- NEST Users - NEST Initiative Mail

nestml generate_target spinnaker failed
by Chris Huyck 10 Jun '25

10 Jun '25

I'm trying to generate a nestml model for spinnaker. I run the generate target and nest, and it works fine. If I change to spinnaker, it crashes with a CoCosManager not found. The spinnaker runs correctly, and I get correct behaviour on my board. I just can't generate target. Has anyone generated spinnaker models recently? -Chris

2 2

NEST Conference 2025 — Register by Wednesday, 11 June (23:59 CEST/UTC+2)!
by Hans Ekkehard Plesser 10 Jun '25

10 Jun '25

Dear Colleagues, We are looking forward to an exciting virtual NEST Conference 2025 on 17–18 June. This year’s program includes keynotes by * Marja-Leena Linne, Tampere University, Finland Astroglia in Neural Circuits: Modeling Synaptic and Network Modulation * Daniela Gandolfi, Università degli Studi di Modena e Reggio Emilia, Italy Full-scale point neuron models of mouse and human hippocampal microcircuits * Bernhard Vogginger, TU Dresden, Germany The SpiNNaker2 neuromorphic system for large-scale brain simulation and energy-efficient AI * Barna Zajzon, Forschungszentrum Jülich, Germany Signal propagation and denoising through topographic modularity of neural circuits complemented by contributed talks, posters and three workshops. You will find the full program at https://events.hifis.net/event/2047/timetable/#all.detailed To register, please go to https://nest-simulator.org/conference. Registration deadline is coming Wednesday, 11 June 2025 23:59 (CEST, UTC+2). We are looking forward to seeing you at the NEST Conference 2025! 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 President, NEST Initiative e.V. 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

1 0

MacOS Homebrew installation issues
by Дарья Снеговская 04 Jun '25

04 Jun '25

Dear all, I met struggles while trying to install NEST on my MacOS Sonoma v. 14.7.6 (Intel). First issue is that I cannot install NEST with PyNEST as it is described in the manual ( https://nest-simulator.readthedocs.io/en/v2.18.0/installation/mac_install.h…) as I get an "Error: invalid option: --with-python". And the second one is that even when I try to install NEST as it is, without PyNEST, then, after a seemingly successful installation I cannot launch neither 'helpindex' nor 'helpdesk' commands. In the first case I get an error message "<path-to-nest>/nest/help/helpindex.hlp: No such file or directory", and in the second, respectively, "<path-to-nest>/nest/index.html does not exist". I guess that occurs because the installation goes wrong at some stage, but I have no idea what to check and how to fix it. Would be grateful for any information, Sincerely yours, Daria.

1 0

Open NEST Developer Video Conference Monday June 2, at 11:30 CEST (UTC+0200)
by Dennis Terhorst 02 Jun '25

02 Jun '25

Dear NEST Users & Developers! I would like to invite you to our next fortnightly Open NEST Developer Video Conference today *Monday June 2, 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/2025-06-02-Open-NEST-Developer-… <https://github.com/nest/nest-simulator/wiki/2025-06-02-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 ---------------------------------------------------------------------------------------------

1 0

Open NEST Developer Video Conference Monday May 19, at 11:30 CEST (UTC+0200)
by Dennis Terhorst 19 May '25

19 May '25

Dear NEST Users & Developers! I would like to invite you to our next fortnightly Open NEST Developer Video Conference today *Monday May 19, 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/2025-05-19-Open-NEST-Developer-… <https://github.com/nest/nest-simulator/wiki/2025-05-19-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 ---------------------------------------------------------------------------------------------

1 0

Open NEST Developer Video Conference Monday May 5, at 11:30 CEST (UTC+0200)
by Dennis Terhorst 05 May '25

05 May '25

Dear NEST Users & Developers! I would like to invite you to our next fortnightly Open NEST Developer Video Conference today *Monday May 5, 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 o Bug report https://github.com/nest/nest-simulator/issues/3489 o Memory measurement, see https://github.com/nest/nest-simulator/issues/3043 The agenda for this meeting is also available online, see https://github.com/nest/nest-simulator/wiki/2025-05-05-Open-NEST-Developer-… <https://github.com/nest/nest-simulator/wiki/2025-05-05-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 ---------------------------------------------------------------------------------------------

1 0

DumpLayerConnections() possible optimization? ...
by Xavier Otazu 29 Apr '25

29 Apr '25

Hello, Some time ago I tool a look at the C++ code of DumpLayerConnections() function and realized the bottleneck is on the get_global_positions_vector() method. In order to avoid this call, could it be possible to define a new function, e.g. DumpLayerConnectionsWithPositions(), where the user can send to the function the positions of the nodes of source and target layers? This way, the calculus of the distance between nodes would be much faster (and it would be possible to avoid the call to get_global_positions_vector() ). In addition, could it be possible to create a function, e.g. GetLocaNodeCollectionPositions(), that returns the positions of (local) nodes? (this positions could be send to the precious DumpLayerConnectionsWithPositions() function). Best, Xavier

1 0

Feedback Requested on NMDA Conductance Model with Dual‑Decay Time Constants in NESTML
by marialaura.degrazia01＠universitadipavia.it 24 Apr '25

24 Apr '25

Dear experts, I am writing to request your feedback about the modification of the standard NMDA conductance β‑function to include two separate decay components. Here our implementation of the related kernel in nestml: kernel g_NMDA' = g_NMDA$ - NMDA_A1_decay1 * (g_NMDA / NMDA_Tau_decay1) - NMDA_A2_decay2 * (g_NMDA /NMDA_Tau_decay2), g_NMDA$' = NMDA_A_rise * (-g_NMDA$ / NMDA_Tau_rise) Do you think that this writing might be the right way to implement it? Thank you very much for your insight. Kind regards, MG

2 1

Fwd: Usage of the nest-server-mpi
by Viktor Vorobev 21 Apr '25

21 Apr '25

Hello, dear nest team! I am trying to launch the experiment, using nest-server-mpi and NRP on the HPC. We also use a module generated by nestml. But I faced the issue, which I so far cannot solve myself... Probably you could help me. We have a working experiment for the nest-server v3.7, which also works with v3.8. I tried to launch nest-simulator in the container on the HPC, but I faced some mpi incompatibility issues, could not solve it fast and gave up for now. Then I installed nest-simulator 3.7 from source on the HPC. The simulation with nest-server also worked. After patching nest-server-mpi (serialization issue) I could launch it on the HPC and communicate with the API, but the experiment didn't work, and I switched to the local nest-simulator container for the test. Locally, in the original nest/nest-simulator:3.7 and 3.8 containers, the nest-server-mpi is not starting. After the fixing the issue (with docopt and serialization) the nest-server-mpi is launching in nest/nest-simulator:dev container. But here is the problem, with this version the experiment is crashing even with nest-server, as well as with nest-server-mpi. And I cannot figure out the reason from the logs and git history... I tried patching versions 3.7 and 3.8, then I can start nest-server-mpi, can use API, but the experiment itself doesn't work. So, the summary: The experiment works with nest-server 3.7 and 3.8, but doesn't work with the patched nest-server-mpi The experiment doesn't work with the nest-server with :dev container What happens in the latest container with the nest-server: nrp-nest-simulator | > nrp-nest-simulator | Apr 03 16:11:15 SimulationManager::set_status [Info]: > nrp-nest-simulator | Temporal resolution changed from 0.1 to 0.1 ms. > nrp-nest-simulator | > nrp-nest-simulator | Apr 03 16:11:15 Install [Info]: > nrp-nest-simulator | loaded module controller_module And that's it, on the other side I get [json.exception.out_of_range.403] key 'data' not found The nest script, which is executed at this moment is nest.ResetKernel() > nest.SetKernelStatus({"resolution": res}) > nest.Install("controller_module") > for i in range(njt): > planner_p = nest.Create("tracking_neuron_nestml", n=N, params={"kp": > plan_params["kp"], "base_rate": plan_params["base_rate"], "pos": True, > "traj": trj, "simulation_steps": len(trj)}) > planner_n = nest.Create("tracking_neuron_nestml", n=N, params={"kp": > plan_params["kp"], "base_rate": plan_params["base_rate"], "pos": False, > "traj": trj, "simulation_steps": len(trj)}) The same piece of code works in nest-server v3.7 and v3.8 What happens in the patched nest-server-mpi v 3.8 or 3.7, here it at least throws an exception nrp-nest-simulator | ======================================== > nrp-nest-simulator | > nrp-nest-simulator | ==> MASTER 0/1743700791.3478301 (route_api_call): > call=GetStatus, args=[[303]], kwargs={} > nrp-nest-simulator | ==> MASTER 0/1743700791.3478405 (GetStatus): sending > call bcast > nrp-nest-simulator | ==> MASTER 0/1743700791.3478618 (GetStatus): sending > data bcast, data=([[303]], {}) > nrp-nest-simulator | ==> MASTER 0/1743700791.3480251 (GetStatus): local > call, args=[NodeCollection(metadata=None, model=spike_recorder, size=1, > first=303)], kwargs={} > nrp-nest-simulator | ==> MASTER 0/1743700791.3480933 (GetStatus): waiting > for response gather > nrp-nest-simulator | ==> MASTER 0/1743700791.3484681 (GetStatus): > received response gather, data=[({'element_type': 'recorder', 'events': > {'senders': array([204]), 'times': array([13.5])}, 'frozen': False, > 'global_id': 303, 'label': 'Brain stem pos', 'local': True, 'model': > 'spike_recorder', 'model_id': 96, 'n_events': 1, 'node_uses_wfr': False, > 'origin': 0.0, 'record_to': 'memory', 'start': 0.0, 'stop': > 1.7976931348623157e+308, 'thread': 0, 'thread_local_id': 152, > 'time_in_steps': False, 'vp': 0},), [{'element_type': 'recorder', 'events': > {'senders': [], 'times': []}, 'frozen': False, 'global_id': 303, 'label': > 'Brain stem pos', 'local': True, 'model': 'spike_recorder', 'model_id': 96, > 'n_events': 0, 'node_uses_wfr': False, 'origin': 0.0, 'record_to': > 'memory', 'start': 0.0, 'stop': 1.7976931348623157e+308, 'thread': 0, > 'thread_local_id': 152, 'time_in_steps': False, 'vp': 1}]] > nrp-nest-simulator | [2025-04-03 19:19:51,348] ERROR in app: Exception on > /api/GetStatus [POST] > nrp-nest-simulator | Traceback (most recent call last): > nrp-nest-simulator | File > "/usr/lib/python3/dist-packages/flask/app.py", line 2070, in wsgi_app > nrp-nest-simulator | response = self.full_dispatch_request() > nrp-nest-simulator | File > "/usr/lib/python3/dist-packages/flask/app.py", line 1515, in > full_dispatch_request > nrp-nest-simulator | rv = self.handle_user_exception(e) > nrp-nest-simulator | File > "/usr/lib/python3/dist-packages/flask_cors/extension.py", line 165, in > wrapped_function > nrp-nest-simulator | return > cors_after_request(app.make_response(f(*args, **kwargs))) > nrp-nest-simulator | File > "/usr/lib/python3/dist-packages/flask/app.py", line 1513, in > full_dispatch_request > nrp-nest-simulator | rv = self.dispatch_request() > nrp-nest-simulator | File > "/usr/lib/python3/dist-packages/flask/app.py", line 1499, in > dispatch_request > nrp-nest-simulator | return > self.ensure_sync(self.view_functions[rule.endpoint])(**req.view_args) > nrp-nest-simulator | File > "/opt/nest/lib/python3.10/site-packages/nest/server/hl_api_server.py", line > 317, in route_api_call > nrp-nest-simulator | return jsonify(response) > nrp-nest-simulator | File > "/usr/lib/python3/dist-packages/flask/json/__init__.py", line 348, in > jsonify > nrp-nest-simulator | f"{dumps(data, indent=indent, > separators=separators)}\n", > nrp-nest-simulator | File > "/usr/lib/python3/dist-packages/flask/json/__init__.py", line 129, in dumps > nrp-nest-simulator | rv = _json.dumps(obj, **kwargs) > nrp-nest-simulator | File "/usr/lib/python3.10/json/__init__.py", line > 238, in dumps > nrp-nest-simulator | **kw).encode(obj) > nrp-nest-simulator | File "/usr/lib/python3.10/json/encoder.py", line > 199, in encode > nrp-nest-simulator | chunks = self.iterencode(o, _one_shot=True) > nrp-nest-simulator | File "/usr/lib/python3.10/json/encoder.py", line > 257, in iterencode > nrp-nest-simulator | return _iterencode(o, 0) > nrp-nest-simulator | File > "/usr/lib/python3/dist-packages/flask/json/__init__.py", line 56, in default > nrp-nest-simulator | return super().default(o) > nrp-nest-simulator | File "/usr/lib/python3.10/json/encoder.py", line > 179, in default > nrp-nest-simulator | raise TypeError(f'Object of type > {o.__class__.__name__} ' > nrp-nest-simulator | TypeError: Object of type int64 is not JSON > serializable > nrp-nest-simulator | [2025-04-03 19:19:51,349] INFO in _internal: > 172.18.0.3 - - [03/Apr/2025 19:19:51] "POST /api/GetStatus HTTP/1.1" 500 - Do you have any clues where I should dig? I would appreciate any help. Best wishes, Viktor

2 2

NEST Conference 2025 - Extension of abstract submission deadline
by Dennis Terhorst 14 Apr '25

14 Apr '25

Dear all, We are inviting contributions to the conference, including talks, "posters" and workshops on specific topics. We are looking forward to your contributions! Due to unrelated organizational circumstances we decided to *extend the abstract submission deadline* for the NEST Conference 2025 *to 30 April*. 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! 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 * Bernhard Vogginger, TU Dresden, Germany as keynote speakers at the conference. For more information on how to submit your contribution, register and participate, please visit the conference website *https://nest-simulator.org/conference* <https://nest-simulator.org/conference> *Important dates* *25 April*2025 - Deadline for NEST Initiative membership applications eligible for fee reduction *30 April*2025 - Extended deadline for submission of contributions *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! on behalf of Hans Ekkehard Plesser and the conference organizing committee best Dennis Terhorst

1 0

2025

2024

2023

2022

2021

2020

2019

NEST Users