June 2022 - NEST Users - NEST Initiative Mail

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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Problem with "import nest"
by Xavier Otazu Porter 04 Jul '22

04 Jul '22

Hello, I have instaled NEST 3.3 (on a Rocky Linux 8.5) from source. After entering python and executing "import nest" I receive the following error. It looks like cannot load some neuron models. I tried to install last git version, but problem persist. Please, some idea? Thanks a lot in advance Xavier python: /home/neurobit/src/nest-simulator/nestkernel/model_manager.h:321: size_t nest::ModelManager::get_num_connection_models() const: Assertion `connection_models_[ 0 ].size() <= invalid_synindex' failed. [dcccluster:979935] *** Process received signal *** [dcccluster:979935] Signal: Aborted (6) [dcccluster:979935] Signal code: (-6) [dcccluster:979935] [ 0] /usr/lib64/libpthread.so.0(+0x12c20)[0x7f8c3a3cdc20] [dcccluster:979935] [ 1] /usr/lib64/libc.so.6(gsignal+0x10f)[0x7f8c398a337f] [dcccluster:979935] [ 2] /usr/lib64/libc.so.6(abort+0x127)[0x7f8c3988ddb5] [dcccluster:979935] [ 3] /usr/lib64/libc.so.6(+0x21c89)[0x7f8c3988dc89] [dcccluster:979935] [ 4] /usr/lib64/libc.so.6(+0x2fa76)[0x7f8c3989ba76] [dcccluster:979935] [ 5] /home/neurobit/local/nest_3.3/lib64/python3.8/site-packages/nest/../../../nest/libnestkernel.so.3(+0x1aad22)[0x7f8c2a878d22] [dcccluster:979935] [ 6] /home/neurobit/local/nest_3.3/lib64/python3.8/site-packages/nest/../../../nest/libnestkernel.so.3(_ZN4nest12ModelManager26register_connection_model_EPNS_14ConnectorModelE+0x32d)[0x7f8c2a80f07d] [dcccluster:979935] [ 7] /home/neurobit/local/nest_3.3/lib64/python3.8/site-packages/nest/../../../nest/libmodels.so.3(_ZN4nest12ModelManager25register_connection_modelINS_24vogels_sprekeler_synapseEEEvRKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEENS_28RegisterConnectionModelFlagsE+0x171)[0x7f8c2b04d071] [dcccluster:979935] [ 8] /home/neurobit/local/nest_3.3/lib64/python3.8/site-packages/nest/../../../nest/libmodels.so.3(_ZN4nest12ModelsModule4initEP14SLIInterpreter+0x2c14)[0x7f8c2afa0404] [dcccluster:979935] [ 9] /home/neurobit/local/nest_3.3/lib64/python3.8/site-packages/nest/../../../nest/libsli.so.3(_ZN9SLIModule7installERSoP14SLIInterpreter+0x59)[0x7f8c29a22369] [dcccluster:979935] [10] /home/neurobit/local/nest_3.3/lib64/python3.8/site-packages/nest/../../../nest/libsli.so.3(_ZN14SLIInterpreter9addmoduleEP9SLIModule+0x44)[0x7f8c299c29f4] [dcccluster:979935] [11] /home/neurobit/local/nest_3.3/lib64/python3.8/site-packages/nest/../../../nest/libnest.so.3(_Z11neststartupPiPPPcR14SLIInterpreterNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEE+0x13cc)[0x7f8c2b6d37ec] [dcccluster:979935] [12] /home/neurobit/local/nest_3.3/lib64/python3.8/site-packages/nest/pynestkernel.so(+0x42475)[0x7f8c2b920475] [dcccluster:979935] [13] /usr/lib64/libpython3.8.so.1.0(+0x1d8faf)[0x7f8c3a9dcfaf] [dcccluster:979935] [14] /usr/lib64/libpython3.8.so.1.0(_PyEval_EvalFrameDefault+0x976)[0x7f8c3a9e5406] [dcccluster:979935] [15] /usr/lib64/libpython3.8.so.1.0(_PyFunction_Vectorcall+0x1bf)[0x7f8c3a9a37af] [dcccluster:979935] [16] /usr/lib64/libpython3.8.so.1.0(_PyEval_EvalFrameDefault+0x5da)[0x7f8c3a9e506a] [dcccluster:979935] [17] /usr/lib64/libpython3.8.so.1.0(_PyEval_EvalCodeWithName+0x3e7)[0x7f8c3a9a23c7] [dcccluster:979935] [18] /usr/lib64/libpython3.8.so.1.0(PyEval_EvalCode+0x23)[0x7f8c3a9a35a3] [dcccluster:979935] [19] /usr/lib64/libpython3.8.so.1.0(+0x25114b)[0x7f8c3aa5514b] [dcccluster:979935] [20] /usr/lib64/libpython3.8.so.1.0(+0x1667e0)[0x7f8c3a96a7e0] [dcccluster:979935] [21] /usr/lib64/libpython3.8.so.1.0(PyVectorcall_Call+0x70)[0x7f8c3a96f390] [dcccluster:979935] [22] /usr/lib64/libpython3.8.so.1.0(_PyEval_EvalFrameDefault+0x68d9)[0x7f8c3a9eb369] [dcccluster:979935] [23] /usr/lib64/libpython3.8.so.1.0(_PyEval_EvalCodeWithName+0x3e7)[0x7f8c3a9a23c7] [dcccluster:979935] [24] /usr/lib64/libpython3.8.so.1.0(_PyFunction_Vectorcall+0x422)[0x7f8c3a9a3a12] [dcccluster:979935] [25] /usr/lib64/libpython3.8.so.1.0(_PyEval_EvalFrameDefault+0x54d9)[0x7f8c3a9e9f69] [dcccluster:979935] [26] /usr/lib64/libpython3.8.so.1.0(_PyFunction_Vectorcall+0x1bf)[0x7f8c3a9a37af] [dcccluster:979935] [27] /usr/lib64/libpython3.8.so.1.0(_PyEval_EvalFrameDefault+0x976)[0x7f8c3a9e5406] [dcccluster:979935] [28] /usr/lib64/libpython3.8.so.1.0(_PyFunction_Vectorcall+0x1bf)[0x7f8c3a9a37af] [dcccluster:979935] [29] /usr/lib64/libpython3.8.so.1.0(_PyEval_EvalFrameDefault+0x5da)[0x7f8c3a9e506a] [dcccluster:979935] *** End of error message *** Aborted (`core' generado) Computer Vision Center<http://www.cvc.uab.cat> CONFIDENTIALITY WARNING<http://www.cvc.uab.es/?page_id=7475>

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Problem with NEST 3.3 installation
by Petia Koprinkova 04 Jul '22

04 Jul '22

Hi,Could you help us with NEST 3.3. installation? The final (check) state give the following error: Executing NEST's testsuite... CMakeFiles/installcheck.dir/build.make:70: recipe for target 'CMakeFiles/installcheck' failed make[3]: *** [CMakeFiles/installcheck] Error 1 CMakeFiles/Makefile2:446: recipe for target 'CMakeFiles/installcheck.dir/all' failed make[2]: *** [CMakeFiles/installcheck.dir/all] Error 2 CMakeFiles/Makefile2:453: recipe for target 'CMakeFiles/installcheck.dir/rule' failed make[1]: *** [CMakeFiles/installcheck.dir/rule] Error 2 Makefile:179: recipe for target 'installcheck' failed make: *** [installcheck] Error 2 We have Ubuntu desctop with installed NEST 2.18 and it works. But for some reason NEST 3.3. failed. Best regards,Petia Koprinkova-Hristova

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Invalid SpikeEvent variables - e.get_sender_node_id()
by Barna Zajzon 04 Jul '22

04 Jul '22

Dear NEST community, I was wondering if there have been some changes from NEST 2.x -> 3.x regarding how the SpikeEvent variables are set and their availability in the handle(SpikeEvent& e) function. With 2.20.0, I could access the sender ID from inside the handle() function. With the current master branch, however, this is not possible anymore (or likely I'm doing it wrong). The following one-line addition to the iaf_cond_exp model (the exact model doesn't really matter): void nest::iaf_cond_exp::handle( SpikeEvent& e ) { assert( e.get_delay_steps() > 0 ); std::cout << "iaf_cond_exp >> e.get_sender_node_id(): " << e.get_sender_node_id() << std::endl << std::flush; if ( e.get_weight() > 0.0 ) ... fails with: python: /home/zbarni/software/packages/nest/znest/nestkernel/event.h:1336: nest::index nest::Event::get_sender_node_id() const: Assertion `sender_node_id_ > 0' failed. Furthermore, the SpikeEvent seems invalid (?), as the e.is_valid() call returns a 0. Is this the expected behavior, and if so, are there any alternatives to access the ID of the sender node in the handle() function? Thank you, Barna -- Barna Zajzon PhD Candidate Computation in Neural Circuits Group Institute of Neuroscience and Medicine (INM-6) Institute for Advanced Simulation (IAS-6) JARA Institute Brain Structure-Function Relationships (INM-10) Jülich Research Centre and JARA 52425 Jülich, Germany http://www.fz-juelich.de/inm/inm-6 ------------------------------------------------------------------------------------------------ ------------------------------------------------------------------------------------------------ Forschungszentrum Juelich GmbH 52425 Juelich Sitz der Gesellschaft: Juelich Eingetragen im Handelsregister des Amtsgerichts Dueren Nr. HR B 3498 Vorsitzender des Aufsichtsrats: MinDir Volker Rieke Geschaeftsfuehrung: Prof. Dr.-Ing. Wolfgang Marquardt (Vorsitzender), Karsten Beneke (stellv. Vorsitzender), Prof. Dr. Astrid Lambrecht, Prof. Dr. Frauke Melchior ------------------------------------------------------------------------------------------------ ------------------------------------------------------------------------------------------------ Neugierige sind herzlich willkommen am Sonntag, den 21. August 2022, von 10:00 bis 17:00 Uhr. Mehr unter: https://www.tagderneugier.de

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Reminder: Free online CNS*2022 satellite tutorials: June 27--July 1
by Ankur Sinha 23 Jun '22

23 Jun '22

Dear all, Apologies for the cross-posts. A final reminder of next week's CNS*2022 free online satellite tutorials (from June 27--July 1): https://ocns.github.io/SoftwareWG/pages/software-wg-satellite-tutorials-at-… Free registration remains open at: https://framaforms.org/incfocns-software-wg-cns2022-satellite-tutorials-reg… To prevent spam/zoom crashing, links to zoom meetings for the tutorial sessions will be limited to registrants only. Therefore, while registration is free, it is required. The satellite tutorials feature sessions on: - Arbor - Brian2 - Introduction to containers - EBRAINS - GeNN - Keras/TensorFlow - LFPy - MOOSE - Neo + Elephant - NEST - NetPyNE - neurolib - NeuroML - NEURON - OSBv2 - RateML Please spread the word, and we look forward to seeing you there. -- Thanks, Regards, Ankur Sinha (He / Him / His) | https://ankursinha.in Research Fellow at the Silver Lab, University College London | http://silverlab.org/ Free/Open source community volunteer at the NeuroFedora project | https://neuro.fedoraproject.org Time zone: Europe/London

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Compartment neuron model - which NEST version?
by Petia Koprinkova 23 Jun '22

23 Jun '22

Hi, Could you tell me which version of NEST supports compartment neuron model?We have installed 2.18 but cm_default is not included. Regards,Petia Koprinkova-Hristova

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Acceleration problem-data transmission
by 叶钧超 20 Jun '22

20 Jun '22

Dear all, Recently, I used software and hardware to accelerate the SNN network based on IZHIKEVICH model on the nest platform. The first step of acceleration is to transport the corresponding neurons to the designated storage place, and then use hardware acceleration. The results show that the hardware acceleration is very effective, but it will lead to extra handling time and high overhead.In order to solve this problem,  I want to know some parameters that change during simulation in which source file is the value of this assigned? Such as: b_ Spikes_ Get_ Value (lag); Best wishes, Chao yjchao1110 yjchao1110(a)qq.com  

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Open NEST Developer Video Conference Monday June 20 2022 11:30 CEST (UTC+2)
by Dennis Terhorst 20 Jun '22

20 Jun '22

Dear NEST Users & Developers! I would like to invite you to our next fortnightly Open NEST Developer Video Conference, today Monday June 20, 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. 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/2022-06-20-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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How to implement double-exponential functions for synapses in C++
by Ravichandran-Schmidt, Pirathitha (SRH Hochschule Heidelberg) 15 Jun '22

15 Jun '22

Dear NEST Community, is there a good way to implement a double-exponential function for synapses in C++ within a nest module? [cid:image001.jpg@01D87B3E.2D9BE590] As I need to implement my own neuron model in C++, I adapted the code from extraction the information from other neuron models (for example: iaf _cond_beta.cpp) and used the following lines f[S::DG_EXC] = -y[ S::DG_EXC ] / node.P_.tau_synAMPA_on; f[S::G_EXC ] = y[ S::DG_EXC ] - y[ S::G_EXC ] / node.P_.tau_synAMPA_off At first, it seemed to work pretty good. But when I swap the values for rise und decay time, the evolution of g_ADP did not change at all (for example: rise_time = 1ms, decay_time = 100ms). I would be happy to get any feedback on it. Thanks, Pira

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About the Izhikevich model
by jcye 10 Jun '22

10 Jun '22

Dear NEST Community, When I use NEST, I find that Izhikevich model has no refractory period. Whether there is a specific reason for this setting or whether the model itself does not have this refractory period? After all, according to my understanding, all neurons in biology have the characteristics of refractory period. I would be happy to get any feedback on it. Thanks, Chao.

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回复：Re: About the Izhikevich model
by jcye 10 Jun '22

10 Jun '22

Dear Professor Hans Ekkehard， Thank you for your answer, which gives me a deeper understanding of Izhikevich model. There is a delay when firing a spike between neurons. If there is an refractory period, can I think that only one spike will be sent in this delay interval. Best wishes, Chao. ------------------ 原始邮件 ------------------ 发件人: "NEST User Mailing List" <hans.ekkehard.plesser(a)nmbu.no>gt;; 发送时间: 2022年6月10日(星期五) 下午4:57 收件人: "NEST User Mailing List"<users(a)nest-simulator.org>gt;; 主题: [NEST Users] Re: About the Izhikevich model   Hi Chao,   In real neurons, the refractory period arises from a combination of biophysical mechanisms. After firing an action potential, the cell needs to recover before it can fire another one. In simplified neuron models, such as most integrate-and-fire models, which do not include these recovery mechanisms, one usually adds an explicit refractory period to capture the effect of the biophysical recovery mechanisms in a mathematically or computationally simple way.   But if a neuron model includes (slow) recovery variables that will prevent it from spiking for some period after firing a spike, adding an explicit refractory period may not be required. Izhikevich decided that this was the case for his model, and thus there is no explicit refractory period that could be set as a parameter. The neuron model has its refractoriness simply "built in", with details depending on the parameters.   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 Home http://arken.nmbu.no/~plesser       On 10/06/2022, 09:31, "jcye" <jc.ye(a)foxmail.com> wrote:   Some people who received this message don't often get email from jc.ye(a)foxmail.com. Learn why this is important   Dear NEST Community,   When I use NEST, I find that Izhikevich model has no refractory period. Whether there is a specific reason for this setting or whether the model itself does not have this refractory period? After all, according to my understanding, all neurons in biology have the characteristics of refractory period. I would be happy to get any feedback on it. Thanks, Chao.

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Free registration is now open for CNS*2022 satellite tutorials: June 27--July 1
by Ankur Sinha 08 Jun '22

08 Jun '22

Dear all, Apologies for the cross-posts. The INCF/OCNS Software Working Group is happy to announce that the schedule for the CNS*2022 satellite tutorials from June 27--July 1 has now been published here: https://ocns.github.io/SoftwareWG/pages/software-wg-satellite-tutorials-at-… Free registration is also now open at: https://framaforms.org/incfocns-software-wg-cns2022-satellite-tutorials-reg… To prevent spam/zoom crashing, links to zoom meetings for the tutorial sessions will be limited to registrants only. Therefore, while registration is free, it is required. The satellite tutorials feature sessions on: - Arbor - Brian2 - Introduction to containers - EBRAINS - GeNN - Keras/TensorFlow - LFPy - MOOSE - Neo + Elephant - NEST - NetPyNE - NeuroLib - NeuroML - NEURON - OSBv2 - RateML Please spread the word, and we look forward to seeing you there! -- Thanks, Regards, Ankur Sinha (He / Him / His) | https://ankursinha.in Research Fellow at the Silver Lab, University College London | http://silverlab.org/ Free/Open source community volunteer at the NeuroFedora project | https://neuro.fedoraproject.org Time zone: Europe/London

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No NEST Developer Video Conference (Pentecost)
by Dennis Terhorst 06 Jun '22

06 Jun '22

Dear NEST Users & Developers! Due to the Pentecost holidays in many countries following the Gregorian calendar we skip today's meeting. Our next fortnightly Open NEST Developer Video Conference will be in two weeks on Monday June 20, 11.30-12.30 CEST (UTC+2). Looking forward to seeing you again soon! Best, 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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Nest dry_run
by 512491013＠qq.com 03 Jun '22

03 Jun '22

Dear all, In the paper“The NEST Dry-Run Mode: Efficient Dynamic Analysis of Neuronal Network Simulation Code”(2017), I found an article about the description of NEST Dry-run Mode, which I am very interested in. However, I don't seem to find relevant information about how to use dry-run in the document. May I ask if there are any relevant examples of using dry-run? best, Cong

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Re: Nest 3.3
by Steffen Graber 01 Jun '22

01 Jun '22

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I can not install Nest 3.3 simulator in Ubuntu 18.04
by salvatore.taffara＠phd.unict.it 31 May '22

31 May '22

Hi to the community, In order to install Nest 3.3 in Ubuntu 18.04 WITHOUTH the Docker, I followed two ways: 1) I downloaded the source zip file from "https://github.com/nest/nest-simulator/tags", then I followed the guide in "https://nest-simulator.readthedocs.io/en/v3.3/installation/linux_install.ht…", in particular the "Installation from source without a virtual Python environment" version. What I obtain is an error in the terminal: salvo@salvo-Aspire-GX-781:~/Downloads/nest-simulator-3.3-build$ cmake -DCMAKE_INSTALL_PREFIX:PATH=/home/nest /home/salvo/Downloads/nest-simulator-3.3-build/ -- Host triple: x86_64-pc-linux -- Target triple: x86_64-pc-linux CMake Error at /usr/share/cmake-3.23/Modules/FindPackageHandleStandardArgs.cmake:230 (message): Could NOT find Python (missing: Python_INCLUDE_DIRS Python_LIBRARIES Development Development.Module Development.Embed) (found suitable version "3.8.13", minimum required is "3.8") Call Stack (most recent call first): /usr/share/cmake-3.23/Modules/FindPackageHandleStandardArgs.cmake:594 (_FPHSA_FAILURE_MESSAGE) /usr/share/cmake-3.23/Modules/FindPython/Support.cmake:3192 (find_package_handle_standard_args) /usr/share/cmake-3.23/Modules/FindPython.cmake:519 (include) cmake/ProcessOptions.cmake:367 (find_package) CMakeLists.txt:129 (nest_process_with_python) -- Configuring incomplete, errors occurred! See also "/home/salvo/Downloads/nest-simulator-3.3-build/CMakeFiles/CMakeOutput.log". See also "/home/salvo/Downloads/nest-simulator-3.3-build/CMakeFiles/CMakeError.log". salvo@salvo-Aspire-GX-781:~/Downloads/nest-simulator-3.3-build$ 2) I also tried to force the following Ubuntu commands to obtain, from the ppa repository, the Nest version that I need (this is the ppa nest site: https://launchpad.net/~nest-simulator/+archive/ubuntu/nest): sudo add-apt-repository ppa:nest-simulator/nest sudo apt-get update sudo apt-get install nest=3.2-0~202202100714~ubuntu18.04.1 But is seems that the only package that is downloaded from this ppa is nest 2.20, in particular: 2.20.1-0~202103121402~ubuntu18.04.1. What can I do to install Nest 3.3 in my Ubuntu 18.04? Best, Salvo

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