NEST Users July 2022

users@nest-simulator.org

18 participants
15 discussions

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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