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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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