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Fwd: Usage of the nest-server-mpi
by Viktor Vorobev 10 Apr '25

10 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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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.

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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.

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

28 Mar '25

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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

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