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NESTML - Error when generating code in an EasyBuild installation
by Pablo Alejandro 20 Mar '25

20 Mar '25

Hi everyone, I am currently working with nest/nestml that was installed with EasyBuild <https://docs.easybuild.io/> (i.e. a tool to manage software in HPC systems). Nest was installed with OpenMPI support (see nest_easybuild.eb attached) and it seems to be working fine. Nestml is failing when I try the stdp tutorial <https://nestml.readthedocs.io/en/latest/tutorials/stdp_windows/stdp_windows…> (see error log slurm-782.out and test.py script attached). I also attached the installation steps for nestml (nestml_easybuild.eb) and the slurm script (run_job_simple.sh) to this email. Could someone please assist me with further debugging this? This looks like an installation problem, but I get no errors if I'm using no synapse models. Thanks -- Pablo Alejandro

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Test message, please ignore
by Hans Ekkehard Plesser 19 Mar '25

19 Mar '25

-- 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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NEST Conference 2025 – registration and call for contributions are open
by Hans Ekkehard Plesser 16 Mar '25

16 Mar '25

Dear colleagues, The NEST Initiative is excited to invite everyone interested in Neural Simulation Technology and the NEST Simulator to the NEST Conference 2025. 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 17/18 June 2025. We are delighted to welcome * Marja-Leena Linne, Tampere University, Finland * Daniela Gandolfi, Università degli Studi di Modena e Reggio Emilia, Italy * Barna Zajzon, Forschungszentrum Jülich, Germany * as keynote speakers at the conference. Registration and submission of contributions are now open! We are inviting contributions to the conference, including talks, "posters" and workshops on specific topics. Please register and submit your contribution(s) via the conference website https://nest-simulator.org/conference Important dates 15 April 2025 - Deadline for submission of contributions 25 April 2025 - Deadline for NEST Initiative membership applications eligible for fee reduction 09 May 2025 - Notification of acceptance 11 June 2025 - Registration deadline 17 June 2025 - NEST Conference 2025 starts 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 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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First LTP interaction in STDP and synaptic time delay in STDP
by iiro.ahokainen＠tuni.fi 10 Mar '25

10 Mar '25

I'm a bit confused with NEST's STDP models. I'm not sure if the issues that I have found are design choices or unintended bugs. To debug stdp models, I added print statements in the stdp_synapse.h file: double minus_dt; while ( start != finish ) { minus_dt = t_lastspike_ - ( start->t_ + dendritic_delay ); std::cout<<"minus_dt: "<<minus_dt<<std::endl; std::cout<<"postspike time: "<<start->t_<<std::endl; ++start; // get_history() should make sure that // start->t_ > t_lastspike - dendritic_delay, i.e. minus_dt < 0 assert( minus_dt < -1.0 * kernel().connection_manager.get_stdp_eps() ); weight_ = facilitate_( weight_, Kplus_ * std::exp( minus_dt / tau_plus_ ) ); } I created two parrot neurons and fed spike times to the first neuron. I set the syn_delay to 0.3 ms. I found two issues: 1. If the spike train consists of only one spike, no STDP updates are performed. I would expect one positive update since the postsynaptic spike arrives 0.3 ms after the presynaptic spike. 2. minus_dt=-0.6 instead of -0.3. The spike separation is 0.3 ms, however for the STDP calculation, one uses 0.6 ms which confuses me. Indeed, simulating with presynaptic spike train [10., 20.] leads to weight change 1.0->35.5443 (lamba=1, mu_plus=mu_minus=0, otherwise defaults). Analytically, the same can be achieved by calculating (1/100 + np.exp(-0.6/20) - np.exp(-9.4/20))*100 = np.float64(35.54432652658074) This confirms that indeed minus_dt=-0.6 ms and that the first LTP STDP interaction is neglected. Are these known issues or new findings? I tested with NEST 3.3 and 3.8 and both had the same issues. I do not understand the point of having dendritic_delay in minus_dt = t_lastspike_ - ( start->t_ + dendritic_delay ), as it is already included in the start->t_ (?).

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Open NEST Developer Video Conference Monday March 10, at 11:30 CET (UTC+0100)
by Dennis Terhorst 10 Mar '25

10 Mar '25

Dear NEST Users & Developers! I would like to invite you to our next fortnightly Open NEST Developer Video Conference today *Monday March 10, 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/2025-03-10-Open-NEST-Developer-… <https://github.com/nest/nest-simulator/wiki/2025-03-10-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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Exponential Euler Support in NESTML
by justin.r.davis＠essie.ufl.edu 05 Mar '25

05 Mar '25

I've got a version of the HH model (via a NESTML file) which seems to be requiring an exponential Euler solver (ie the one commonly used for e^x dependent biologic systems) to most efficiently solve the equations*. From my reading of the NESTML code generator tools source, only rk45 and forward-Euler are supported. The difference between Euler and Exponential Euler doesn't seem that significant, so I wanted to see if I could get the exponential version implemented....however, what's become unclear to me is whether or not this is a limitation of NEST, NESTML or the underlying solvers and how I'd go about getting a different solver implemented. Are there any guides around on how one would implement a new solver and/or information which would help me figure this out. thx. jrd *=forward Euler does work for some (might work with even smaller timestep) cases, but it requires a time step of 0.01ms. I'm comparing with a Brian2 version of the model running with a 0.1ms time step with it's natively supported exponential Euler solver which is what is making me look into other solvers for my NESTML-based code.

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Open NEST Developer Video Conference Monday February 24, at 11:30 CET (UTC+0100)
by Dennis Terhorst 24 Feb '25

24 Feb '25

Dear NEST Users & Developers! I would like to invite you to our next fortnightly Open NEST Developer Video Conference today *Monday February 24, 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/2025-02-24-Open-NEST-Developer-… <https://github.com/nest/nest-simulator/wiki/2025-02-24-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/ Phone +49 2461 61-85062 ---------------------------------------------------------------------- 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), Karsten Beneke (stellv. Vorsitzender), Prof. Dr. Ir. Pieter Jansens ----------------------------------------------------------------------

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export NEST_MLMODULES=nestmlmodule breaks nest
by Chris Huyck 14 Feb '25

14 Feb '25

I've been using nestml with pynn and nest for some time. I think I built a new model (combining a synapse and a neuron) and it broke nest. So, I can start an environment that has nest, and run nest (sli), pynest and pynn files with nest. However, if I export NEST_MLMODULES=nestmlmodule it breaks nest (sli). That is, I invoke nest, and it says it can't find nestmlmodule. However, if I start a new shell, and do not export NEST_MLMODULES I can run python, import nest, then nest.Install("./nestmlmodule") # in the right directory neuron = nest.Create("iaf_cond_beta_neuron") If I then export NEST_MLMODULES=nestmlmodule I can't import nest from python. Somewhere in the middle of all this, I reran nestml to create just the iaf_cond_beta_neuron, so that's the library I'm using. I'm pretty sure that library works fine. Any idea how to fix it? -Chris From: Chris Huyck <C.Huyck(a)mdx.ac.uk> Sent: 31 January 2025 12:10 To: NEST User Mailing List <users(a)nest-simulator.org> Subject: [NEST Users] Re: nestml synapses in pyNN I'm trying to use my own short term potentiation model with an existing model. The model is the IF_cond_exp model from PyNN. I tried your nestml integrate and fire models from Git.../nestml/master/models/neurons, and none seem to be the IF_cond_exp model. The closest I could find was the iaf_cond_beta_neuron. Am I missing something. Is the IF_cond_exp model done somewhere in nestml? (I'm relatively vested in that IF_cond_exp model. I need the nestml neuron model before I can properly use the nestml synapse model.) -Chris From: Charl Linssen <nest-users(a)turingbirds.com<mailto:nest-users@turingbirds.com>> Sent: 23 July 2024 11:25 To: users(a)nest-simulator.org<mailto:users@nest-simulator.org> Subject: [NEST Users] Re: nestml synapses in pyNN You don't often get email from nest-users(a)turingbirds.com<mailto:nest-users@turingbirds.com>. Learn why this is important<https://aka.ms/LearnAboutSenderIdentification> Hi Chris, Thank you for writing in! It would be great to have a better compatibility and better documentation for using NESTML models in pyNN, but as of now this is not yet in place, please let us know if you have any tips or experience to share. On SpiNNaker, only neuron models are supported for now, we have an open position for a student project to implement synaptic plasticity as well! With kind regards, Charl On Mon, Jul 22, 2024, at 16:32, Chris Huyck wrote: I've taken your noisy_synapse model and got that to run in pyNest. When I try it in PyNN it fails (can't find weight if you set w, weight not an argument if you use weight). I understand that you don't support pyNN. Do you support SpiNNaker (as it's a target)? If so, how do you access the model on SpiNNaker? (I only access SpiNNaker through PyNN). -Chris _______________________________________________ NEST Users mailing list -- users(a)nest-simulator.org<mailto:users@nest-simulator.org> To unsubscribe send an email to users-leave(a)nest-simulator.org<mailto:users-leave@nest-simulator.org>

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nestml synapses in pyNN
by Chris Huyck 14 Feb '25

14 Feb '25

I've taken your noisy_synapse model and got that to run in pyNest. When I try it in PyNN it fails (can't find weight if you set w, weight not an argument if you use weight). I understand that you don't support pyNN. Do you support SpiNNaker (as it's a target)? If so, how do you access the model on SpiNNaker? (I only access SpiNNaker through PyNN). -Chris

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nestml doesn't work on synapse models
by Chris Huyck 12 Feb '25

12 Feb '25

I've got a new conda environment. I compile nest (3.7) from a tarball and it runs. I pip install pyNN I pip install nestml (which now gives me nestml8.0.0. Is there some way to tell the version without just uninstalling it?) The neuron models work. The synapse models fail to nestml I tried my models, but went to the noisy_synapse and static_synapse models (from git) Both fail in nest_code_generator.py line 267 (variables_special_cases = ...) Any thoughts about how to get synapses to work in nestml? -Chris

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