- NEST Users - NEST Initiative Mail

New Continuous Integration Setup and Porting Tests to Python
by Hans Ekkehard Plesser 02 May '23

02 May '23

Dear NEST Developers and Users, Those of you following the NEST Github repository will have noticed a high level of activity last week and an all new appearance of Github actions for NEST (see https://github.com/nest/nest-simulator/actions/runs/4858443145 for an example). First of all, thanks to a major effort by Dennis Terhorst in particular, we have a completely re-organized continuous integration test setup. A considerably larger set of static code checks is now run independent of each other in a first stage of testing before NEST is build on Linux and macOS runners for actual testing. Furthermore, documentation is also linted and test-built. Overall, this setup runs faster and provides more information and assurances. Second, we have started a major effort to port all tests from the SLI-based testsuite to Python using pytest, so that we eventually will be able to remove the SLI interpreter and still have a full set of tests for NEST. Over time, the number of tests in `testsuite/{unittests, regressiontests, mpitests}` will decrease as tests are moved to `testsuite/pytests`. In that directory, new tests are distributed into several subdirectories according the the part of NEST they cover. Those directories are all prefixed with `sli2py_` for now; the prefix will be dropped when the transition is complete. We have tried to come up with good pytest test designs, but we are still developing our skills and style in this area. In general, consider tests in the sli2py_ directories as reference. Tests in the main pytests directory and its other subdirectories are mostly written in older unittest style and have not undergone thorough review. We plan to bring them ajour later. As a side effect of this transition, the number of tests reported by the testsuite has increased significantly. This has mainly two reasons: Many *.sli test files contained multiple tests but were counted only as one. And pytest's parametrize support allows us to run tests more systematically across models. If you would like to join our effort in porting tests form SLI to Python, why not drop by the Open NEST Developer VC on Monday? Best, 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<mailto:hans.ekkehard.plesser@nmbu.no> Home http://arken.nmbu.no/~plesser

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Synaptic dynamics equation?
by bstrohmer＠gmail.com 25 Apr '23

25 Apr '23

Hi All, I am using the aeif_cond_alpha neuron model in NEST and the synaptic dynamics are calculated together with the membrane potential of the neuron model. I understand that the synapse uses an alpha function. However, it is unclear what the actual equation is for calculating the synaptic conductance. After looking through the documentation and C++ code it was still unclear to me, however, I found this journal article which defines an equation for the synaptic conductance (equation 4), https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0057134. Is this the correct equation? Thanks for any help! Best, Beck

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Open NEST Developer Video Conference Monday Apr 24 2023 11:30 CET (UTC+1)
by Dennis Terhorst 24 Apr '23

24 Apr '23

Dear NEST Users & Developers! I would like to invite you to our next fortnightly Open NEST Developer Video Conference, today Monday April 24, 11.30-12.30 CET (UTC+1). 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. Feel free to join the meeting also if it's just to bring your own quick questions for direct discussion in the in-depth section. 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/2023-04-24-Open-NEST-Developer-… Looking forward to seeing you! 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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Reloading and debugging a nestml module
by gustavo.patow＠udg.edu 22 Apr '23

22 Apr '23

Hi, Continuing with my exploration, I am now developing my own nestML module. I successfully compiled it and ran it without errors or problems. However, the result was not what I expect, so I modified the nestML code, compiled it, and... well, I tried to re-install it with nest.Install("nestmlmodule") and I get an error that the module was already loaded. When I try to rerun my simulation, I get the old result, not the new one. How do I do to reload the module? I've searched through the documentation and I do not find any reload, reinstall, or anything similar... Is there any other way than killing everything and starting over from scratch? By the way, are there any debug tools for a nestML module? I tend to make zillions of mistakes, and any way of inspecting the behavior of the module and the state of the internal variables would be of incredible help! thanks!!! gus.-

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Basic problems running nestml
by gustavo.patow＠udg.edu 15 Apr '23

15 Apr '23

Dear all, While I try to solve my doubts on the other thread, I decided to try nestml on my own. For this, I installed docker and did: wget https://raw.githubusercontent.com/steffengraber/nest-docker/master/docker-c… and then: docker-compose up nest-jupyterlab as explained here: https://nest-simulator.readthedocs.io/en/latest/installation/docker.html#do… Then, I created a silly Python file that simply does: import matplotlib.pyplot as plt import nest import numpy as np import os from pynestml.frontend.pynestml_frontend import generate_nest_target NEST_SIMULATOR_INSTALL_LOCATION = nest.ll_api.sli_func("statusdict/prefix ::") generate_nest_target(input_path="izhikevich.nestml", target_path="/tmp/nestml-component", logging_level="ERROR", codegen_opts={"nest_path": NEST_SIMULATOR_INSTALL_LOCATION}) where izhikevich.nestml is nothing else than a brute-force copy and paste of https://github.com/nest/nestml/blob/master/models/neurons/izhikevich.nestml It should be trivial, but then I get: -- N E S T -- Copyright (C) 2004 The NEST Initiative Version: 3.4 Built: Mar 31 2023 12:33:35 This program is provided AS IS and comes with NO WARRANTY. See the file LICENSE for details. Problems or suggestions? Visit https://www.nest-simulator.org Type 'nest.help()' to find out more about NEST. WARNING:root:PyGSL is not available. The stiffness test will be skipped. WARNING:root:Error when importing: No module named 'pygsl' line 44:4 extraneous input 'equations' expecting {NEWLINE, 'end', 'inline', 'recordable', NAME} line 48:4 extraneous input 'parameters' expecting {NEWLINE, 'end', 'inline', 'recordable', 'kernel', NAME} line 59:4 missing 'end' at 'input' line 63:4 extraneous input 'output' expecting {NEWLINE, 'end', NAME} line 77:24 mismatched input '<EOF>' expecting {'end', 'elif', 'else'} [6,GLOBAL, ERROR]: Error occurred during parsing: abort Traceback (most recent call last): File "/opt/data/Izhikevich.py", line 10, in <module> generate_nest_target(input_path="izhikevich.nestml", File "/usr/local/lib/python3.10/dist-packages/pynestml/frontend/pynestml_frontend.py", line 229, in generate_nest_target generate_target(input_path, target_platform="NEST", target_path=target_path, logging_level=logging_level, File "/usr/local/lib/python3.10/dist-packages/pynestml/frontend/pynestml_frontend.py", line 199, in generate_target raise Exception("Error(s) occurred while processing the model") Exception: Error(s) occurred while processing the model which I do not understand. The syntaxis of nestml seems clear, no "end", right? Then, what am I doing wrong? Thanks! gus.- PS: I still have my doubts, as explained in the other thread, but I thought this is a different issue... sorry if I did wrong!!!

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Population of Izhikevich-like neurons
by gustavo.patow＠udg.edu 11 Apr '23

11 Apr '23

Dear All, My name is Gustavo (Gus) and I am a complete newbie at NEST, so probably this will be a stupid question. However, I have thoroughly;y searched the documentation for nest-desktop, nest, nestml, and this mailing list, but couldn't find an appropriate answer. So, if this is a stupid question, sorry! Well, I want to model a population of Izhikevich-like neurons, as described in this paper: Chen, L., Campbell, S.A. Exact mean-field models for spiking neural networks with adaptation. J Comput Neurosci 50, 445–469 (2022). https://doi.org/10.1007/s10827-022-00825-9 arXiv: https://arxiv.org/abs/2203.08341 code: https://senselab.med.yale.edu/ModelDB/ShowModel?model=267382#tabs-1 Basically, it is a light variant of the original model in Izhikevich's 2003 paper, with a standard synaptic current I = g S (e_r - u_k), with S the gating variable following its own first-order differential equation, and assuming an intrinsic current with a Lorentzian distribution (and probably something else that I do not remember right now). I also wanted to take this opportunity to learn nest at the same time, so I decided to start with NEST-Desktop online (I have an account at EBRAINS), but couldn't figure out how to exactly configure the standard Izhikevich model to be the one in the paper, and also couldn't find a mechanism to plug a gating variable, or a way to specify the intrinsic current, and also couldn't find a Lorentzian distribution among the options for the current generators... So, I guess I should go deeper. Is that right? Can I solve this with merely nest-desktop? Then, I started to look at some examples in nestml, including the Izhikevich one, and I think that, if I have to modify it, it is feasible. I am fluent in Python, and reading the Izhikevich tutorial seemed reasonable to me: https://nestml.readthedocs.io/en/latest/tutorials/izhikevich/nestml_izhikev… So, my final question... is this the way to go? Should I write my neuron model as a new variant of the original one, perhaps in nestml? Should I include the gating variable inside this model, or is there another mechanism for that? Then, I guess I need to build a current generator, right? Can I have more than one (1 for the external stimulus, 1 for the intrinsic current)? Is this plan sound? Are there any shortcuts for what I want to do? Any hints or tips you could share? In any case, THANKS FOR THE PATIENCE!!! cheers gus.-

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structural_plasticity.py set initial Ca
by Abbey Durell 31 Mar '23

31 Mar '23

I'm trying to set the initial Calcium concentration for this model with no luck. I've tried self.model_params = {'tau_m': 10.0, # membrane time constant (ms) ... 'Ca': 0.1 #initial calcium concentration } This method doesn't throw an exception but it also doesn't change the initial calcium concentration. I've also tried self.nodes_e.set(Ca=0.1) which throws an exception nest.lib.hl_api_exceptions.NESTErrors.DictError: DictError in SLI function SetStatus_id: Unused dictionary items: Ca Any suggestions?

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structural_plasticity.py change connection rules
by Abbey Durell 28 Mar '23

28 Mar '23

I'm running the structural_plasticity.py example and would like to make some modifications. I was able to change the initial Ca value with the help of Charl. Now I'm trying to specify connection rules such as disallowing autapses. Does anyone have any suggestions on how I can implement this in the structural plasticity example? I'm not CS major but I am able to compile and run nest locally.

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Open NEST Developer Video Conference Monday Mar 13 2023 11:30 CET (UTC+1)
by Jochen Martin Eppler 27 Mar '23

27 Mar '23

Dear NEST Users & Developers! I would like to invite you to our next fortnightly Open NEST Developer Video Conference, today Monday March 27, 11.30-12.30 CET (UTC+1). 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. Feel free to join the meeting also if it's just to bring your own quick questions for direct discussion in the in-depth section. 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/2023-03-27-Open-NEST-Developer-… Looking forward to seeing you! Cheers, Jochen! ------------------ 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 -- Dr. Jochen Martin Eppler (he/him) Simulation and Data Lab Neuroscience Jülich Supercomputing Centre Institute for Advanced Simulation --------------------------------------------------------------------- Forschungszentrum Juelich GmbH 52425 Juelich Sitz der Gesellschaft: Juelich Eingetragen im Handelsregister des Amtsgerichts Dueren Nr. HR B 3498 Vorsitzender des Aufsichtsrats: MinDir Stefan Müller Geschaeftsfuehrung: Prof. Dr.-Ing. Wolfgang Marquardt (Vorsitzender), Karsten Beneke (stellv. Vorsitzender), Dr. Ir. Pieter Jansens, Prof. Dr. Astrid Lambrecht, Prof. Dr. Frauke Melchior ---------------------------------------------------------------------

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MPI error when using GetConnections
by Xavier Otazu 17 Mar '23

17 Mar '23

Hello, I am trying to normalize connection weights using a code similar to the one on the Documentation (see code below). I receive an error when assigning the modified weights on the last line of the for loop below (only when I use several MPI processes). That is, when using mpirun -np 1 python3 test_DumpLayerConnections.py I do not receive any error, but when using 4 MPI processes: mpirun -np 4 python3 test_DumpLayerConnections.py I receive the following error when trying to start a Simulation: Mar 16 11:13:53 NodeManager::prepare_nodes [Info]: Preparing 675 nodes for simulation. [dcccluster:747534] *** An error occurred in MPI_Allgather [dcccluster:747534] *** reported by process [2696478721,0] [dcccluster:747534] *** on communicator MPI_COMM_WORLD [dcccluster:747534] *** MPI_ERR_TRUNCATE: message truncated [dcccluster:747534] *** MPI_ERRORS_ARE_FATAL (processes in this communicator will now abort, [dcccluster:747534] *** and potentially your MPI job) I can avoid this error by commenting the last for loop assignament (the normalized weights assignment operation). I am using NEST 3.3 (compiled with MPI option) and Python 3.8.12. I guess it could be related to the DumpLayerConnections bug I told you some days ago. Thanks a lot in advance! Xavier import nest import numpy as np pos = nest.spatial.grid(shape = [30,30] ) input = nest.Create('iaf_psc_alpha', positions=pos) layer_0 = nest.Create('iaf_psc_alpha', positions=pos) layer_1 = nest.Create('iaf_psc_alpha', positions=pos) conn_neur = {'rule':'pairwise_bernoulli', 'use_on_source': True, 'mask': {'grid':{'shape':[9,9]}} } nest.CopyModel('static_synapse', 'syn_1_model') syn_0 = {'synapse_model': 'static_synapse'} syn_1 = {'synapse_model': 'syn_1_model'} nest.Connect(input, layer_0, conn_neur, syn_0) nest.Connect(input, layer_1, conn_neur, syn_1) nest.DumpLayerConnections(input, layer_0, 'static_synapse', 'conn.txt') nest.DumpLayerConnections(input, layer_1, 'syn_1_model', 'conn.txt') for neuron in layer_0: conn = nest.GetConnections(target=neuron, synapse_model='static_synapse') w = np.array(conn.weight) if (w.size>1): w_normed = w / sum(abs(w)) # L1-norm w_nparray = 2. * w_normed conn.weight = w_nparray.tolist() nest.Simulate(100)

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Open NEST Developer Video Conference Monday Mar 13 2023 11:30 CET (UTC+1)
by Dennis Terhorst 13 Mar '23

13 Mar '23

Dear NEST Users & Developers! I would like to invite you to our next fortnightly Open NEST Developer Video Conference, today Monday March 13, 11.30-12.30 CET (UTC+1). 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. Feel free to join the meeting also if it's just to bring your own quick questions for direct discussion in the in-depth section. 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/2023-03-13-Open-NEST-Developer-… Looking forward to seeing you! 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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Coredump with DumpLayerConnections
by Xavier Otazu 13 Mar '23

13 Mar '23

Hello, For the following code, I receive a coredump (it throws and assertion from grid_layer.h) (output at the end). When not connecting 'input' to 'layer_1', everything works fine. It looks like it does not like to connect a layer to more than one target layer. Thanks a lot in advance! import nest pos = nest.spatial.grid(shape = [3,3] ) input = nest.Create('iaf_psc_alpha', positions=pos) layer_0 = nest.Create('iaf_psc_alpha', positions=pos) layer_1 = nest.Create('iaf_psc_alpha', positions=pos) conn_neur = {'rule':'pairwise_bernoulli', 'use_on_source': True, 'mask': {'grid':{'shape':[3,3]}} } nest.Connect(input, layer_0, conn_neur) nest.Connect(input, layer_1, conn_neur) nest.DumpLayerConnections(input, layer_0, 'static_synapse', 'conn.txt') The output message is: python3: /home/neurobit/src/nest_3.3_src/nestkernel/grid_layer.h:223: nest::Position<D> nest::GridLayer<D>::lid_to_position(nest::index) const [with int D = 2; nest::index = long unsigned int]: Assertion `lid < dims_[ 0 ]' failed. [dcccluster:326996] *** Process received signal *** [dcccluster:326996] Signal: Aborted (6) [dcccluster:326996] Signal code: (-6) [dcccluster:326996] [ 0] /lib64/libpthread.so.0(+0x12c20)[0x7fb317ec0c20] [dcccluster:326996] [ 1] /lib64/libc.so.6(gsignal+0x10f)[0x7fb31739637f] [dcccluster:326996] [ 2] /lib64/libc.so.6(abort+0x127)[0x7fb317380db5] [dcccluster:326996] [ 3] /lib64/libc.so.6(+0x21c89)[0x7fb317380c89] [dcccluster:326996] [ 4] /lib64/libc.so.6(+0x2fa76)[0x7fb31738ea76] [dcccluster:326996] [ 5] /home/neurobit/local/nest_3.3/lib64/python3.8/site-packages/nest/../../../nest/libnestkernel.so(+0x1d7783)[0x7fb2fcbf7783] [dcccluster:326996] [ 6] /home/neurobit/local/nest_3.3/lib64/python3.8/site-packages/nest/../../../nest/libnestkernel.so(_ZNK4nest9GridLayerILi2EE12get_positionEm+0xa)[0x7fb2fcbf779a] [dcccluster:326996] [ 7] /home/neurobit/local/nest_3.3/lib64/python3.8/site-packages/nest/../../../nest/libnestkernel.so(_ZN4nest5LayerILi2EE16dump_connectionsERSoSt10shared_ptrINS_14NodeCollectionEES3_INS_13AbstractLayerEERK5Token+0x525)[0x7fb2fcbfca75] [dcccluster:326996] [ 8] /home/neurobit/local/nest_3.3/lib64/python3.8/site-packages/nest/../../../nest/libnestkernel.so(_ZN4nest22dump_layer_connectionsERK5TokenSt10shared_ptrINS_14NodeCollectionEES5_R12lockPTRDatumISoXadL_ZN14SLIInterpreter11OstreamtypeEEEE+0x35c)[0x7fb2fcc1530c] [dcccluster:326996] [ 9] /home/neurobit/local/nest_3.3/lib64/python3.8/site-packages/nest/../../../nest/libnestkernel.so(_ZNK4nest10NestModule37DumpLayerConnections_os_g_g_lFunction7executeEP14SLIInterpreter+0xfc)[0x7fb2fcb491dc] [dcccluster:326996] [10] /home/neurobit/local/nest_3.3/lib64/python3.8/site-packages/nest/../../../nest/libsli.so(_ZN13FunctionDatum7executeEP14SLIInterpreter+0x2b)[0x7fb2f7c0975b] [dcccluster:326996] [11] /home/neurobit/local/nest_3.3/lib64/python3.8/site-packages/nest/../../../nest/libsli.so(_ZN14SLIInterpreter8execute_Em+0x1b2)[0x7fb2f7c06b32] [dcccluster:326996] [12] /home/neurobit/local/nest_3.3/lib64/python3.8/site-packages/nest/../../../nest/libsli.so(_ZN14SLIInterpreter7executeERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEE+0x1ea)[0x7fb2f7c06e7a] [dcccluster:326996] [13] /home/neurobit/local/nest_3.3/lib64/python3.8/site-packages/nest/pynestkernel.so(+0x38669)[0x7fb2ff200669] [dcccluster:326996] [14] /lib64/libpython3.8.so.1.0(+0x173db8)[0x7fb31846adb8] [dcccluster:326996] [15] /lib64/libpython3.8.so.1.0(_PyEval_EvalFrameDefault+0x976)[0x7fb3184d8406] [dcccluster:326996] [16] /lib64/libpython3.8.so.1.0(_PyFunction_Vectorcall+0x1bf)[0x7fb3184967af] [dcccluster:326996] [17] /lib64/libpython3.8.so.1.0(_PyEval_EvalFrameDefault+0x5da)[0x7fb3184d806a] [dcccluster:326996] [18] /lib64/libpython3.8.so.1.0(_PyEval_EvalCodeWithName+0x3e7)[0x7fb3184953c7] [dcccluster:326996] [19] /lib64/libpython3.8.so.1.0(_PyFunction_Vectorcall+0x422)[0x7fb318496a12] [dcccluster:326996] [20] /lib64/libpython3.8.so.1.0(_PyEval_EvalFrameDefault+0x5da)[0x7fb3184d806a] [dcccluster:326996] [21] /lib64/libpython3.8.so.1.0(_PyFunction_Vectorcall+0x1bf)[0x7fb3184967af] [dcccluster:326996] [22] /lib64/libpython3.8.so.1.0(_PyEval_EvalFrameDefault+0x54d9)[0x7fb3184dcf69] [dcccluster:326996] [23] /lib64/libpython3.8.so.1.0(_PyEval_EvalCodeWithName+0x3e7)[0x7fb3184953c7] [dcccluster:326996] [24] /lib64/libpython3.8.so.1.0(PyEval_EvalCode+0x23)[0x7fb3184965a3] [dcccluster:326996] [25] /lib64/libpython3.8.so.1.0(+0x22b09a)[0x7fb31852209a] [dcccluster:326996] [26] /lib64/libpython3.8.so.1.0(+0x250fa2)[0x7fb318547fa2] [dcccluster:326996] [27] /lib64/libpython3.8.so.1.0(+0x10312c)[0x7fb3183fa12c] [dcccluster:326996] [28] /lib64/libpython3.8.so.1.0(PyRun_SimpleFileExFlags+0x369)[0x7fb318400fe3] [dcccluster:326996] [29] /lib64/libpython3.8.so.1.0(Py_RunMain+0x2ef)[0x7fb318549b6f] [dcccluster:326996] *** End of error message ***

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Re: how to customize Ion channels and receptor types of "cm_default" neuron model through nestml
by 王梓瑞 09 Mar '23

09 Mar '23

Hi, Charl Thanks for your reply. And sorry about taking such a long time in this question. My main research interest is the biophysical model of glutamatergic cortico-striatal projections. I previous constructed a striatal circuit (contain two neuron populations MSN and FSI) using simple Integrate-and-fire model, and it successfully reproduced the firing state of striatum MSN and FSI. In that case I simplified the glutamatergic cortical input from multi-synapse to single synapse. Since glutamatergic cortico-striatal projections consist of AMPA and NMDA receptors, I then changed the simple Integrate-and-fire model to multi-synapse Integrate-and-fire model using NESTML. But the results didn't seem good, and got even worse when I handly tuned some parameters. I have been confused for a long time and I thought my multi-synapse definition might account for this. I read about "cm_default" neuron model on NEST model directory, which you described containing AMPA_NMDA receptors. And the difference between your definition on this receptor and mine is the term of NMDA ratio (ratio of NMDA versus AMPA channels). So I thought that might help me resolve this issue and that's why I wrote to ask how to customize receptor types of "cm_default" neuron model through NESTML. So briefly: I wonder how I can apply the NMDA ratio in my own multi-synapse Integrate-and-fire model or is it possible to extract the AMPA_NMDA receptors from "cm_default". And I read about the "cm_default" neuron model on NEST model directory, and you described like "For receptors, the choice is AMPA, GABA or NMDA or AMPA_NMDA. Ion channels and receptor types can be customized with NESTML." ------------------------------------------------------------------ Sender:Charl Linssen <nest-users(a)turingbirds.com> Sent At:2022 Dec. 8 (Thu.) 16:56 Recipient:users <users(a)nest-simulator.org> Subject:[NEST Users] Re: how to customize Ion channels and receptor types of "cm_default" neuron model through nestml Dear Zirui, Thank you for writing in. Just to double-check, the compartmental ("cm_default") model in NEST is intended for use in morphologically detailed models, containing dozens or hundreds of compartments. If your model can be described by only a few compartments, it could be easier to manually define these (define say a separate membrane potential and dendritic potential and the coupling between them; see https://nestml.readthedocs.io/en/v5.1.0/tutorials/active_dendrite/nestml_ac… <https://nestml.readthedocs.io/en/v5.1.0/tutorials/active_dendrite/nestml_ac… > for an example). If you do indeed need the full morpological complexity in your simulations, then the cm_default model is indeed the way to go. We are currently working on extending NESTML to support defining the biophysics in NESTML (ion channels, membrane dynamics etc.) and then combining this with a morphology in NEST. For a prototype of this functionality, please see the branch in https://github.com/nest/nestml/pull/772 <https://github.com/nest/nestml/pull/772 >. The current effort there is focused on adding the ability to specify different ion channels in a more flexible manner. If you could describe a little bit more about your use case and what exactly you are trying to achieve, we could probably give you some more specific advice. Cheers, Charl On Mon, Dec 5, 2022, at 05:54, 王梓瑞 wrote: Dear nest community, I wonder if any of you know how to customize Ion channels and receptor types of "cm_default" neuron model through nestml. I noticed some information on Extending NESTML- Running NESTML with custom templates, but I still found myself confused due to my poor understanding. Is there any way to acquire the .nestml file of the cm_default neuron model? Thank you. Best, Zirui _______________________________________________ NEST Users mailing list -- users(a)nest-simulator.org <mailto:users@nest-simulator.org > To unsubscribe send an email to users-leave(a)nest-simulator.org <mailto:users-leave@nest-simulator.org >

2 2

Ubuntu issue with version 3.4 and roll back to version 3.3
by Ing Jyh Tsang 07 Mar '23

07 Mar '23

Hi, I am using Ubuntu and just updated to Nest 3.4 however I get the following error: Feb 26 15:53:59 SLIStartup [Fatal]: SLI initialisation file not found at /build/nest-xF9H0B/nest-3.4/debian/nest/usr/share/nest/sli/sli-init.sli. Please check your NEST installation. Moreover, is there a simple way to roll back and install Nest 3.3 , such as: sudo apt install nest=3.3? Thanks, Inton

3 4

Deepcopy problem with connections
by Xavier Otazu 01 Mar '23

01 Mar '23

Hello, For the below code I get an error related to __cinit__ (Cython) when performing a deepcopy that includes a nest.spatial specification. I am using NEST 3.3 and Python 3.8.12 Best, Xavier ---- import nest import copy my_dict = {'rule': 'pairwise_bernoulli', 'p': nest.spatial_distributions.gaussian(nest.spatial.distance, std=1.0), 'mask': {'circular': {'radius': 4.}}} new_dict = copy.deepcopy(my_dict) Traceback (most recent call last): File "<stdin>", line 1, in <module> File "/usr/lib64/python3.8/copy.py", line 146, in deepcopy y = copier(x, memo) File "/usr/lib64/python3.8/copy.py", line 230, in _deepcopy_dict y[deepcopy(key, memo)] = deepcopy(value, memo) File "/usr/lib64/python3.8/copy.py", line 172, in deepcopy y = _reconstruct(x, memo, *rv) File "/usr/lib64/python3.8/copy.py", line 270, in _reconstruct state = deepcopy(state, memo) File "/usr/lib64/python3.8/copy.py", line 146, in deepcopy y = copier(x, memo) File "/usr/lib64/python3.8/copy.py", line 230, in _deepcopy_dict y[deepcopy(key, memo)] = deepcopy(value, memo) File "/usr/lib64/python3.8/copy.py", line 161, in deepcopy rv = reductor(4) File "stringsource", line 2, in pynestkernel.SLIDatum.__reduce_cython__ TypeError: no default __reduce__ due to non-trivial __cinit__

2 2

Free NESTML and NEST Desktop Workshop (27.03.2023)
by Jens Bruchertseifer 27 Feb '23

27 Feb '23

Hello everyone, we are pleased to announce that NESTML and NEST Desktop will be represented at the satellite training sessions (https://flagship.kip.uni-heidelberg.de/jss/HBPm?mI=252&m=showAgenda&showAbs…) as part of the HBP Summit 2023 in Marseille! These sessions will take place on *27 March 2023*. Participation is free of charge, but a registration is mandatory. Please note that only a limited number of participants can register - at the moment there are still places available! The registration page is https://flagship.kip.uni-heidelberg.de/jss/HBPm?meetingID=252. You might need to create a free EBRAINS account for that, if you do not have one yet. The abstract of the workshop can be found below, as well as on the conference page. We also have a dedicated page for this tutorial with detailed information on the topics covered (https://clinssen.github.io/HBP-summit-2023-workshop/). Catering will be provided on site. We are looking forward to meeting you at the workshop! On behalf of the tutorial organizers, Jens Bruchertseifer PS: Please have also a look at the other exciting topics at the training session! ;) ----- License to Spike - A NEST Desktop and NESTML Workshop NEST is an established, open-source simulator for spiking neuronal networks, which can capture a high degree of detail of biological network structures while retaining high performance and scalability from laptops to HPC [1]. This tutorial provides hands-on experience in building and simulating neuron, synapse, and network models. It introduces several tools and front-ends to implement modeling ideas most efficiently. Participants do not have to install software as all tools can be accessed via the cloud. First, we look at NEST Desktop [2], a web-based graphical user interface (GUI), which allows the exploration of essential concepts in computational neuroscience without the need to learn a programming language. This advances both the quality and speed of teaching in computational neuroscience. To get acquainted with the GUI, we will create and analyze a balanced two-population network. In the second half of the session, we will create a new, custom neuron model that extends the capabilities of NEST Simulator by introducing new mechanisms, such as an active spiking dendritic compartment. NESTML [3] makes it quick and easy it is to implement and simulate model variants. A neuronal plasticity rule is then introduced, which allows a network to be trained by means of reinforcement learning. This is accomplished by combinating a typical spike-timing dependent plasticity learning rule with a global neuromodulatory dopamine signal. We will use the new learning rule to train a stimulus preference in the balanced network. Citations [1] https://nest-simulator.readthedocs.org/ [2] https://nest-desktop.readthedocs.org/ [3] https://nestml.readthedocs.org/

1 0

NEST Conference 2023 – Save the date & registration
by Hans Ekkehard Plesser 27 Feb '23

27 Feb '23

Dear Colleagues, The NEST Initiative is excited to invite everyone interested in Neural Simulation Technology and the NEST Simulator to the NEST Conference 2023. The NEST Conference provides an opportunity for the NEST Community to meet, exchange success stories, swap advice, learn about current developments in and around NEST spiking network simulation and its application. We particularly encourage young scientists to participate in the conference! This year's conference will take place as a virtual event on 15-16 June 2023. Register now! For more information please visit the conference website https://nest-simulator.org/conference We are looking forward to seeing you all in June! Hans Ekkehard Plesser and colleagues [Image] -- 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<mailto:hans.ekkehard.plesser@nmbu.no> Home http://arken.nmbu.no/~plesser

1 0

Open NEST Developer Video Conference Monday Feb 27 2023 11:30 CET (UTC+1)
by Dennis Terhorst 27 Feb '23

27 Feb '23

Dear NEST Users & Developers! I would like to invite you to our next fortnightly Open NEST Developer Video Conference, today Monday February 27, 11.30-12.30 CET (UTC+1). * Special topic for the in-depth today will be the introduction to "NEAT" a Neural Analysis Toolkit by @WillemWybo. * Additionally, @heplesser will shed more light on performance optimizations described in #2617: Integrating "deliver events first". Feel free to join the meeting also if it's just to bring your own quick 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/2023-02-27-Open-NEST-Developer-… Looking forward to seeing you! 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

1 0

RunManager and STDP connections
by Xavier Otazu 27 Feb '23

27 Feb '23

Hello, In my model I am using STDP synapse connections. When running simulations with nest.Simulate(), everything seems to work fine. When using nest.Run() inside a "with RunManager():" execution is *MUCH* faster, but STDP connections are not updated. Is it a correct behaviour? Thanks a lot in advance, Xavier

3 5

how to record local field potential from the network
by 王梓瑞 21 Feb '23

21 Feb '23

Dear nest community, Is there anyone know how to record local field potential from the network since I only found spike/weight recorder in NEST. Thank you. Best, Zirui

3 2

Collect the calcium concentration of the neuron without structural plasticity
by Maryada Maryada 18 Feb '23

18 Feb '23

Dear NEST Users, I would like to "record" or read calcium concentration of the neurons (let's say aeif_cond_exp). For now Ca variable is 0 before and after I simulate, however the neuron spikes. Is there any neuron model that supports this, or do I need to edit the nestml of the desired model to achieve this. If so, a sample code snippet would be helpful. -- Thanks and Regards *Maryada*

2 2

Open NEST Developer Video Conference Monday Feb 13 2023 11:30 CET (UTC+1)
by Dennis Terhorst 13 Feb '23

13 Feb '23

Dear NEST Users & Developers! I would like to invite you to our next fortnightly Open NEST Developer Video Conference, today Monday February 13, 11.30-12.30 CET (UTC+1). Feel free to join the meeting also if it's just to bring your own quick 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/2023-02-13-Open-NEST-Developer-… Looking forward to seeing you! 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

1 0

Fastest way to transfer dense connectivity data in a parallel simulation?
by Robin Gilbert De Schepper 01 Feb '23

01 Feb '23

Hi all! In the world of biophysical detail, it's commonplace that the connectome is generated with algorithms that specify connections as dense tabular data, with each row specifying a synaptic location on a cell pair (SONATA for example). A) In NEST I can't really find the opportunity to fit this data into any of the connection rules: I want to specify pairwise connections from the multiset A to multiset B. - Is this possible with `pairwise bernoulli`, or do the inputs have to be strict sets? - The probability step is superfluous, can it be skipped? B) Then there's the fact that NEST parallelizes transparently, but since this data was generated in parallel by tiling the biological volume, I have neatly fragmented data already available on each node in the distributed cluster. It would be such a waste to communicate all the data to each node, for NEST to communicate and distribute them back another way. The data is too big to allgather and fit into memory of any single node. Not only is this a lot of overhead to implement, but NEST will throw away all but `1 / Nnodes` of the data on each node again, leaving me with a reshuffled version of my starting data. Is there a way to bypass the transparency and to imperatively declare the cells and connections on each machine? -- Robin De Schepper, MSc (they/them) Department of Brain and Behavioral Sciences Unit of Neurophysiology University of Pavia, Italy Via Forlanini 6, 27100 Pavia - Italy Tel: (+39) 038298-7607 http://www-5.unipv.it/dangelo/ Interested in large scale network modelling? Discover our framework <https://bsb.readthedocs.io/en/latest/>: <https://github.com/dbbs-lab/bsb>

3 7

Re: Update: Ablating and executing a small subset of the Allen V1 model (layer23) using cpp intermediate objects where possible.
by Nicolai Haug 31 Jan '23

31 Jan '23

Hi Russell, Being able to easily build and simulate SONATA networks with NEST is hopefully imminent. We currently have a pull request under review which will add native NEST support for networks described by the SONATA format, see https://github.com/nest/nest-simulator/pull/2595. With our implementation, 64 GB of memory is more than sufficient for building and simulating the entire point neuron version of the Allen V1 model. Regarding a downscaled version of the V1 model, this cannot be achieved solely through the JSON configuration file for this particular model. This is due to all layers (V1 nodes) and associated edges being contained in single HDF5 files. In order to use a downscaled V1 model in the context of the upcoming NEST functionality, you would actually need to construct a new set of SONATA files that contain just the nodes and associated edges you are interested in. That is, you have to parse each nodes and edges .h5 and .csv file, extract the relevant entries, create new files and store the relevant entries in correctly named datasets and in the correct order. Unfortunately, I do not know of any examples that can guide you in this endeavour. You could try to reach out to the SONATA developers here https://github.com/AllenInstitute/sonata. They might have some ideas or even readily available examples. Hope this helps! Best regards, Nicolai

1 0

Need help Compiling NEST to use inside Julia
by Russell Jarvis 31 Jan '23

31 Jan '23

Dear Nest mailing list. I am trying to compile NEST to use inside Julia. Surprisingly or unsuprisingly Julia has great tools to support building external modules in cpp and c source code. I am using the tool BinaryBuilder.jl On a linux system with julia installed\, if I type: julia <ENTER> using Pkg Pkg.add("BinaryBuilder.jl") using BinaryBuilder BinaryBuilder.run_wizard() By following the wizard options, I can download the source code https://github.com/nest/nest-simulator.git and build the source tree in an alpine linux sand box. The building of the source tree in Alpine linux is related to how Julia does cross platform builds, an Alpine micro linux build is included with the Julia binary. From there I can optionally include the Binary file: Libtool_jll.jl Then the binary builder drops me into Alpine Linux environment, in order to test out (monkey patch a workable build script). When I navigate to: /workspace/srcdir/nest-simulator-3.3 I can run: sandbox:${WORKSPACE}/srcdir/nest-simulator-3.3 # cmake -DCMAKE_INSTALL_PREFIX=$prefix -DCMAKE_TOOLCHAIN_FILE=${CMAKE_TARGET_TOOLCHAIN} -DCMAKE_BUILD_TYPE=Release -Dwith-python=OFF -Dwith-warning=ON -Dwith-ltdl=ON and then run I get this output: Re-run cmake no build system arguments -- Could NOT find Doxygen (missing: DOXYGEN_EXECUTABLE) -- Host triple: x86_64-pc-linux -- Target triple: x86_64-pc-linux -- Could NOT find Readline (missing: READLINE_LIBRARY NCURSES_LIBRARY READLINE_INCLUDE_DIR) -- Could NOT find GSL (missing: GSL_INCLUDE_DIR GSL_LIBRARY GSL_CBLAS_LIBRARY) (found version "") -- Check the abort exitcode. -- Check the abort exitcode. -- Check the segmentation fault exitcode. -- Check the segmentation fault exitcode. -- Check whether the compiler ignores cmath makros. -- Check whether the compiler ignores cmath makros. OFF -- Check whether the compiler does NOT include <*.h> headers ISO conformant. -- Check whether the compiler does NOT include <*.h> headers ISO conformant. OFF -- Check whether the compiler respects symbolic signal names in signal.h. -- Check whether the compiler respects symbolic signal names in signal.h. OFF -- Check static template member declaration. -- Check static template member declaration. OFF -- Check for STL vector capacity base unity. -- Check for STL vector capacity base unity. ON -- Check for STL vector capacity doubling strategy. -- Check for STL vector capacity doubling strategy. ON -- Check whether the compiler fails with ICE. -- Check whether the compiler fails with ICE. OFF -- Check if ::nan is available from cmath. -- Check if ::nan is available from cmath. ON -- Check if ::isnan is available from cmath. -- Check if ::isnan is available from cmath. ON -- Check if Random123 generators work. PLEASE_FILL_OUT-NOTFOUND -- Check if Random123 generators work. OFF -- NEST version: 3.3 -------------------------------------------------------------------------------- NEST Configuration Summary -------------------------------------------------------------------------------- Build type : Release Target System : Linux Cross Compiling : TRUE C compiler : GNU 4.8.5 (/opt/bin/x86_64-linux-gnu-libgfortran3-cxx03/x86_64-linux-gnu-gcc) C compiler flags : -O2 -Wall -fopenmp -O3 -DNDEBUG C++ compiler : GNU 4.8.5 (/opt/bin/x86_64-linux-gnu-libgfortran3-cxx03/x86_64-linux-gnu-g++) C++ compiler flags : -O2 -std=c++11 -Wall -fopenmp -O3 -DNDEBUG Build dynamic : ON Built-in modules : models User modules : None Python bindings : No Use threading : Yes (OpenMP: -fopenmp) Use GSL : No Use Readline : No Use libltdl : Yes (LTDL 2.4.6) Includes : /opt/x86_64-linux-gnu/x86_64-linux-gnu/sys-root/usr/local/include Libraries : /opt/x86_64-linux-gnu/x86_64-linux-gnu/sys-root/usr/local/lib/libltdl.so Use doxygen : No Use MPI : No Detailed timers : No Use MUSIC : No Use libneurosim : No Use Boost : Yes (Boost 1.79.0) Includes : /workspace/destdir/include Libraries : Use SIONlib : No -------------------------------------------------------------------------------- The NEST executable will be installed to: /workspace/destdir/bin/ NEST dynamic libraries and user modules will be installed to: /workspace/destdir/lib/nest/ Documentation and examples will be installed to: /workspace/destdir/share/doc/nest/ To set necessary environment variables, add the following line to your ~/.bashrc : source /workspace/destdir/bin/nest_vars.sh -------------------------------------------------------------------------------- ATTENTION! You are about to compile NEST without the GNU Scientific Library or your GSL is too old (before v1.11). This means that conductance-based neuron models and some random number generators will not be available. -------------------------------------------------------------------------------- You can now build and install NEST with make make install make installcheck If you experience problems with the installation or the use of NEST, please see https://www.nest-simulator.org/frequently_asked_questions or go to https://www.nest-simulator.org/community to find out how to join the user mailing list. -- Configuring done -- Generating done -- Build files have been written to: /workspace/srcdir/nest-simulator-3.3 sandbox:${WORKSPACE}/srcdir/nest-simulator-3.3 # sandbox:${WORKSPACE}/srcdir/nest-simulator-3.3/make: but when I try to run make I hit this error: [ 26%] Building CXX object nestkernel/CMakeFiles/nestkernel.dir/recording_backend_ascii.cpp.o cd /workspace/srcdir/nest-simulator-3.3/nestkernel && /opt/bin/x86_64-linux-gnu-libgfortran3-cxx03/x86_64-linux-gnu-g++ --sysroot=/opt/x86_64-linux-gnu/x86_64-linux-gnu/sys-root/ -Dnestkernel_EXPORTS -I/workspace/srcdir/nest-simulator-3.3/thirdparty -I/workspace/srcdir/nest-simulator-3.3/libnestutil -I/workspace/srcdir/nest-simulator-3.3/sli -I/workspace/srcdir/nest-simulator-3.3/nestkernel -I/workspace/srcdir/nest-simulator-3.3/nestkernel/spatial -O2 -std=c++11 -Wall -fopenmp -O3 -DNDEBUG -fPIC -fopenmp -MD -MT nestkernel/CMakeFiles/nestkernel.dir/recording_backend_ascii.cpp.o -MF CMakeFiles/nestkernel.dir/recording_backend_ascii.cpp.o.d -o CMakeFiles/nestkernel.dir/recording_backend_ascii.cpp.o -c /workspace/srcdir/nest-simulator-3.3/nestkernel/recording_backend_ascii.cpp In file included from /opt/x86_64-linux-gnu/x86_64-linux-gnu/include/c++/4.8.5/bits/stl_algobase.h:64:0, from /opt/x86_64-linux-gnu/x86_64-linux-gnu/include/c++/4.8.5/bits/char_traits.h:39, from /opt/x86_64-linux-gnu/x86_64-linux-gnu/include/c++/4.8.5/ios:40, from /opt/x86_64-linux-gnu/x86_64-linux-gnu/include/c++/4.8.5/istream:38, from /opt/x86_64-linux-gnu/x86_64-linux-gnu/include/c++/4.8.5/sstream:38, from /workspace/srcdir/nest-simulator-3.3/thirdparty/compose.hpp:36, from /workspace/srcdir/nest-simulator-3.3/nestkernel/recording_backend_ascii.cpp:24: /opt/x86_64-linux-gnu/x86_64-linux-gnu/include/c++/4.8.5/bits/stl_pair.h: In instantiation of ‘constexpr std::pair<_T1, _T2>::pair(const _T1&, const _T2&) [with _T1 = long unsigned int; _T2 = nest::RecordingBackendASCII::DeviceData]’: /opt/x86_64-linux-gnu/x86_64-linux-gnu/include/c++/4.8.5/bits/stl_pair.h:281:72: required from ‘constexpr std::pair<typename std::__decay_and_strip<_Tp>::__type, typename std::__decay_and_strip<_T2>::__type> std::make_pair(_T1&&, _T2&&) [with _T1 = const long unsigned int&; _T2 = nest::RecordingBackendASCII::DeviceData; typename std::__decay_and_strip<_T2>::__type = nest::RecordingBackendASCII::DeviceData; typename std::__decay_and_strip<_Tp>::__type = long unsigned int]’ /workspace/srcdir/nest-simulator-3.3/nestkernel/recording_backend_ascii.cpp:69:108: required from here /opt/x86_64-linux-gnu/x86_64-linux-gnu/include/c++/4.8.5/bits/stl_pair.h:113:31: error: use of deleted function ‘nest::RecordingBackendASCII::DeviceData::DeviceData(const nest::RecordingBackendASCII::DeviceData&)’ : first(__a), second(__b) { } ^ In file included from /workspace/srcdir/nest-simulator-3.3/nestkernel/recording_backend_ascii.cpp:33:0: /workspace/srcdir/nest-simulator-3.3/nestkernel/recording_backend_ascii.h:195:10: note: ‘nest::RecordingBackendASCII::DeviceData::DeviceData(const nest::RecordingBackendASCII::DeviceData&)’ is implicitly deleted because the default definition would be ill-formed: struct DeviceData ^ /workspace/srcdir/nest-simulator-3.3/nestkernel/recording_backend_ascii.h:195:10: error: use of deleted function ‘std::basic_ofstream<char>::basic_ofstream(const std::basic_ofstream<char>&)’ In file included from /workspace/srcdir/nest-simulator-3.3/nestkernel/recording_device.h:27:0, from /workspace/srcdir/nest-simulator-3.3/nestkernel/recording_backend_ascii.cpp:27: /opt/x86_64-linux-gnu/x86_64-linux-gnu/include/c++/4.8.5/fstream:599:11: note: ‘std::basic_ofstream<char>::basic_ofstream(const std::basic_ofstream<char>&)’ is implicitly deleted because the default definition would be ill-formed: class basic_ofstream : public basic_ostream<_CharT,_Traits> ^ /opt/x86_64-linux-gnu/x86_64-linux-gnu/include/c++/4.8.5/fstream:599:11: error: use of deleted function ‘std::basic_ostream<char>::basic_ostream(const std::basic_ostream<char>&)’ In file included from /opt/x86_64-linux-gnu/x86_64-linux-gnu/include/c++/4.8.5/istream:39:0, from /opt/x86_64-linux-gnu/x86_64-linux-gnu/include/c++/4.8.5/sstream:38, from /workspace/srcdir/nest-simulator-3.3/thirdparty/compose.hpp:36, from /workspace/srcdir/nest-simulator-3.3/nestkernel/recording_backend_ascii.cpp:24: /opt/x86_64-linux-gnu/x86_64-linux-gnu/include/c++/4.8.5/ostream:58:11: note: ‘std::basic_ostream<char>::basic_ostream(const std::basic_ostream<char>&)’ is implicitly deleted because the default definition would be ill-formed: class basic_ostream : virtual public basic_ios<_CharT, _Traits> ^ /opt/x86_64-linux-gnu/x86_64-linux-gnu/include/c++/4.8.5/ostream:58:11: error: use of deleted function ‘std::basic_ios<char>::basic_ios(const std::basic_ios<char>&)’ In file included from /opt/x86_64-linux-gnu/x86_64-linux-gnu/include/c++/4.8.5/ios:44:0, from /opt/x86_64-linux-gnu/x86_64-linux-gnu/include/c++/4.8.5/istream:38, from /opt/x86_64-linux-gnu/x86_64-linux-gnu/include/c++/4.8.5/sstream:38, from /workspace/srcdir/nest-simulator-3.3/thirdparty/compose.hpp:36, from /workspace/srcdir/nest-simulator-3.3/nestkernel/recording_backend_ascii.cpp:24: /opt/x86_64-linux-gnu/x86_64-linux-gnu/include/c++/4.8.5/bits/basic_ios.h:66:11: note: ‘std::basic_ios<char>::basic_ios(const std::basic_ios<char>&)’ is implicitly deleted because the default definition would be ill-formed: class basic_ios : public ios_base ^ In file included from /opt/x86_64-linux-gnu/x86_64-linux-gnu/include/c++/4.8.5/ios:42:0, from /opt/x86_64-linux-gnu/x86_64-linux-gnu/include/c++/4.8.5/istream:38, from /opt/x86_64-linux-gnu/x86_64-linux-gnu/include/c++/4.8.5/sstream:38, from /workspace/srcdir/nest-simulator-3.3/thirdparty/compose.hpp:36, from /workspace/srcdir/nest-simulator-3.3/nestkernel/recording_backend_ascii.cpp:24: /opt/x86_64-linux-gnu/x86_64-linux-gnu/include/c++/4.8.5/bits/ios_base.h:786:5: error: ‘std::ios_base::ios_base(const std::ios_base&)’ is private ios_base(const ios_base&); ^ In file included from /opt/x86_64-linux-gnu/x86_64-linux-gnu/include/c++/4.8.5/ios:44:0, from /opt/x86_64-linux-gnu/x86_64-linux-gnu/include/c++/4.8.5/istream:38, from /opt/x86_64-linux-gnu/x86_64-linux-gnu/include/c++/4.8.5/sstream:38, from /workspace/srcdir/nest-simulator-3.3/thirdparty/compose.hpp:36, from /workspace/srcdir/nest-simulator-3.3/nestkernel/recording_backend_ascii.cpp:24: /opt/x86_64-linux-gnu/x86_64-linux-gnu/include/c++/4.8.5/bits/basic_ios.h:66:11: error: within this context class basic_ios : public ios_base ^ In file included from /workspace/srcdir/nest-simulator-3.3/nestkernel/recording_device.h:27:0, from /workspace/srcdir/nest-simulator-3.3/nestkernel/recording_backend_ascii.cpp:27: /opt/x86_64-linux-gnu/x86_64-linux-gnu/include/c++/4.8.5/fstream:599:11: error: use of deleted function ‘std::basic_ios<char>::basic_ios(const std::basic_ios<char>&)’ class basic_ofstream : public basic_ostream<_CharT,_Traits> ^ /opt/x86_64-linux-gnu/x86_64-linux-gnu/include/c++/4.8.5/fstream:599:11: error: use of deleted function ‘std::basic_filebuf<char>::basic_filebuf(const std::basic_filebuf<char>&)’ /opt/x86_64-linux-gnu/x86_64-linux-gnu/include/c++/4.8.5/fstream:72:11: note: ‘std::basic_filebuf<char>::basic_filebuf(const std::basic_filebuf<char>&)’ is implicitly deleted because the default definition would be ill-formed: class basic_filebuf : public basic_streambuf<_CharT, _Traits> ^ In file included from /opt/x86_64-linux-gnu/x86_64-linux-gnu/include/c++/4.8.5/ios:43:0, from /opt/x86_64-linux-gnu/x86_64-linux-gnu/include/c++/4.8.5/istream:38, from /opt/x86_64-linux-gnu/x86_64-linux-gnu/include/c++/4.8.5/sstream:38, from /workspace/srcdir/nest-simulator-3.3/thirdparty/compose.hpp:36, from /workspace/srcdir/nest-simulator-3.3/nestkernel/recording_backend_ascii.cpp:24: /opt/x86_64-linux-gnu/x86_64-linux-gnu/include/c++/4.8.5/streambuf:802:7: error: ‘std::basic_streambuf<_CharT, _Traits>::basic_streambuf(const std::basic_streambuf<_CharT, _Traits>&) [with _CharT = char; _Traits = std::char_traits<char>]’ is private basic_streambuf(const basic_streambuf& __sb) ^ In file included from /workspace/srcdir/nest-simulator-3.3/nestkernel/recording_device.h:27:0, from /workspace/srcdir/nest-simulator-3.3/nestkernel/recording_backend_ascii.cpp:27: /opt/x86_64-linux-gnu/x86_64-linux-gnu/include/c++/4.8.5/fstream:72:11: error: within this context class basic_filebuf : public basic_streambuf<_CharT, _Traits> ^ In file included from /opt/x86_64-linux-gnu/x86_64-linux-gnu/include/c++/4.8.5/bits/stl_algobase.h:64:0, from /opt/x86_64-linux-gnu/x86_64-linux-gnu/include/c++/4.8.5/bits/char_traits.h:39, from /opt/x86_64-linux-gnu/x86_64-linux-gnu/include/c++/4.8.5/ios:40, from /opt/x86_64-linux-gnu/x86_64-linux-gnu/include/c++/4.8.5/istream:38, from /opt/x86_64-linux-gnu/x86_64-linux-gnu/include/c++/4.8.5/sstream:38, from /workspace/srcdir/nest-simulator-3.3/thirdparty/compose.hpp:36, from /workspace/srcdir/nest-simulator-3.3/nestkernel/recording_backend_ascii.cpp:24: /opt/x86_64-linux-gnu/x86_64-linux-gnu/include/c++/4.8.5/bits/stl_pair.h: In instantiation of ‘constexpr std::pair<typename std::__decay_and_strip<_Tp>::__type, typename std::__decay_and_strip<_T2>::__type> std::make_pair(_T1&&, _T2&&) [with _T1 = const long unsigned int&; _T2 = nest::RecordingBackendASCII::DeviceData; typename std::__decay_and_strip<_T2>::__type = nest::RecordingBackendASCII::DeviceData; typename std::__decay_and_strip<_Tp>::__type = long unsigned int]’: /workspace/srcdir/nest-simulator-3.3/nestkernel/recording_backend_ascii.cpp:69:108: required from here /opt/x86_64-linux-gnu/x86_64-linux-gnu/include/c++/4.8.5/bits/stl_pair.h:281:72: error: use of deleted function ‘constexpr std::pair<_T1, _T2>::pair(std::pair<_T1, _T2>&&) [with _T1 = long unsigned int; _T2 = nest::RecordingBackendASCII::DeviceData]’ return __pair_type(std::forward<_T1>(__x), std::forward<_T2>(__y)); ^ /opt/x86_64-linux-gnu/x86_64-linux-gnu/include/c++/4.8.5/bits/stl_pair.h:128:17: note: ‘constexpr std::pair<_T1, _T2>::pair(std::pair<_T1, _T2>&&) [with _T1 = long unsigned int; _T2 = nest::RecordingBackendASCII::DeviceData]’ is implicitly deleted because the default definition would be ill-formed: constexpr pair(pair&&) = default; ^ /opt/x86_64-linux-gnu/x86_64-linux-gnu/include/c++/4.8.5/bits/stl_pair.h:128:17: error: use of deleted function ‘nest::RecordingBackendASCII::DeviceData::DeviceData(nest::RecordingBackendASCII::DeviceData&&)’ In file included from /workspace/srcdir/nest-simulator-3.3/nestkernel/recording_backend_ascii.cpp:33:0: /workspace/srcdir/nest-simulator-3.3/nestkernel/recording_backend_ascii.h:195:10: note: ‘nest::RecordingBackendASCII::DeviceData::DeviceData(nest::RecordingBackendASCII::DeviceData&&)’ is implicitly deleted because the default definition would be ill-formed: struct DeviceData ^ /workspace/srcdir/nest-simulator-3.3/nestkernel/recording_backend_ascii.h:195:10: error: use of deleted function ‘std::basic_ofstream<char>::basic_ofstream(const std::basic_ofstream<char>&)’ /workspace/srcdir/nest-simulator-3.3/nestkernel/recording_backend_ascii.cpp: In member function ‘virtual void nest::RecordingBackendASCII::enroll(const nest::RecordingDevice&, const DictionaryDatum&)’: /workspace/srcdir/nest-simulator-3.3/nestkernel/recording_backend_ascii.cpp:69:110: error: no matching function for call to ‘std::map<long unsigned int, nest::RecordingBackendASCII::DeviceData>::insert(std::pair<long unsigned int, nest::RecordingBackendASCII::DeviceData>)’ auto p = device_data_[ t ].insert( std::make_pair( node_id, DeviceData( modelname, vp_node_id_string ) ) ); ^ /workspace/srcdir/nest-simulator-3.3/nestkernel/recording_backend_ascii.cpp:69:110: note: candidates are: In file included from /opt/x86_64-linux-gnu/x86_64-linux-gnu/include/c++/4.8.5/map:61:0, from /workspace/srcdir/nest-simulator-3.3/thirdparty/compose.hpp:39, from /workspace/srcdir/nest-simulator-3.3/nestkernel/recording_backend_ascii.cpp:24: /opt/x86_64-linux-gnu/x86_64-linux-gnu/include/c++/4.8.5/bits/stl_map.h:594:7: note: std::pair<typename std::_Rb_tree<_Key, std::pair<const _Key, _Tp>, std::_Select1st<std::pair<const _Key, _Tp> >, _Compare, typename _Alloc::rebind<std::pair<const _Key, _Tp> >::other>::iterator, bool> std::map<_Key, _Tp, _Compare, _Alloc>::insert(const value_type&) [with _Key = long unsigned int; _Tp = nest::RecordingBackendASCII::DeviceData; _Compare = std::less<long unsigned int>; _Alloc = std::allocator<std::pair<const long unsigned int, nest::RecordingBackendASCII::DeviceData> >; typename std::_Rb_tree<_Key, std::pair<const _Key, _Tp>, std::_Select1st<std::pair<const _Key, _Tp> >, _Compare, typename _Alloc::rebind<std::pair<const _Key, _Tp> >::other>::iterator = std::_Rb_tree_iterator<std::pair<const long unsigned int, nest::RecordingBackendASCII::DeviceData> >; std::map<_Key, _Tp, _Compare, _Alloc>::value_type = std::pair<const long unsigned int, nest::RecordingBackendASCII::DeviceData>] insert(const value_type& __x) ^ /opt/x86_64-linux-gnu/x86_64-linux-gnu/include/c++/4.8.5/bits/stl_map.h:594:7: note: no known conversion for argument 1 from ‘std::pair<long unsigned int, nest::RecordingBackendASCII::DeviceData>’ to ‘const value_type& {aka const std::pair<const long unsigned int, nest::RecordingBackendASCII::DeviceData>&}’ /opt/x86_64-linux-gnu/x86_64-linux-gnu/include/c++/4.8.5/bits/stl_map.h:602:9: note: template<class _Pair, class> std::pair<typename std::_Rb_tree<_Key, std::pair<const _Key, _Tp>, std::_Select1st<std::pair<const _Key, _Tp> >, _Compare, typename _Alloc::rebind<std::pair<const _Key, _Tp> >::other>::iterator, bool> std::map<_Key, _Tp, _Compare, _Alloc>::insert(_Pair&&) [with _Pair = _Pair; <template-parameter-2-2> = <template-parameter-1-2>; _Key = long unsigned int; _Tp = nest::RecordingBackendASCII::DeviceData; _Compare = std::less<long unsigned int>; _Alloc = std::allocator<std::pair<const long unsigned int, nest::RecordingBackendASCII::DeviceData> >] insert(_Pair&& __x) ^ /opt/x86_64-linux-gnu/x86_64-linux-gnu/include/c++/4.8.5/bits/stl_map.h:602:9: note: template argument deduction/substitution failed: /opt/x86_64-linux-gnu/x86_64-linux-gnu/include/c++/4.8.5/bits/stl_map.h:598:32: error: no type named ‘type’ in ‘struct std::enable_if<false, void>’ template<typename _Pair, typename = typename ^ /opt/x86_64-linux-gnu/x86_64-linux-gnu/include/c++/4.8.5/bits/stl_map.h:615:7: note: void std::map<_Key, _Tp, _Compare, _Alloc>::insert(std::initializer_list<std::pair<const _Key, _Tp> >) [with _Key = long unsigned int; _Tp = nest::RecordingBackendASCII::DeviceData; _Compare = std::less<long unsigned int>; _Alloc = std::allocator<std::pair<const long unsigned int, nest::RecordingBackendASCII::DeviceData> >] insert(std::initializer_list<value_type> __list) ^ /opt/x86_64-linux-gnu/x86_64-linux-gnu/include/c++/4.8.5/bits/stl_map.h:615:7: note: no known conversion for argument 1 from ‘std::pair<long unsigned int, nest::RecordingBackendASCII::DeviceData>’ to ‘std::initializer_list<std::pair<const long unsigned int, nest::RecordingBackendASCII::DeviceData> >’ /opt/x86_64-linux-gnu/x86_64-linux-gnu/include/c++/4.8.5/bits/stl_map.h:644:7: note: std::map<_Key, _Tp, _Compare, _Alloc>::iterator std::map<_Key, _Tp, _Compare, _Alloc>::insert(std::map<_Key, _Tp, _Compare, _Alloc>::const_iterator, const value_type&) [with _Key = long unsigned int; _Tp = nest::RecordingBackendASCII::DeviceData; _Compare = std::less<long unsigned int>; _Alloc = std::allocator<std::pair<const long unsigned int, nest::RecordingBackendASCII::DeviceData> >; std::map<_Key, _Tp, _Compare, _Alloc>::iterator = std::_Rb_tree_iterator<std::pair<const long unsigned int, nest::RecordingBackendASCII::DeviceData> >; std::map<_Key, _Tp, _Compare, _Alloc>::const_iterator = std::_Rb_tree_const_iterator<std::pair<const long unsigned int, nest::RecordingBackendASCII::DeviceData> >; std::map<_Key, _Tp, _Compare, _Alloc>::value_type = std::pair<const long unsigned int, nest::RecordingBackendASCII::DeviceData>] insert(const_iterator __position, const value_type& __x) ^ /opt/x86_64-linux-gnu/x86_64-linux-gnu/include/c++/4.8.5/bits/stl_map.h:644:7: note: candidate expects 2 arguments, 1 provided /opt/x86_64-linux-gnu/x86_64-linux-gnu/include/c++/4.8.5/bits/stl_map.h:655:9: note: template<class _Pair, class> std::map<_Key, _Tp, _Compare, _Alloc>::iterator std::map<_Key, _Tp, _Compare, _Alloc>::insert(std::map<_Key, _Tp, _Compare, _Alloc>::const_iterator, _Pair&&) [with _Pair = _Pair; <template-parameter-2-2> = <template-parameter-1-2>; _Key = long unsigned int; _Tp = nest::RecordingBackendASCII::DeviceData; _Compare = std::less<long unsigned int>; _Alloc = std::allocator<std::pair<const long unsigned int, nest::RecordingBackendASCII::DeviceData> >] insert(const_iterator __position, _Pair&& __x) ^ /opt/x86_64-linux-gnu/x86_64-linux-gnu/include/c++/4.8.5/bits/stl_map.h:655:9: note: template argument deduction/substitution failed: /workspace/srcdir/nest-simulator-3.3/nestkernel/recording_backend_ascii.cpp:69:110: note: cannot convert ‘std::make_pair(_T1&&, _T2&&) [with _T1 = const long unsigned int&; _T2 = nest::RecordingBackendASCII::DeviceData; typename std::__decay_and_strip<_T2>::__type = nest::RecordingBackendASCII::DeviceData; typename std::__decay_and_strip<_Tp>::__type = long unsigned int]((* & nest::RecordingBackendASCII::DeviceData(std::basic_string<char>((*(const std::basic_string<char>*)(& modelname))), std::basic_string<char>((*(const std::basic_string<char>*)(& vp_node_id_string))))))’ (type ‘std::pair<long unsigned int, nest::RecordingBackendASCII::DeviceData>’) to type ‘std::map<long unsigned int, nest::RecordingBackendASCII::DeviceData>::const_iterator {aka std::_Rb_tree_const_iterator<std::pair<const long unsigned int, nest::RecordingBackendASCII::DeviceData> >}’ auto p = device_data_[ t ].insert( std::make_pair( node_id, DeviceData( modelname, vp_node_id_string ) ) ); ^ In file included from /opt/x86_64-linux-gnu/x86_64-linux-gnu/include/c++/4.8.5/map:61:0, from /workspace/srcdir/nest-simulator-3.3/thirdparty/compose.hpp:39, from /workspace/srcdir/nest-simulator-3.3/nestkernel/recording_backend_ascii.cpp:24: /opt/x86_64-linux-gnu/x86_64-linux-gnu/include/c++/4.8.5/bits/stl_map.h:670:9: note: template<class _InputIterator> void std::map<_Key, _Tp, _Compare, _Alloc>::insert(_InputIterator, _InputIterator) [with _InputIterator = _InputIterator; _Key = long unsigned int; _Tp = nest::RecordingBackendASCII::DeviceData; _Compare = std::less<long unsigned int>; _Alloc = std::allocator<std::pair<const long unsigned int, nest::RecordingBackendASCII::DeviceData> >] insert(_InputIterator __first, _InputIterator __last) ^ /opt/x86_64-linux-gnu/x86_64-linux-gnu/include/c++/4.8.5/bits/stl_map.h:670:9: note: template argument deduction/substitution failed: /workspace/srcdir/nest-simulator-3.3/nestkernel/recording_backend_ascii.cpp:69:110: note: candidate expects 2 arguments, 1 provided auto p = device_data_[ t ].insert( std::make_pair( node_id, DeviceData( modelname, vp_node_id_string ) ) ); ^ /workspace/srcdir/nest-simulator-3.3/nestkernel/recording_backend_ascii.cpp: In member function ‘void nest::RecordingBackendASCII::DeviceData::open_file()’: /workspace/srcdir/nest-simulator-3.3/nestkernel/recording_backend_ascii.cpp:266:9: error: use of deleted function ‘std::basic_ofstream<char>& std::basic_ofstream<char>::operator=(const std::basic_ofstream<char>&)’ file_ = std::ofstream( filename.c_str() ); ^ In file included from /workspace/srcdir/nest-simulator-3.3/nestkernel/recording_device.h:27:0, from /workspace/srcdir/nest-simulator-3.3/nestkernel/recording_backend_ascii.cpp:27: /opt/x86_64-linux-gnu/x86_64-linux-gnu/include/c++/4.8.5/fstream:599:11: note: ‘std::basic_ofstream<char>& std::basic_ofstream<char>::operator=(const std::basic_ofstream<char>&)’ is implicitly deleted because the default definition would be ill-formed: class basic_ofstream : public basic_ostream<_CharT,_Traits> ^ /opt/x86_64-linux-gnu/x86_64-linux-gnu/include/c++/4.8.5/fstream:599:11: error: use of deleted function ‘std::basic_ostream<char>& std::basic_ostream<char>::operator=(const std::basic_ostream<char>&)’ In file included from /opt/x86_64-linux-gnu/x86_64-linux-gnu/include/c++/4.8.5/istream:39:0, from /opt/x86_64-linux-gnu/x86_64-linux-gnu/include/c++/4.8.5/sstream:38, from /workspace/srcdir/nest-simulator-3.3/thirdparty/compose.hpp:36, from /workspace/srcdir/nest-simulator-3.3/nestkernel/recording_backend_ascii.cpp:24: /opt/x86_64-linux-gnu/x86_64-linux-gnu/include/c++/4.8.5/ostream:58:11: note: ‘std::basic_ostream<char>& std::basic_ostream<char>::operator=(const std::basic_ostream<char>&)’ is implicitly deleted because the default definition would be ill-formed: class basic_ostream : virtual public basic_ios<_CharT, _Traits> ^ /opt/x86_64-linux-gnu/x86_64-linux-gnu/include/c++/4.8.5/ostream:58:11: error: use of deleted function ‘std::basic_ios<char>& std::basic_ios<char>::operator=(const std::basic_ios<char>&)’ In file included from /opt/x86_64-linux-gnu/x86_64-linux-gnu/include/c++/4.8.5/ios:44:0, from /opt/x86_64-linux-gnu/x86_64-linux-gnu/include/c++/4.8.5/istream:38, from /opt/x86_64-linux-gnu/x86_64-linux-gnu/include/c++/4.8.5/sstream:38, from /workspace/srcdir/nest-simulator-3.3/thirdparty/compose.hpp:36, from /workspace/srcdir/nest-simulator-3.3/nestkernel/recording_backend_ascii.cpp:24: /opt/x86_64-linux-gnu/x86_64-linux-gnu/include/c++/4.8.5/bits/basic_ios.h:66:11: note: ‘std::basic_ios<char>& std::basic_ios<char>::operator=(const std::basic_ios<char>&)’ is implicitly deleted because the default definition would be ill-formed: class basic_ios : public ios_base ^ In file included from /opt/x86_64-linux-gnu/x86_64-linux-gnu/include/c++/4.8.5/ios:42:0, from /opt/x86_64-linux-gnu/x86_64-linux-gnu/include/c++/4.8.5/istream:38, from /opt/x86_64-linux-gnu/x86_64-linux-gnu/include/c++/4.8.5/sstream:38, from /workspace/srcdir/nest-simulator-3.3/thirdparty/compose.hpp:36, from /workspace/srcdir/nest-simulator-3.3/nestkernel/recording_backend_ascii.cpp:24: /opt/x86_64-linux-gnu/x86_64-linux-gnu/include/c++/4.8.5/bits/ios_base.h:789:5: error: ‘std::ios_base& std::ios_base::operator=(const std::ios_base&)’ is private operator=(const ios_base&); ^ In file included from /opt/x86_64-linux-gnu/x86_64-linux-gnu/include/c++/4.8.5/ios:44:0, from /opt/x86_64-linux-gnu/x86_64-linux-gnu/include/c++/4.8.5/istream:38, from /opt/x86_64-linux-gnu/x86_64-linux-gnu/include/c++/4.8.5/sstream:38, from /workspace/srcdir/nest-simulator-3.3/thirdparty/compose.hpp:36, from /workspace/srcdir/nest-simulator-3.3/nestkernel/recording_backend_ascii.cpp:24: /opt/x86_64-linux-gnu/x86_64-linux-gnu/include/c++/4.8.5/bits/basic_ios.h:66:11: error: within this context class basic_ios : public ios_base ^ In file included from /workspace/srcdir/nest-simulator-3.3/nestkernel/recording_device.h:27:0, from /workspace/srcdir/nest-simulator-3.3/nestkernel/recording_backend_ascii.cpp:27: /opt/x86_64-linux-gnu/x86_64-linux-gnu/include/c++/4.8.5/fstream:599:11: error: use of deleted function ‘std::basic_filebuf<char>& std::basic_filebuf<char>::operator=(const std::basic_filebuf<char>&)’ class basic_ofstream : public basic_ostream<_CharT,_Traits> ^ /opt/x86_64-linux-gnu/x86_64-linux-gnu/include/c++/4.8.5/fstream:72:11: note: ‘std::basic_filebuf<char>& std::basic_filebuf<char>::operator=(const std::basic_filebuf<char>&)’ is implicitly deleted because the default definition would be ill-formed: class basic_filebuf : public basic_streambuf<_CharT, _Traits> ^ In file included from /opt/x86_64-linux-gnu/x86_64-linux-gnu/include/c++/4.8.5/ios:43:0, from /opt/x86_64-linux-gnu/x86_64-linux-gnu/include/c++/4.8.5/istream:38, from /opt/x86_64-linux-gnu/x86_64-linux-gnu/include/c++/4.8.5/sstream:38, from /workspace/srcdir/nest-simulator-3.3/thirdparty/compose.hpp:36, from /workspace/srcdir/nest-simulator-3.3/nestkernel/recording_backend_ascii.cpp:24: /opt/x86_64-linux-gnu/x86_64-linux-gnu/include/c++/4.8.5/streambuf:810:7: error: ‘std::basic_streambuf<_CharT, _Traits>& std::basic_streambuf<_CharT, _Traits>::operator=(const std::basic_streambuf<_CharT, _Traits>&) [with _CharT = char; _Traits = std::char_traits<char>]’ is private operator=(const basic_streambuf&) { return *this; }; ^ In file included from /workspace/srcdir/nest-simulator-3.3/nestkernel/recording_device.h:27:0, from /workspace/srcdir/nest-simulator-3.3/nestkernel/recording_backend_ascii.cpp:27: /opt/x86_64-linux-gnu/x86_64-linux-gnu/include/c++/4.8.5/fstream:72:11: error: within this context class basic_filebuf : public basic_streambuf<_CharT, _Traits> ^ make[2]: *** [nestkernel/CMakeFiles/nestkernel.dir/build.make:818: nestkernel/CMakeFiles/nestkernel.dir/recording_backend_ascii.cpp.o] Error 1 make[2]: Leaving directory '/workspace/srcdir/nest-simulator-3.3' make[1]: *** [CMakeFiles/Makefile2:772: nestkernel/CMakeFiles/nestkernel.dir/all] Error 2 make[1]: Leaving directory '/workspace/srcdir/nest-simulator-3.3' make: *** [Makefile:146: all] Error 2 I wonder if the problem might be the GCC version? From this source it looks like 4.8.5 is the default GCC version https://github.com/JuliaPackaging/Yggdrasil/blob/master/RootFS.md#compiler-… GCC Binutils libgfortran SONAME libstdc++ SONAME string ABI 4.8.5 2.24 libgfortran.so.3 libstdc++.so.6.0.19 cxx03 5.2.0 2.25.1 libgfortran.so.3 libstdc++.so.6.0.21 cxx11 6.1.0* 2.26 libgfortran.so.3 libstdc++.so.6.0.22 cxx11 7.1.0 2.27 libgfortran.so.4 libstdc++.so.6.0.23 cxx11 8.1.0 2.31 libgfortran.so.5 libstdc++.so.6.0.25 cxx11 9.1.0 2.33.1 libgfortran.so.5 libstdc++.so.6.0.26 cxx11 10.2.0 2.34 libgfortran.so.5 libstdc++.so.6.0.28 cxx11 11.1.0 2.36 libgfortran.so.5 libstdc++.so.6.0.29 cxx11 Also I wonder if any one has any hints about what to try? I have noticed the Ubuntu Nest dependencies in the Dockerfile here: https://github.com/nest/nest-docker/blob/master/src/base/Dockerfile-build-b… Many of those dependencies have Alpine counter parts, but I'd rather not try to randomly install them. Russell.

3 5

Open NEST Developer Video Conference Monday Jan 30 2023 11:30 CET (UTC+1)
by Dennis Terhorst 30 Jan '23

30 Jan '23

Dear NEST Users & Developers! I would like to invite you to our next fortnightly Open NEST Developer Video Conference, today Monday January 30, 11.30-12.30 CET (UTC+1). Feel free to join the meeting also if it's just to bring your own quick 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/2023-01-30-Open-NEST-Developer-… Looking forward to seeing you! 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

1 0

current recording for gap junction
by Hanjia Jiang 30 Jan '23

30 Jan '23

Dear all, I would like to ask if there is a way to measure the actual current that is transmitted through the gap junction in NEST. With the example file gap_junctions_two_neuron.py, I tried to use weight_recorder for the gap junction, but only got a constant value of 0.5 (which is the "weight" set in this file). It seems the "weight" here is only the conductance in nS, after I quickly read the reference Hahne et al., 2015 <https://www.frontiersin.org/articles/10.3389/fninf.2015.00022/full>. Is there a way in PyNEST to record the gap junction current? Thank you for answering! p.s. This is because I am developing astrocyte network models with NEST, which uses a "sic_connection" (slow inward current connection) that is adapted from gap_junction. I am trying to record its current in PyNEST if possible. Unfortunately because the other collaborators developed the sic_connection back then a while ago, I myself do not have an answer to this. I will try other indirect methods, if there is no way to do such a recording in PyNEST. If you have any relevant suggestions, please also kindly let me know. Thanks again. Happy new year, Han-Jia

2 1

Subsetting and executing a small subset of the Allen V1 model (layer23) using cpp intermediate objects where possible.
by Russell Jarvis 28 Jan '23

28 Jan '23

Hi there, I would like to subset and execute the subset of the Allen V1 model. I am also hoping to store intermediate simulation configuration files not as Python code, but if possible as cpp code. I am wondering if there is a way of storing the matrices in a cpp native way? Forinstance I have noticed the class https://github.com/nest/nest-simulator/blob/master/nestkernel/connection_ma… I think that this would class may have I acquired the config.json file from DropBox and all of the assoicated hdf5, and csv files from here: https://www.dropbox.com/sh/w5u31m3hq6u2x5m/AAB0B6OLRyLJwxCKjuWrG26pa/simula… I have found the nodes in the model pertaining to only layer 23 by wrangling data frames in Julia (see the code below). Calling the method `extract_subset` is slower than I would like. I suspect it would be faster to use the SL or /nest_kernel more directly, but I don't know what interventions I would need to do to get the PyNest instance to dump its intermediate objects in a cpp native way. I wonder if any one has any hints on how to do this? subset0 = get_layer_sub_net("i23Htr3a") subset1 = get_layer_sub_net("i23Pvalb") subset2 = get_layer_sub_net("i23Sst") subset3 = get_layer_sub_net("e23Cux2") For instance I would like to be able to use the nestkernel CLI to save using Pkg using Conda using PyCall ENV["PYTHON"] = $HOME/.julia/conda/3/lib/python3.10/ Pkg.build("PyCall") py""" def init_sim_to_call_from_julia():#slice_start,slice_end,nest=None,sim=None) import os, sys import math import numpy as np from bmtk.simulator import pointnet from bmtk.simulator.pointnet.pyfunction_cache import synaptic_weight from bmtk.simulator.pointnet.io_tools import io import nest import h5py try: nest.Install('glifmodule') except Exception as e: pass @synaptic_weight def DirectionRule_others(edges, src_nodes, trg_nodes): src_tuning = src_nodes['tuning_angle'].values tar_tuning = trg_nodes['tuning_angle'].values sigma = edges['weight_sigma'].values nsyn = edges['nsyns'].values syn_weight = edges['syn_weight'].values delta_tuning_180 = np.abs(np.abs(np.mod(np.abs(tar_tuning - src_tuning), 360.0) - 180.0) - 180.0) w_multiplier_180 = np.exp(-(delta_tuning_180 / sigma) ** 2) return syn_weight * w_multiplier_180 * nsyn @synaptic_weight def DirectionRule_EE(edges, src_nodes, trg_nodes): src_tuning = src_nodes['tuning_angle'].values tar_tuning = trg_nodes['tuning_angle'].values x_tar = trg_nodes['x'].values x_src = src_nodes['x'].values z_tar = trg_nodes['z'].values z_src = src_nodes['z'].values sigma = edges['weight_sigma'].values nsyn = edges['nsyns'].values syn_weight = edges['syn_weight'].values delta_tuning_180 = np.abs(np.abs(np.mod(np.abs(tar_tuning - src_tuning), 360.0) - 180.0) - 180.0) w_multiplier_180 = np.exp(-(delta_tuning_180 / sigma) ** 2) delta_x = (x_tar - x_src) * 0.07 delta_z = (z_tar - z_src) * 0.04 theta_pref = tar_tuning * (np.pi / 180.) xz = delta_x * np.cos(theta_pref) + delta_z * np.sin(theta_pref) sigma_phase = 1.0 phase_scale_ratio = np.exp(- (xz ** 2 / (2 * sigma_phase ** 2))) # To account for the 0.07 vs 0.04 dimensions. This ensures the horizontal neurons are scaled by 5.5/4 (from the # midpoint of 4 & 7). Also, ensures the vertical is scaled by 5.5/7. This was a basic linear estimate to get the # numbers (y = ax + b). theta_tar_scale = abs(abs(abs(180.0 - np.mod(np.abs(tar_tuning), 360.0)) - 90.0) - 90.0) phase_scale_ratio = phase_scale_ratio * (5.5 / 4.0 - 11.0 / 1680.0 * theta_tar_scale) return syn_weight * w_multiplier_180 * phase_scale_ratio * nsyn def main(config_file): configure = pointnet.Config.from_json(config_file) configure.build_env() graph = pointnet.PointNetwork.from_config(configure) sim = pointnet.PointSimulator.from_config(configure, graph) node_info = list(graph.get_node_populations()) dfv1 = node_info[0].nodes_df() pop_names = { k:v for k,v in zip(dfv1.index,dfv1["pop_name"].values) } dfv1e = dfv1[dfv1["ei"] == "e"].index dfv1i = dfv1[dfv1["ei"] == "i"].index dfv1e_pop = dfv1[dfv1["ei"] == "e"]["pop_name"].values dfv1i_pop = dfv1[dfv1["ei"] == "i"]["pop_name"].values lgn = node_info[1].nodes_df() lgne = lgn[lgn["ei"] == "e"].index return nest,sim,node_info,dfv1e,dfv1i,lgne,dfv1e_pop,dfv1i_pop,pop_names #,lgni nest,sim,node_info,dfv1e,dfv1i,lgne,dfv1e_pop,dfv1i_pop,pop_names = main('config.json') # ,lgni return (nest,sim,node_info,dfv1e,dfv1i,lgne,dfv1e_pop,dfv1i_pop,pop_names) """ (nest,sim,node_info,dfv1e,dfv1i,lgne,dfv1e_pop,dfv1i_pop,pop_names) = py"init_sim_to_call_from_julia"() function get_layer_sub_net(target) subset = Int64[] for (k,v) in pairs(pop_names) if v==target println(k,v) append!(subset,k) end end subset end subset0 = get_layer_sub_net("i23Htr3a") subset1 = get_layer_sub_net("i23Pvalb") subset2 = get_layer_sub_net("i23Sst") subset3 = get_layer_sub_net("e23Cux2") layer_23_ids = [] layer_23_ids = vcat(layer_23_ids,subset0) layer_23_ids = vcat(layer_23_ids,subset1) layer_23_ids = vcat(layer_23_ids,subset2) layer_23_ids = vcat(layer_23_ids,subset3) py"""def get_conns_from_py_nest(nest,sim,slice_start,nodes=None): conns = nest.GetConnections(nest.NodeCollection([slice_start])) nodes = nest.NodeCollection([slice_start]) node_ = nodes.get() dict_ = conns.get() return (dict_["source"],dict_["target"],dict_["weight"]) """ function extract_subset(nest,sim,subset) N = 230924+1#+17400#230901 exc_matrix = spzeros(N,N) @inbounds for srcv in ProgressBars.ProgressBar(subset) result = py"get_conns_from_py_nest"(nest,sim,srcv) @inbounds for (x,y,z) in zip(Vector{Int64}(result[1]),Vector{Int64}(result[2]),Vector{Float64}(result[3])) exc_matrix[y,x] = z end end exc_matrix end exc_matrix = extract_subset(nest,sim,layer_23_ids) Thanks for your help :) Russell.

1 1

NEST 3.3 installation error
by Petia Koprinkova 16 Jan '23

16 Jan '23

Dear NEST Developers, We are trying to install NEST 3.3 on a Linux machine in Windows 11 desktop computer and the following error report was obtained: -- Docs:https://docs.pytest.org/en/stable/how-to/capture-warnings.html - generated xml file: /nest-3.3.0-build/reports/07_pynesttests.xml - =========================== short testsummary info ============================ FAILED share/nest/testsuite/pytests/test_NodeCollection.py::TestNodeCollection::test_array_indexing FAILEDshare/nest/testsuite/pytests/test_NodeCollection.py::TestNodeCollection::test_array_indexing_bools FAILEDshare/nest/testsuite/pytests/test_NodeCollection.py::TestNodeCollection::test_slice_with_unsorted_raisesFAILEDshare/nest/testsuite/pytests/test_connect_arrays.py::TestConnectArrays::test_connect_array_list FAILEDshare/nest/testsuite/pytests/test_connect_arrays.py::TestConnectArrays::test_connect_arrays_additional_synspec_params FAILEDshare/nest/testsuite/pytests/test_connect_arrays.py::TestConnectArrays::test_connect_arrays_different_weights_delays FAILEDshare/nest/testsuite/pytests/test_connect_arrays.py::TestConnectArrays::test_connect_arrays_differnt_alpha FAILEDshare/nest/testsuite/pytests/test_connect_arrays.py::TestConnectArrays::test_connect_arrays_float_rtype FAILEDshare/nest/testsuite/pytests/test_connect_arrays.py::TestConnectArrays::test_connect_arrays_no_delays FAILED share/nest/testsuite/pytests/test_connect_arrays.py::TestConnectArrays::test_connect_arrays_no_weights FAILEDshare/nest/testsuite/pytests/test_connect_arrays.py::TestConnectArrays::test_connect_arrays_nonunique FAILEDshare/nest/testsuite/pytests/test_connect_arrays.py::TestConnectArrays::test_connect_arrays_nonunique_dict_conn_spec FAILEDshare/nest/testsuite/pytests/test_connect_arrays.py::TestConnectArrays::test_connect_arrays_receptor_type FAILEDshare/nest/testsuite/pytests/test_connect_arrays.py::TestConnectArrays::test_connect_arrays_rtype FAILEDshare/nest/testsuite/pytests/test_connect_arrays.py::TestConnectArrays::test_connect_arrays_threaded =========== 15 failed, 669 passed, 15skipped, 27 warnings in 43.13s =========== make[3]: *** [CMakeFiles/installcheck.dir/build.make:71:CMakeFiles/installcheck] Error 1 make[2]: *** [CMakeFiles/Makefile2:465:CMakeFiles/installcheck.dir/all] Error 2 make[1]: *** [CMakeFiles/Makefile2:472:CMakeFiles/installcheck.dir/rule] Error 2 make: *** [Makefile:179: installcheck]Error 2 Could you please help to resolve it?Best regards,Petia Koprinkova-Hristova

2 3

Open NEST Developer Video Conference Monday Jan 16 2023 11:30 CET (UTC+1)
by Dennis Terhorst 16 Jan '23

16 Jan '23

Dear NEST Users & Developers! I would like to invite you to our next fortnightly Open NEST Developer Video Conference, today Monday January 16, 11.30-12.30 CET (UTC+1). Feel free to join the meeting also if it's just to bring your own quick 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/2023-01-16-Open-NEST-Developer-… Looking forward to seeing you! 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

1 0

Error installing extension module
by bstrohmer＠gmail.com 13 Jan '23

13 Jan '23

I would like to install a custom neuron model in NEST so I followed the instructions for the nest-extension-module. It is able to build the .so files but it errors during the final install of the project as seen in the below message. Install the project... -- Install configuration: "" -- Installing: /home/bs/git_repos/extension/nest-simulator/result/include/piftestmodule/pif_psc_alpha.h -- Installing: /home/bs/git_repos/extension/nest-simulator/result/lib/nest/piftestmodule.so -- Installing: /home/bs/git_repos/extension/nest-simulator/result/lib/nest/libpiftestmodule.so Traceback (most recent call last): File "<string>", line 1, in <module> File "/home/bs/git_repos/extension/nest-simulator/result/lib/python3.8/site-packages/nest/__init__.py", line 444 err = AttributeError(f"Cannot set attribute '{attr}' on module 'nest'") I am trying to install one of the example neurons provided first (pif_psc_alpha) so I do not expect that it is an issue within the source files. Thanks for any advice in correcting this issue!

4 6

stdp_dopamine_synapse model
by Behnam Ghazinouri 05 Jan '23

05 Jan '23

Hi all, Happy new year! I have a question about the "stdp_dopamine_synapse" model. In the documentation, they mentioned that they used it as a benchmark the model in [1], based on [2]. In [1], in the section "2.2 Benchmark Network Models", they have C_1 and C_2. They just mentioned these two parameters are constant coefficients. My question is: Does NEST implement these equations? If yes, how can I find the values of C_1 and C_2? (they are not listed under the nest.GetValues() and are not in the table of the documentation). If not, what is the exact model that the NEST implemented for "stdp_dopamine_synapse"? Best regards, Behnam [1] Potjans W, Morrison A, Diesmann M (2010). Enabling functional neural circuit simulations with distributed computing of neuromodulated plasticity. Frontiers in Computational Neuroscience, 4:141. DOI: https://doi.org/10.3389/fncom.2010.00141 <https://doi.org/10.3389/fncom.2010.00141> [2] Izhikevich EM (2007). Solving the distal reward problem through linkage of STDP and dopamine signaling. Cerebral Cortex, 17(10):2443-2452. DOI: https://doi.org/10.1093/cercor/bhl152 <https://doi.org/10.1093/cercor/bhl152>

2 1

Open NEST Developer Video Conference Monday Dec 19 2022 11:30 CET (UTC+1)
by Dennis Terhorst 19 Dec '22

19 Dec '22

Dear NEST Users & Developers! I would like to invite you to our next fortnightly Open NEST Developer Video Conference, today Monday December 19, 11.30-12.30 CET (UTC+1). 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/2022-12-19-Open-NEST-Developer-… As I will not be joining today, I delegated chairing the meeting. Looking forward to seeing you again next year! Merry Christmas and a happy new year! 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

1 0

how to customize Ion channels and receptor types of "cm_default" neuron model through nestml
by 王梓瑞 08 Dec '22

08 Dec '22

Dear nest community, I wonder if any of you know how to customize Ion channels and receptor types of "cm_default" neuron model through nestml. I noticed some information on Extending NESTML- Running NESTML with custom templates, but I still found myself confused due to my poor understanding. Is there any way to acquire the .nestml file of the cm_default neuron model? Thank you. Best, Zirui

2 1

Open NEST Developer Video Conference Monday Dec 5 2022 11:30 CET (UTC+1)
by Dennis Terhorst 05 Dec '22

05 Dec '22

Dear NEST Users & Developers! I would like to invite you to our next fortnightly Open NEST Developer Video Conference, today Monday December 5, 11.30-12.30 CET (UTC+1). Feel free to join the meeting also if it's just to bring your own questions for direct discussion in the in-depth section. Special topic for the in-depth discussion for today are / Hackathon Results / 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/2022-12-05-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

1 0

docker questions
by 1538356357＠qq.com 05 Dec '22

05 Dec '22

I use Docker to create a nest environment. The version is v2.16.0 But when I execute the code as follows，vt_dummy = nest.Create("global_volume_transmitter", 1, {'deliver_interval': 10})， , I encounter an error, the error is pynestkernel.NESTError: UnknownModelName in GetDefaults_l: /global_volume_transmitter is not a known model name. Please check the modeldict for a list of available models . but after I use the nest2.16 source code to install, the same code executes successfully. I don't know why

2 3

About Polling Algorithm
by 1538356357＠qq.com 22 Nov '22

22 Nov '22

Dear NEST community： We all know that distributed computing is carried out in Nest, and neurons are distributed to each neuron through polling. However, considering the load balancing and sparsity of communication, this is a NP hard problem. Should we adopt some other methods, such as directed graph segmentation technology. Whether this will be considered in Nest, or whether graph segmentation is helpful in SNN simulation. If you can spare time to reply, thank you very much

2 1

Open NEST Developer Video Conference Monday Nov 21 2022 11:30 CET (UTC+1)
by Dennis Terhorst 21 Nov '22

21 Nov '22

Dear NEST Users & Developers! I would like to invite you to our next fortnightly Open NEST Developer Video Conference, today Monday November 21, 11.30-12.30 CET (UTC+1). Feel free to join the meeting also if it's just to bring your own questions for direct discussion in the in-depth section. Special topic for the in-depth discussion for today are mechanisms around /Tsodyks-style synapses/ 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/2022-11-21-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

1 0

errors when using command"d1_pop.set({"V_m":nest.random.uniform(-80.0, -55.0)})"
by 王梓瑞 15 Nov '22

15 Nov '22

Dear NEST community, Thank you so much for your previous suggestions on writing my own neuron model with NESTML. I constructed a multiple synapses version of simple integrate-and-fire ("iaf_cond_beta_multisynapse") neuron based on the existing "iaf_cond_beta" neuron model. And I did this by simply adding two synaptic channels (AMPA and NMDA) without changing the structure of the neuron model. But when I called this model on NEST to set the initial membrane potentials from a uniform distribution (from 280 to 255 mV), for example:"d1_pop.set({"V_m":nest.random.uniform(-80.0, -55.0)})", an error reporting NESTErrors.TypeMismatch: "TypeMismatch in SLI function SetStatus_id: Expected datatype: doubletype Provided datatype: parametertype" appeared. So I wonder is there any coding errors in my own neuron model, since it worked just fine when I set the initial membrane potentials to a number like -80, and how can I fix this error. Best, Zirui

2 1

Re: weight_recorder with large number of synapses
by Hans Ekkehard Plesser 14 Nov '22

14 Nov '22

Hello Alice, Setting repeated recording windows is currently not possible (but maybe create a feature request on Github). What you can do is the following n1 = nest.Create('iaf_psc_delta', params={'I_e': 1000.}) n2 = nest.Create('iaf_psc_delta') wr = nest.Create('weight_recorder', params={'origin': 0., 'start': 0, 'stop': 1000}) nest.CopyModel('stdp_synapse', 'stdp_synapse_rec', {'weight_recorder': wr}) nest.Connect(n1, n2, syn_spec={'synapse_model': 'stdp_synapse_rec', 'weight': 20}) nest.Connect(n2, sr) t_block = 5000 for k in range(10): wr.origin = k * t_block nest.Simulate(t_block) This will simulate in 5s blocks and record weights only during the first 1s of each block. The actual recording windows are given by (origin+start, origin+stop]. You need to do this with Simulate() calls since you need to change the origin parameter; therefore RunManager + run() does not work. You could also record to file if that is an option for your workflow, by setting wr.record_to = 'ascii'. If you want to combine that with a loop, you need to set wr.label to a different value for each loop iteration, otherwise data will be overwritten for each round through the loop. Best, 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<mailto:hans.ekkehard.plesser@nmbu.no> Home http://arken.nmbu.no/~plesser From: Alice Geminiani <alice.geminiani(a)polimi.it> Reply to: NEST User Mailing List <users(a)nest-simulator.org> Date: Friday, 11 November 2022 at 18:47 To: "users(a)nest-simulator.org" <users(a)nest-simulator.org> Subject: [NEST Users] weight_recorder with large number of synapses Some people who received this message don't often get email from alice.geminiani(a)polimi.it. Learn why this is important<https://aka.ms/LearnAboutSenderIdentification> Dear NEST users, I am trying to record weights from a network with about 1.5 million synapses, for simulations of a 30-minute protocol, and using the weight_recorder causes memory errors. Is there a way to record only in specific time instants of the simulation (e.g. every 5 minutes)? Thanks a lot! Cheers, Alice ---------------------------- Alice Geminiani, PhD PostDoctoral Researcher NeuroEngineering And medical Robotics Laboratory - NEARLab Department of Electronics, Information and Bioengineering - DEIB Politecnico di Milano Neurocomputational laboratory Department of Brain and Behavioral Sciences University of Pavia

1 0

weight_recorder with large number of synapses
by Alice Geminiani 11 Nov '22

11 Nov '22

Dear NEST users, I am trying to record weights from a network with about 1.5 million synapses, for simulations of a 30-minute protocol, and using the weight_recorder causes memory errors. Is there a way to record only in specific time instants of the simulation (e.g. every 5 minutes)? Thanks a lot! Cheers, Alice ---------------------------- Alice Geminiani, PhD PostDoctoral Researcher NeuroEngineering And medical Robotics Laboratory - NEARLab Department of Electronics, Information and Bioengineering - DEIB Politecnico di Milano Neurocomputational laboratory Department of Brain and Behavioral Sciences University of Pavia

1 0

how to construct multiple synapse simple integrate-and-fire model
by 王梓瑞 07 Nov '22

07 Nov '22

Hi, I planned to use simple integrate-and-fire model (iaf_cond_beta) to construct the cortico-striatal network, but then it appeared some issues. Since striatum neurons have multiple synapses (AMPA and NMDA for example), ‘iaf_cond_beta’ seemed not to support multiple synapse input. I searched the whole Model directory and found multiple synapse neuron models like “aeif_cond_beta_multisynapse”, “aeif_cond_alpha_multisynapse” and “aeif_psc_alpha_multisynaps”. So I wondered if there’s a multiple synapse version of simple integrate-and-fire model (iaf_cond_beta), or can I construct a multiple synapse simple integrate-and-fire model through nestml. Thank you Best, Zirui

2 1

Open NEST Developer Video Conference Monday Nov 7 2022 11:30 CET (UTC+1)
by Dennis Terhorst 07 Nov '22

07 Nov '22

Dear NEST Users & Developers! I would like to invite you to our next fortnightly Open NEST Developer Video Conference, today Monday November 7, 11.30-12.30 CET (UTC+1). (note the changed timezone!) Feel free to join the meeting also if it's just to bring your own questions for direct discussion in the in-depth section. Special topic for the in-depth discussion for today is /Eligibility Propagation/ 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/2022-11-07-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

1 0

Tips for getting a scaled-down version of the Allen Brain V1 model to work using NEST/Sonata/BMTK?
by Russell Jarvis 27 Oct '22

27 Oct '22

I am just wondering if anyone in the Nest community has any tips for running the Allen Brain V1 model? A lot of the code and Sonata/HDF5 files are hosted on DropBox. model_nest_2.20 - Dropbox <https://www.dropbox.com/sh/w5u31m3hq6u2x5m/AAA1ZQrM-4pgfK5dlRtWYdJNa/GLIF%2…> I have been busy trying to get the model to work with PyGeNN and even Julia. It occurred to me that I should probably start with what has been known to work, ie Nest. Thanks for any advice. Russell. -- Russell Jarvis (he/him) PhD Personal Website <https://russelljjarvis.github.io/home/> *I respectfully acknowledge the Traditional Owners of the land on which we work and learn, and pay respect to the First Nations Peoples and their elders, past, present and future.* *phone: *614 <623-404-9322>44576301 *email:* russelljarvis(a)protonmail.com

1 0

Dendritic Arbors at Scale
by Ryan O'Loughlin 26 Oct '22

26 Oct '22

Hello NEST community, I am at the outset of a large project and I would like to start off with the right simulator. Perhaps someone here can advise on the viability of NEST for my particular needs. I will be modeling neuromorphic hardware with some unique design constraints, such as: - A complex dendritic arbor - Dendrite potentials may be coupled with their neighbors - Several dendrites may feed into other dendrites (a several-layer-deep dendritic tree) - The arbor eventually feeds into the soma which has typical LIF behavior, with a membrane potential determined by the sum of all directly connected dendrites - The solution for the leaky-integrator term of dendrites must be drawn from a precalculated lookup table The question here is how best to facilitate these dendritic nuances within NEST? Any counsel on whether it makes sense to pursue modeling such a system in NEST would be highly appreciated. We would like to eventually scale to the maximum number of neurons our hardware/clusters and your simulator can facilitate. Thank you, Ryan

2 1

Problems with Github CI on macOS / Temporary solution
by Hans Ekkehard Plesser 25 Oct '22

25 Oct '22

Dear NEST Developers, For the last few days, all CI builds on macOS have failed. This is most likely due to Homebrew now providing libomp 15.0 instead of 14.0, see issue #2515 (https://github.com/nest/nest-simulator/issues/2515). I have temporarily disabled OpenMP-dependent tests for the macOS builds (#2516). Please pull current master into all open PRs so that most of the macOS tests can run. Please note that considerable recent improvements in the code base (systematic use of nullptr #2496, of "and" and "or" instead of && and || #2498, removal of "void" arguments, systematic use of "override" and removal of "virtual" where not needed #2493; removal of unused imports #2490 as well as #2479) may lead to some merge conflicts. Please resolve them in the spirit of the new style and consult the listed PRs if in doubt about what is the new style. 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<mailto:hans.ekkehard.plesser@nmbu.no> Home http://arken.nmbu.no/~plesser

1 0

Open NEST Developer Video Conference Monday Oct 24 2022 11:30 CEST (UTC+2)
by Dennis Terhorst 24 Oct '22

24 Oct '22

Dear NEST Users & Developers! I would like to invite you to our next fortnightly Open NEST Developer Video Conference, today Monday October 24, 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. Special topic for the in-depth discussion for today are /Compressed Spikes/ 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/2022-10-24-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

1 0

Open NEST Developer Video Conference Monday Oct 10 2022 11:30 CEST (UTC+2)
by Dennis Terhorst 10 Oct '22

10 Oct '22

Dear NEST Users & Developers! I would like to invite you to our next fortnightly Open NEST Developer Video Conference, today Monday October 10, 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. Special topic for the in-depth discussion for today is the /NEST implementation of eligibility propagation/. 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/2022-10-10-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

1 0

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

2 2

NEST, CMake, Xcode, Eclipse & Co: the magic -G
by Hans Ekkehard Plesser 07 Oct '22

07 Oct '22

Dear NEST Developers, I would like to share some insights I gained over the last few days concerning NEST and IDEs. As you might know, we have some instructions for how to use NEST with IDEs (https://nest-simulator-sg.readthedocs.io/en/latest/developer_space/workflow…), but these instructions are at best complicated and at worst awfully outdated. I now discover the magic -G flag for CMake (https://cmake.org/cmake/help/latest/manual/cmake-generators.7.html), where CMake does all the heavy configuration lifting for you. Proceed as follows: - Create a build directory - Prepare your normal cmake invocation and add - for XCode: -GXcode - for Eclipse: -G"Eclipse CDT4 - Unix Makefiles" - Then open the build directory in XCode or Eclipse For other build systems, run cmake –help and see if your system is listed. Unfortunately, VSCode seems unsupported at the moment. In Xcode, you can then choose the "install" target and run it to build NEST and afterwards the "nest" target to run nest—and it will stop in the debugger if you just set a breakpoint or something goes wrong. There are still a few problems, and if any of you have more experience than me with setting up Xcode or Eclipse problems, we can maybe work it out together: 1. In Eclipse, the project will only include files in the build directory, not the source code. How to fix that? 2. Xcode * Files are ordered a bit strangely (subfolders for headers and non-headers) and "libnestutil" is shown as "nestutil" in the folder list * The "installcheck" target does not work because Xcode runs everything in the conda "base" environment—how to either force a "conda activate nest" before each run or explicitly set PYTHONPATH? * I have not yet found out how to run PyNEST from Xcode, which would also depend on conda activate/Pythonpath setting Once we have a little more experience, I will prepare a PR to update the IDE instructions. Best, 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<mailto:hans.ekkehard.plesser@nmbu.no> Home http://arken.nmbu.no/~plesser

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using mpi4py with nest | parallel write to a file
by Aadhar Sharma 28 Sep '22

28 Sep '22

Hi there! I am using the structural plasticity module to simulate large-scale networks on HPC. The way I run these simulations with MPI creates a large number of small data files (.npy) which I organize into a HDF5 file in a post hoc manner. This has hitherto not been a problem, however, I recently increased the size of my simulations and the number of files that I create exceeds my HPCinode quota. So, I have to come up with a way of handling all these files or the way I export them. Ideally, I would like to concurrently write to a file (like zarr) with multiple processes. However, parallel zarr writes are only optimal when the chunk size are uniform. For me, they are not uniform---so, I abandoned the idea of using zarr. Currently, I am trying to use mpi4py to gather the data I want and save it through a mother MPI process. I ran some test simulations and all was fine (see attached script). However, when I use structural plasticity with mpi4py I get an error that: "nest.lib.hl_api_exceptions.DimensionMismatch: ('DimensionMismatch in SetStatus_id: Expected dimension size: 1\nProvided dimension size: 20', 'DimensionMismatch', <SLILiteral: SetStatus_id>, ': Expected dimension size: 1\nProvided dimension size: 20". I believe that mpi4py somehow interferes with nest's internal mpi mechanism. Perhaps it signals nest kernel to use 1 process rather than the mentioned 20. If I remove the mpi4py import call, all works fine. So, I cannot run the simulation using this mpi4py hack. Do you notice something wrong with my approach? I'm just beginning to use mpi4py, so I may be missing something here. Alternatively, could you recommend a way to reduce the number of exported files. For example, through zarr or other file formats which support parallel writes. I'd appreciate any suggestions. Thanks! pyNEST version: 2.20.2 python version: Python 3.7.10 mpiexec/mpirun version: MPI Library for Linux* OS, Version 2021.3 Best, Ady

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[Precise Spikes]small bug in ./pynest/examples/hpc_benchmark.py (nest-3.3)
by Tianxiang Lyu 26 Sep '22

26 Sep '22

Hi, all! I try to replace "iaf_psc_alpha" with "iaf_psc_alpha_ps" and "poisson_generator" with "poisson_generator_ps" for using precise spikes neuron template in the simulation However, there are somethings wrong with the logs related to SLI with which I hadn't been familiar: (If the randomizing of membrane potentials is removed, hpc_benchmark.py could run as usual) Traceback (most recent call last): File "./hpc_benchmark.py", line 456, in <module> run_simulation() File "./hpc_benchmark.py", line 362, in run_simulation sr = build_network(logger) File "./hpc_benchmark.py", line 227, in build_network nest.GetLocalNodeCollection(E_neurons).V_m = random_vm File "/GPUFS/sysu_hpcedu_302/lvtx/tools/nest-simulator/3.3-intel-2021/lib64/python3.8/site-packages/nest/lib/hl_api_types.py", line 543, in __setattr__ self.set({attr: value}) File "/GPUFS/sysu_hpcedu_302/lvtx/tools/nest-simulator/3.3-intel-2021/lib64/python3.8/site-packages/nest/lib/hl_api_types.py", line 477, in set sli_func('SetStatus', self._datum, params) File "/GPUFS/sysu_hpcedu_302/lvtx/tools/nest-simulator/3.3-intel-2021/lib64/python3.8/site-packages/nest/ll_api.py", line 165, in sli_func sli_run(slifun) # SLI support code to execute s on args File "/GPUFS/sysu_hpcedu_302/lvtx/tools/nest-simulator/3.3-intel-2021/lib64/python3.8/site-packages/nest/ll_api.py", line 115, in catching_sli_run raise exceptionCls(commandname, message) nest.lib.hl_api_exceptions.TypeMismatch: TypeMismatch in SLI function SetStatus_id: Expected datatype: doubletype Provided datatype: parametertype How could I fix that? Or another way to implement randomizing of membrane potentials? Tianxiang Lyu Department of Mechanic Sun Yet-Sen University No. 66, Gongchang Road, Guangming District, Shenzhen, 518107, P. R. China

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Open NEST Developer Video Conference Monday Sep 26 2022 11:30 CEST (UTC+2)
by Dennis Terhorst 26 Sep '22

26 Sep '22

Dear NEST Users & Developers! I would like to invite you to our next fortnightly Open NEST Developer Video Conference, today Monday September 26, 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/2022-09-26-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 save and reload an already trained network created with Nest Simulator?
by salvatore.taffara＠phd.unict.it 21 Sep '22

21 Sep '22

Hi, can anyone answer to my question in subject? I am using Nest 3.3. Thanks in advance, Salvo

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which neuron model supports shunting inhibition
by Aadhar Sharma 14 Sep '22

14 Sep '22

Hi all! I want to use investigate the effects of shunting inhibition in one of my experiments. I tried iaf_cond_alpha, but couldn't reproduce the shunting effect. Could someone please suggest which neuron model to use? There should be a way to also change the V_th, V_rest, C_m, tau_m or g_L for this model. I am working with NEST 2.20.2 Best, Ady

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Open NEST Developer Video Conference Monday Aug 15 2022 11:30 CEST (UTC+2)
by Dennis Terhorst 12 Sep '22

12 Sep '22

Dear NEST Users & Developers! I would like to invite you to our next fortnightly Open NEST Developer Video Conference, today Monday August 15, 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/2022-08-15-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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Upcoming conference in Computational Neuroscience - Neuromatch 2022
by Alberto Antonietti 30 Aug '22

30 Aug '22

Dear NEST users and developers, I am glad to invite you to the upcoming fifth edition of the Neuromatch Conference (NMC), which will take place online on September 27-28! The scope of NMC 2022 includes computational neuroscience and machine learning work that has a biological link. We are excited to have a slate of excellent speakers and panelists lined up including: - Keynotes from Larry Abbott, Rosa Chan, Ida Momennejad and Mac Shine - Panel on spiking computation: Priya Panda, Katie Schuman, and Peter Suma - Panel on the future of scientific publishing: Tim Behrens, Simine Vazire, and Abeni Wickham - Bridging-the-gap with computational psychiatry: Xiaosi Gu and Quentin Huys Registration costs are set at 15 USD to cover technical costs, and if this is a difficulty, the fee can be waived without questions. **Important dates** September 5, 2022: Abstract submission deadline September 7, 2022: Abstract acceptance and live talk selection news September 22, 2022: Video submission deadline for flashtalks September 27 - 28, 2022: NMC 2022 Each of the two conference days will have two sessions, each of which is 4 hours long. Here are the hours for each of the sessions, as they would occur across five time zones from around the world: Read more at http://conference.neuromatch.io I hope to see many of you there! Best, Alberto

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Spike->Synapse->Update
by lvtx＠mail2.sysu.edu.cn 25 Aug '22

25 Aug '22

I wrote a simple python code(without nest) for a E-I random balanced network with poisson noise stimulus. Then I try to build it on nest. However, the response firing rates are changed.(not a computing error) Is there anything wrong? neurons -> spike synapse -> wait delay post_neurons -> add weight from connected synapses to corresponding input channel neurons -> update ODE each step I figured out that without connections but with poisson noise input, the firing rates of my python code is the same as the code on nest. (Seems that the ODE calculations are the same in my python code and nest) However, the firing rates show differ greatly when I add the connections on both.

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Open NEST Developer Video Conference Monday Aug 15 2022 11:30 CEST (UTC+2)
by Hans Ekkehard Plesser 15 Aug '22

15 Aug '22

Dear NEST Users & Developers! I would like to invite you to our next fortnightly Open NEST Developer Video Conference, today Monday August 15, 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/2022-08-15-Open-NEST-Developer-… Looking forward to seeing you again soon! Best regards, Hans Ekkehard Plesser ------------------ 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<mailto: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 -- 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<mailto:hans.ekkehard.plesser@nmbu.no> Home http://arken.nmbu.no/~plesser

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Compiling nest-simulator from source
by Daniel Naoumenko 11 Aug '22

11 Aug '22

Hi, I've been trying to compile the latest version on github (c1cebdc) without success. The system is a HPC running RHEL7. Pre-installed software includes gsl-2.7, cmake 3.17.5 and openMPI-1.10.3-gnu, although I have tried variations with similar results. I've created a fresh conda environment with packages necessary for nest and nestml: conda create --name pythonfornestml -c conda-forge boost readline ipython pyqt wxpython cython pip install mpi4py cmake -DCMAKE_INSTALL_PREFIX:PATH=/headnode1/dnao/nest-installs/nest3-23.07.2022 \ -Dwith-mpi=ON \ /headnode1/dnao/gitnest/nest-simulator make make fails at 47%. I have uploaded the make output here: https://drive.google.com/file/d/1FXVsidFLXYvnHk4Tob2zDi4wQJJNW-yw/view?usp=… As well as the output of cmake to show the build configuration: https://drive.google.com/file/d/1HWH_KqILEyQYujzd4B1ma4ZrzUXbG231/view?usp=… Thank you in advance for any assistance.

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Fwd: Building nest 3.3
by Mikael Lindahl 05 Aug '22

05 Aug '22

Hi, I am trying to build NEST on debian 11 with cmake 3.16.9 and conda python=3.9. I have attached my installation script asswell as the full logs for make and install steps. ( I run the script with using source to conda activate will play nice) During "make install" I get the following message error -- Set runtime path of "/home/mikael/git/bgmodel/nest/dist/install/nest-simulator-3.3/lib/python3.9/site-packages/nest/pynestkernel.so" to "$ORIGIN/../lib/nest:$ORIGIN/../../lib/nest:$ORIGIN/../../../nest:/home/mikael/opt/anaconda3/envs/nest-3.3/lib" running install_egg_info /home/mikael/opt/anaconda3/envs/nest-3.3/lib/python3.9/site-packages/setuptools/command/install.py:34: SetuptoolsDeprecationWarning: setup.py install is deprecated. Use build and pip and other standards-based tools. warnings.warn( running egg_info creating nest_simulator.egg-info writing nest_simulator.egg-info/PKG-INFO writing dependency_links to nest_simulator.egg-info/dependency_links.txt writing requirements to nest_simulator.egg-info/requires.txt writing top-level names to nest_simulator.egg-info/top_level.txt writing manifest file 'nest_simulator.egg-info/SOURCES.txt' reading manifest file 'nest_simulator.egg-info/SOURCES.txt' writing manifest file 'nest_simulator.egg-info/SOURCES.txt' Copying nest_simulator.egg-info to /home/mikael/git/bgmodel/nest/dist/install/nest-simulator-3.3/lib/python3.9/site-packages/nest_simulator-3.3-py3.9.egg-info Traceback (most recent call last): File "<string>", line 1, in <module> File "/home/mikael/opt/anaconda3/envs/nest-3.3/lib/python3.9/site-packages/pkg_resources/__init__.py", line 477, in get_distribution dist = get_provider(dist) File "/home/mikael/opt/anaconda3/envs/nest-3.3/lib/python3.9/site-packages/pkg_resources/__init__.py", line 353, in get_provider return working_set.find(moduleOrReq) or require(str(moduleOrReq))[0] File "/home/mikael/opt/anaconda3/envs/nest-3.3/lib/python3.9/site-packages/pkg_resources/__init__.py", line 897, in require needed = self.resolve(parse_requirements(requirements)) File "/home/mikael/opt/anaconda3/envs/nest-3.3/lib/python3.9/site-packages/pkg_resources/__init__.py", line 783, in resolve raise DistributionNotFound(req, requirers) pkg_resources.DistributionNotFound: The 'nest-simulator' distribution was not found and is required by the application And for make installcheck i get this error Scanning dependencies of target installcheck Executing NEST's testsuite... make[3]: *** [CMakeFiles/installcheck.dir/build.make:61: CMakeFiles/installcheck] Error 1 make[2]: *** [CMakeFiles/Makefile2:524: CMakeFiles/installcheck.dir/all] Error 2 make[1]: *** [CMakeFiles/Makefile2:531: CMakeFiles/installcheck.dir/rule] Error 2 make: *** [Makefile:178: installcheck] Error 2 It took 160 seconds Anyone who knows how to solve this? /Mikael -- Mikael Lindahl Phd Phone: +46735119429 Email: m <lindahlm(a)csc.kth.se>ickelindahl(a)gmail.com

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Open NEST Developer Video Conference Monday Aug 1 2022 11:30 CEST (UTC+2)
by Dennis Terhorst 01 Aug '22

01 Aug '22

Dear NEST Users & Developers! I would like to invite you to our next fortnightly Open NEST Developer Video Conference, today Monday August 1, 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/2022-08-01-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

1 0

How to use the update block in NESTML?
by lea.driessens＠ensea.fr 31 Jul '22

31 Jul '22

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.

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Open NEST Developer Video Conference Monday July 18 2022 11:30 CEST (UTC+2)
by Dennis Terhorst 18 Jul '22

18 Jul '22

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

1 0

Access weight_recorder data during simulation
by francescojamal.sheiban＠polimi.it 15 Jul '22

15 Jul '22

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

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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

1 0

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

2 3

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.

2 1

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>

3 2

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

4 11

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

2 1

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

1 0

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

1 0

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

2 2

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  

2 1

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

1 0

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

3 3

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.

3 3

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.

1 0

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

1 0

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

1 0

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

1 0

Re: Nest 3.3
by Steffen Graber 01 Jun '22

01 Jun '22

1 1

I can not install Nest 3.3 simulator in Ubuntu 18.04
by salvatore.taffara＠phd.unict.it 01 Jun '22

01 Jun '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

2 1

CNS*2022 satellite tutorials: free online sessions: June 27--July 1
by Ankur Sinha 31 May '22

31 May '22

Dear all, Apologies for the cross posts. https://ocns.github.io/SoftwareWG/pages/software-wg-satellite-tutorials-at-… The INCF/OCNS Software working group is organising 5 days of free online satellite tutorials ahead of the CNS*2022 conference. These tutorials will run from June 27--July 1 and feature sessions on: - Arbor - Brian2 - Introduction to containers - EBRAINS - GeNN - Keras/TensorFlow - LFPy - MOOSE - Neo + Elephant - NEST - NetPyNE - NeuroLib - NeuroML - NEURON - OSBv2 - RateML More information on the schedule and (free) registration will be published in the next week or so. Please do mark your calendars and spread to word to your colleagues, students, and anyone else who these may interest. For more information on the INCF/OCNS Software working group and how you can join our community, please visit our website: https://ocns.github.io/SoftwareWG/ -- 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

1 0

Integration between ROS node and NEST
by salvatore.taffara＠phd.unict.it 30 May '22

30 May '22

Dear Nest community, I should import numerical data (not spiking data) obtained from a dynamic simulator called CoppeliaSim (ex VRep) into a Nest script. To do this I thought of using a ROS subscriber node that receives the data using a topic. I ask you, how do I interface Nest with Ros in order to import the data? Greetings, Except

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Test NEST performance
by 512491013＠qq.com 30 May '22

30 May '22

Dear all, Recently, I've been trying to test NEST's performance(with and without MPI). But with PyNEST, it's hard to do more detailed testing with tools like Gprof. Only some print-time and memory methods can be inserted into the C++ source code for testing. Is there a C++ front-end interface that can call NEST C++ source code for testing? Of course, I used some of Python's performance testing tools, but only to the interface, not C++ in action. I'd appreciate any tips on how to test NEST's performance! Cong

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Open NEST Developer Video Conference Monday May 23 2022 11:30 CEST (UTC+2)
by Dennis Terhorst 22 May '22

22 May '22

Dear NEST Users & Developers! I would like to invite you to our next fortnightly Open NEST Developer Video Conference, tomorrow Monday May 23, 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/2022-05-23-Open-NEST-Developer-… Since I will not be available for the meeting, Hans Ekkehard Plesser has kindly agreed to chair the meeting. 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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NEST Conference 2022 - Extension of abstract submission deadline
by Hans Ekkehard Plesser 10 May '22

10 May '22

Dear all, The abstract submission deadline for the (virtual) NEST Conference 2022 has been extended to Wednesday, 25 May. We are looking forward to your contributions! The NEST Conference provides an opportunity for the NEST Community to meet, exchange success stories, swap advice, learn about current developments in and around NEST spiking network simulation and its application. This year's conference will again take place as a virtual conference on Thursday/Friday 23/24 June 2022. We are inviting contributions to the conference, including talks, "posters" and workshops on specific topics. Important dates 25 May 2022 — Deadline for submission of contributions 03 June 2022 — Notification of acceptance 17 June 2022 — Registration deadline 23 June 2022 — NEST Conference 2022 starts For more information on how to submit your contribution, register and participate, please visit the conference website https://nest-simulator.org/conference We are looking forward to seeing you all in June! Hans Ekkehard Plesser and the conference organizing committee -- 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<mailto:hans.ekkehard.plesser@nmbu.no> Home http://arken.nmbu.no/~plesser

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NEST Conference 2022 - Extension of abstract submission deadline
by Hans Ekkehard Plesser 10 May '22

10 May '22

Dear all, The abstract submission deadline for the (virtual) NEST Conference 2022 has been extended to Wednesday, 25 May. We are looking forward to your contributions! The NEST Conference provides an opportunity for the NEST Community to meet, exchange success stories, swap advice, learn about current developments in and around NEST spiking network simulation and its application. This year's conference will again take place as a virtual conference on Thursday/Friday 23/24 June 2022. We are inviting contributions to the conference, including talks, "posters" and workshops on specific topics. Important dates 25 May 2022 — Deadline for submission of contributions 03 June 2022 — Notification of acceptance 17 June 2022 — Registration deadline 23 June 2022 — NEST Conference 2022 starts For more information on how to submit your contribution, register and participate, please visit the conference website https://nest-simulator.org/conference We are looking forward to seeing you all in June! Hans Ekkehard Plesser and the conference organizing committee -- 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<mailto:hans.ekkehard.plesser@nmbu.no> Home http://arken.nmbu.no/~plesser

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Job opportunity
by Elena Pastorelli 09 May '22

09 May '22

Dear NEST developers, I would like to share with you a job opportunity that could be of interest for the community. APE Lab (Rome, Italy) is looking for a motivated and enthusiast candidate for activities aimed at system software development and application porting on advanced HPC platforms, in the framework of the RED-SEA <https://jobs.dsi.infn.it/borseassegni/pdf/getfile.php?filename=24338.pdf> project. Application submission details <https://jobs.dsi.infn.it/borseassegni/pdf/getfile.php?filename=24338.pdf> here (English version in the second part of the document), deadline: 20/05/2022 APE Lab is a INFN (National Institute of Nuclear Physic) initiative started in 1984 with the goal of connecting theoretical physics and technology through the development of custom distributed and parallel computing systems. Since then, APE Lab has generated unique know-how, enabling cutting-edge research in HPC (High Performance Computing) with leading roles in the HPC community. APE Lab has participated in several EU-funded projects, the last of which being RED-SEA. The RED-SEA project prepares a new-generation European Network Interconnect, capable of powering the EU Exascale systems to come, leveraging efficient European interconnect technology (BXI) associated with a standard and mature technology (Ethernet), in full coordination with other EU-funded initiatives. The INFN task in RED-SEA is two-fold: 1. to design and implement the network interface card (APEnetX) based on PCIe interface to communicate with CPU and GPU accelerators, and prototyped exploiting Xilinx Alveo FPGAs. 2. to support the co-design approach for network design activities focusing in particular on NEST application as a benchmark. Job Details Task: contribution to development of scalable network simulator based on Omnet++ framework as well as to the Linux Kernel Driver of the Network Interface Card. Requirements: 24 months of demonstrated experience in software development and knowledge/development of linux kernel driver. Knowledge of simulator architectures, coding and use of MPI framework would be an advantage. Best, Elena Pastorelli -- This email has been checked for viruses by Avast antivirus software. https://www.avast.com/antivirus

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Open NEST Developer Video Conference Monday May 9 2022 11:30 CEST (UTC+2)
by Dennis Terhorst 09 May '22

09 May '22

Dear NEST Users & Developers! I would like to invite you to our next fortnightly Open NEST Developer Video Conference, today Monday May 9, 11.30-12.30 CEST (UTC+2). Feel free to join the meeting also 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/2022-05-09-Open-NEST-Developer-… Looking forward to seeing you 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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NEST Conference 2022 — Abstract submission deadline Wednesday 11 May
by Hans Ekkehard Plesser 04 May '22

04 May '22

Dear Colleagues, I would like to remind you that the deadline for abstract submission to the virtual NEST Conference 2022 is approaching fast: You have until next Wednesday, 11 May 2022, to submit your contribution (talk, "poster", or workshop) via the conference website https://nest-simulator.org/conference. The NEST Conference provides an opportunity for the NEST Community to meet, exchange success stories, swap advice, learn about current developments in and around NEST spiking network simulation and its application. We explicitly encourage young scientists to participate in the conference! This year's conference will again take place as a virtual conference on Thursday/Friday 23/24 June 2022. Important dates 11 May 2022 - Deadline for submission of contributions 03 June 2022 - Notification of acceptance 17 June 2022 - Registration deadline 23 June 2022 - NEST Conference 2022 starts We are looking forward to seeing you all in June! Hans Ekkehard Plesser and the conference organizing committee -- 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<mailto:hans.ekkehard.plesser@nmbu.no> Home http://arken.nmbu.no/~plesser

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problems with step_current_generator parallelization
by Jan Střeleček 28 Apr '22

28 Apr '22

Dear NEST developers, In our group, we're working on a model of the primary visual cortex and use step_current_source generators to simulate the input current of the LGN neurons. We noticed that the simulation time of our model was very sensitive to the number of step_current_sources. When trying to narrow down the cause, we found out that this might be due to an issue with the parallelization of the step_current_source_generators. The resulting simple system in which the problem can be observed is attached below, simple_example.py. It essentially creates NSstep_current_generators and injects them into NLneurons with fixed indegree. The iaf_cond_exp neuron model is used here. The increment in the number of step_current sources does not benefit from a multithreading performance boost as one would expect. This is compared to the performance boost for the number of neurons; see the technical details below. Our estimated guess is that the difference between 1 and 32 threads is 10 to 20 times slower than the parallelization suggests. Technical details: The relative slowdown due to the parallelization of step_current_sources was measured using linear regression over simulation time = a NL + b NS. See slowdown_example.png. The ratio b/a was then calculated. This ratio was then measured in dependence on the number of threads. A bigger difference between the ratio for 1 thread and 32 threads means a greater problem in parallelization in step_current_generators. Some additional results: - interval_dependence.png - the slowdown does not depend on amplitude_times in the step_current_source function - indegree_dependence.png - the slowdown depends on the indegree of nest.Connect(source, neurons). Specifically, the slowdown is worse for low indegree values. This shows the slowdown depends on the number of step_current_sources created, not on the injections themselves. Are you aware of some lack of parallelization of the step_current_source or current the injection itself? If so, are there any plans for improving it? best regards, Jan Střeleček

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Tsodyks model, examples, burst generation
by Dennis Terhorst 28 Apr '22

28 Apr '22

Dear all, in the past weeks there was some on- and off-list discussion around the Tsodyks models and examples in NEST and I want to put some files out here that might be interesting for more people. Around 2019 we were trying to port some old scripts to more recent versions of NEST and did some basic plots. There are descriptions and PyNEST examples available in the docs Model Directory [1, 2, 3], and the example Notebook in the docs runs with NEST 3.x. Additionally the short-term burst behavior can be reproduced with the attached scripts (taken from the pre-3.x repository and updated to 3.x syntax, still a bit untidy), but to my knowledge this was not yet transferred into a PyNEST version. There has also been some discussion on the mailing list some time ago [4], but I couldn't find any results that have surfaced on the list here, though I know of some work going on in this direction in different groups. It would be interesting to hear about your perspective and see where we can combine experience! best, Dennis [1]: https://nest-simulator.readthedocs.io/en/v3.3/models/index.html#short-term-… [2]: https://nest-simulator.readthedocs.io/en/v3.3/models/tsodyks_synapse.html [3]: https://nest-simulator.readthedocs.io/en/v3.3/models/tsodyks2_synapse.html [4]: https://nest-simulator.org/mailinglist/hyperkitty/list/users@nest-simulator… -- Dipl.-Phys. Dennis Terhorst Coordinator Software Development Institute of Neuroscience and Medicine (INM-6) Computational and Systems Neuroscience & Theoretical Neuroscience, Institute for Advanced Simulation (IAS-6) Jülich Research Centre, Member of the Helmholz Association and JARA 52425 Jülich, Germany Building 15.22 Room 4004 Phone +49 2461 61-85062 Fax +49 2461 61- 9460 d.terhorst(a)fz-juelich.de

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Any objections to renaming hh_cond_*_traub models?
by Hans Ekkehard Plesser 25 Apr '22

25 Apr '22

Dear NEST Users, As discussed a long time ago (see towards the end of the discussion in https://github.com/nest/nest-simulator/issues/329), the hh_cond_exp_traub model included in NEST is far from the model by Traub and Miles (1991) which inspired it. The model in NEST was implemented as part of the work on the Brette et al (2007) review paper. I am considering to create a pull request that will 1. rename the models to hh_brette_2007* in keeping with NEST naming guidelines for paper-specific models 2. change the threshold parameter V_T to be the actual threshold for spike emission (currently the criterium is V_m >= V_T + 30 and falling V_m) I was therefore wondering if anyone of you 1. uses the hh_cond_* models at all 2. would object to those changes? Depending on whether the models are being used or not, I'd either implement the renaming via deprecation or directly. Best, 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<mailto:hans.ekkehard.plesser@nmbu.no> Home http://arken.nmbu.no/~plesser

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Open NEST Developer Video Conference Monday April 25 2022 11:30 CEST (UTC+2)
by Dennis Terhorst 25 Apr '22

25 Apr '22

Dear NEST Users & Developers! I would like to invite you to our next fortnightly Open NEST Developer Video Conference, today Monday April 25, 11.30-12.30 CEST (UTC+2). Special feature today will be a discussion of the available, but maybe not so widely known astrocyte model implementation in NEST. Feel free to join the meeting also 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 * Astrocyte models in NEST The agenda for this meeting is also available online, see https://github.com/nest/nest-simulator/wiki/2022-04-25-Open-NEST-Developer-… Looking forward to seeing you 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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Developer info: calibrate() is now called pre_run_hook()
by Hans Ekkehard Plesser 21 Apr '22

21 Apr '22

Dear NEST Developers! If you are just using NEST, you can ignore this message. If you are coding models at the C++ level, I just want to share this information to reduce the risk of confusion: The good old calibrate() method found in all neuron models has now been renamed to pre_run_hook(), see https://github.com/nest/nest-simulator/pull/2336. Thanks to Pooja for implementing this. I'd suggest that you merge the master branch into any open development branches to bring them up to date on this change. Best, 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<mailto:hans.ekkehard.plesser@nmbu.no> Home http://arken.nmbu.no/~plesser

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Re: Kernel death when recording from 300+ cells for 2mins+
by Hans Ekkehard Plesser 19 Apr '22

19 Apr '22

Hello Rachael, Could you post a minimal script or Jupyter notebook reproducing the problem? Does the problem only occur on the Neurorobotics platform or can you reproduce it locally on your computer as well? 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<mailto:hans.ekkehard.plesser@nmbu.no> Home http://arken.nmbu.no/~plesser On 13/04/2022, 13:20, "Rachael Stentiford" <rachael.stentiford(a)brl.ac.uk<mailto:rachael.stentiford@brl.ac.uk>> wrote: Some people who received this message don't often get email from rachael.stentiford(a)brl.ac.uk. Learn why this is important<http://aka.ms/LearnAboutSenderIdentification> Apologies for so many emails. Looks like i jumped the gun a little and i am still having this issue. So if anyone does have any ideas, I would welcome the help. Cheers, Rachael ________________________________ From: Rachael Stentiford <rachael.stentiford(a)brl.ac.uk> Sent: Wednesday, April 13, 2022 11:46 AM To: users(a)nest-simulator.org <users(a)nest-simulator.org> Subject: Re: Kernel death when recording from 300+ cells for 2mins+ Looks like i have solved this issue now. For those interested in the solution, i have switched from using the efficient method for splitting a simulation into multiple intervals described in the docs, which has the clean up functions outside of the loop, to just using nest.Simulate() in the loop so the clean up functions are called each time. Cheers, Rachael ________________________________ From: Rachael Stentiford <rachael.stentiford(a)brl.ac.uk> Sent: Tuesday, April 12, 2022 6:32 PM To: users(a)nest-simulator.org <users(a)nest-simulator.org> Subject: [NEST Users] Kernel death when recording from 300+ cells for 2mins+ Dear all, I hope you are doing well. I am having an issue using pyNEST which i haven't come across before and have been unable to find answer to elsewhere. I am working with Python 3.8 and Nest 2.18 (which is the version currently used by the Neurorobotics platform). I have a network of 6 x 360 neurons, and i am trying to record spikes from 360 of these. However, I am finding that if i try to simulate for more than ~2 mins i run into problems. In jupyter notebooks I get a kernel death error, but even just running a standard python script NEST dies. I can simulate for longer if i only record from a single neuron. Previously I have used networks of 4 x 180 neurons and recorded from 180 for 10+ minutes without an issue. I have tried splitting up the simulation into multiple intervals, as explained in the docs, and saving spikes in between. This would mean there are fewer spikes to save each time, but this doesn't appear to help. Ideally i would like to record from 360 cells for around 30 mins. Have any of you come across a similar issue in the past, or have any suggestions for how I could fix this issue? Thanks for your help! Rachael ------------------------- Dr Rachael Stentiford (she/her) Research Associate in Neurobotics Bristol Robotics Laboratory University of the West of England Bristol BS16 1QY

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Kernel death when recording from 300+ cells for 2mins+
by Rachael Stentiford 13 Apr '22

13 Apr '22

Dear all, I hope you are doing well. I am having an issue using pyNEST which i haven't come across before and have been unable to find answer to elsewhere. I am working with Python 3.8 and Nest 2.18 (which is the version currently used by the Neurorobotics platform). I have a network of 6 x 360 neurons, and i am trying to record spikes from 360 of these. However, I am finding that if i try to simulate for more than ~2 mins i run into problems. In jupyter notebooks I get a kernel death error, but even just running a standard python script NEST dies. I can simulate for longer if i only record from a single neuron. Previously I have used networks of 4 x 180 neurons and recorded from 180 for 10+ minutes without an issue. I have tried splitting up the simulation into multiple intervals, as explained in the docs, and saving spikes in between. This would mean there are fewer spikes to save each time, but this doesn't appear to help. Ideally i would like to record from 360 cells for around 30 mins. Have any of you come across a similar issue in the past, or have any suggestions for how I could fix this issue? Thanks for your help! Rachael ------------------------- Dr Rachael Stentiford (she/her) Research Associate in Neurobotics Bristol Robotics Laboratory University of the West of England Bristol BS16 1QY

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