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Re: Problems in simulation restore
by Hans Ekkehard Plesser 11 Mar '24

11 Mar '24

Dear Petia, Please excuse my late reply to your questions about restoring NEST simulations. For some reason, your mail had disappeared from my computer. The behaviour you observe is as expected. When storing and then re-loading and continuing the simulation, a number of things will be different in the second part of the simulation: * Any spikes that were in transit from pre- to postsynaptic neuron are lost. * Random number generators re-start from a different point then where they stopped. * Internal properties of neuron models, such as the state of GSL-based ODE integrators for nonlinear neuron models. There is currently no way to avoid this loss of information. Best regards, Hans Ekkehard -- Prof. Dr. Hans Ekkehard Plesser 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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Opt out of MPI during an MPI run
by Robin Gilbert De Schepper 11 Mar '24

11 Mar '24

Hi! Is there a way to disable the following fatal error? Perhaps an environment variable to tell NEST not to try to initialize MPI: [FATAL] [2024.3.1 12:15:12 /home/robin/git/nest-simulator/nestkernel/mpi_manager.cpp:203 @ MPIManager::initialize()] : You seem to be using NEST via an MPI launcher like mpirun, mpiexec or srun although NEST was not compiled with MPI support. Please see the NEST documentation about parallel and distributed computing. Exiting. I know I could rebuild with MPI support, and set the communicator to a communicator containing just that rank, on each rank, but this is during unit testing where nest is just imported, so a quick opt-out would be less work. -- Robin De Schepper, PhD (they/them) Department of Brain and Behavioral Sciences Unit of Neurophysiology University of Pavia, Italy Via Forlanini 6, 27100 Pavia - Italy Tel: (+39) 038298-7607 http://www-5.unipv.it/dangelo/

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

11 Mar '24

Dear NEST Users & Developers! I would like to invite you to our next fortnightly Open NEST Developer Video Conference today *Monday March 11, 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 o Todo's for the 3.7 release The agenda for this meeting is also available online, see https://github.com/nest/nest-simulator/wiki/2024-03-11-Open-NEST-Developer-… <https://github.com/nest/nest-simulator/wiki/2024-03-11-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 Juelich GmbH 52425 Juelich Sitz der Gesellschaft: Juelich Eingetragen im Handelsregister des Amtsgerichts Dueren Nr. HR B 3498 Vorsitzender des Aufsichtsrats: MinDir Stefan Müller Geschaeftsfuehrung: Prof. Dr. Astrid Lambrecht (Vorsitzende), Karsten Beneke (stellv. Vorsitzender), Dr. Ir. Pieter Jansens ----------------------------------------------------------------------

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GetConnections() enhancement request
by Xavier Otazu 08 Mar '24

08 Mar '24

Hi! In order to perform connections weight normalization, I am using the GetConnections() function to obtain the input connections for every neuron. That is, I use a code like for i in range(number_of neurons) conn[i] = GetConnections(my_source, my_target[i], ...) Later in the code, I use conn[i].weight to perform my normalization. It implies that for big networks (number_of_neurons=10k) I have to call GetConnections() around 10k times. Hence, the execution time is huge. Could it be possible that you enhance GetConnections() (or define a new function) in order to return the connections for all the neurons in the target in array with the same longitude as the number of neurons in target instead of the number of connections? That is, indexed by neurons instead of indexed by connections. I understand that present implementation of GetConnections() visits all the connections and return only the input connections to target. I do not want to tell developers how to do it :-) but I believe it could be implemented by visiting all the connections (related to target) just ONCE and copy each one to the corresponding output array indexed by neuron. This way, it would be a single call to GetConnections() (plus the time needed to internally manage the assignment to the output array), instead of 10k times. It would be very much appreciated. Thanks a lot in advance! Xavier

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Virtual NEST Conference 2024 / Abstract Submission and Registration Open
by Hans Ekkehard Plesser 05 Mar '24

05 Mar '24

Dear Colleagues, The NEST Initiative is excited to invite everyone interested in Neural Simulation Technology and the NESTSimulator to the NEST Conference 2024. The NEST Conference provides an opportunity for the NEST Community to meet, exchange success stories, swap advice, learn about current developments in and around NEST spiking network simulation and its application. We explicitly encourage young scientists to participate in the conference! This year's conference will again take place as a virtual conference on Monday/Tuesday 17/18 June 2024. We are delighted to welcome * Tadashi Yamazaki (University of Electro-Communications, Tokyo) * Behnam Ghazinouri (Ruhr University Bochum) * Benedetta Gambosi (Politecnico di Milano) * Tobias Gemmeke (RWTH Aachen University) as keynote speakers at the conference. Registration and submission of contributions are now open! We are inviting contributions to the conference, including talks, "posters" and workshops on specific topics. Please register and submit your contribution(s) via the conference website https://nest-simulator.org/conference. Important dates 15 April 2024 - Deadline for submission of contributions 26 April 2024 - Deadline for NEST Initiative membership applications eligible for fee reduction 08 May 2024 - Notification of acceptance 07 June 2024 - Registration deadline 17 June 2024 - NEST Conference 2024 starts We are looking forward to seeing you all in June! Hans Ekkehard Plesser and the conference organizing committee [Image] -- Prof. Dr. Hans Ekkehard Plesser 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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Open NEST Developer Video Conference Monday February 26, at 11:30 CET (UTC+0100)
by Dennis Terhorst 26 Feb '24

26 Feb '24

Dear NEST Users & Developers! I would like to invite you to our next fortnightly Open NEST Developer Video Conference today *Monday February 26, 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 o MPI tests port to Python #3102 <https://github.com/nest/nest-simulator/pull/3102> The agenda for this meeting is also available online, see https://github.com/nest/nest-simulator/wiki/2024-02-26-Open-NEST-Developer-… <https://github.com/nest/nest-simulator/wiki/2024-02-26-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 Juelich GmbH 52425 Juelich Sitz der Gesellschaft: Juelich Eingetragen im Handelsregister des Amtsgerichts Dueren Nr. HR B 3498 Vorsitzender des Aufsichtsrats: MinDir Stefan Müller Geschaeftsfuehrung: Prof. Dr. Astrid Lambrecht (Vorsitzende), Karsten Beneke (stellv. Vorsitzender), Dr. Ir. Pieter Jansens ----------------------------------------------------------------------

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SLIInterpreter --> Key '/Install' does not exist in dictionary
by Willem Wybo 21 Feb '24

21 Feb '24

Dear all, I’m trying to run nestml with the latest nest master branch commit (8e85268ca512e0f509240fb5ef06f62a4e61a67e) but I get an error when calling the `nest.Install()` function. -- Install configuration: "" -- Installing: /Users/wybo/miniconda3/envs/nest-multiscale/lib/nest/concmech_mockup_module.so Traceback (most recent call last): File "/Users/wybo/Code/NEST/nestml/tests/nest_compartmental_tests/compile_test.py", line 23, in <module> nest.Install("concmech_mockup_module") File "/Users/wybo/miniconda3/envs/nest-multiscale/lib/python3.12/site-packages/nest/ll_api.py", line 216, in stack_checker_func return f(*args, **kwargs) ^^^^^^^^^^^^^^^^^^ File "/Users/wybo/miniconda3/envs/nest-multiscale/lib/python3.12/site-packages/nest/lib/hl_api_simulation.py", line 332, in Install return sr("(%s) Install" % module_name) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/Users/wybo/miniconda3/envs/nest-multiscale/lib/python3.12/site-packages/nest/ll_api.py", line 103, in catching_sli_run raise exceptionCls(commandname, message) nest.lib.hl_api_exceptions.NESTErrors.DictError: DictError in SLI function SLIInterpreter::execute: Key '/Install' does not exist in dictionary. Did anybody experience the same problem, or know what might cause it? Best regards, Willem ---------------------- Dr. Willem Wybo 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), Karsten Beneke (stellv. Vorsitzender), Dr. Ir. Pieter Jansens ------------------------------------------------------------------------------------------------ ------------------------------------------------------------------------------------------------

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Tripsitter: A Psychedelics, Ketamine, & Cannabis Encyclopedia
by Leon Vergara 21 Feb '24

21 Feb '24

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Problems when using a mask inside the conn_dict on 3 or 4 MPI processes
by Kempter, Miriam 20 Feb '24

20 Feb '24

Dear NEST Community, while adapting my model to run on multiple MPI processes, I have been running into some problems connected with the usage of masks inside the connectivity dictionary for a 2D-spatially distributed population. You can find a minimal example containing further details in the attachments in the form of a .txt file. Please just change "txt" with "py" for execution. The following explanation also references to the example. My setup: - NEST version 3.4 - Python version 3.10 - Executed with mpirun inside a conda environment "mpirun -np 4 python3 minEx_4MPIprocesses_problem.py" - System: Ubuntu 22.04 - The same problem occurred when the model was executed on JURECA. Problem description: While using multiple MPI processes: 1. Create circular mask. See line 119 Create a spatial 2D-Population of neurons "neurons". See line 125-132 2. Select some of the neurons as source neurons. See line 154 3. Set up the connection dictionary with a mask inside. See line 157-163 4. For each source neuron: See line 173 Connect the source neurons with the neurons population using the connection dictionary See line 183 Where does the Problem occur?: The error occurs at the point when the nest.Connect(…) call is executed in the loop at line 183 when each source neuron is connected. When does the Problem occur?: Its occurrance depends on whether or not a mask is used inside the connection-dict given to the nest.Connect(...) function. If the mask is removed as in the conn-dict. in line 164-169, no error is produced in none of the used settings (however the result is not as desired). If the mask is used, the way the problem shows itself depends on the number of MPI processes used, and on the setting of the number of neurons, extent, mask radius, number of source neurons and if edge wrap is used. - For 1 and 2 MPI procs the model is running correctly, independent of the used conn-dict and setting. - For 3 MPI procs either the model runs but the distance between connected neurons does not correspond to the given mask dimensions. In other words: The established connections are longer/shorter than the mask should allow. Or execution leads to an error code output ("segmentation fault") from mpirun and job abortion. The terminal output for an example run can be seen in the attached file "minEx_4MPIprocesses_problem_error_output_3_MPI" - For 4 MPI procs either, the model runs correctly, or it leads to an error code output ("segmentation fault") and the model not terminating. (When executed in the terminal the keyboard command "str+c" is needed to stop the execution. The terminal output for an example run can be seen in the attached file "minEx_4MPIprocesses_problem_error_output_4_MPI" If the model is executed with the same setting on 3 and 4 MPI procs there are 3 possible combinations of above described problems. 1. The model runs and terminates on both, however the distances created on 3 MPI procs are wrong. 2. The model works with 4 MPI procs but creates the "segmentation fault" error on 3 MPI processes. 3. The model creates a "segmentation fault" error on both. Please keep in mind that whether an error occurs and in which form highly depends on the used setting. In the minimal example I provide different settings which represent the above described cases. However, it might not cover everything that can occur. Workaround: For my own use-case I found a rather computing-time consuming workaround. It involves applying nest.SelectNodesByMask() on every source neuron, and from the resulting set choosing the targets using the desired probability. This requires multiple additional loops and also communicating the position data of every neuron to every MPI process in the beginning. Using this approach, the connection distances seem to be correct and no error occurs while executing the model. However, while writing this I'm questioning if I actually tested it enough. So there might be some not yet discovered problems. Is there something that I overlooked or approached wrong when using masks in the connectivity dict on multiple MPI processes? Thanks in advance! Best, Miriam Kempter ------------------------------------------------------------------------------------------------ ------------------------------------------------------------------------------------------------ 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), Dr. Ir. Pieter Jansens ------------------------------------------------------------------------------------------------ ------------------------------------------------------------------------------------------------

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Weights assignment error with mpirun
by Xavier Otazu 12 Feb '24

12 Feb '24

Hi! I am trying to implement weight normalization (as you show in your documentation). It works well (see below code) when executed "normally" (or when using" mpirun -np 1"), but it hangs (it just do not respond) when executed using mpirun. It hangs when I try to execute nest.Simulate() after weigth assignment. If I remove the "conn.weight = w_nparray" instruction in the following code, it works without hang. I use NEST 3.6 and python3, compiled with python, mpi, sionlib and music. Thanks a lot in advance! import nest import numpy as np pos = nest.spatial.grid(shape = [30,30] ) input = nest.Create('iaf_psc_alpha', positions=pos) layer_0 = nest.Create('iaf_psc_alpha', positions=pos) layer_1 = nest.Create('iaf_psc_alpha', positions=pos) conn_neur = {'rule':'pairwise_bernoulli', 'use_on_source': True, 'mask': {'grid':{'shape':[9,9]}} } nest.CopyModel('static_synapse', 'syn_1_model') syn_0 = {'synapse_model': 'static_synapse'} syn_1 = {'synapse_model': 'syn_1_model'} nest.Connect(input, layer_0, conn_neur, syn_0) nest.Connect(input, layer_1, conn_neur, syn_0) nest.DumpLayerConnections(input, layer_0, 'static_synapse', 'conn.txt') nest.DumpLayerConnections(input, layer_1, 'syn_1_model', 'conn.txt') nest.Simulate(100) for neuron in layer_0: conn = nest.GetConnections(source=input, target=neuron, synapse_model='static_synapse') w = np.array(conn.weight) if (w.size>1): w_normed = w / sum(abs(w)) # L1-norm w_nparray = 2. * w_normed conn.weight = w_nparray nest.Simulate(100)

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