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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

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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

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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.

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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 ---------------------------------------------------------------------------------------------

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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 ---------------------------------------------------------------------------------------------

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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 ---------------------------------------------------------------------------------------------

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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

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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

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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

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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

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install issue: MUSIC working from SLI but not pyNEST
by Paolo Marzolo 14 Apr '25

14 Apr '25

Hey all! First time poster here on the mailing list, so don't hesitate to correct me or ask for more information. I'm building a container to package a simulation, but I've ran into an unusual issue that I can't seem to fix: MUSIC proxy nodes are found and created correctly from NEST SLI, but raise `nest.lib.hl_api_exceptions.NESTErrors.UnknownModelName` when created from pyNEST. Here's some more info about my setup. - Both MUSIC and NEST are built from source (`git clone --depth 1 --branch v3.7 https://github.com/nest/nest-simulator/`) - I've tried both `-Dwith-music=ON` and `-Dwith-music=$MUSIC_INSTALL_DIR` to no avail. I'll keep the latter. - other flags are `-Dwith-mpi=ON -Dwith-openmp=ON -Dwith-ltdl=ON` - here are the relevant sections of the cmake output (full output at the end) ``` #18 11.02 Python bindings : Yes (Python 3.10.17: /sim/venv/bin/python3) #18 11.02 Includes : /usr/local/include/python3.10 #18 11.02 Libraries : #18 11.02 Cython : Yes (Cython 3.0.12: /sim/venv/bin/cython) #18 11.02 MPI4Py : Yes (/sim/venv/lib/python3.10/site-packages/mpi4py/include) ... #18 11.02 Use MUSIC : Yes (MUSIC 1.2.1) #18 11.02 Includes : /sim/install/music/include #18 11.02 Libraries : /sim/install/music/lib/libmusic.so ``` - the presence of MUSIC version in `cmake` output makes me hopeful that it's found correctly - image based on Debian 12 (`FROM python:3.10-slim-bookworm AS runner`) - first thing i do is create a venv and set it as first in path (`ENV PATH="$VIRTUAL_ENV/bin:$PATH"`) - when i attempt to run the [MUSIC with pyNEST example](https://nest-simulator.readthedocs.io/en/stable/tutorials/music_tutorial/music_tutorial_2.html) i get `nest.lib.hl_api_exceptions.NESTErrors.UnknownModelName: UnknownModelName in SLI function Create_l_i: /music_event_in_proxy is not a known model name.`, while running the [MUSIC in SLI example](https://nest-simulator.readthedocs.io/en/stable/tutorials/music_tutorial/music_tutorial_sli.html) works correctly - i read the [official Dockerfile](https://github.com/nest/nest-docker/blob/master/src/3.8/Dockerf… but I couldn't spot any steps I might be missing, the [cmake options](https://nest-simulator.readthedocs.io/en/stable/installation/cmake_options.html#cmake-options), the [install_music.sh script](https://github.com/nest/nest-simulator/blob/master/build_support/in…, the [docker entrypoint](https://github.com/nest/nest-docker/blob/master/src/3.8/entrypo… and the $NEST_INSTALL_DIR/bin/nest_vars.sh scripts, but I didn't find anything other than what I already had. - I'm guessing this is user error on my part, hence the mailing list instead of github issues. If necessary I can share a smaller version of the dockerfile... not sure what else to try. On one hand, I'd think of a compilation issue, but the cmake output and the fact that SLI works correctly makes me doubt so. On the other, I might be missing an env var, but from what I could gather in pyNEST `nest.node_models` is asked to the kernel, which correctly creates the node when called from the SLI... Is there any esoteric configuration I might've missed? I'll take any and all suggestions! Thanks a lot, Paolo full cmake output: ``` #18 11.02 -------------------------------------------------------------------------------- #18 11.02 NEST Configuration Summary #18 11.02 -------------------------------------------------------------------------------- #18 11.02 #18 11.02 Target System : Linux #18 11.02 Cross Compiling : FALSE #18 11.02 C compiler : GNU 12.2.0 (/usr/bin/cc) #18 11.02 C compiler flags : -Wall -fopenmp -O2 -fdiagnostics-color=auto #18 11.02 C++ compiler : GNU 12.2.0 (/usr/bin/c++) #18 11.02 C++ compiler flags : -std=c++17 -Wall -fopenmp -O2 -fdiagnostics-color=auto #18 11.02 Build dynamic : ON #18 11.02 #18 11.02 Built-in modelset : full #18 11.02 #18 11.02 Python bindings : Yes (Python 3.10.17: /sim/venv/bin/python3) #18 11.02 Includes : /usr/local/include/python3.10 #18 11.02 Libraries : #18 11.02 Cython : Yes (Cython 3.0.12: /sim/venv/bin/cython) #18 11.02 MPI4Py : Yes (/sim/venv/lib/python3.10/site-packages/mpi4py/include) #18 11.02 #18 11.02 Documentation : No #18 11.02 #18 11.02 Use threading : Yes (OpenMP: -fopenmp) #18 11.02 Libraries : /usr/lib/gcc/x86_64-linux-gnu/12/libgomp.so;/usr/lib/x86_64-linux-gnu/libpthread.a #18 11.02 #18 11.02 Use GSL : Yes (GSL 2.7.1) #18 11.02 Includes : /usr/include #18 11.02 Libraries : /usr/lib/x86_64-linux-gnu/libgsl.so;/usr/lib/x86_64-linux-gnu/libgslcblas.so #18 11.02 #18 11.02 Use Readline : Yes (GNU Readline 8.2) #18 11.02 Includes : /usr/include #18 11.02 Libraries : /usr/lib/x86_64-linux-gnu/libreadline.so;/usr/lib/x86_64-linux-gnu/libncurses.so #18 11.02 #18 11.02 Use libltdl : Yes (LTDL 2.4.7) #18 11.02 Includes : /usr/include #18 11.02 Libraries : /usr/lib/x86_64-linux-gnu/libltdl.so #18 11.02 #18 11.02 Use MPI : Yes (MPI: /usr/bin/mpicxx) #18 11.02 Includes : /usr/lib/x86_64-linux-gnu/openmpi/include;/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi #18 11.02 Libraries : /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi_cxx.so;/usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so #18 11.02 Launcher : /usr/bin/mpiexec -n <np> <prog> <args> #18 11.02 #18 11.02 Detailed timers : No #18 11.02 #18 11.02 Use MUSIC : Yes (MUSIC 1.2.1) #18 11.02 Includes : /sim/install/music/include #18 11.02 Libraries : /sim/install/music/lib/libmusic.so #18 11.02 #18 11.02 Use libneurosim : No #18 11.02 #18 11.02 Use Boost : Yes (Boost 1.74.0) #18 11.02 Includes : /usr/include #18 11.02 Libraries : #18 11.02 #18 11.02 Use SIONlib : No #18 11.02 #18 11.02 Use HDF5 : No #18 11.02 #18 11.02 For details on setting specific flags for your MPI launcher command, see the #18 11.02 CMake documentation at https://cmake.org/cmake/help/latest/module/FindMPI.html #18 11.02 #18 11.02 -------------------------------------------------------------------------------- #18 11.02 #18 11.02 The NEST executable will be installed to: #18 11.02 /sim/install/nest/bin/ #18 11.02 #18 11.02 NEST dynamic libraries and user modules will be installed to: #18 11.02 /sim/install/nest/lib/nest/ #18 11.02 #18 11.02 PyNEST will be installed to: #18 11.02 /sim/install/nest/lib/python3.10/site-packages #18 11.02 #18 11.02 To set necessary environment variables, add the following line #18 11.02 to your ~/.bashrc : #18 11.02 source /sim/install/nest/bin/nest_vars.sh #18 11.02 #18 11.02 -------------------------------------------------------------------------------- #18 11.02 #18 11.02 You can now build and install NEST with #18 11.02 make #18 11.02 make install #18 11.02 make installcheck #18 11.02 #18 11.02 If you experience problems with the installation or the use of NEST, #18 11.02 please see https://www.nest-simulator.org/frequently_asked_questions #18 11.02 or go to https://www.nest-simulator.org/community to find out how to #18 11.02 join the user mailing list. #18 11.02 ```

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Open NEST Developer Video Conference Monday April 7, at 11:30 CEST (UTC+0200)
by Dennis Terhorst 07 Apr '25

07 Apr '25

Dear NEST Users & Developers! I would like to invite you to our next fortnightly Open NEST Developer Video Conference today *Monday April 7, 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/2025-04-07-Open-NEST-Developer-… <https://github.com/nest/nest-simulator/wiki/2025-04-07-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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using NEST in C++ examples
by johnpapad24＠gmail.com 02 Apr '25

02 Apr '25

Dear NEST team, I would like to intergrate nest in my c++ project however I couldn't find any examples on how to use nest in the C++ programing language. Can you give me some simple examples like conecting 3 neurons? Thanks in advance.

2 1

using NEST in C++ examples
by johnpapad24＠gmail.com 01 Apr '25

01 Apr '25

Dear NEST team, I would like to intergrate nest in my c++ project however I couldn't find any examples on how to use nest in the C++ programing language. Can you give me some simple examples like conecting 3 neurons? Thanks in advance.

1 0

What exactly should one do to customize one's own extension module?
by Alex Serenko 28 Mar '25

28 Mar '25

2 1

Documentation
by Peter Mason 25 Mar '25

25 Mar '25

To Jessica Mitchell. using::: https://nest-jessica-mitchell.readthedocs.io/en/stable/documentation_workfl… Should this read 'bottom right of the screen' ? Also the 'Stable' page raises an Error Peter [image: image.png]

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Disconnecting a recurrently connected population fails
by Willem Wybo 24 Mar '25

24 Mar '25

Dear Nest users, I’ve been trying to disconnect a population of neurons that is recurrently connected to itself. This works for a simple connection rule, like conn_spec=‘all_to_all’, but it fails for a more complex rule, like, conn_spec={'rule': 'pairwise_bernoulli', 'p': 1.0, 'allow_autapses': False}. When connecting two different populations to each other, disconnecting works with this rule. However, when connecting to the same population, the output of nest.GetConnections states that there are no connections, and calling nest.Disconnect() results in an error: nest.lib.hl_api_exceptions.NESTErrors.The connection does not exist: The connection does not exist in SLI function Disconnect_g_g_D_D: Deletion of connection is not possible. I’ve added a minimal example reproducing the issue in the attachment, Nest version is 3.8.0-post0.dev0. Btw, I’ve gotten this issue in a network model that was developed for Nest 3.5, so it seemed to work in that version. Best regards, Willem ---------------------- Dr. Willem Wybo, group leader Peter Grünberg Institute 15 - Neuromorphic Software Ecosystems Forschungszentrum Jülich www.fz-juelich.de/pgi/PGI-15 ——————————— ------------------------------------------------------------------------------------------------ ------------------------------------------------------------------------------------------------ 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 (stellv. Vorsitzende), Prof. Dr. Ir. Pieter Jansens, Prof. Dr. Laurens Kuipers ------------------------------------------------------------------------------------------------ ------------------------------------------------------------------------------------------------

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

24 Mar '25

Dear NEST Users & Developers! I would like to invite you to our next fortnightly Open NEST Developer Video Conference today *Monday March 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/2025-03-24-Open-NEST-Developer-… <https://github.com/nest/nest-simulator/wiki/2025-03-24-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/ --------------------------------------------------------------------------------------------- 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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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

1 0

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

1 0

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_ (?).

3 3

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 ---------------------------------------------------------------------------------------------

1 0

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.

5 5

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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