Video Conference today *Monday October 06 at 11:30 CEST (UTC+0200).* As usual, in the Project team round, a contact person of each team will give a short statement summarizing ongoing and planned work in the team and highlight 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. Feel free to join the meeting also if it’s just to bring your own quick questions for direct discussion in the in-depth section. Agenda 1. Welcome 2. Review of NEST User Mailing List <https://www.nest-simulator.org/mailinglist/hyperkitty/list/users@nest-simul…> 3. Project team <https://github.com/nest/nest-simulator/projects> round 4. In-depth discussion * #3582 > release 3.9! * Report from NEST tutorials The agenda for this meeting is also available online, see https://github.com/nest/nest-simulator/wiki/2025-10-06-Open-NEST-Developer-… Looking forward to seeing you soon! Cheers, Jessica Mitchell > *Log-in information* >> >> We use a virtual conference room provided by DFN >> <https://www.dfn.de/en/> (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 >> <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 <mailto: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 >> <http://vcc.zih.tu-dresden.de/index.php?linkid=1.1.3.4> >> -- -------------------------- Dr. Jessica Mitchell (she/her) Documentation Specialist for Research Software Institute for Advanced Simulation (IAS-6) Computational and Systems Neuroscience & JARA-Institut Brain Structure-Function Relationships (INM-10) Jülich Research Centre and JARA Jülich, Germany Email:j.mitchell@fz-juelich.de Forschungszentrum Jülich GmbH 52425 Jülich Sitz der Gesellschaft: Jülich Eingetragen im Handelsregister des Amtsgerichts Düren Nr. HR B 3498 Vorsitzender des Aufsichtsrats: MinDir Stefan Müller Geschaeftsfuehrung: Prof. Dr. Astrid Lambrecht (Vorsitzende), Dr. Stephanie Bauer (stellvertretende Vorsitzende), Prof. Dr. Ir. Pieter Jansens, Prof. Dr. Laurens Kuipers

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NEST 3.9 released
by Hans Ekkehard Plesser 25 Sep '25

25 Sep '25

Dear NEST Users, It is a great pleasure to annouce the release of NEST 3.9 which brings numerous improvements contributed by 24 developers through over 1200 commits to the NEST code base. Key enhancements include * Enhanced e-prop plasticity with biologically inspired features<https://github.com/nest/nest-simulator/pull/3207> * Re-organised tripartite connectivity generation to support multiple primary connection rules<https://github.com/nest/nest-simulator/pull/3204> * Windows docker instructions for installation<https://github.com/nest/nest-simulator/pull/3521> * Updates built-in timer documentation<https://github.com/nest/nest-simulator/pull/3490> * Extended detailed neuron documentation<https://github.com/nest/nest-simulator/pull/3448> * Enhanced gunicorn options in NEST Server<https://github.com/nest/nest-simulator/pull/3380> * Support for per-thread timers and timing MPI synchronization<https://github.com/nest/nest-simulator/pull/3378> * A logger for nest-server-mpi<https://github.com/nest/nest-simulator/pull/3365> and many bug fixes and code maintenance. I’d like to thank all who have contributed to making NEST 3.9 possible, in particular Jessica Mitchell who joined Dennis Terhorst in our release team and saw the completion of NEST 3.9—thanks a lot! Enjoy NEST 3.9! Hans Ekkehard -- Prof. Dr. Hans Ekkehard Plesser Research Committee Chair, Faculty of Science and Technology Head, Department of Data Science 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

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