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how to construct multiple synapse simple integrate-and-fire model
by 王梓瑞 07 Nov '22

07 Nov '22

Hi, I planned to use simple integrate-and-fire model (iaf_cond_beta) to construct the cortico-striatal network, but then it appeared some issues. Since striatum neurons have multiple synapses (AMPA and NMDA for example), ‘iaf_cond_beta’ seemed not to support multiple synapse input. I searched the whole Model directory and found multiple synapse neuron models like “aeif_cond_beta_multisynapse”, “aeif_cond_alpha_multisynapse” and “aeif_psc_alpha_multisynaps”. So I wondered if there’s a multiple synapse version of simple integrate-and-fire model (iaf_cond_beta), or can I construct a multiple synapse simple integrate-and-fire model through nestml. Thank you Best, Zirui

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Open NEST Developer Video Conference Monday Nov 7 2022 11:30 CET (UTC+1)
by Dennis Terhorst 07 Nov '22

07 Nov '22

Dear NEST Users & Developers! I would like to invite you to our next fortnightly Open NEST Developer Video Conference, today Monday November 7, 11.30-12.30 CET (UTC+1). (note the changed timezone!) Feel free to join the meeting also if it's just to bring your own questions for direct discussion in the in-depth section. Special topic for the in-depth discussion for today is /Eligibility Propagation/ As usual, in the Project team round, a contact person of each team will give a short statement summarizing ongoing work in the team and 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. 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/2022-11-07-Open-NEST-Developer-… Looking forward to seeing you again soon! Cheers, Dennis Terhorst ------------------ Log-in information ------------------ We use a virtual conference room provided by DFN (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 - 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

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Tips for getting a scaled-down version of the Allen Brain V1 model to work using NEST/Sonata/BMTK?
by Russell Jarvis 27 Oct '22

27 Oct '22

I am just wondering if anyone in the Nest community has any tips for running the Allen Brain V1 model? A lot of the code and Sonata/HDF5 files are hosted on DropBox. model_nest_2.20 - Dropbox <https://www.dropbox.com/sh/w5u31m3hq6u2x5m/AAA1ZQrM-4pgfK5dlRtWYdJNa/GLIF%2…> I have been busy trying to get the model to work with PyGeNN and even Julia. It occurred to me that I should probably start with what has been known to work, ie Nest. Thanks for any advice. Russell. -- Russell Jarvis (he/him) PhD Personal Website <https://russelljjarvis.github.io/home/> *I respectfully acknowledge the Traditional Owners of the land on which we work and learn, and pay respect to the First Nations Peoples and their elders, past, present and future.* *phone: *614 <623-404-9322>44576301 *email:* russelljarvis(a)protonmail.com

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Dendritic Arbors at Scale
by Ryan O'Loughlin 26 Oct '22

26 Oct '22

Hello NEST community, I am at the outset of a large project and I would like to start off with the right simulator. Perhaps someone here can advise on the viability of NEST for my particular needs. I will be modeling neuromorphic hardware with some unique design constraints, such as: - A complex dendritic arbor - Dendrite potentials may be coupled with their neighbors - Several dendrites may feed into other dendrites (a several-layer-deep dendritic tree) - The arbor eventually feeds into the soma which has typical LIF behavior, with a membrane potential determined by the sum of all directly connected dendrites - The solution for the leaky-integrator term of dendrites must be drawn from a precalculated lookup table The question here is how best to facilitate these dendritic nuances within NEST? Any counsel on whether it makes sense to pursue modeling such a system in NEST would be highly appreciated. We would like to eventually scale to the maximum number of neurons our hardware/clusters and your simulator can facilitate. Thank you, Ryan

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Problems with Github CI on macOS / Temporary solution
by Hans Ekkehard Plesser 25 Oct '22

25 Oct '22

Dear NEST Developers, For the last few days, all CI builds on macOS have failed. This is most likely due to Homebrew now providing libomp 15.0 instead of 14.0, see issue #2515 (https://github.com/nest/nest-simulator/issues/2515). I have temporarily disabled OpenMP-dependent tests for the macOS builds (#2516). Please pull current master into all open PRs so that most of the macOS tests can run. Please note that considerable recent improvements in the code base (systematic use of nullptr #2496, of "and" and "or" instead of && and || #2498, removal of "void" arguments, systematic use of "override" and removal of "virtual" where not needed #2493; removal of unused imports #2490 as well as #2479) may lead to some merge conflicts. Please resolve them in the spirit of the new style and consult the listed PRs if in doubt about what is the new style. Best regards, Hans Ekkehard -- Prof. Dr. Hans Ekkehard Plesser Head, 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 Oct 24 2022 11:30 CEST (UTC+2)
by Dennis Terhorst 24 Oct '22

24 Oct '22

Dear NEST Users & Developers! I would like to invite you to our next fortnightly Open NEST Developer Video Conference, today Monday October 24, 11.30-12.30 CEST (UTC+2). Feel free to join the meeting also if it's just to bring your own questions for direct discussion in the in-depth section. Special topic for the in-depth discussion for today are /Compressed Spikes/ As usual, in the Project team round, a contact person of each team will give a short statement summarizing ongoing work in the team and 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. 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/2022-10-24-Open-NEST-Developer-… Looking forward to seeing you again soon! Cheers, Dennis Terhorst ------------------ Log-in information ------------------ We use a virtual conference room provided by DFN (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 - 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

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Open NEST Developer Video Conference Monday Oct 10 2022 11:30 CEST (UTC+2)
by Dennis Terhorst 10 Oct '22

10 Oct '22

Dear NEST Users & Developers! I would like to invite you to our next fortnightly Open NEST Developer Video Conference, today Monday October 10, 11.30-12.30 CEST (UTC+2). Feel free to join the meeting also if it's just to bring your own questions for direct discussion in the in-depth section. Special topic for the in-depth discussion for today is the /NEST implementation of eligibility propagation/. As usual, in the Project team round, a contact person of each team will give a short statement summarizing ongoing work in the team and 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. 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/2022-10-10-Open-NEST-Developer-… Looking forward to seeing you again soon! Cheers, Dennis Terhorst ------------------ Log-in information ------------------ We use a virtual conference room provided by DFN (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 - 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

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Assertion error during connection when using CopyModel and own neuron model
by Barna Zajzon 07 Oct '22

07 Oct '22

Dear all, I'm encountering the following error python: /home/zbarni/software/packages/nest/znest/nestkernel/model_manager.h:296: nest::Model* nest::ModelManager::get_node_model(nest::index) const: Assertion `m < node_models_.size()' failed. when using the following code: nest.SetKernelStatus({'total_num_virtual_procs':16, 'local_num_threads':16}) nest.Install('my_neuron_module') for iin range(16): nest.CopyModel('MyNeuron', f'MyNeuron_{i}') neurons = nest.Create('MyNeuron_0', 2) nest.Connect(neurons, neurons) The script uses a neuron model that I wrote in C++ and is loaded without errors. The error is thrown upon nest.Connect(), and goes away if I create the neurons using `MyNeuron` and not `MyNeuron_x` (copied) or if the #vp and #threads is 1. I've used the model with NEST 2.20.0 without problems, but I'd like to port the code to the latest version. Maybe I'm just missing something new functionality/API related to CopyModel and multiprocessing - have there been any critical changes in the model requirements? Any help would be greatly appreciated. Barni

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NEST, CMake, Xcode, Eclipse & Co: the magic -G
by Hans Ekkehard Plesser 07 Oct '22

07 Oct '22

Dear NEST Developers, I would like to share some insights I gained over the last few days concerning NEST and IDEs. As you might know, we have some instructions for how to use NEST with IDEs (https://nest-simulator-sg.readthedocs.io/en/latest/developer_space/workflow…), but these instructions are at best complicated and at worst awfully outdated. I now discover the magic -G flag for CMake (https://cmake.org/cmake/help/latest/manual/cmake-generators.7.html), where CMake does all the heavy configuration lifting for you. Proceed as follows: - Create a build directory - Prepare your normal cmake invocation and add - for XCode: -GXcode - for Eclipse: -G"Eclipse CDT4 - Unix Makefiles" - Then open the build directory in XCode or Eclipse For other build systems, run cmake –help and see if your system is listed. Unfortunately, VSCode seems unsupported at the moment. In Xcode, you can then choose the "install" target and run it to build NEST and afterwards the "nest" target to run nest—and it will stop in the debugger if you just set a breakpoint or something goes wrong. There are still a few problems, and if any of you have more experience than me with setting up Xcode or Eclipse problems, we can maybe work it out together: 1. In Eclipse, the project will only include files in the build directory, not the source code. How to fix that? 2. Xcode * Files are ordered a bit strangely (subfolders for headers and non-headers) and "libnestutil" is shown as "nestutil" in the folder list * The "installcheck" target does not work because Xcode runs everything in the conda "base" environment—how to either force a "conda activate nest" before each run or explicitly set PYTHONPATH? * I have not yet found out how to run PyNEST from Xcode, which would also depend on conda activate/Pythonpath setting Once we have a little more experience, I will prepare a PR to update the IDE instructions. Best, Hans Ekkehard -- Prof. Dr. Hans Ekkehard Plesser Head, 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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using mpi4py with nest | parallel write to a file
by Aadhar Sharma 28 Sep '22

28 Sep '22

Hi there! I am using the structural plasticity module to simulate large-scale networks on HPC. The way I run these simulations with MPI creates a large number of small data files (.npy) which I organize into a HDF5 file in a post hoc manner. This has hitherto not been a problem, however, I recently increased the size of my simulations and the number of files that I create exceeds my HPCinode quota. So, I have to come up with a way of handling all these files or the way I export them. Ideally, I would like to concurrently write to a file (like zarr) with multiple processes. However, parallel zarr writes are only optimal when the chunk size are uniform. For me, they are not uniform---so, I abandoned the idea of using zarr. Currently, I am trying to use mpi4py to gather the data I want and save it through a mother MPI process. I ran some test simulations and all was fine (see attached script). However, when I use structural plasticity with mpi4py I get an error that: "nest.lib.hl_api_exceptions.DimensionMismatch: ('DimensionMismatch in SetStatus_id: Expected dimension size: 1\nProvided dimension size: 20', 'DimensionMismatch', <SLILiteral: SetStatus_id>, ': Expected dimension size: 1\nProvided dimension size: 20". I believe that mpi4py somehow interferes with nest's internal mpi mechanism. Perhaps it signals nest kernel to use 1 process rather than the mentioned 20. If I remove the mpi4py import call, all works fine. So, I cannot run the simulation using this mpi4py hack. Do you notice something wrong with my approach? I'm just beginning to use mpi4py, so I may be missing something here. Alternatively, could you recommend a way to reduce the number of exported files. For example, through zarr or other file formats which support parallel writes. I'd appreciate any suggestions. Thanks! pyNEST version: 2.20.2 python version: Python 3.7.10 mpiexec/mpirun version: MPI Library for Linux* OS, Version 2021.3 Best, Ady

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