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

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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

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

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

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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

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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

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

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

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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

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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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stp synapse nestml errror
by Chris Huyck 18 Sep '24

18 Sep '24

I'm trying to make a Hebbian Short Term plasticity model. I got the stdp_synapse working, and then tried to change that to stp. I kept getting the error stp_synapse not found in pynest. So, I just started from the static synapse, and modified that to get an stp_synapse that wasn't Hebbian. When I introduced the post_synaptic neuron into the model, the stp_synapse not found error returns. Oddly, in the generated files (.h, .cpp, in stp_synapse__with_iaf_cond_exp_neuron and iaf_cond_exp_neuron__with_stp_synapse) there is a function for register stdp_synapse. (If you want to duplicate this, just change the stdp_synapse model name to stp_synapse). -Chris

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Regular LIF with adaptive threshold
by jona.m.scholz＠gmail.com 13 Sep '24

13 Sep '24

Hello everyone, just a quick question in case anybody knows: is there a LIF model that has an adaptive spike threshold in NEST? I know there's the GLIF model which can have a threshold, but it seems to bring other deviations from the conventional LIF model that I want to avoid. There's also the adaptive exponential integrate and fire model, but again I don't want the exponential part. It's not a problem if no such model exists in NEST, I am only asking so I don't reimplement an existing model. Any feedback would be appreciated. Kind regards, Jona

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Open NEST Developer Video Conference Monday September 9, at 11:30 CEST (UTC+0200)
by Dennis Terhorst 09 Sep '24

09 Sep '24

Dear NEST Users & Developers! I would like to invite you to our next fortnightly Open NEST Developer Video Conference today *Monday September 9, 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/2024-09-09-Open-NEST-Developer-… <https://github.com/nest/nest-simulator/wiki/2024-09-09-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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Invitation for Article Submissions
by David Wack 05 Sep '24

05 Sep '24

Greetings Everyone, Paul John Werbos, Rajendra D Badgaiyan, Konstantinos Slavakis, and I are bringing key researchers together in a focused project on 'Modeling brain circuits as intelligent systems'. Here's a link to find out more about the project: https://www.frontiersin.org/researchtopic/64421. This topic is an extension of a US NSF push led by Dr. Werbos in 2007. We believe that members of this community would have much to offer and we would like to invite you to participate. If you are interested, please let me know directly, and I will send an invitation link: dswack(a)buffalo.edu<mailto:dswack@buffalo.edu> We are trying to finalize the leading group of participating authors in the next two weeks, so we can start publishing our work before the topic closes on 07 March 2025. Our Research Topic will be hosted in Frontiers in Systems Neuroscience Impact Factor: 3.1 Cite Score: 6.0 Frontiers will provide a team to help develop and promote our project, and we'll have a dedicated space in the journal to showcase our collective work and to amplify its impact and visibility. I'm looking forward to seeing your work and exploring this emerging topic together. I really think we can push this field forward as a team. All the best, dave David S. Wack, PhD dswack(a)buffalo.edu Associate Professor, Depts. of Nuclear Medicine and Biomedical Engineering University at Buffalo, USA P.S. Frontiers is a publisher created by scientists for scientists. We created Research Topics to give emerging research communities a platform. They bring together leading researchers to accelerate the development of cutting-edge research themes. As an open access publisher, Frontiers applies article publishing charges (APCs) to make research freely open and available for all. You can find more information here. If you encounter any technical issue, contact support(a)frontiersin.org<mailto:support@frontiersin.org>, with s0WY7RwlpCx5JEP as reference. David S. Wack, PhD Associate Professor Depts. of Nuclear Medicine And Biomedical Engineering University at Buffalo tel: 716 829-2648 cell: 716 319-4853 email: dswack(a)buffalo.edu or : dswack(a)gmail.com

1 0

Open NEST Developer Video Conference Monday August 26, at 11:30 CEST (UTC+0200)
by Dennis Terhorst 26 Aug '24

26 Aug '24

Dear NEST Users & Developers! I would like to invite you to our next fortnightly Open NEST Developer Video Conference today *Monday August 26, 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/2024-08-26-Open-NEST-Developer-… <https://github.com/nest/nest-simulator/wiki/2024-08-26-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 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 July 29, at 11:30 CEST (UTC+0200)
by Dennis Terhorst 12 Aug '24

12 Aug '24

Dear NEST Users & Developers! I would like to invite you to our next fortnightly Open NEST Developer Video Conference today *Monday July 29, 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/2024-07-29-Open-NEST-Developer-… <https://github.com/nest/nest-simulator/wiki/2024-07-29-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

Inject analog signal in a neuron
by Maryada Maryada 08 Aug '24

08 Aug '24

Dear NEST Users, Could anyone recommend the best way to inject a fluctuating current over time. A sample signal [image: image.png] -- Thanks and Regards *Maryada*

3 2

Order or Computation
by carriere.maxime93＠gmail.com 08 Aug '24

08 Aug '24

Hello everyone, I am trying to replicate our brain-constrained model to NEST. In our model the computation of the inhibition occurs before the inhibition. I believe it's the other way round in NEST. I was wondering, where the order of computation was implemented in NEST and if that was possible to change it. Best, Maxime

2 1

Open NEST Developer Video Conference Monday July 15, at 11:30 CEST (UTC+0200)
by Dennis Terhorst 24 Jul '24

24 Jul '24

Dear NEST Users & Developers! I would like to invite you to our next fortnightly Open NEST Developer Video Conference today *Monday July 15, 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/2024-07-15-Open-NEST-Developer-… <https://github.com/nest/nest-simulator/wiki/2024-07-15-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 ----------------------------------------------------------------------

3 3

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

3 10

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

3 2

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

1 0

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

3 4

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

1 0

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

3 5

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

1 0

About example structural plasticity?
by Thanh Binh To 21 May '24

21 May '24

1 0

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

2 5

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

1 0

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

1 0

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/

2 1

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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