- NEST Users - NEST Initiative Mail

by lea.driessens＠ensea.fr

Hello, We are trying to plot an exponential synaptic trace in a custom made synapse model made with NESTML, and to do that we are trying to use the print function within the model. But when we try to print something or to change the value of a variable (initialized in the state block) inside the update block, nothing happens. We started with a simple string "Hello", and nothing was printed. We then tried to add 1 to a variable initialized to 0 and its value didn't change. If the print command is written in the onReceive block, it works without problems; as for the variable, its value can be changed in the onReceive block, but if we print its value in the onReceive block and change the value in the update block, we see that the value is not updated from 0. Since we would like to get the value of the synaptic trace to plot its change during simulation, we would need to get the value of the trace not just when a spike is received (there would be no point) but more often. Do you know what we could do? (And why the update block is not working properly?) Best regards, Léa D.

2 years, 4 months

4
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Open NEST Developer Video Conference Monday July 18 2022 11:30 CEST (UTC+2)

by Dennis Terhorst

Dear NEST Users & Developers! I would like to invite you to our next fortnightly Open NEST Developer Video Conference, today Monday July 18, 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/2022-07-18-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

2 years, 5 months

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Access weight_recorder data during simulation

by francescojamal.sheiban＠polimi.it

Dear all, I was wondering if it is possible to access the events collected by a weight_recorder during a simulation: I am able to collect and plot the recorded data once the simulation is over, but I found no information about accessing the device in real-time. Specifically, I would like to know if there is a way to pass the data as input to a custom NESTML synapse model dynamically during a simulation. Best regards, Francesco Sheiban

2 years, 5 months

2
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Decreased simulation speed using nest v2.20.1 compared to v2.2.2

by Hartmut Schmidt

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

2 years, 5 months

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Get MPI time

by 512491013＠qq.com

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

2 years, 5 months

2
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NEST mini app?

by itaru.kitayama＠gmail.com

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.

2 years, 5 months

2
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Problem with "import nest"

by Xavier Otazu Porter

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>

2 years, 5 months

3
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Problem with NEST 3.3 installation

by Petia Koprinkova

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

2 years, 5 months

4
11
0 0

Invalid SpikeEvent variables - e.get_sender_node_id()

by Barna Zajzon

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

2 years, 5 months

2
1
0 0

Open NEST Developer Video Conference Monday July 4 2022 11:30 CEST (UTC+2)

by Dennis Terhorst

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

2 years, 5 months

1
0
0 0

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