NEST Users January 2021

users@nest-simulator.org

19 participants
17 discussions

Error in Simulate
by Petia Koprinkova 15 Jan '21

15 Jan '21

We have encountered the following error: Traceback (most recent call last): File "all_v2.py", line 364, in <module> nest.Simulate(sim_time) File"/opt/soft/nest-2.18.0/lib64/python3.6/site-packages/nest/ll_api.py",line 246, in stack_checker_func return f(*args, **kwargs) File"/opt/soft/nest-2.18.0/lib64/python3.6/site-packages/nest/lib/hl_api_simulation.py",line 66, in Simulate sr('ms Simulate') File"/opt/soft/nest-2.18.0/lib64/python3.6/site-packages/nest/ll_api.py",line 132, in catching_sli_run raise exceptionCls(commandname, message) nest.ll_api.C++Exception: ('C++Exception in Simulate_d:std::bad_alloc', 'C++Exception', <SLILiteral: Simulate_d>, ':std::bad_alloc') Could you help to resolve it? Best regards,Petia Koprinkova-Hristova

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Trouble about the spiking time will increase and get so bigger with the simulation epoch increasing.
by enguang zhou 13 Jan '21

13 Jan '21

Deal all, I am recording the spiking time of neurons after every simulation, and I find that the time beginning of every simulation isn't all 0 except the first simulation. So how can I set to recording spiking time beginning from 0 during all simulations? By now I am processing that for every simulation spiking time recording by deleting all the time used before a specific simulation epoch. Hope for your answer,thanks! Enguang

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Problems with installation of NEST on MAC
by Vittorio De Falco 12 Jan '21

12 Jan '21

Dear Users of NEST, I have downloaded and installed nest on my MAC. I was able to configure it. When I launch make I receive the following error Undefined symbols for architecture x86_64: "___kmpc_critical", referenced from: SLIInterpreter::message(int, char const*, char const*, char const*) const in interpret.cc.o "___kmpc_end_critical", referenced from: SLIInterpreter::message(int, char const*, char const*, char const*) const in interpret.cc.o "___kmpc_global_thread_num", referenced from: SLIInterpreter::message(int, char const*, char const*, char const*) const in interpret.cc.o "_omp_in_parallel", referenced from: Name::insert(std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> > const&) in name.cc.o ld: symbol(s) not found for architecture x86_64 clang: error: linker command failed with exit code 1 (use -v to see invocation) make[2]: *** [sli/libsli.dylib] Error 1 make[1]: *** [sli/CMakeFiles/sli_lib.dir/all] Error 2 make: *** [all] Error 2 I have already installed it successfully the previous week, but for example I have problem when I launch an example code from NEST (one_neuron.py), because import nest is recognised, while "import nest.voltage_trace" is not found ModuleNotFoundError: No module named 'nest.voltage_trace' Sorry I am a little bit confused. When I try to launch a code in a folder different from the nest-simulator folder "import nest" is not recognised. Could you please explain me better how to solve such an issue? Thank you very much for your support. Best, Vittorio *************************************************************** * Postdoctoral Researcher in Mathematics * University of Naples "Federico II" * Department of Mathematics and Application "R. Caccioppoli" * Via Cintia, IT-80126 Naples, Italy * CELL: +39 340 544 70 15 ****************************************************************

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spatiotemporal Poisson generator
by Abolfazl Ziaeemehr 08 Jan '21

08 Jan '21

Hello everyone, Is it possible to include a *spatiotemporal poisson generator* in the simulation? I am trying to apply a current to a population of neurons which is something like this? [image: Selection_001.png] where `i` is the index of the neuron and `t` is the current time of the simulation. Thank you for any guidance. best, -- Abolfazl Ziaeemehr PhD in Computational Neuroscience Institute for Advanced Studies in Basic Sciences (IASBS) Page: iasbs.ac.ir/~a.ziaeemehr https://github.com/Ziaeemehr

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I want to know the derivative equation of iaf_psc_alpha neuron model to design some algorithms for neural network
by enguang zhou 06 Jan '21

06 Jan '21

Hi everyone, I have a very big problem now again for the iaf neuron(such as iaf_psc_alpha), which is I don't know know differential equation for the neuron model, so I can't get the derivative of voltage about some other variable, such as derivative of voltage versus synapse weight. The point is I do need to know the derivative equation of iaf_psc_alpha neuron model to design some algorithm for neural network. For the paper mentioned below, I still can't figure out the exact derivative equation of voltage or voltage state equation. https://link.springer.com/article/10.1007/s004220050570 By the way, At last meeting, I wanted to ask that but my device had trouble when host asked, so awkward. Hope for your answer. Thank you. Enguang

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How does the synapse weight influence 'iaf_psc_alpha' neuron(or any other neuron you know) to send a spike?
by enguang zhou 04 Jan '21

04 Jan '21

Hello everyone, As the title says, can someone help me answer this? I am really confused about this. Because I need to know how to control the neuron spiking from the mathematical formula, and I check out the iaf_psc_alpha.cpp and its .h file, and I can't get a clue how does the synapse weight value influence the neuron spiking. I would be appreciate if you can tell me how to check out the code in nest_simualator. Thank you. Enguang

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Open NEST Developer Video Conference Monday 4 January 2021 11:30 CET (UTC+1)
by Dennis Terhorst 04 Jan '21

04 Jan '21

Dear NEST Users & Developers! I would like to wish you all a Happy New Year and invite you to our first fortnightly Open NEST Developer Video Conference of this year, today Monday 4 January, 11.30-12.30 CET (UTC+1). Today we have a special feature discussion on * Python module installation Additionally, 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 Python module installation The agenda for this meeting is also available online, see https://github.com/nest/nest-simulator/wiki/2021-01-04-Open-NEST-Developer-… Looking forward to seeing you 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 Users January 2021