- NEST Users - NEST Initiative Mail

nestml syntax problem
by Chris Huyck 19 Jul '24

19 Jul '24

I was using an old version of nest (3.5) and nestml. Someone sent me a nestml model, and that worked. I wanted to make my own model, but the tutorials had a different format. In particular, it seems like the first line of code in the tutorials start with model, and the old version started with neuron of synapse. So, I thought it was time to upgrade, so installed nest 3.7, and pip-ed nestml. (I also installed PyNN as that's the way I typically work.) When I imported generate_target (through python 3.12), I got the typical PyGSL warning; I think that's because I'm using python 3.12 not 3.11, and I don't think it matters in this case. Then I ran the generate_target and I got an error mismatched input 'model' expecting {newline, 'neuron', 'synapse} I expect there's something like a yacc table that specifies the syntax, and somehow I've got the old syntax. I've tried it with several version of nestml 7.0.2, 7.0.0, 6.0.0 and 5.0.0. I think 5.0.0 had the old syntax. I've tried several models from the library, and the Izhikevich tutorial. Any thoughts about how to fix it? -Chris

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e-prop tutorial missing data file
by Xavier Otazu 04 Jul '24

04 Jul '24

Hi! Looking at the e-prop tutorial (https://nest-simulator.readthedocs.io/en/v3.7/auto_examples/eprop_plasticit…), the chaos_handwriting.txt datafile is needed. Where can I find this file? Thanks a lot in advance! Xavier

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Open NEST Developer Video Conference Monday July 1, at 11:30 CEST (UTC+0200)
by Dennis Terhorst 01 Jul '24

01 Jul '24

Dear NEST Users & Developers! I would like to invite you to our next fortnightly Open NEST Developer Video Conference today *Monday July 1, 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/2024-07-01-Open-NEST-Developer-… <https://github.com/nest/nest-simulator/wiki/2024-07-01-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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Questions about Neuron Update Mechanism and Spike Event Handling in Source Code
by anh.phan＠tuni.fi 25 Jun '24

25 Jun '24

Hi, I've been trying to read through the source code to understand this, but I'm still having trouble figuring it out. From what I can see, the neurons are updated using a for loop, meaning each neuron is updated one at a time. The update function for each neuron can run for multiple timesteps, but I'm unclear on how its B_.input_buffer_ gets updated while the update function is running. If it doesn't get updated during this process, wouldn't it miss some spike events? Additionally, how does the code ensure that neurons updated one at a time for all simulation steps do not miss any spike events? Thank you for your help! Best regards, Anh Phan

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Developers: Please pull Master to your branches / NumPy 2.0 changes
by Hans Ekkehard Plesser 20 Jun '24

20 Jun '24

Dear Colleagues, This mail is mainly for those of you who contribute to NEST Simulator development. NumPy 2.0, released last Sunday, has some minor changes that broke existing tests and examples. This has now been fixed in the master branch (PRs #3226, #3227). Please pull master into all your branches—otherwise, the testsuite will fail on Github and your contributions cannot be merged. Best, 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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Open NEST Developer Video Conference Monday June 3, at 11:30 CEST (UTC+0200)
by Dennis Terhorst 09 Jun '24

09 Jun '24

Dear NEST Users & Developers! I would like to invite you to our next fortnightly Open NEST Developer Video Conference today *Monday June 3, at 11:30 CEST (UTC+0200).* Despite many people attending conferences this week, we will briefly meet to offer attention also to smaller questions or more general topics that you may bring. The Project team round, might however be quite short today. Feel free to join the meeting and bring your own quick questions for direct discussion or just to hear what's going on in and around NEST. 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/2024-06-03-Open-NEST-Developer-… <https://github.com/nest/nest-simulator/wiki/2024-06-03-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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NEST Conference 2024 — Register by Friday!
by Hans Ekkehard Plesser 04 Jun '24

04 Jun '24

Dear NEST Users, We are looking forward to an exciting Virtual NEST Conference 2024 on Monday/Tuesday 17./18. June 2024. This years program includes keynotes by Tadashi Yamazaki, University of Electro-Communications, Japan Diversity and inclusion: Distributed simulation of multiple brain and body models in multiple simulators on multiple computers across multiple organizations Benedetta Gambosi, University of Pavia A multiarea model predicts the changes in thalamocortical beta oscillations caused by dopamine depletion in basal ganglia and cerebellum Tobias Gemmeke, RWTH Aachen Accelerated Simulation of Biological Neural Networks Behnam Ghazinouri, Ruhr-Universität Bochum The attractor dynamics of behavioral flexibility in spatial and reversal learning complemented by contributed talks, posters and a workshop Introducing Arbor. For the full program an to register, please see https://nest-simulator.org/conference. Registration deadline is this FRIDAY, 7 June 2024. We are looking forward to seeing you at the NEST Conference 2024! Hans Ekkehard Plesser -- 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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About example structural plasticity?
by Thanh Binh To 21 May '24

21 May '24

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Problem in STDP Windows tutorial notebook
by Ashraf Ul Islam Shihab 15 May '24

15 May '24

Hi, In nestml/doc/tutorials/stdp_windows notebook, in cell 3, I see an example of fetching model name, neuron name, and synapse name from nestml/models/neurons/iaf_psc_delta_neuron.nestml, which appears to have only model inside of it. It tries to extract the names from a format of 1. model <name>: 2. neuron <name>: 3. synapse <name>: But the iaf_psc_delta_neuron.nestml file from the latest build doesn't have any structure as neuron <name>: to my best knowledge. Please let me know if there is any fix for this problem. I went ahead and tried to edit the generate_code_for function from NESTCodeGeneratorUtils class. It can be found here <https://pastebin.com/Qz8JwinA>. But it gives an error as follows: > [6,GLOBAL, ERROR]: An error occurred while importing the `nest` module in > Python. Please check your NEST installation-related environment variables > and paths, or specify ``nest_version`` manually in the code generator > options. > An exception has occurred, use %tb to see the full traceback. Best, Ashraf Ul Islam Shihab Graduate Research Assistant Department of Electrical and Computer Engineering Boise State University (BSU) Boise, Idaho 83725 Email: ashrafshihab(a)u.boisestate.edu

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gsl import error after update (plus: NEST on WSL)
by Patricio Orio 09 May '24

09 May '24

Hello, I have been trying NEST under the WSL in Windows and I am glad to say that it works! I think that getting NEST working correctly under the WSL may attract more users, to both NEST and the WSL. BTW (this is a side note), I have noticed that some Python codes (unrelated to NEST) run a little faster (15-20%) under the WSL than in Windows itself. Anyway, nest works perfectly on the WSL using either Spyder as IDE or JupyterLab. However, after a while the installation breaks. After doing any upgrade via "conda upgrade --all" (once it was NEST itself updated), when I try to import NEST I get the error transcribed below, which ends in "ImportError: libgsl.so.25: cannot open shared object file: No such file or directory". I have narrowed down the problem to this: when installing NEST, the package "conda-forge::gsl-2.7-he838d99_0" is installed along. Then, if I do any "conda update --all" (or I guess that if I install any other package that uses gsl), the package gets updated "conda-forge::gsl-2.7-he838d99_0 --> pkgs/main::gsl-2.7.1-h6e86dc7_1". Then here: https://nest-simulator.org/mailinglist/hyperkitty/list/users@nest-simulator… I found out that "If you upgrade your environment, you might have to cmake and compile NEST anew in order for it to pick up the new version.". So I thought that a force-reinstall of nest might do the trick, but it didn't. Moreover, I did the following: - start a new, clean environment - install gsl before nest (I got main::gsl-2.7.1-h6e86dc7_1) - then install nest-simulator. But the error appears again. FINALLY, I did "conda install conda-forge::gsl", it picked gsl-2.7-he838d99_0 and now NEST works again!! So it seems that the problem is specific with gsl-2.7.1 (and/or whatever version is in main?). I don't want to end up using NEST in a frozen environment where nothing can be added or changed, neither before nor after installing NEST. Although I found the workaround, I guess you may find a way of this not happening at all. Thank you and best regards Patricio. In [1]: import nest --------------------------------------------------------------------------- ImportError Traceback (most recent call last) Cell In[1], line 1 ----> 1 import nest File ~/miniconda3/lib/python3.12/site-packages/nest/__init__.py:64 61 import sys # noqa 62 import types # noqa ---> 64 from .ll_api_kernel_attributes import KernelAttribute # noqa 66 try: 67 import versionchecker # noqa: F401 File ~/miniconda3/lib/python3.12/site-packages/nest/ll_api_kernel_attributes.py:22 1 # -*- coding: utf-8 -*- 2 # 3 # ll_api_kernel_attributes.py (...) 19 # You should have received a copy of the GNU General Public License 20 # along with NEST. If not, see <http://www.gnu.org/licenses/>. ---> 22 from .ll_api import spp, sps, sr, stack_checker 25 class KernelAttribute: 26 """ 27 Descriptor that dispatches attribute access to the nest kernel. 28 """ File ~/miniconda3/lib/python3.12/site-packages/nest/ll_api.py:53 48 # Make MPI-enabled NEST import properly. The underlying problem is that the 49 # shared object pynestkernel dynamically opens other libraries that open 50 # yet other libraries. 51 sys.setdlopenflags(os.RTLD_NOW | os.RTLD_GLOBAL) ---> 53 from . import pynestkernel as kernel # noqa pylint: disable=no-name-in-module 55 __all__ = [ 56 "check_stack", 57 "connect_arrays", (...) 69 "take_array_index", 70 ] 73 engine = kernel.NESTEngine() ImportError: libgsl.so.25: cannot open shared object file: No such file or directory

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Open NEST Developer Video Conference Monday May 6, at 11:30 CEST (UTC+0200)
by Dennis Terhorst 06 May '24

06 May '24

Dear NEST Users & Developers! I would like to invite you to our next fortnightly Open NEST Developer Video Conference today *Monday May 6, 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/2024-05-06-Open-NEST-Developer-… <https://github.com/nest/nest-simulator/wiki/2024-05-06-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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NEST on Google Colab?
by Alvin Spivey 03 May '24

03 May '24

I'm trying to install and use NEST on google Colab, but it's not importing: !pip install -Uqq nest !pip install -Uqq nestml !pip install -Uqq pysilsub import nest import nestml import numpy as np import matplotlib.pyplot as plt from pysilsub import observers from nestml.network import Network from nestml.models import ConeNakaRushton Am I able to use NEST on Google Colab? -- Alvin J. Spivey, Ph.D. (c) 843.267.8055

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Open NEST Developer Video Conference Monday April 22, at 11:30 CEST (UTC+0200)
by Dennis Terhorst 22 Apr '24

22 Apr '24

Dear NEST Users & Developers! I would like to invite you to our next fortnightly Open NEST Developer Video Conference today *Monday April 22, 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/2024-04-22-Open-NEST-Developer-… <https://github.com/nest/nest-simulator/wiki/2024-04-22-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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NEST Conference 2024 - Extension of abstract submission deadline
by Hans Ekkehard Plesser 16 Apr '24

16 Apr '24

Dear all, The abstract submission deadline for the NEST Conference 2024 has been extended to 30 April. We are looking forward to your contributions! [Image] 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. This year's conference will again take place as a virtual conference on Monday/Tuesday 17/18 June 2024. We are inviting contributions to the conference, including talks, "posters" and workshops on specific topics. For more information on how to submit your contribution, register and participate, please visit the conference website https://nest-simulator.org/conference Important dates 26 April 2024 - Deadline for NEST Initiative membership applications eligible for fee reduction 30 April 2024 - Extended deadline for submission of contributions 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 -- 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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NEST Conference 2024 - reminder for abstract submission deadline on 15 April 2024
by Hans Ekkehard Plesser 09 Apr '24

09 Apr '24

Dear all, The abstract submission deadline for the virtual NEST Conference 2024 is approaching (15 April 2024). We are looking forward to your contributions! 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. This year's conference will again take place as a virtual conference on Monday/Tuesday 17/18 June 2024. We are inviting contributions to the conference, including talks, "posters" and workshops on specific topics. 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 For more information on how to submit your contribution, register and participate, please visit the conference website https://nest-simulator.org/conference We are looking forward to seeing you all in June! Hans Ekkehard Plesser and the conference organizing committee -- 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 April 8, at 11:30 CEST (UTC+0200)
by Hans Ekkehard Plesser 08 Apr '24

08 Apr '24

Dear NEST Users & Developers! I would like to invite you to our next fortnightly Open NEST Developer Video Conference today Monday April 8, 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. Special topic today is the status of the upcoming NEST 3.7 release. 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 * NEST Conference 2024<http://www.nest-initiative.org/conference>: Submission Deadline 15 April 2024 * NEST 3.7 RC1 Status * Reduce number of warnings (see, e.g., https://github.com/nest/nest-simulator/actions/runs/8566897766) * Porting tests from SLI to Py The agenda for this meeting is also available online, see https://github.com/nest/nest-simulator/wiki/2024-03-25-Open-NEST-Developer-… Looking forward to seeing you soon! Cheers, Hans Ekkehard Plesser 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 * 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<tel:+493020097938800> 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 -- 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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Questions regarding the iaf_psc_exp model
by anh.phan＠tuni.fi 02 Apr '24

02 Apr '24

Hello, I have some questions regarding the iaf_psc_exp model. When it receives current from a current generator (with static synapse), does that current go to receptor_type 0 and not be filtered through an exponential kernel? Secondly, I would like to confirm if the exponential PSCs follow the exponential function:: i_syn(t) = (q / tau_syn) * exp(-t / tau_syn) * Θ(t) , where Θ(t) is the Heaviside step function defined as Θ(t) = 1 fot t >0 and Θ(t) = 0 otherwise. Additionally, is q chosen to be equal to tau_syn? Thank you very much! Best regards, Anh Phan

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

25 Mar '24

Dear NEST Users & Developers! I would like to invite you to our next fortnightly Open NEST Developer Video Conference today *Monday March 25, 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. Special topic today is the status of the /upcoming NEST 3.7 release/. 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/2024-03-25-Open-NEST-Developer-… <https://github.com/nest/nest-simulator/wiki/2024-03-25-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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NESTML sample random distributions - assertion failed
by chiara de luca 19 Mar '24

19 Mar '24

Dear NESTML community, I have a problem with random number generator in the new version of nestml. Specifically, I am using nest 3.6.0 nestml 7.0 This is what I would like to do: whenever creating a neuron with a set of parameters defined by the user, each parameter should be affected by a "gaussian error" with defined variability. I tried to use the internal random_normal() function but with the current version I am getting some issues there. Specifically, whenever trying to call such function from the "internals", "parameters", "state" blocks the model is correctly generated (no errors returned) but exits with en error whenever trying to "install". The error is the following Assertion failed: (tid < static_cast< size_t >( vp_specific_rngs_.size() )), function get_vp_specific_rng, file my/path/to/miniforge3/conda-bld/nest-simulator_1707218961774/work/nestkernel/random_manager.h, line 173. [1] 32875 abort python test.py Such problem does not exist for random_normal() called within the update and equations blocks. Attached some minimal code to reproduce the error. Best, Chiara

2 3

DumpLayerConnections() enhancement request
by Xavier Otazu 18 Mar '24

18 Mar '24

Hi! I am using DumpLayerConnections() with two layers with around 100x100 nodes each layer. Every layer node is connected to around 100 nodes on the other layer. Calling the DumpLayerConnections() takes around 10-15 minutes to save connections to file. I know it is a too general request, but it would be nice if this function is faster. In my particular case, I obtain these connections in a previous step using GetConnections(). I guess (hence I am probably wrong) that DumpLayerConnections() calls GetConnections(). If I am right, I believe it could be an interesting enhancement to implement a DumpLayerConnections() function with input parameters that are a set of connections, that is, something like: myconn = nest.GetConnections(layer1, layer2, ...) nest.DumpLayerConnections(myconn) Thanks a lot in advance! Xavier

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ValueError: 'Wmax' is not allowed in syn_spec when connecting with mask or kernel
by anh.phan＠tuni.fi 14 Mar '24

14 Mar '24

I am working with a 2D spatially-structured neural network and aim to employ STDP synapses to establish connections between neurons. However, I encountered an error stating 'ValueError: 'Wmax' is not allowed in syn_spec when connecting with mask or kernel,' along with similar issues for parameters such as tau_plus, alpha, lambda, and others. Could you give me some guidance on how to properly configure these parameters? Thank you very much.

2 2

SelectNodesByMask() and DumpLayerConnections() combination problem
by Xavier Otazu 14 Mar '24

14 Mar '24

Hello, Looking at the documentation, I understand that the output of SelectNodesByMask() is a NodeCollection, and the 'layer' input parameters of DumpLayerConnections() is also a NodeCollection. Hence, I understand that I can combine these two parameters, but when I do it (see code below) I receive the error: nest.lib.hl_api_exceptions.LayerExpected: LayerExpected in SLI function DumpLayerConnections_os_g_g_l Am I missing something? Thanks a lot in advance! Xavier -------- import nest # Layers creation pos = nest.spatial.grid(shape = [100,100] ) input_l = nest.Create('iaf_psc_alpha', positions=pos) layer_0 = nest.Create('iaf_psc_alpha', positions=pos) conn_neur = {'rule':'pairwise_bernoulli', 'mask': {'grid':{'shape':[10,10]}} } syn_0 = {'synapse_model': 'static_synapse'} nest.Connect(input_l, layer_0, conn_neur, syn_0) # GetNodesByMask mask_specs = {'lower_left':[-0.25,-0.25], 'upper_right':[0.25,0.25]} mask_obj = nest.CreateMask(masktype='rectangular', specs=mask_specs, anchor=[0.0,0.0]) center_neur = nest.SelectNodesByMask(layer_0,[0.0,0.0],mask_obj) nest.DumpLayerConnections(input_l,center_neur, 'static_synapse', 'conn.txt')

3 2

Strange interaction between NEST and IPython
by Hans Ekkehard Plesser 12 Mar '24

12 Mar '24

Dear Python experts among the NEST Users! I just notice a strange interaction between NEST and Ipython. In a freshly started Ipython, I execute the following three statements import nest n = nest.Create('parrot_neuron', positions=nest.spatial.free([(x, 0) for x in range(10000)])) n The last one takes extraordinarily long, over 10 seconds, I think. But if I instead do print(n) it executes instantaneously. Also, if I do the same thing in python directly, just entering n shows the NodeCollection immediately. Can anyone reproduce this and does anyone have an idea what might be going on? I am on macOS 14.3.1 with Python 3.12.2, Ipython 8.22.2, and have checked with NEST 3.6 and a branch of recent master. Best, 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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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

2 1

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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