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Decreased simulation speed using nest v2.20.1 compared to v2.2.2
by Hartmut Schmidt 13 Jul '22

13 Jul '22

Hi, I recently upgraded from nest v2.2.2 to v2.20.1 and experienced a decrease in simulation speed. I tested it using the /brunel_alpha_nest.py/ example script that is available in both versions. For better comparison I set the option /to_file/ in the new version to /False/. Simulating the network for 10s using v2.2.2 I get: 100 %: network time: 9999.0 ms, realtime factor: 0.0672 Simulation finished. Brunel network simulation (Python) Number of neurons : 12500 Number of synapses: 15637600 Exitatory : 12512500 Inhibitory : 3125000 Excitatory rate : 28.84 Hz Inhibitory rate : 28.78 Hz Building time : 5.56 s Simulation time : 149.01 s Using v2.20.1: 100 %: network time: 9999.0 ms, realtime factor: 0.0601 Simulation finished. Brunel network simulation (Python) Number of neurons : 12500 Number of synapses: 15637600 Exitatory : 12512500 Inhibitory : 3125000 Excitatory rate : 28.84 Hz Inhibitory rate : 28.78 Hz Building time : 2.39 s Simulation time : 168.58 s Adding /'total_num_virtual_procs': 48/and running it for 100s on a 48 core node using v2.2.2 I get: Simulation time : 98.49 s Using v2.20.1: Simulation time : 120.08 s Both versions are build with OpenMp support and without mpi. Is this expected or do you have any idea where this behavior comes from? Thank you in advance! Best, Hartmut

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Get MPI time
by 512491013＠qq.com 06 Jul '22

06 Jul '22

Dear all, I used 10 PyNQ nodes to run SNN using mpirun, which is faster than a single node. but I want to know how long each node takes to start MPI and wait for MPI_all_gether to end. Where do I need to print the time in the source code?Or what tools can I use to test MPI communication times?（my nest version is 2.14） Best regards Cong

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NEST mini app?
by itaru.kitayama＠gmail.com 05 Jul '22

05 Jul '22

Hello, I've worked on OpenMP-based offloading of NEST for the past couple of years, but due to the lack of C++ runtime library support on the device, it's no success. If someone in this NEST developer community happens to have a validated minimal NEST code written in C++ with OpenMP, could you share it with me so I can extend it to be offloadable one? Thanks, Itaru.

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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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Open NEST Developer Video Conference Monday July 4 2022 11:30 CEST (UTC+2)
by Dennis Terhorst 04 Jul '22

04 Jul '22

Dear NEST Users & Developers! I would like to invite you to our next fortnightly Open NEST Developer Video Conference, today Monday July 4, 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/2022-07-04-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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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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