December 2024 - NEST Users - NEST Initiative Mail

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

2 3

`tsodyks_synapse` and `tsodyks2_synapse` models have different behavior for short term depression
by Pavel Haman 21 Dec '24

21 Dec '24

Hello, I have followed the example script comparing `tsodyks_synapse` and `tsodyks2_synapse` models, which can be found here: https://nest-simulator.readthedocs.io/en/stable/auto_examples/evaluate_tsod… Using the parameter set for depression instead of facilitation I found that `tsodyks2_synapse` model leads to weird peaks of synaptic currents (at least I would not expect that for short term depression) - during the second stimulation the weight rescaling seems to be shifted by one spike compared to tsodyks_synapse (as if parameter "u" would be updated after rescaling the weight instead of before). Does anybody know why is there this difference between the two synapse models? Thank you. All the best, PH

3 7

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

1 0

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

1 0

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

2 7

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.

3 4

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

1 0

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

2 1

About Resonate and Fire Neuron Model?
by Thanh Binh To 02 Dec '24

02 Dec '24

2 5

2024

2023

2022

2021

2020

2019

NEST Users December 2024