- NEST Users - NEST Initiative Mail

Test message, please ignore
by Hans Ekkehard Plesser 09 Jan '25

09 Jan '25

This message is a test. -- 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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Test and a Happy New Year!
by Jochen Martin Eppler 07 Jan '25

07 Jan '25

Cheers Jochen!  

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Assistance with Installing NESTML
by atiye nejadebrahim 26 Dec '24

26 Dec '24

Dear all, I have installed NEST from source in a conda environment and attempted to install NESTML both via conda and manually. However, I consistently encounter the following error: pynestml.exceptions.generated_code_build_exception.GeneratedCodeBuildException: Error occurred during 'make all'! More detailed error messages can be found in stderr. I have tried adding it to the path, but despite installing pynestml, it still cannot locate it. Could you please assist me in resolving this issue and successfully installing NESTML to create a new module? Thank you in advance for your help! Best regards,Atiyeh Atiyeh Nezhadebrahim,Scientific Researcher

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Using nest server to run nestml models
by pabloabur＠gmail.com 17 Dec '24

17 Dec '24

Hi Everyone, Does nest server currently support nestml models? I couldn't find examples in the documentation (even though `nestml-server` binary exists in nest3.8 docker image). Ideally, I would like to run it with MPI too. I can run a simple example (`python test.py`) with `nest-server` running from a docker container, but the same code fails if I use `nestml-server`: ``` docker run -it --rm -e LOCAL_USER_ID=`id -u $USER` -p 52425:52425 nest/nest-simulator:3.8 nest-server start ``` works, but ``` docker run -it --rm -e LOCAL_USER_ID=`id -u $USER` -p 52426:52426 nest/nest-simulator:3.8 nestml-server start ``` fails with ``` Traceback (most recent call last): File "/usr/local/lib/python3.10/dist-packages/urllib3/connection.py", line 199, in _new_conn sock = connection.create_connection( File "/usr/local/lib/python3.10/dist-packages/urllib3/util/connection.py", line 85, in create_connection raise err File "/usr/local/lib/python3.10/dist-packages/urllib3/util/connection.py", line 73, in create_connection sock.connect(sa) ConnectionRefusedError: [Errno 111] Connection refused The above exception was the direct cause of the following exception: Traceback (most recent call last): File "/usr/local/lib/python3.10/dist-packages/urllib3/connectionpool.py", line 789, in urlopen response = self._make_request( File "/usr/local/lib/python3.10/dist-packages/urllib3/connectionpool.py", line 495, in _make_request conn.request( File "/usr/local/lib/python3.10/dist-packages/urllib3/connection.py", line 441, in request self.endheaders() File "/usr/lib/python3.10/http/client.py", line 1278, in endheaders self._send_output(message_body, encode_chunked=encode_chunked) File "/usr/lib/python3.10/http/client.py", line 1038, in _send_output self.send(msg) File "/usr/lib/python3.10/http/client.py", line 976, in send self.connect() File "/usr/local/lib/python3.10/dist-packages/urllib3/connection.py", line 279, in connect self.sock = self._new_conn() File "/usr/local/lib/python3.10/dist-packages/urllib3/connection.py", line 214, in _new_conn raise NewConnectionError( urllib3.exceptions.NewConnectionError: <urllib3.connection.HTTPConnection object at 0x7fb8b63ea440>: Failed to establish a new connection: [Errno 111] Connection refused The above exception was the direct cause of the following exception: Traceback (most recent call last): File "/usr/lib/python3/dist-packages/requests/adapters.py", line 439, in send resp = conn.urlopen( File "/usr/local/lib/python3.10/dist-packages/urllib3/connectionpool.py", line 843, in urlopen retries = retries.increment( File "/usr/local/lib/python3.10/dist-packages/urllib3/util/retry.py", line 519, in increment raise MaxRetryError(_pool, url, reason) from reason # type: ignore[arg-type] urllib3.exceptions.MaxRetryError: HTTPConnectionPool(host='localhost', port=52425): Max retries exceeded with url: /exec (Caused by NewConnectionError('<urllib3.connection.HTTPConnection object at 0x7fb8b63ea440>: Failed to establish a new connection: [Errno 111] Connection refused')) During handling of the above exception, another exception occurred: Traceback (most recent call last): File "/home/pablo/git/nest-client/test_server.py", line 4, in <module> response = nsc.from_file('examples/NESTClient_script.py', return_vars='n_events') File "/home/pablo/git/nest-client/nest_client/nest_client.py", line 68, in from_file return self.exec_script(script, return_vars) File "/home/pablo/git/nest-client/nest_client/nest_client.py", line 56, in exec_script response = requests.post(self.url + 'exec', json=params, headers=self.headers) File "/usr/lib/python3/dist-packages/requests/api.py", line 119, in post return request('post', url, data=data, json=json, **kwargs) File "/usr/lib/python3/dist-packages/requests/api.py", line 61, in request return session.request(method=method, url=url, **kwargs) File "/usr/lib/python3/dist-packages/requests/sessions.py", line 544, in request resp = self.send(prep, **send_kwargs) File "/usr/lib/python3/dist-packages/requests/sessions.py", line 657, in send r = adapter.send(request, **kwargs) File "/usr/lib/python3/dist-packages/requests/adapters.py", line 516, in send raise ConnectionError(e, request=request) requests.exceptions.ConnectionError: HTTPConnectionPool(host='localhost', port=52425): Max retries exceeded with url: /exec (Caused by NewConnectionError('<urllib3.connection.HTTPConnection object at 0x7fb8b63ea440>: Failed to establish a new connection: [Errno 111] Connection refused')) ``` The simple python code used is shown below. ``` from nest_client import NESTClient nsc = NESTClient() response = nsc.from_file('examples/NESTClient_script.py', return_vars='n_events') n_events = response['data'] print('Number of events:', n_events) ``` No nestml models are being tested for now because I don't know which functions should be used to generate code with `nest-client` e.g. ``` from pynestml.codegeneration.nest_code_generator_utils import NESTCodeGeneratorUtils module_name, neuron_model_name, synapse_model_name = \ NESTCodeGeneratorUtils.generate_code_for( "neuron.nestml", "synapse.nestml", post_ports=["post_spikes"], codegen_opts=codegen_opts ) ``` should be rewritten to use `from nest_client import NESTClient`. Thanks in advance, Pablo Alejandro

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Open NEST Developer Video Conference Monday December 16, at 11:30 CET (UTC+0100)
by Dennis Terhorst 16 Dec '24

16 Dec '24

Dear NEST Users & Developers! I would like to invite you to our next fortnightly Open NEST Developer Video Conference today *Monday December 16, 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/2024-12-16-Open-NEST-Developer-… <https://github.com/nest/nest-simulator/wiki/2024-12-16-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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Issue In testing of a trained network
by Aditya Srivastava 10 Dec '24

10 Dec '24

I have built a nest model with a reverse stdp approach in which with time I'm trying to reduce the spikes in training data which is a normal bearing metal data and then during testing I'll try to test it on a anomalous data which should produce opposite results to that of training data so now firstly I made it in brian and it worked fine but here in nest after training the model when I have to test it then again the synaptic weights are changing which should not happen during testing. In brian I had put the learning rate as 0 thats why it was working fine but in Nest I am not able to find a way to test a model by freezing the weights. So I tried something which I'm not sure is the correct approach so can anyone please review this approach or if suggest a better approach for testing these kind of models. Also I want to mention one thing that with my current approach the weights are freezing but as I'm assigning input spikes from anomalous signal and start testing, the kernel is getting died which usually happens when there is a some issue in nest network. nest.ResetKernel() # Simulation parameters dt = 0.01 # Simulation time step in ms nest.SetKernelStatus({"resolution": dt}) N = 16 # Number of neurons gmax = 3 neuron_params = { "tau_m": 140.0, # Membrane time constant in ms "E_L": -70.6, # Resting potential (in mV) "V_th": -40.4, # Threshold potential (in mV) "V_reset": -70.6, # Reset potential (in mV) "V_m":0.0, } nest.CopyModel("stdp_synapse_hom", "stdp_synapse_exc", {"weight":gmax,"alpha":1,"Wmax":gmax, "tau_plus": 20.0,"lambda": -0.0005, "mu_minus": 0, "mu_plus": 0}) nest.CopyModel("stdp_synapse_hom", "stdp_synapse_inh", {"weight":-gmax/(N-1),"alpha":1,"Wmax":-gmax, "tau_plus": 20.0,"lambda": 0.005, "mu_minus": 0, "mu_plus": 0}) G_spike_gen = nest.Create("spike_generator", N) G_input = nest.Create("parrot_neuron", N) G_hidden = nest.Create("iaf_psc_delta", N,params=neuron_params) G_output = nest.Create("iaf_psc_delta", 1,params=neuron_params) S_in = nest.Connect(G_spike_gen, G_input, "one_to_one") # Connect input to hidden layer with excitatory STDP synapses S_exc = nest.Connect(G_input, G_hidden,"one_to_one",syn_spec = "stdp_synapse_exc") # Retrieve the neuron IDs for G_input and G_hidden input_ids = G_input.tolist() hidden_ids = G_hidden.tolist() # Get the existing excitatory connections and extract their source-target ID pairs exc_connections = nest.GetConnections(G_input, G_hidden) exc_connection_pairs = set(zip(exc_connections.get("source"), exc_connections.get("target"))) for i in input_ids: for h in hidden_ids: if (i, h) not in exc_connection_pairs: nc1 = nest.NodeCollection([i]) nc2 = nest.NodeCollection([h]) nest.Connect(nc1, nc2, syn_spec= "stdp_synapse_inh") S_out = nest.Connect(G_hidden, G_output,"all_to_all",syn_spec = {"weight": 40.4/N}) def train_net(signals, spike_tol=0): output_spike_recorder = nest.Create("spike_recorder") output_membrane_recorder = nest.Create("voltmeter", 1) nest.Connect(G_output, output_spike_recorder) # Record output layer spikes nest.Connect(output_membrane_recorder, G_output, "one_to_one") while True: recorder_for_epoch = nest.Create("spike_recorder") nest.Connect(G_output, recorder_for_epoch) for signal in signals: indices, times = process_signal(signal) # Get the indices and times offset = nest.GetKernelStatus()["biological_time"] for i in range(N): times_for_neuron = [t+offset for j,t in enumerate(times) if indices[j] == i] G_spike_gen[i].set(spike_times = times_for_neuron) nest.Simulate(len(signal)*(1/SAMPLE_RATE)*1000) output_spikes_num = len(recorder_for_epoch.get()["events"]["times"]) print("# of output spikes: " + str(output_spikes_num)) del recorder_for_epoch if output_spikes_num <= spike_tol: print("Training finished") break return output_membrane_recorder, output_spike_recorder def synapse_freeze(): conn = nest.GetConnections() sources = conn.get("source") targets = conn.get("target") weights = conn.get("weight") # Store as a list of tuples connections = list(zip(sources, targets, weights)) # Replace dynamic synapses with static synapses for s,t,w in connections: nc1 = nest.NodeCollection([s]) nc2 = nest.NodeCollection([t]) conn_t = nest.GetConnections(nc1,nc2) model=nest.GetConnections(nc1,nc2).get("synapse_model") if model=="stdp_synapse_exc": nest.Disconnect(nc1,nc2,syn_spec = {"synapse_model":"stdp_synapse_exc"}) nest.Connect(nc1,nc2,syn_spec = {"synapse_model":"static_synapse","weight":w}) if model=="stdp_synapse_inh": nest.Disconnect(nc1,nc2,syn_spec = {"synapse_model":"stdp_synapse_inh"}) nest.Connect(nc1,nc2,syn_spec = {"synapse_model":"static_synapse","weight":w}) print("Switched to static synapses with trained weights.") def inference(signal): output_spike_recorder_t = nest.Create("spike_recorder") output_membrane_recorder_t = nest.Create("voltmeter", 1) nest.Connect(G_output, output_spike_recorder_t) # Record output layer spikes nest.Connect(output_membrane_recorder_t, G_output, "one_to_one") indices, times = process_signal(signal) # Prepare test signal offset = nest.GetKernelStatus()["biological_time"] for i in range(N): times_for_neuron = [t+offset for j,t in enumerate(times) if indices[j] == i] G_spike_gen[i].set(spike_times = times_for_neuron) nest.Simulate(len(signal)*(1/SAMPLE_RATE)*1000) # Run simulation output_spikes_num = len(output_spike_recorder_t.get()["events"]["times"]) print("# of output spikes: " + str(output_spikes_num)) return output_membrane_recorder_t, output_spike_recorder_t

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Request for Assistance with Synaptic Weight Normalization
by Peter Mason 02 Dec '24

02 Dec '24

I am currently working on a project involving synaptic weight normalization using the guidelines provided in the NEST simulator documentation. I have implemented the normalization process; however, I encountered some questions that I would appreciate your insights on. 1. Normalization Value: I found that the normalization value for a neuron with approximately 190 synapses is around 420, which I do not fully understand. This looks like the total weight of the neuron synapses. Could you provide clarification on how the normalisation value is determined? 2. Simulation State Preservation: I would like to save and restore the state of synaptic weights to maintain the simulation's behaviour across sessions. Below is the pseudocode I intend to use: Save synaptic weights: w = array of current weights of neuron connections normalization_factor = sum of absolute weights if normalization_factor != 0: normalized_weights = w / normalization_factor save normalized_weights to file Load synaptic weights: read normalized_weights from file assign loaded weights back to connection I would like to know if you have any suggestions for improving this pseudocode or if there are best practices I should consider. Thank you for your time and assistance. I look forward to your response.

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Open NEST Developer Video Conference Monday December 2, at 11:30 CET (UTC+0100)
by Dennis Terhorst 02 Dec '24

02 Dec '24

Dear NEST Users & Developers! I would like to invite you to our next fortnightly Open NEST Developer Video Conference today *Monday December 2, 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/2024-12-02-Open-NEST-Developer-… <https://github.com/nest/nest-simulator/wiki/2024-12-02-Open-NEST-Developer-…> Today Jessica will be chairing the meeting. 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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Open NEST Developer Video Conference Monday November 18, at 11:30 CET (UTC+0100)
by Dennis Terhorst 02 Dec '24

02 Dec '24

Dear NEST Users & Developers! I would like to invite you to our next fortnightly Open NEST Developer Video Conference today *Monday November 18, 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/2024-11-18-Open-NEST-Developer-… <https://github.com/nest/nest-simulator/wiki/2024-11-18-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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About Resonate and Fire Neuron Model?
by Thanh Binh To 02 Dec '24

02 Dec '24

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Generating and building code in NESTML
by Shavika Rastogi 25 Nov '24

25 Nov '24

Hello everyone, I am Shavika Rastogi, a PhD student at the International Centre for Neuromorphic Systems, Western Sydney University, Australia. I currently use NEST and NESTML to write and test any arbitrary neuron model. Before writing my own neuron model, I wanted to test neuron models already existing in NESTML. I am using NEST and NESTML using docker. I am running the Izhikevich tutorial available in the documentation ( https://nestml.readthedocs.io/en/latest/tutorials/izhikevich/nestml_izhikev…). As per this tutorial, we can generate and build code using the following statement : "module_name,neuron_model_name=NESTCodeGeneratorUtils.generate_code_for("izhikevich_solution.nestml")" When I am using this function, I get the following error : "AttributeError: 'NESTCodeGeneratorUtils' object has no attribute 'generate_code_for'" Does anyone know whether the generate_code_for() function exists in the NESTCodeGeneratorUtils package? If not, what could be the alternative function we can use for generating and building neuron models ? Thanks in advance. With Warm Regards Shavika Rastogi, Research Scholar (Dual Award PhD) International Centre for Neuromorphic Systems The MARCS Institute of Brain, Behaviour and Development Western Sydney University Sydney, Australia & Biocomputation Research Group University of Hertfordshire, UK

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Re: NESTML Dopa Synapse - Error during parsing
by Jona Scholz 15 Nov '24

15 Nov '24

Hello everyone, quick update on my problem: I was using the latest .nestml models from the main branch with NESTML version 8.0.0-rc3. There is a slight difference between these and apparently that caused it. It works now and I hope everyone has a great weekend. Kind regards, Jona

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NESTML Dopa Synapse - Error during parsing
by Jona Scholz 13 Nov '24

13 Nov '24

Dear NESTML enthusiasts, I'm trying to do the NESTML dopamine-modulated STDP synapse tutorial ( https://nestml.readthedocs.io/en/latest/tutorials/stdp_dopa_synapse/stdp_do…) and get an error during the first code generation (see bottom of the message). This is the line where it fails: NESTCodeGeneratorUtils.generate_code_for("../../../models/neurons/iaf_psc_delta_neuron.nestml", nestml_stdp_dopa_model, ...) I am running the tutorial notebook as is, except for a change in the neuron model path. I changed it like this: NESTCodeGeneratorUtils.generate_code_for("iaf_psc_delta_neuron.nestml", nestml_stdp_dopa_model, ...) With this model https://github.com/nest/nestml/blob/master/models/neurons/iaf_psc_delta_neu… in the same folder as the notebook. I am using NESTML version 8.0.0rc3 and Nest 3.8. If I only generate code for the neuron model everything is fine. module_name, neuron_model_name = NESTCodeGeneratorUtils.generate_code_for( "iaf_psc_delta_neuron.nestml") [100%] Built target nestml_24dea23d173448c9b2a52d4f6a232dbd_module_module Install the project... Additionally, in the SFA tutorial I am able to change the neuron model and run it without any problems ( https://nestml.readthedocs.io/en/latest/tutorials/spike_frequency_adaptatio… ). With all of that said, here is the error: [1,GLOBAL, INFO]: List of files that will be processed: [2,GLOBAL, INFO]: /home/jona/rstdp-gym/iaf_psc_delta_neuron.nestml [3,GLOBAL, INFO]: /home/jona/rstdp-gym/neuromodulated_stdp_synapse.nestml [4,GLOBAL, INFO]: Target platform code will be generated in directory: '/home/jona/rstdp-gym/target' [5,GLOBAL, INFO]: Target platform code will be installed in directory: '/tmp/nestml_target_8uqeeze7' -- N E S T -- Copyright (C) 2004 The NEST Initiative Version: 3.8.0 Built: Aug 27 2024 04:33:09 This program is provided AS IS and comes with NO WARRANTY. See the file LICENSE for details. Problems or suggestions? Visit https://www.nest-simulator.org Type 'nest.help()' to find out more about NEST. [6,GLOBAL, INFO]: The NEST Simulator version was automatically detected as: v3.8.0 [7,GLOBAL, INFO]: Given template root path is not an absolute path. Creating the absolute path with default templates directory '/home/jona/mambaforge/envs/neuro/lib/python3.11/site-packages/pynestml/codegeneration/resources_nest/point_neuron' [8,GLOBAL, INFO]: Given template root path is not an absolute path. Creating the absolute path with default templates directory '/home/jona/mambaforge/envs/neuro/lib/python3.11/site-packages/pynestml/codegeneration/resources_nest/point_neuron' [9,GLOBAL, INFO]: Given template root path is not an absolute path. Creating the absolute path with default templates directory '/home/jona/mambaforge/envs/neuro/lib/python3.11/site-packages/pynestml/codegeneration/resources_nest/point_neuron' [10,GLOBAL, INFO]: The NEST Simulator installation path was automatically detected as: /home/jona/mambaforge/envs/neuro [11,GLOBAL, INFO]: Start processing '/home/jona/rstdp-gym/iaf_psc_delta_neuron.nestml'! [13,GLOBAL, INFO]: Start processing '/home/jona/rstdp-gym/neuromodulated_stdp_synapse.nestml'! [14,GLOBAL, ERROR]: Error occurred during parsing: abort [15,iaf_psc_delta_neuron_nestml, WARNING, [43:0;85:0]]: Model 'iaf_psc_delta_neuron_nestml' contains errors. No code generated! line 37:13 mismatched input '(' expecting NEWLINE line 39:4 extraneous input 'onReceive' expecting {<EOF>, NEWLINE, 'model'} line 40:8 extraneous input ' ' expecting {<EOF>, NEWLINE, 'model'} line 40:4 extraneous input ' ' expecting {<EOF>, NEWLINE, 'model'} line 43:8 extraneous input ' ' expecting {<EOF>, NEWLINE, 'model'} line 46:8 extraneous input 'c' expecting {<EOF>, NEWLINE, 'model'} line 46:4 extraneous input ' ' expecting {<EOF>, NEWLINE, 'model'} line 49:8 extraneous input ' ' expecting {<EOF>, NEWLINE, 'model'} line 52:8 extraneous input 'c' expecting {<EOF>, NEWLINE, 'model'} line 55:8 extraneous input 'emit_spike' expecting {<EOF>, NEWLINE, 'model'} line 55:4 extraneous input ' ' expecting {<EOF>, NEWLINE, 'model'} line 59:8 extraneous input ' ' expecting {<EOF>, NEWLINE, 'model'} line 63:8 extraneous input 'w' expecting {<EOF>, NEWLINE, 'model'} line 64:8 extraneous input 'w' expecting {<EOF>, NEWLINE, 'model'} line 65:8 extraneous input 'c' expecting {<EOF>, NEWLINE, 'model'} line 66:8 extraneous input 'n' expecting {<EOF>, NEWLINE, 'model'} line 66:0 extraneous input '\n' expecting {<EOF>, NEWLINE, 'model'} Any help is appreciated. Kind regards, Jona

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Open NEST Developer Video Conference Monday November 4, at 11:30 CET (UTC+0100)
by Dennis Terhorst 04 Nov '24

04 Nov '24

Dear NEST Users & Developers! I would like to invite you to our next fortnightly Open NEST Developer Video Conference today *Monday November 4, 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/2024-11-04-Open-NEST-Developer-… <https://github.com/nest/nest-simulator/wiki/2024-11-04-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 ----------------------------------------------------------------------

1 0

Simulation execution time for extended runs
by Peter Mason 01 Nov '24

01 Nov '24

The simulation of C.elegans now is implemented in a multi processing environment. The simulation of each individual object and various observation tools such as visualisation, matplotlib spike data plotting and configuration of the simulation parameters have their own process. An issue has arisen with only one object being simulated in that the execution 'time' for the constant 'simulation step time', increases with subsequent call to pynn.nest.Simulate(self.simulation_step). I presume nest continues the simulation from the previous iteration state. A crude plot suggests that the time increase is linear. Eventually the simulation stalls. I have a recorder connected to each of the 302 nodes and multiple recorders connected to some of the nodes. These use multiprocessor queues and a manged list to transfer data and as far as I can tell they do not overflow. I have disabled the recorders by not connecting them to the neurons and the phenomenon persists. It looks as if the issue is in the nest simulation. I have increased the process priority to -1. It does not help. Also does anyone know of the work of Ramin Hasani at Wien. He seems to have done the same thing and is now using 19 neurons to steer a car. How can I get a copy of the report of work done by him and his students? Peter Mason

1 1

NEST & NESTML do things right :)
by Hans Ekkehard Plesser 24 Oct '24

24 Oct '24

Dear NEST Users, I have just published a paper in Frontiers in Neuroinformatics Plesser HE (2024) Commentary: Accelerating spiking neural network simulations with PymoNNto and PymoNNtorch. Front. Neuroinform. 18:1446620. doi: 10.3389/fninf.2024.1446620 confirming that NEST/NESTML provide correct simulations. I just wanted to let you know about this result because a paper earlier this year had included a figure showing that NEST got different results than several other simulators. It turned out that exact integration is exact as the name says, while forward Euler is not. Best, Hans Ekkehard -- Prof. Dr. Hans Ekkehard Plesser Research Committee Chair, Faculty of Science and Technology Head, Department of Data Science Department of Data Science Faculty of Science and Technology Norwegian University of Life Sciences PO Box 5003, 1432 Aas, Norway Phone +47 6723 1560 Email hans.ekkehard.plesser(a)nmbu.no<mailto:hans.ekkehard.plesser@nmbu.no> Home http://arken.nmbu.no/~plesser

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Application-Oriented Hackathons
by Kunkel, Susanne 21 Oct '24

21 Oct '24

Dear NEST Users, We would like to inquire your interest in Application-Oriented Hackathons, and are thus reaching out to you with this survey: https://ictsurvey.helmholtz-muenchen.de/index.php?r=survey/index&sid=234889… which will be active till 25 October, 2024. For now, we plan to organize two such hackathons: 1. in Aachen, Germany in the week 9-13 December, 2024 2. in Aas, Norway in the week 23-27 June, 2025 These in-person events would allow you to bring your ideas for new NEST features and get started implementing them with the help of experienced NEST developers. Please note that your participation would be at your own expense. We look forward to your feedback! Best wishes, Susanne Kunkel on behalf of NEST Initiative ------------------------------------------------------------------------------------------------ ------------------------------------------------------------------------------------------------ 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 ------------------------------------------------------------------------------------------------ ------------------------------------------------------------------------------------------------

1 1

Open NEST Developer Video Conference Monday October 21, at 11:30 CEST (UTC+0200)
by Dennis Terhorst 21 Oct '24

21 Oct '24

Dear NEST Users & Developers! I would like to invite you to our next fortnightly Open NEST Developer Video Conference today *Monday October 21, 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/2024-10-21-Open-NEST-Developer-… <https://github.com/nest/nest-simulator/wiki/2024-10-21-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 ----------------------------------------------------------------------

1 0

MPI-based error on v3.8
by Ady Sharma 20 Oct '24

20 Oct '24

Hi all! What I'm doing: I've used v2.20.2 on HPC (bwForCluster NEMO) for my large-scale simulations involving structural plasticity. Now I'm trying to move to v3.8. How am I doing this? I built NESTv3.8 on my HPC workspace following the cmake instructions mentioned at: https://nest-simulator.readthedocs.io/en/v3.8/installation/cmake_options.ht… Here's an overview of my build and installation commands: ``` source /<some_path>/NESTv3.8/bin/activate # activate a fresh python venv (v3.9.7) [optional] module load mpi/openmpi/4.0-gnu-9.2 # cmake version 3.30.4 cmake --debug-find \ -DMPI_C_COMPILER=$(which mpicc) \ -DMPI_CXX_COMPILER=$(which mpicxx) \ -DMPI_HOME=$(which mpirun) \ -Dwith-mpi=ON \ -Dwith-openmp=ON \ -DCYTHON_EXECUTABLE=/<some_path>/intel/oneapi/2022.1/intelpython/latest/bin/cython \ -DCMAKE_INSTALL_PREFIX:PATH=/<some_path>/nest-simulator-3.8-build \ /<path_to_extracted_tar>/nest-simulator-3.8/ # if I don't specify the Cython path, cmake picks an outdated (uncompatible) cython version. I did not try the -Dcythonize-pynest=OFF option because I don't know how to build PyNEST from a pre-cythonized pynestkernel.pyx. make make install make installcheck ``` Once this finishes, I do the usual `source`-ing of `nest_vars.sh`. I also add the NEST path to my python venv's `site-packages`. This has always worked for all NEST versions I ever installed. `installcheck` finishes with 1 error. See below: ``` THE NEST TESTSUITE DISCOVERED PROBLEMS The following tests failed | regressiontests.issue-1703.py Please report test failures by creating an issue at https://github.com/nest/nest-simulator/issues --------------------------------------------------------------------------- make[3]: *** [CMakeFiles/installcheck] Error 1 make[2]: *** [CMakeFiles/installcheck.dir/all] Error 2 make[1]: *** [CMakeFiles/installcheck.dir/rule] Error 2 make: *** [installcheck] Error 2 ``` THE WARNING: Ignoring this, if I proceed with pyNEST in the venv by `import nest`, I get the following warning: ``` -------------------------------------------------------------------------- WARNING: There is at least non-excluded one OpenFabrics device found, but there are no active ports detected (or Open MPI was unable to use them). This is most certainly not what you wanted. Check your cables, subnet manager configuration, etc. The openib BTL will be ignored for this job. Local host: n4669 -------------------------------------------------------------------------- n4669.nemo.privat.74030PSM2 no hfi units are active (err=23) -------------------------------------------------------------------------- Open MPI failed an OFI Libfabric library call (fi_endpoint). This is highly unusual; your job may behave unpredictably (and/or abort) after this. Local host: n4669 Location: mtl_ofi_component.c:627 Error: Invalid argument (22) -------------------------------------------------------------------------- -- N E S T -- Copyright (C) 2004 The NEST Initiative Version: 3.8.0 Built: Oct 10 2024 16:21:41 This program is provided AS IS and comes with NO WARRANTY. See the file LICENSE for details. Problems or suggestions? Visit https://www.nest-simulator.org Type 'nest.help()' to find out more about NEST. ``` THE CRASH: If I ignore this warning and proceed to submit a job, the execution eventually crashes with exit code: 134. If you'd like to see the crash dump, check this MD file on GitLab.: https://gitlab.rz.uni-freiburg.de/as2013/mpi-hpc-nestv3.8.git Any idea what's going wrong here? If I follow the same build and installation steps on my local machine (other than specifying the Cython path in cmake; because no need). Neither do I get any warnings nor does any simulation crash. I'm guessing this has to do with the build and installation on the cluster. I'd appreciate any input. Thanks! Best, Ady

2 9

aeif_cond_beta_multisynapse in NESTML
by tanguy.damart＠protonmail.com 11 Oct '24

11 Oct '24

Hello everyone, Is there a NESTML version of the NEST model aeif_cond_beta_multisynapse ? (https://nest-simulator.readthedocs.io/en/stable/models/aeif_cond_beta_multi…) If not, is there any difficulties that I might face implementing it in NESTML that I need to be aware of ? (Like how to handle multiple types of synapses). Best, Tanguy

3 3

Open NEST Developer Video Conference Monday October 7, at 11:30 CEST (UTC+0200)
by Dennis Terhorst 07 Oct '24

07 Oct '24

Dear NEST Users & Developers! I would like to invite you to our next fortnightly Open NEST Developer Video Conference today *Monday October 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/2024-10-07-Open-NEST-Developer-… <https://github.com/nest/nest-simulator/wiki/2024-10-07-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/ 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 ----------------------------------------------------------------------

1 0

Enhancement of C++ implementation of DumpLayerConnections()
by Xavier Otazu 27 Sep '24

27 Sep '24

Hi! After using some PyNEST functions and modifying the C++ implementation of DumpLayerConnections(), I was thinking on a possible further improvement of this function (or creating a new function). But since I do not know the design and architecture of C++ nestkernel code, I prefer to ask. In my code I normalize the presynaptic connections of every neuron. To do this, I originally do something like for i in range(len(target_layer)) conn[i] = nest.GetConnections(source_layer, target_layer, synapse_model) normalize(conn) Since I am using MPI and the loop iterates over all the neurons, I modified the previous code to local_nodes = nest.GetLocalNodeCollection(target_layer) local_nodes = nest.NodeCollection(local_nodes) for i in range(len(local_nodes)) conn[i] = nest.GetConnections(source_layer, local_nodes, synapse_model) normalize(conn) This last code is faster that the previous one (I guess that local_nodes variable is local to every MPI process and, as a consequence, GetConnections() is more efficient because it only works with local nodes instead of with all of them). Using the idea of the GetLocalNodeCollection(), I was thinking it could be used into the C++ implementation of DumpLayerConnections(). Presently, this function obtain all the connections between source and target layers. Could it be possible to call the equivalent C++ implementation of GetLocalCollection()? I understand that the problem is that, since DumpLayerConnections() needs the spatial information of the layers, the node collections obtained with GetLocalNodeCollection() (I guess similarly its C++ implementation) does not have this spatial information. As a second possibility, I was thinking on adding a new method (GetSpatialInformation()) and enhancing DumpLayerConnections() (or add a new function). The GetSpatialInformation() function could return the spatial information of a collection of nodes (the ones obtained by GetLocalNodeCollection() ). The DumpLayerConnections() (or a new function) could be enhanced by changing the target layer parameter to a pair of parameters that contain the local nodes collection and their spatial information. Something like DumpLaterConnections(source_layer, local_nodes_collection, spatial_information, synapse_model). This way DumpLayerConnections() will only used local nodes and would be much faster. Sorry for the technical email. Xavier

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Open NEST Developer Video Conference Monday September 23, at 11:30 CEST (UTC+0200)
by Dennis Terhorst 23 Sep '24

23 Sep '24

Dear NEST Users & Developers! I would like to invite you to our next fortnightly Open NEST Developer Video Conference today *Monday September 23, 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/2024-09-23-Open-NEST-Developer-… <https://github.com/nest/nest-simulator/wiki/2024-09-23-Open-NEST-Developer-…> Looking forward to seeing you soon! Cheers, Dennis Terhorst Log-in information We use a virtual conference room provided by DFN <https://www.dfn.de/en/> (Deutsches Forschungsnetz). You can use the web client to connect. We however encourage everyone to use a headset for better audio quality or even a proper video conferencing system (see below) or software when available. Web client * Visit https://conf.dfn.de/webapp/conference/97938800 <https://conf.dfn.de/webapp/conference/97938800> * Enter your name and allow your browser to use camera and microphone * The conference does not need a PIN to join, just click join and you’re in. In case you see a dfnconf logo and the phrase “Auf den Meetingveranstalter warten”, just be patient, the meeting host needs to join first (a voice will tell you). VC system/software How to log in with a video conferencing system, depends on you VC system or software. * Using the H.323 protocol (eg Polycom): |vc.dfn.net##97938800| or |194.95.240.2##97938800| * Using the SIP protocol:97938800@vc.dfn.de <mailto:97938800@vc.dfn.de> * By telephone: |+49-30-200-97938800| For those who do not have a video conference system or suitable software, Polycom provides a pretty good free app for iOS and Android, so you can join from your tablet (Polycom RealPresence Mobile, available from AppStore/PlayStore). Note that firewalls may interfere with videoconferencing in various and sometimes confusing ways. For more technical information on logging in from various VC systems, please see http://vcc.zih.tu-dresden.de/index.php?linkid=1.1.3.4 <http://vcc.zih.tu-dresden.de/index.php?linkid=1.1.3.4> -- Dipl.-Phys. Dennis Terhorst Coordinator Software Development Institute for Advanced Simulation (IAS-6) Computational and Systems Neuroscience & JARA-Institute Brain Structure-Function Relationships (INM-10) Institute of Neuroscience and Medicine Jülich Research Center, Member of the Helmholz Association 52425 Jülich, Germany http://www.csn.fz-juelich.de/ 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 ----------------------------------------------------------------------

1 0

stdp synapse nestml erro
by Chris Huyck 20 Sep '24

20 Sep '24

I'm working with the nestml 7.0.2. I got the example models from https://github.com/nest/nestml/blob/v7.0.2/models/neurons/hill_tononi.nestml this git tree. I tried three different stdp models including stdp_triplet_naive.nestml. All give AssertionError: Synapses only support one spiking input port when I generate_target in python. -Chris

2 7

Discuss NEST @ Bernstein Conference in Frankfurt 29 Sep–2 Oct
by Hans Ekkehard Plesser 19 Sep '24

19 Sep '24

Dear NEST Users, I just wanted to let you know that I and a number of other NEST developers will attend the Bernstein Conference in Frankfurt from 29 September to 2 October this year. If you would like to discuss anything related to NEST, let me know so we can arrange to meet. You are also welcome to drop by the EBRAINS booth, where we will have NEST stickers 😊. If you are going to present work done with NEST, we’d appreciate it if you put a “nest::simulated()” logo on your slides or poster (see https://github.com/nest/nest-simulator/tree/master/doc/logos) and let us know about your talk/poster number in advance. Best Hans Ekkehard -- Prof. Dr. Hans Ekkehard Plesser Head of Research, 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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