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Weights assignment error with mpirun
by Xavier Otazu 12 Feb '24

12 Feb '24

Hi! I am trying to implement weight normalization (as you show in your documentation). It works well (see below code) when executed "normally" (or when using" mpirun -np 1"), but it hangs (it just do not respond) when executed using mpirun. It hangs when I try to execute nest.Simulate() after weigth assignment. If I remove the "conn.weight = w_nparray" instruction in the following code, it works without hang. I use NEST 3.6 and python3, compiled with python, mpi, sionlib and music. Thanks a lot in advance! 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_0) nest.DumpLayerConnections(input, layer_0, 'static_synapse', 'conn.txt') nest.DumpLayerConnections(input, layer_1, 'syn_1_model', 'conn.txt') nest.Simulate(100) for neuron in layer_0: conn = nest.GetConnections(source=input, 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 nest.Simulate(100)

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cannot open shared object file (pynestkernel.so)
by Willem Wybo 08 Feb '24

08 Feb '24

I’m trying to run NEST on Jureca, but I get an error: Traceback (most recent call last): File "/p/project/jinm60/users/wybo1/Code/NEAST_models/BBP/tests/run_all_tests.py", line 2, in <module> import nest.lib.hl_api_exceptions as nestexceptions File "/p/home/jusers/wybo1/jureca/nest/nest-install/lib64/python3.11/site-packages/nest/__init__.py", line 64, in <module> from .ll_api_kernel_attributes import KernelAttribute # noqa ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/p/home/jusers/wybo1/jureca/nest/nest-install/lib64/python3.11/site-packages/nest/ll_api_kernel_attributes.py", line 22, in <module> from .ll_api import spp, sps, sr, stack_checker File "/p/home/jusers/wybo1/jureca/nest/nest-install/lib64/python3.11/site-packages/nest/ll_api.py", line 53, in <module> from . import pynestkernel as kernel # noqa pylint: disable=no-name-in-module ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ ImportError: libltdl.so.7: cannot open shared object file: No such file or directory Apparently it doesn’t find pynestkernel.so (I think?). However, this file is definitely there. wybo1@jrlogin09 ~/.../site-packages/nest> pwd /p/home/jusers/wybo1/jureca/nest/nest-install/lib64/python3.11/site-packages/nest wybo1@jrlogin09 ~/.../site-packages/nest> ls __init__.py __pycache__ lib ll_api.py ll_api_kernel_attributes.py logic math pynest-init.sli pynestkernel.so random raster_plot.py server spatial spatial_distributions versionchecker.py visualization.py voltage_trace.py The problem also only manifests itself while running from a SLURM script. I followed the install instruction here: https://nest-simulator.readthedocs.io/en/stable/installation/noenv_install.… And source the nest_vars.sh file according to the instructions: `source /p/home/jusers/wybo1/jureca/nest/nest-install/bin/nest_vars.sh` Also, `make installcheck` passes successfully (both from the login node and from a slurm script). Cheers, Willem ---------------------- Dr. Willem Wybo Peter Grünberg Institute 15 - Neuromorphic Software Ecosystems Forschungszentrum Jülich www.fz-juelich.de/pgi/PGI-15<http://www.fz-juelich.de/pgi/PGI-15> ---------------------- ------------------------------------------------------------------------------------------------ ------------------------------------------------------------------------------------------------ Forschungszentrum Jülich GmbH 52425 Jülich Sitz der Gesellschaft: Jülich Eingetragen im Handelsregister des Amtsgerichts Düren Nr. HR B 3498 Vorsitzender des Aufsichtsrats: MinDir Stefan Müller Geschäftsführung: Prof. Dr. Astrid Lambrecht (Vorsitzende), Karsten Beneke (stellv. Vorsitzender), Dr. Ir. Pieter Jansens ------------------------------------------------------------------------------------------------ ------------------------------------------------------------------------------------------------

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STDP synapse t_spike and t_lastspike clarification
by prao2＠uw.edu 07 Feb '24

07 Feb '24

Dear all, I am trying to develop a new synapse model that uses the activity of the postsynaptic neuron. I'm looking at the STDP synapse to understand how it gets the target neuron history, and I wanted to clarify: are t_spike and t_lastspike the time stamps for the last spike of the presynaptic or postsynaptic neuron? I am looking at the send method of stdp_synapse.h (https://github.com/nest/nest-simulator/blob/91a02ed98017224deabe25e8e08bcfd…) Thanks in advance! Best, Priyanka Rao

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Problems in simulation restore
by Petia Koprinkova 06 Feb '24

06 Feb '24

Hi, We've discovered the following problem in restoring network simulation: if the simulation stops for some reason restoring it form the network status kept in files does not yield the same results as in case when the simulation was not interrupted and finishes normally. In our experiment we run a script twice as follows: 1. Create a network and simulate for some period of time. 2. Record the current network status in terms of connections and membrane potentials and store them in files at the end of script.3. End the script 4. Start the script again restoring the network structure from files.5. Run simulation till the end of desired time. The spiking activity of the network is different if we run simulation without interruption or if we run it in the manner described here: https://nest-simulator.readthedocs.io/en/stable/auto_examples/store_restore… i.e. if we run a script with following steps:1. Run simulation for some time.2. Get connections and membrane potentials3. Reset kernel4. Create again the network5. Simulate till the end of desired time. Please help to resolve the problem. Best,Petia Koprinkova-Hristova

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Question about membrane potential recording
by Petia Koprinkova 31 Jan '24

31 Jan '24

Hi, We recently discovered that multimeter returns membrane potential in some unordered way so if we want to record the last state of a group of neurons and then to continue simulation from exactly the same state we were unable to reconstruct it properly. Is there a way to record the membrane potential together with neuron ID? Best,Petia Koprinkova-Hristova

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Assert failed running hpc_benchmark
by Michele Martinelli 29 Jan '24

29 Jan '24

Dear NEST Users & Developers, we're currently working on a custom OpenMPI BTL (supporting a custom FPGA-based NIC) at the National Institute for Nuclear Physics in Rome, Italy and we have an error when running hpc_benchmark(this test is currently used as simple validation test) with 2 processes (one on each of 2 hosts), the command we run is like: mpirun -n 2 -H host1:1,host2:1 --bynode --report-bindings -mca btl apelink,self,sm python hpc_benchmark.py (apelink is our custom BTL component) but then we see this error: python: [...]/NEST_with_local_ompi/nest-simulator-3.6/nestkernel/target_table.cpp:107: void nest::TargetTable::add_target(size_t, size_t, const nest::TargetData&): Assertion `syn_id < secondary_send_buffer_pos_[ tid ][ lid ].size()' failed. [host:23979] *** Process received signal *** [host:23979] Signal: Aborted (6) [host:23979] Signal code: (-6) My guess is that we are transferring something incorrectly (maybe during the initialization/setup phase?), but I'm not sure what the assert expects to have in secondary_send_buffer_pos_[ tid ][ lid ].size() and how this field should be set. Best, Michele

2 1

Open NEST Developer Video Conference Monday January 29, at 11:30 CET (UTC+0100)
by Dennis Terhorst 29 Jan '24

29 Jan '24

Dear NEST Users & Developers! I would like to invite you to our next fortnightly Open NEST Developer Video Conference today *Monday January 29, at 11:30 CET (UTC+0100).* As usual, in the Project team round, a contact person of each team will give a short statement summarizing ongoing and planned work in the team and highlight cross-cutting points that need discussion among the teams. The remainder of the meeting we would go into a bunch of topics that came up and that were 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 o Changed Model registration for NEST Models (from last meeting) o Proposed new model with an approximation for nonlinear NMDA receptors (#2979 <https://github.com/nest/nest-simulator/pull/2979>) o Proposed multi-state models (#3069 <https://github.com/nest/nest-simulator/pull/3069>) o Report from LASCON IX The agenda for this meeting is also available online, see https://github.com/nest/nest-simulator/wiki/2024-01-29-Open-NEST-Developer-… <https://github.com/nest/nest-simulator/wiki/2024-01-29-Open-NEST-Developer-…> Looking forward to seeing you soon! Cheers, Dennis Terhorst Log-in information We use a virtual conference room provided by DFN <https://www.dfn.de/en/> (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 <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 <http://vcc.zih.tu-dresden.de/index.php?linkid=1.1.3.4> -- Dipl.-Phys. Dennis Terhorst Coordinator Software Development Institute for Advanced Simulation (IAS-6), Computational and Systems Neuroscience & JARA-Institute Brain Structure-Function Relationships (INM-10) Institute of Neuroscience and Medicine Jülich Research Center, Member of the Helmholz Association 52425 Jülich, Germany http://www.csn.fz-juelich.de/ Phone +49 2461 61-85062 ---------------------------------------------------------------------- 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. Astrid Lambrecht (Vorsitzende), Karsten Beneke (stellv. Vorsitzender), Dr. Ir. Pieter Jansens ----------------------------------------------------------------------

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Google Gemini NESTML code
by Alvin Spivey 26 Jan '24

26 Jan '24

I'm using Google Bard's Gemini to learn NESTML. It's giving me some unexpected results: import nestml from nestml.network import Network from nestml.models import ConeNakaRushton # Define network with Naka-Rushton cone model for primate 'cone_type' cones network = Network() cone_population = network.add_population("cones", ConeNakaRushton(species= "human", cone_type=cone_type)) The NESTML network and models packages don't seem to exist. Also, how do I find more information about the network and models packages (or packages in general) for NESTML? -- Alvin J. Spivey, Ph.D. (c) 843.267.8055

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Open NEST Developer Video Conference Monday January 15, at 11:30 CET (UTC+0100)
by Dennis Terhorst 15 Jan '24

15 Jan '24

Dear NEST Users & Developers! 🎈🎉🎈 Happy New Year! 🎈🎊🎈 I would like to invite you to our first fortnightly Open NEST Developer Video Conference in 2024, today *Monday January 15, at 11:30 CET (UTC+0100).* As usual, in the Project team round, a contact person of each team will give a short statement summarizing ongoing and planned work in the team and highlight 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/2024-01-15-Open-NEST-Developer-… <https://github.com/nest/nest-simulator/wiki/2024-01-15-Open-NEST-Developer-…> Looking forward to seeing you soon! Cheers, Dennis Terhorst Log-in information We use a virtual conference room provided by DFN <https://www.dfn.de/en/> (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 <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 <http://vcc.zih.tu-dresden.de/index.php?linkid=1.1.3.4> -- Dipl.-Phys. Dennis Terhorst Coordinator Software Development Institute of Neuroscience and Medicine Computational and Systems Neuroscience (INM-6) & Institute for Advanced Simulation (IAS-6) Theoretical Neuroscience & JARA (INM-10) Jülich Research Center, Member of the Helmholz Association 52425 Jülich, Germany http://www.csn.fz-juelich.de/ Phone +49 2461 61-85062 ---------------------------------------------------------------------- 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. Astrid Lambrecht (Vorsitzende), Karsten Beneke (stellv. Vorsitzender), Dr. Ir. Pieter Jansens ----------------------------------------------------------------------

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NEST Conference 2024 — Save the date 17/18 June 2024
by Hans Ekkehard Plesser 21 Dec '23

21 Dec '23

Dear Colleagues, The NEST Initiative is excited to invite everyone interested in Neural Simulation Technology and the NEST Simulator to the NEST Conference 2024. Save the date for the virtual conference taking place on June 17–18, 2024! The annual 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! Registration and abstract submission will open early next year. For more information on the event please visit the conference website https://nest-simulator.org/conference. We are looking forward to seeing you in June and wish you happy holidays and a good start into the new year! Hans Ekkehard Plesser and colleagues [Image] -- Prof. Dr. Hans Ekkehard Plesser 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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Adding weight to synaptic currents
by atiye nejadebrahim 04 Dec '23

04 Dec '23

Dear All, I am going to add weights for excitatory and inhibitory synaptic currents according to this equation: can you help me how I can add S(Wji) to a simple neuron model like one I attached to this email?Thanks and BR, Atiyeh

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No NEST Open Developer VC today
by Hans Ekkehard Plesser 04 Dec '23

04 Dec '23

Dear all! Due to an on-site Hackathon today, we will not have a NEST Open Developer VC. See you on 18 December for the final VC of the year! Hans Ekkehard -- Prof. Dr. Hans Ekkehard Plesser 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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conda env deactivate PYTHONPATH
by anduls＠web.de 30 Nov '23

30 Nov '23

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Hardware computing bottlenecks for NEST simulations
by cagnol＠ksvi.mff.cuni.cz 23 Nov '23

23 Nov '23

Dear colleagues, We are procuring a new small computing cluster on which we want to primarily run NEST simulations. Our models are medium in size (100s of thousands of neurons) but we run them for relatively long biological times (100s of seconds), so the network setup duration is mostly irrelevant for us. What we would like to ask is if there is any insight into the current NEST simulator in terms of what are the hardware bottlenecks of these types of simulations. Are we going to do better with investing into more cores or higher clock speeds or more cache, or faster RAM? I understand that this is a complex multi-factor optimization question, but any insights or links to existing material that would allow us to form an informed decision would be greatly appreciated. Best regards, Remy Cagnol.

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NEST & Python 3.12
by Hans Ekkehard Plesser 23 Nov '23

23 Nov '23

Dear NEST Users! I am happy to report that I have successfully built NEST with Python 3.12. Right now, there are just one little problem: Unittest.assertDictContainsSubset() has been removed in Python 3.12, so five tests fail currently. This is fixed by https://github.com/nest/nest-simulator/pull/2997. Best regards, Hans Ekkehard -- Prof. Dr. Hans Ekkehard Plesser 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 install
by 1538356357＠qq.com 23 Nov '23

23 Nov '23

When installing Nest, I encountered the following error " Traceback (most recent call last): File "<stdin>", line 1, in <module> File "/home/yao/Documents/nest-simulator-2.16.0-build/lib/python2.7/site-packages/nest/__init__.py", line 70, in <module> from . import pynestkernel as _kernel # noqa ImportError: dynamic module does not define module export function (PyInit_pynestkernel) " I tried nest 2.16.0, nest 2.20.0, and nest 2.18.0, but all encountered this error. I haven't encountered it before, so I would like to ask for advice on how to do it

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The buffering mechanism of neurons and synapses in nest
by 1538356357＠qq.com 23 Nov '23

23 Nov '23

When I check the nest source code, the updates for each neuron are based on the ringbuffer. Its size is max_ Delay.The code defines moduli, whose size should be max as analyzed earlier_ Delay+min_ Delay, But I don't quite understand the mechanism of moduli because it involves the minimum delay of many neuron update steps, the size of ringbuffer, and the size of moduli. Can I see the relevant detailed information there, or can you guide me

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Open NEST Developer Video Conference Monday November 20, at 11:30 CET (UTC+0100)
by Dennis Terhorst 20 Nov '23

20 Nov '23

Dear NEST Users & Developers! I would like to invite you to our next fortnightly Open NEST Developer Video Conference today *Monday November 20, at 11:30 CET (UTC+0100).* As usual, in the Project team round, a contact person of each team will give a short statement summarizing ongoing and planned work in the team and highlight 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/2023-11-20-Open-NEST-Developer-… <https://github.com/nest/nest-simulator/wiki/2023-11-20-Open-NEST-Developer-…> Looking forward to seeing you soon! Cheers, Dennis Terhorst Log-in information We use a virtual conference room provided by DFN <https://www.dfn.de/en/> (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 <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 <http://vcc.zih.tu-dresden.de/index.php?linkid=1.1.3.4> -- Dipl.-Phys. Dennis Terhorst Coordinator Software Development Institute of Neuroscience and Medicine Computational and Systems Neuroscience (INM-6) & Institute for Advanced Simulation (IAS-6) Theoretical Neuroscience & JARA (INM-10) Jülich Research Center, Member of the Helmholz Association 52425 Jülich, Germany http://www.csn.fz-juelich.de/ Phone +49 2461 61-85062 ---------------------------------------------------------------------- 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. Astrid Lambrecht (Vorsitzende), Karsten Beneke (stellv. Vorsitzender), Dr. Ir. Pieter Jansens ----------------------------------------------------------------------

2 1

NEST make installcheck / Potential problems due to Pylint 3
by Hans Ekkehard Plesser 20 Nov '23

20 Nov '23

Dear NEST users and developers, Pylint was recently updated to version 3, which changed the way in which pylintrc is discovered (https://github.com/pylint-dev/pylint/issues/8862). This seems to break pytest. So if “make installcheck” gives you the message Executing NEST's testsuite... Error: PyNEST testing requested, but 'pytest' cannot be run. Testing also requires the 'pytest-xdist' and 'pytest-timeout' extensions. And running pytest --version gives you a long error trace ending in ImportError: cannot import name 'PYLINTRC' from 'pylint.config' ... and pylint --version shows version 3.x.x, you need to downgrade to “pylint<3”. https://github.com/nest/nest-simulator/pull/2996 updates our environment file accordingly. Best, Hans Ekkehard -- Prof. Dr. Hans Ekkehard Plesser 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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recording I_syn
by atiye nejadebrahim 13 Nov '23

13 Nov '23

Hello all, I need to record I_sys from the neurons of network, but when I use .recordables for my neuron defined, I_syn isn't included in recording. can you help me how can I make I_sys recordable?Thanks for your help. Best, Atiyeh

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Replay Poisson input
by Maryada Maryada 08 Nov '23

08 Nov '23

Dear NEST Users, Is there an easy way to replay the poisson input other than saving spike timings and using spike_generator to replay. -- Thanks and Regards *Maryada*

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Open NEST Developer Video Conference Monday November 6, at 11:30 CET (UTC+0100)
by Dennis Terhorst 06 Nov '23

06 Nov '23

Dear NEST Users & Developers! I would like to invite you to our next fortnightly Open NEST Developer Video Conference today Monday November 6, at 11:30 CET (UTC+0100). As usual, in the Project team round, a contact person of each team will give a short statement summarizing ongoing and planned work in the team and highlight 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/2023-11-06-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 -- Dipl.-Phys. Dennis Terhorst Coordinator Software Development Institute of Neuroscience and Medicine Computational and Systems Neuroscience (INM-6) & Institute for Advanced Simulation (IAS-6) Theoretical Neuroscience & JARA (INM-10) Jülich Research Center, Member of the Helmholz Association 52425 Jülich, Germany http://www.csn.fz-juelich.de/ Phone +49 2461 61-85062 ---------------------------------------------------------------------- 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. Astrid Lambrecht (Vorsitzende), Karsten Beneke (stellv. Vorsitzender), Dr. Ir. Pieter Jansens ----------------------------------------------------------------------

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4 Neuron Test--Multimeter Connect Error
by Allen Rabayda 29 Oct '23

29 Oct '23

Dear Community, Anyone have suggestions to fix multimeter1 to neuron[0] connect error in my simple 4 neuron test? 'nest.Connect(mm_iz1, n_iz2[0])' Error: 'ArgumentType', <SLILiteral: Connect>, ': The type of the second parameter did not match the argument(s) of this function.' My code attached. Thx for any suggestions. Regards, --Allen

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Open NEST Developer Video Conference Monday October 23 2023 11:30 CEST (UTC+2)
by Dennis Terhorst 23 Oct '23

23 Oct '23

Dear NEST Users & Developers! I would like to invite you to our next fortnightly Open NEST Developer Video Conference, today Monday October 23, 11.30-12.30 CEST (UTC+2). Also 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/2023-10-23-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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Open NEST Developer Video Conference Monday October 16 2023 11:30 CEST (UTC+2)
by Dennis Terhorst 16 Oct '23

16 Oct '23

Dear NEST Users & Developers! I would like to invite you to our next fortnightly Open NEST Developer Video Conference, today Monday October 16, 11.30-12.30 CEST (UTC+2). Also 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. In the in-depth discussion I would like to go through some proposed changes in the CI setup to get some feedback and learn about your perspectives on these topics. 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/2023-10-16-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

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Open NEST Developer Video Conference Monday October 9 2023 11:30 CEST (UTC+2)
by Dennis Terhorst 09 Oct '23

09 Oct '23

Dear NEST Users & Developers! I would like to invite you to our next fortnightly Open NEST Developer Video Conference, today Monday October 9, 11.30-12.30 CEST (UTC+2). Also 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/2023-10-09-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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Simple Additive STDP Dynamics (`stdp_synapse`) only seeing LTD not LTP
by Tony Lee 02 Oct '23

02 Oct '23

Hi, I'm attempting to recreate the STDP dynamic figure like that of [this figure](https://www.jneurosci.org/content/jneuro/20/23/8812/F1.large.jpg?wi… (from [this paper](https://www.jneurosci.org/content/20/23/8812)). However, no matter how I tune the time-constants and transmission delays, it seems that the potentiation side of the dynamics is just missing. I've checked the NEST ML equations and C++ header files and they look fine. Thus, I am needing a second opinion to see if I am missing something obvious. [Here](https://gist.github.com/aoot/9409b939e891a1c823cc7defe97ab479) is the code in ipynb form and the figure I have (missing the LTP side). Thank you, Anthony

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NEST 3.6 released
by Hans Ekkehard Plesser 28 Sep '23

28 Sep '23

Dear NEST Users! It is a great pleasure to inform you that we have released NEST 3.6 which brings a number of exciting enhancements in particular * Support for astrocytes and a first astrocyte model * A new glif_psc_double_alpha model * Much improved performance, especially for highly threaded simulations * Improved security for NEST Server * Minor changes to the volume transmitter syntax and to rarely used kernel attributes * Many tests ported to pytest and modernized * Lots of minor improvements and bug fixes For more information, see - https://nest-simulator.readthedocs.io/en/v3.6/whats_new/v3.6/index.html - https://github.com/nest/nest-simulator/releases/tag/v3.6 I would like to thank all NEST developers who contributed to this release and the NEST release team, especially Dennis, for making this release a reality. Best wishes straight from the Bernstein Conference in Berlin, Hans Ekkehard -- Prof. Dr. Hans Ekkehard Plesser 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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CMake error
by atiye nejadebrahim 28 Sep '23

28 Sep '23

Dear All, I am trying to install nest from source in miniconda3 (ubuntu) and following this instruction (Install from source in a conda environment — NEST Simulator Documentation),but at this step, cmake -DCMAKE_INSTALL_PREFIX:PATH=$CONDA_PREFIX /home/atiye/Downloads/nest-simulator-3.5 I face with this error: CMake Error: CMake was unable to find a build program corresponding to "Unix Makefiles". CMAKE_MAKE_PROGRAM is not set. You probably need to select a different build tool.CMake Error: CMAKE_CXX_COMPILER not set, after EnableLanguageCMake Error: CMAKE_C_COMPILER not set, after EnableLanguage-- Configuring incomplete, errors occurred! Can you help me to remove this error and install nest?Thanks.Best, Atiyeh | | | | Install from source in a conda environment — NEST Simulator Documentation This is the documentation index for the NEST, a simulator for spiking neuronal networks. | | |

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Open NEST Developer Video Conference Monday September 25 2023 11:30 CEST (UTC+2)
by Hans Ekkehard Plesser 25 Sep '23

25 Sep '23

1. Dear NEST Users & Developers! I would like to invite you to our next fortnightly Open NEST Developer Video Conference, today Monday September 25, 11.30-12.30 CEST (UTC+2). Also 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 1. Welcome 2. Review of NEST User Mailing List<https://www.nest-simulator.org/mailinglist/hyperkitty/list/users@nest-simul…> 3. Project team<https://github.com/nest/nest-simulator/projects> round 4. In-depth discussion * NEST 3.6 Release * Next steps * Two hints for productive work * Semantics of tripartite connections (https://github.com/nest/nest-simulator/pull/2955; see in particular this proposal<https://github.com/nest/nest-simulator/pull/2955#issuecomment-1733030870>) * New way of registering connections (https://github.com/nest/nest-simulator/pull/2956) The agenda for this meeting is also available online, see https://github.com/nest/nest-simulator/wiki/2023-09-25-Open-NEST-Developer-… Looking forward to seeing you! Cheers, Hans Ekkehard ------------------ 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<tel:+493020097938800> 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 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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error in making new module
by atiye nejadebrahim 21 Sep '23

21 Sep '23

Dear all, I installed nest from source according to this instruction (Install NEST from source — NEST Simulator Documentation) but when I run this code to make a module, I face with following error. Can you help me to solve it? import matplotlib as mplimport matplotlib.pyplot as pltimport nestimport numpy as npimport osfrom pynestml.frontend.pynestml_frontend import generate_nest_target NEST_SIMULATOR_INSTALL_LOCATION = nest.ll_api.sli_func("statusdict/prefix ::") generate_nest_target(input_path="/home/atiye/nestml/models/neurons/hh_psc_alpha1.nestml", target_path="/home/atiye/new_neuron2", module_name="hh_psc_alpha1_module", suffix="_nestml", logging_level="ERROR", # try "INFO" for more debug information codegen_opts={"nest_path": NEST_SIMULATOR_INSTALL_LOCATION})nest.Install("hh_psc_alpha1_module") errors:cd /home/atiye/New\ folder ; /usr/bin/env /bin/python3 /home/atiye/.vscode-server/extensions/ms-python.python-2023.16.0/pythonFiles/lib/python/debugpy/adapter/../../debugpy/launcher 52383 -- /home/atiye/New\ folder/hh_motor_neuron.py -- N E S T -- Copyright (C) 2004 The NEST Initiative Version: 3.5 Built: Jul 13 2023 04:45:54 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. -- N E S T -- Copyright (C) 2004 The NEST Initiative Version: 3.5 Built: Jul 13 2023 04:45:54 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. -- The CXX compiler identification is GNU 11.3.0-- Detecting CXX compiler ABI info-- Detecting CXX compiler ABI info - done-- Check for working CXX compiler: /usr/bin/g++ - skipped-- Detecting CXX compile features-- Detecting CXX compile features - done -------------------------------------------------------hh_psc_alpha1_module Configuration Summary------------------------------------------------------- C++ compiler : /usr/bin/g++Build static libs : OFFC++ compiler flags : NEST compiler flags : -g -O2 -ffile-prefix-map=/build/nest-gCkf8Z/nest-3.5-0ubuntu1ppa1-1389=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -std=c++11 -Wall -fopenmp -O2 -fdiagnostics-color=autoNEST include dirs : -I/build/nest-gCkf8Z/nest-3.5-0ubuntu1ppa1-1389/debian/nest/usr/include/nest -I/usr/include -I/usr/include -I/usr/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/includeNEST libraries flags : -L/build/nest-gCkf8Z/nest-3.5-0ubuntu1ppa1-1389/debian/nest/usr/lib/nest -lnest -lsli -fopenmp /usr/lib/x86_64-linux-gnu/libltdl.so /usr/lib/x86_64-linux-gnu/libreadline.so /usr/lib/x86_64-linux-gnu/libncurses.so /usr/lib/x86_64-linux-gnu/libgsl.so /usr/lib/x86_64-linux-gnu/libgslcblas.so /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so ------------------------------------------------------- You can now build and install 'hh_psc_alpha1_module' using make make install The library file libhh_psc_alpha1_module.so will be installed to /build/nest-gCkf8Z/nest-3.5-0ubuntu1ppa1-1389/debian/nest/usr/lib/nestThe module can be loaded into NEST using (hh_psc_alpha1_module) Install (in SLI) nest.Install(hh_psc_alpha1_module) (in PyNEST) CMake Warning (dev) in CMakeLists.txt: No cmake_minimum_required command is present. A line of code such as cmake_minimum_required(VERSION 3.22) should be added at the top of the file. The version specified may be lower if you wish to support older CMake versions for this project. For more information run "cmake --help-policy CMP0000".This warning is for project developers. Use -Wno-dev to suppress it. -- Configuring done-- Generating done-- Build files have been written to: /home/atiye/new_neuron2[ 66%] Building CXX object CMakeFiles/hh_psc_alpha1_module_module.dir/hh_psc_alpha1_module.o[ 66%] Building CXX object CMakeFiles/hh_psc_alpha1_module_module.dir/hh_psc_alpha1_nestml.o/home/atiye/new_neuron2/hh_psc_alpha1_module.cpp:26:10: fatal error: connection_manager_impl.h: No such file or directory 26 | #include "connection_manager_impl.h" | ^~~~~~~~~~~~~~~~~~~~~~~~~~~compilation terminated.make[2]: *** [CMakeFiles/hh_psc_alpha1_module_module.dir/build.make:76: CMakeFiles/hh_psc_alpha1_module_module.dir/hh_psc_alpha1_module.o] Error 1make[2]: *** Waiting for unfinished jobs..../home/atiye/new_neuron2/hh_psc_alpha1_nestml.cpp:29:10: fatal error: numerics.h: No such file or directory 29 | #include "numerics.h" | ^~~~~~~~~~~~compilation terminated.make[2]: *** [CMakeFiles/hh_psc_alpha1_module_module.dir/build.make:90: CMakeFiles/hh_psc_alpha1_module_module.dir/hh_psc_alpha1_nestml.o] Error 1make[1]: *** [CMakeFiles/Makefile2:110: CMakeFiles/hh_psc_alpha1_module_module.dir/all] Error 2make: *** [Makefile:156: all] Error 2Traceback (most recent call last): File "/home/atiye/.local/lib/python3.10/site-packages/pynestml/codegeneration/nest_builder.py", line 176, in build subprocess.check_call(make_all_cmd, stderr=stderr, stdout=stdout, shell=shell, File "/usr/lib/python3.10/subprocess.py", line 369, in check_call raise CalledProcessError(retcode, cmd)subprocess.CalledProcessError: Command '['make', '-j8', 'all']' returned non-zero exit status 2. During handling of the above exception, another exception occurred: Traceback (most recent call last): File "/home/atiye/New folder/hh_motor_neuron.py", line 11, in <module> generate_nest_target(input_path="/home/atiye/nestml/models/neurons/hh_psc_alpha1.nestml", File "/home/atiye/.local/lib/python3.10/site-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 "/home/atiye/.local/lib/python3.10/site-packages/pynestml/frontend/pynestml_frontend.py", line 198, in generate_target if not process() == 0: File "/home/atiye/.local/lib/python3.10/site-packages/pynestml/frontend/pynestml_frontend.py", line 351, in process _builder.build() File "/home/atiye/.local/lib/python3.10/site-packages/pynestml/codegeneration/nest_builder.py", line 183, in build raise GeneratedCodeBuildException(stages_exception[current_stage])pynestml.exceptions.generated_code_build_exception.GeneratedCodeBuildException: Error occurred during 'make all'! More detailed error messages can be found in stderr. Thanks a lotBest, Atiyeh

2 1

MPI launcher
by atiye nejadebrahim 20 Sep '23

20 Sep '23

Dear all, During running my network in nest, I faced with this error, can you help me how can I remove this error?you seem to be using NEST via an MPI launcher like mpirun, mpiexec or srun although NEST was not compiled with MPI support. Best, Atiyeh

3 2

No Open NEST Developer VC today
by Hans Ekkehard Plesser 11 Sep '23

11 Sep '23

Dear Colleagues, There will be no NEST Developer Video Conference today. See you again on 25 September at 11.30! Best, Hans Ekkehard -- Prof. Dr. Hans Ekkehard Plesser 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

A problem running a .nestml file
by Hedyeh Rezaei 01 Sep '23

01 Sep '23

Dear all, I have installed nestml via conda and developed a code describing an LIF neuron with bi-exponential synaptic currents including NMDA, while the charge mediated by AMPA and NMDA receptors are not independent. When I try to compile the .nestml file, it gives me an error as: from pynestml.frontend.pynestml_frontend import generate_nest_target WARNING:root:PyGSL is not available. The stiffness test will be skipped. WARNING:root:Error when importing: No module named 'pygsl' In [2]: generate_nest_target(input_path="/home/hrezaei/neuron_model_NMDA.nestml", ...: target_path="/tmp/nestml-component", ...: logging_level="ERROR") line 61:4 extraneous input 'end' expecting {DEDENT, 'function', 'state', 'parameters', 'internals', 'update', 'equations', 'input', 'output'} line 63:4 extraneous input 'equations' expecting {<EOF>, NEWLINE, 'neuron', 'synapse'} line 64:8 extraneous input ' ' expecting {<EOF>, NEWLINE, 'neuron', 'synapse'} line 67:8 extraneous input 'kernel' expecting {<EOF>, NEWLINE, 'neuron', 'synapse'} line 70:8 extraneous input 'kernel' expecting {<EOF>, NEWLINE, 'neuron', 'synapse'} ... r"""Generate and build code for NEST Simulator. Parameters A dictionary containing additional options for the target code generator. """ I was wondering what the reason could be. I would appreciate it if you could help. Thanks in advance. Best, Hedyeh

3 4

OpenMP: only one thread is used
by Stefan Dvoretskii 30 Aug '23

30 Aug '23

Hello all, I am trying to use as much parallelism as possible on my computing grid. In this sense, I combine MPI+OpenMP. MPI processes are spawned fine, but OpenMP threads always amount to 1, no matter that I set local_num_threads correctly ( https://nest-simulator.readthedocs.io/en/latest/hpc/slurm_script.html#set-l…) as well as all SLURM variables. I am sure I have compiled nest with OpenMP too. I use slightly modified izhikevich neurons with stdp synapses. Can the model specifics be the cause of underutilizing available threads? Or is there something else in the system that could be the reason for that? Best regards, -- Stefan Dvoretskii

4 5

Network simulation of Hanuschkin (2010) - precise spike times
by Evgenia Kartsaki 28 Aug '23

28 Aug '23

Hello, I am trying to simulate the network of a model with precise spike times as in Hanuschkin (2010), which is based on the balanced random network of Brunel (2000). As far as I understand the model of Hanuschkin exists already in NEST here: https://nest-simulator.readthedocs.io/en/v3.5/models/iaf_psc_exp_ps.html . However, I haven't found an example of the network simulation. I have tried using the Brunel network (https://nest-simulator.readthedocs.io/en/stable/auto_examples/brunel_delta_…) with the iaf_psc_exp_ps model, but I got a firing rate (excitatory or inhibitory) of 0 Hz. I would appreciate any advice on that! Thanks in advance, Jenny

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Open NEST Developer Video Conference Monday August 28 2023 11:30 CEST (UTC+2)
by Dennis Terhorst 28 Aug '23

28 Aug '23

Dear NEST Users & Developers! I would like to invite you to our next fortnightly Open NEST Developer Video Conference, today Monday August 28, 11.30-12.30 CEST (UTC+2). Also 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/2023-08-28-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

Finalization of release procedure: NEST 3.5
by Dennis Terhorst 24 Aug '23

24 Aug '23

Dear all, After the quite silent NEST 3.5 release on GitHub in July we have waited a bit to publish the DOI record. Now we have completed the last step of the release process and I am happy to announce the completed NEST Simulator 3.5. When using this version of NEST in your work you can cite it as Haug et al. (2023). NEST 3.5. Zenodo. https://doi.org/10.5281/zenodo.8069926 As usual the full citation record and other citation formats for this and other versions are available on Zenodo. Thanks to all of you for being in this enthusiastic community and a very special thanks to everyone that contributed to this release! We're looking forward to the exciting scientific results you may produce with this tool! Best, Dennis -- Dipl.-Phys. Dennis Terhorst Coordinator Software Development Institute of Neuroscience and Medicine Computational and Systems Neuroscience (INM-6) & Institute for Advanced Simulation (IAS-6) Theoretical Neuroscience & JARA (INM-10) Jülich Research Center, Member of the Helmholz Association 52425 Jülich, Germany http://www.csn.fz-juelich.de/ Phone +49 2461 61-85062 ---------------------------------------------------------------------- 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. Astrid Lambrecht (Vorsitzende), Karsten Beneke (stellv. Vorsitzender), Dr. Ir. Pieter Jansens ----------------------------------------------------------------------

1 0

GetConnections is too slow- can i obtain connection ids as I connect the neurons? (nest v2.20)
by Angeliki Papadimitriou 24 Aug '23

24 Aug '23

Hello, I have a serious bottleneck in terms of runtime in my simulations. I have a modular cortical network and i need to 'manually' change weights in some specific connections before i start the simulation. The modularity means that this happens inside a for loop for all populations pairs. so, before simulation starts i have a function that goes over all population pairs and does this: AMPA_conns = nest.GetConnections(source=pre_pop,target=post_pop, synapse_model='AMPA_synapse_longrange') # RETRIEVE ALL AMPA CONNECTIONS BETWEEN SOURCE AND TARGET POPULATION nest.SetStatus(AMPA_conns, {'weight': pattern_weight}) # CHANGE CONNECTION WEIGHT NMDA_conns = nest.GetConnections(source=pre_pop,target=post_pop, synapse_model='NMDA_synapse_longrange') # RETRIEVE ALL NMDA CONNECTIONS BETWEEN SOURCE AND TARGET POPULATION nest.SetStatus(NMDA_conns, {'weight': pattern_weight * nmda2ampa_ratio}) # CHANGE CONNECTION WEIGHT commenting out these 4 lines reduces my runtime by 8 hours. for reference, the model consists of ~27000neurons, is created in 20 minutes (nodes generated and connections drawn) and the actual simulation runs for about 15 minutes. so my question is: is there a way to obtain the connection ids as i draw the connections (right after the nest.Connect() function) so that i can store them in a data structure and avoid this expensive operation of searching? or perhaps it is the setstatus that makes it expensive? *I havent yet migrated to nest v3, this concerns version 2.20. thank you for your time! angeliki

2 5

asynchronicity between spikes and firing pattern
by atiye nejadebrahim 24 Aug '23

24 Aug '23

Dear All, I made a HH neuron model and I can get an action potential from it. but it seems there is a problem in spikes. Action potential shape show one spike, but spike recorder shows several spikes and there is not any synchronicity between them. can you help me why? my second question is about spike generation, when I use I_e current for injecting current to the neuron, I can record spikes, but when I use step current generators, no spike shows. can you help me why?Thank you for your consideration. Best, Atiyeh Dear All, I made a HH neuron model and I can get an action potential from it. but it seems there is a problem in spikes. Action potential shape show one spike, but spike recorder shows several spikes and there is not any synchronicity between them. can you help me why? my second question is about spike generation, when I use I_e current for injecting current to the neuron, I can record spikes, but when I use step current generators, no spike shows. can you help me why?Thank you for your consideration. Best, Atiyeh

3 6

asynchronicity between spikes and firing pattern
by atiye nejadebrahim 22 Aug '23

22 Aug '23

Dear All, I made a HH neuron model and I can get an action potential from it. but it seems there is a problem in spikes. Action potential shape show one spike, but spike recorder shows several spikes and there is not any synchronicity between them. can you help me why? my second question is about spike generation, when I use I_e current for injecting current to the neuron, I can record spikes, but when I use step current generators, no spike shows. can you help me why?Thank you for your consideration. Best, Atiyeh

1 0

Multimeter data while multiple runs
by Maryada Maryada 22 Aug '23

22 Aug '23

Dear NEST Users, I am simulating my network multiple times (split simulation). I tried but nest.simulate(100) in a for loop and with RunManager() with nest.RunManager(): df_mul = pd.DataFrame() for _ in np.arange(0,3,1): nest.Run(150.0) df_mul = pd.concat([df_mul,pd.DataFrame(mult.get('events'))]) However in both case, it only record NaN [image: image.png] -- Thanks and Regards *Maryada*

3 3

Open NEST Developer Video Conference Monday July 17 2023 11:30 CEST (UTC+2)
by Dennis Terhorst 14 Aug '23

14 Aug '23

Dear NEST Users & Developers! I would like to invite you to our next fortnightly Open NEST Developer Video Conference, today Monday August 14, 11.30-12.30 CEST (UTC+2). Also 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. In the in-depth discussion I would like to go through some proposed changes in the CI setup to get some feedback and learn about your perspectives on these topics. 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 * NEST with "Salsa" The agenda for this meeting is also available online, see https://github.com/nest/nest-simulator/wiki/2023-08-14-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 1

Maintaining connection weights outside synapse
by Stefan Dvoretskii 07 Aug '23

07 Aug '23

Hello all, I am trying to implement a sort of plasticity that keeps the sum of all outgoing weights of the neuron constant. It would require not only knowing the weights of all synapses at a simulation timestep, but also setting them externally with this knowledge, i.e. setting weights outside of single synapse context. Is there any way I could implement it efficiently in NEST? Thanks in advance! Best regards, -- Stefan Dvoretskii

3 4

Synapses support only one spiking input port
by Stefan Dvoretskii 02 Aug '23

02 Aug '23

Hello, I am using an example synapse model which utilizes both post and pre spikes (nestml/models/synapses/stdp_nn_symm.nestml at master · nest/nestml (github.com) <https://github.com/nest/nestml/blob/master/models/synapses/stdp_nn_symm.nes…> ). I get an error: ... File "/dss/dsshome1/00/ge72puf2/.conda/envs/nest/lib/python3.8/site-packages/pynestml/codegeneration/nest_code_generator.py", line 469, in _get_synapse_model_namespace assert len(namespace["pre_ports"]) <= 1, "Synapses only support one spiking input port" AssertionError: Synapses only support one spiking input port It is confusing: can I or can I not use a model with 2 synaptic inputs (post and pre)? Is that a version thing? Best regards, -- Stefan

4 6

NEST Compilation Issue on openSUSE Machine - Missing <mach-o/dyld.h> Header
by Jesus Espinoza 01 Aug '23

01 Aug '23

Dear NEST Community, I hope this email finds you well. I am encountering some challenges while attempting to compile the NEST simulator on an openSUSE machine. I am using the provided CMake command, which has worked successfully on my Ubuntu machine with the required libraries and environment loaded. However, on the openSUSE machine, the compilation process fails with an error related to the <mach-o/dyld.h> header, which seems specific to macOS. The CMake command I am using is as follows: ``` conda activate python_for_nest module load gsl/2.6 openmpi/cxx-4.1.1 cmake -Dwith-python=ON \ -Dwith-gsl=ON \ -Dwith-openmp=ON \ -DMPI_CXX_COMPILER=$(which mpic++) \ -DMPI_C_COMPILER=$(which mpicc) \ -Dwith-mpi=ON \ -DCMAKE_INSTALL_PREFIX:PATH=${PREFIX} ${SRC} ``` The error messages I encounter during the compilation are as follows, all mach-related: ``` Building C object CMakeFiles/cmTC_4dc4e.dir/HAVE_MACH_O_DYLD_H.c.o /usr/bin/cc -o CMakeFiles/cmTC_4dc4e.dir/HAVE_MACH_O_DYLD_H.c.o -c /home/espinoza/opt/nest/master/nest-simulator-build/CMakeFiles/CheckIncludeFiles/HAVE_MACH_O_DYLD_H.c /home/espinoza/opt/nest/master/nest-simulator-build/CMakeFiles/CheckIncludeFiles/HAVE_MACH_O_DYLD_H.c:2:10: fatal error: mach-o/dyld.h: No such file or directory 2 | #include <mach-o/dyld.h> | ^~~~~~~~~~~~~~~ compilation terminated. gmake[1]: *** [CMakeFiles/cmTC_4dc4e.dir/build.make:85: CMakeFiles/cmTC_4dc4e.dir/HAVE_MACH_O_DYLD_H.c.o] Fehler 1 gmake[1]: Verzeichnis „/home/espinoza/opt/nest/master/nest-simulator-build/CMakeFiles/CMakeTmp“ wird verlassen gmake: *** [Makefile:140: cmTC_4dc4e/fast] Fehler 2 ``` From my understanding, `<mach-o/dyld.h>` is primarily used for macOS, and its absence on openSUSE is causing the compilation error. I kindly request any hint or advice for resolving this issue. Is there any way I can modify the CMake command or the environment to ensure successful compilation on the openSUSE machine? Additionally, if there are any specific libraries or configurations that need to be adjusted for openSUSE, I would greatly appreciate your guidance. To further investigate the issue, I will attach the `CMakeError.log` and `CMakeOutput.log` files to this email. Thank you very much for your time and support. Any insights or suggestions you can provide will be invaluable in resolving this problem. Best regards, Jesús Espinoza -- Jesús Espinoza Bergische Universität Wuppertal Fakultät für Mathematik und Naturwissenschaften Wissenschaftliches Rechnen und Hochleistungsrechnen Gaußstraße 20 42119 Wuppertal Germany E-Mail: espinozavalverd{at}uni-wuppertal.de

3 2

Results of simulation using `fixed_indegree` seem to depend on `total_num_virtual_procs`
by Jesus Espinoza 31 Jul '23

31 Jul '23

Hello everyone, I am writing to the NEST mailing list as I have encountered an issue in my simulation script, and I would greatly appreciate your insights. The problem I am facing is that the membrane potential time course for a simulation with a fixed indegree seems to be dependent on the number of virtual processes (`total_num_virtual_procs`). Interestingly, this behavior does not occur for simulations with all-to-all connectivity. The simulation involves a network with the following architecture: 5 `spike_generator` nodes connected to 5 `parrot_neuron` nodes with (all-to-all), which are further connected to 5 `iaf_psc_delta` neurons (all-to-all). The connections between the `iaf_psc_delta` neurons have an `fixed_indegree` of 2. A voltmeter is used to monitor the membrane potentials of these 5 neurons, and the simulation runs for 100 ms. The issue arises when I vary the number of virtual processes (`total_num_virtual_procs`). I have tested the values 1, 2, and 4, and I have noticed that the plot of the membrane potentials at the end of the simulation differs for each `total_num_virtual_procs` value. Additionally, when I print the table of connections, I observe that the weights between the `iaf_psc_delta` neurons are also influenced by the number of virtual processes. I have attached the simulation script and three images showing the plot for each `total_num_virtual_procs` value. The experiments were conducted on my personal Ubuntu machine. The version of NEST that I am using is the latest at the time of writing this message, with commit `b9514cce789fb0b2c0dfbd9d0894d3986f743021`, authored by Abigail Morrison <morrison(a)fz-juelich.de> on Tue Jul 18 23:46:22 2023 +0200. I would be grateful for any suggestions or explanations regarding this issue, as it hinders the reproducibility of my results. Thank you in advance for your valuable help and support. Best regards, Jesus Espinoza. -- Jesús Espinoza Bergische Universität Wuppertal Fakultät für Mathematik und Naturwissenschaften Wissenschaftliches Rechnen und Hochleistungsrechnen Gaußstraße 20 42119 Wuppertal Germany E-Mail: espinozavalverd{at}uni-wuppertal.de

4 4

CXX compiler change path
by Stefan Dvoretskii 27 Jul '23

27 Jul '23

Hello, when running code generator(NESTCodeGeneratorUtils.generate_code_for), I encounter an error: -- The CXX compiler identification is unknown CMake Error at CMakeLists.txt:95 (project): The CMAKE_CXX_COMPILER: /home/conda/feedstock_root/build_artifacts/nest-simulator_1633676998878/_build_env/bin/x86_64-conda-linux-gnu-c++ is not a full path to an existing compiler tool. Tell CMake where to find the compiler by setting either the environment variable "CXX" or the CMake cache entry CMAKE_CXX_COMPILER to the full path to the compiler, or to the compiler name if it is in the PATH. I have tried to set CXX variable to one of the compilers I have on the system, but it did not work. I don't know how to set CMAKE_CXX_COMPILER in this context. Maybe someone could give me an advice on that? Best regards, -- Stefan

2 2

Axonal delay
by ali.ghadiri1375＠gmail.com 26 Jul '23

26 Jul '23

Hi everyone, How can I implement axonal delay in synapse models of NEST?

3 2

Open NEST Developer Video Conference Monday July 17 2023 11:30 CEST (UTC+2)
by Dennis Terhorst 17 Jul '23

17 Jul '23

Dear NEST Users & Developers! I would like to invite you to our next fortnightly Open NEST Developer Video Conference, today Monday July 17, 11.30-12.30 CEST (UTC+2). Also 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/2023-07-17-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

Casting in NESTML
by chiara de luca 06 Jul '23

06 Jul '23

Hello everyone, just a small question about NESML. I would like to cast a variable from float to integer in the onReceive block of a custom synapse model. Is there an easy way to do that? Can't find anything in documentation about that. Thank you! Chiara

2 1

Open NEST Developer Video Conference Monday July 3 2023 11:30 CEST (UTC+2)
by Dennis Terhorst 03 Jul '23

03 Jul '23

Dear NEST Users & Developers! I would like to invite you to our next fortnightly Open NEST Developer Video Conference, today Monday July 3, 11.30-12.30 CEST (UTC+2). Also 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. Special topic today will be a discussion on dependency management. 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/2023-07-03-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

Re: Connection by dendrite
by Jona Scholz 02 Jul '23

02 Jul '23

Hello Anno and Willem, thank you for your replies. Anno's description of the problem is exactly what I was trying to express. It's too bad that generating connectivity like this can not be achieved as easily as I had hoped. Either way, that answers my question. The reference to the blue brain project is very interesting. Their work seems to be relevant to several of my problems. Thank you both :) Kind regards, Jona

1 0

Repeated simulations of the same specified connectivity
by Daniel Esposito 30 Jun '23

30 Jun '23

I want to initialize a network with some random connectivity, following some standard connectivity rules, like is achieved by standard use of the nest.Connect function.Then I want to make several runs of this network, with the same connectivity. I learned however that this is not a straightforward thing to do repeated runs of the same network in NEST. Although I saw different solutions online, it is not clear that there is a 'standard' solution for how to achieve this goal of just initializing the network with the same connectivity several times, which seems fairly simple. This link <https://nest-simulator.readthedocs.io/en/stable/auto_examples/store_restore…> here, for example, shows how to store and restore a network, but it seems like overshoot for my purpose (the described problem is a network with plasticity). I also thought of creating a network, extract the connectivity, and then impose this connectivity in new networks, following what is explained here <https://nest-simulator.readthedocs.io/en/v3.4/synapses/connection_managemen…> in the 'Connecting sparse matrices with array indexing' section, but it's a bit tedious to implement (I started implementing it) and error prone. The alternative I'm thinking of now is to just re create the network on each pass of my loop with standard NEST functions, but giving the same random seed to NEST before making the connectivity each time. After the connectivity is done, I'd pass a new random seed, sampled from numpy's random number generator, and so each simulation would be a different repeat. I was wondering whether this very simple approach I propose would work, or whether I'm missing something. Thanks

1 0

Re: Connection by dendrite
by Jona Scholz 30 Jun '23

30 Jun '23

Hello Anno, thank you for your reply. Not sure what using compartments entails, but I'm guessing I only need distance dependent connection probabilities. The probability should be 1 if a dendrite is close enough to a given neuron and 0 otherwise. Another point that may be relevant: it should be possible to have multiple connections between a pair of neurons. Each connection should be able to learn with a variation of STDP. Is this supported by default? Kind regards, Jona

3 2

EBRAINS — Survey on use of tools and services
by Hans Ekkehard Plesser 30 Jun '23

30 Jun '23

Dear NEST Users, As you may know, the Human Brain Project is coming to an end in September and we are currently working hard on planning the future of the EBRAINS Research Infrastructure. In this context, EBRAINS has started a survey to determine the interest in tools and services provided by EBRAINS. The results of this survey will inform decisions on priorities for funding applications. We hope you could contribute to this survey by filling it in at https://wiki.ebrains.eu/bin/view/Collabs/slu-hbpb/25.06/ and would in particular hope that you would tick the boxes for NEST and related tools such as NESTML, NEST Desktop, Elephant (listed as Electrophysiology Analysis Toolkit) and LFPy. For the question "Relationship status on HBP and EBRAINS", if you are not working in an HBP-affiliated lab, "Stakeholder" is probably the most suitable answer, as there is no explicit category for "Tool User" or "Tool Contributor". Information on all tools listed in the survey is available under https://wiki.ebrains.eu/bin/view/Collabs/slu-hbpb/Tools%20description/ or the "Tools description" link on the left edge of the survey page. 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

Connection by dendrite
by jona.m.scholz＠gmail.com 29 Jun '23

29 Jun '23

Hello everyone, first off some disclaimers (feel free to skip). I'm new to the space and don't know what I'm talking about. I'm also sorry if this is question is redundant, but I couldn't find an answer to it. Imagine a spatial network where neurons have free positions. Each neuron has associated dendrites, which are also just points in space. 2 neurons are connected if and only if the dendrite of 1 neuron is very close to the other neuron. I've created an image to show what I mean, but couldn't upload it here. It's under this link: https://ibb.co/nfh9hbn Is there a good way to achieve this? If there is not, what would be the best way to implement it? The pointers I'm looking for are along the lines of "yes use function x" or "no, you have to implement it in python" or maybe even "you can add this connectivity to our C++ back-end if you do this and that". Kind regards, Jona

2 1

Open NEST Developer Video Conference Monday June 19 2023 11:30 CEST (UTC+2)
by Dennis Terhorst 19 Jun '23

19 Jun '23

Dear NEST Users & Developers! I would like to invite you to our next fortnightly Open NEST Developer Video Conference, today Monday June 19, 11.30-12.30 CEST (UTC+2). Also 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/2023-06-19-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

correlated gaussian noise
by saeed taghavi 14 Jun '23

14 Jun '23

is there a way to generate correlated Gaussian white noise in the NEST? It is stated that the "noise_generator" can be used to inject a "Gaussian white” noise current into a node, also it is stated that all targets of a noise generator receive different currents. I am looking for a way to produce correlated white noise, or equally send the same noise to all targets of the "noise_generator". In the next step, I like to have a small duration of noisy current, then inject the same current into different neurons at different times. Best, Saeed

2 1

problem with cmake directory
by atiye nejadebrahim 12 Jun '23

12 Jun '23

Hi all, I am running a nestml code and I have updated cmake,But I always receive this error ¨no such file or directory cmake¨. all .cpp and .h files are built and just the last .so file is remained. Can you help me how I can remove this error? Best,Atiyeh

2 2

GetConnections in distributed simulation
by Petia Koprinkova 06 Jun '23

06 Jun '23

Dear NEST Support team, We are trying to get the weights of stdp synapses during a distributed simulation. According to NEST documentation and our experience function GetConnections returns only local connections but not all connections in our model. Could you please advise us how to get all connections in such a case? Best regards, Petia Koprinkova-Hristova

4 8

Adding gap junctions using NESTML
by bstrohmer＠gmail.com 06 Jun '23

06 Jun '23

Hi everyone, has anyone successfully added a gap junction to an existing model using NESTML? I would like to add gap junction support to the aeif_cond_alpha neuron model but it is unclear how this can be done within NESTML. As suggested by Charl, I started to look into updating the jinja templates but I am not sure this will be possible since both the input/output of the neuron and the model's equation must be updated to support gap junctions. If anyone has any suggestions or if anyone has NESTML code for adding a gap junction to an existing model, I would be very appreciative. Thanks!

4 13

Open NEST Developer Video Conference Monday June 5 2023 11:30 CEST (UTC+2)
by Dennis Terhorst 05 Jun '23

05 Jun '23

Dear NEST Users & Developers! I would like to invite you to our next fortnightly Open NEST Developer Video Conference, today Monday June 5, 11.30-12.30 CEST (UTC+2). Also 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/2023-06-05-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

NEST Conference 2023 - registration deadline: 5 June 2023
by Hans Ekkehard Plesser 02 Jun '23

02 Jun '23

Dear all, This year's NEST Conference will again take place as a virtual conference on Thursday/Friday 15/16 June 2023. You can still register until Monday next week, June 5. More information on the program and how to register can be found on 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

1 0

Handle input/output relation of device to node connection
by Robin Gilbert De Schepper 22 May '23

22 May '23

Hello NEST users, I'm trying to connect some devices in a black box manner and run into this error: ``` nest.lib.hl_api_exceptions.NESTErrors.IllegalConnection: IllegalConnection in SLI function Connect_g_g_D_D: Creation of connection is not possible because: Source node does not send output. Note that recorders must be connected as Connect(neuron, recorder). ``` Is there a way for me to inspect whether I should nest.Connect(A, B) or nest.Connect(B, A), or should I catch this error and try the inverse? Is this the only `IllegalConnection` error that can be thrown, or should I parse the error message? (which is prone to changes) -- 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/

2 2

NEST on AMD
by Alberto Antonietti 22 May '23

22 May '23

Dear NEST users, We are going to buy some nodes for the departmental HPC cluster and they are currently oriented towards nodes with AMD processors (e.g., AMD EPYC 7413 and AMD EPYC 9654 2). On HPC, in the past years we have always been using Intel-based nodes (e.g., Xeon Gold). I just wanted to check if there are possible issues in using these nodes or if others have already been using multi-CPU AMD nodes successfully. Thank you and have a great weekend! Best, Alberto -- Alberto Antonietti, Ph.D. Assistant Professor Nearlab - NeuroEngineering And medical Robotics Laboratory Department of Electronics, Information and Bioengineering Politecnico di Milano http://www.nearlab.polimi.it/

3 3

Open NEST Developer Video Conference Monday May 22 2023 11:30 CEST (UTC+2)
by Dennis Terhorst 22 May '23

22 May '23

Dear NEST Users & Developers! I would like to invite you to our next fortnightly Open NEST Developer Video Conference, today Monday May 22, 11.30-12.30 CEST (UTC+2). One point of discussion will be the required preparations for the next hackathon (overflow of last meeting). Also 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/2023-05-22-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

How to repeatedly stimulate random neurons in a population ?
by adrien.dhollande＠etu.u-paris.fr 10 May '23

10 May '23

Hi, I am in trouble here: I would like to stimulate every delta_t a random subset of neurons in a population. Should I create, for a population of size N, N generators and independently connect them to the N neurons, each spike generator provided with a random spike time series. Or is there a clever way to do it ? Thanks for any help! Best, Adrien

2 3

All-to-all connection and gating variable
by gustavo.patow＠udg.edu 10 May '23

10 May '23

Dear friends, Thanks to all your help, I've successfully reproduced the behavior of the modified Izhikevich neuron described in the 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 But when I try to connect a population of neurons among themselves, I have problems. In particular, imagine I create 10 neurons with the following Python code: neurons = nest.Create("izhikevich_ODE", 10) Then, I found in some of the examples that the neurons do not come connected, and to connect them all-to-all, I had to do the following: nest.Connect(neurons, neurons, 'all_to_all') Is that right? Then, in the NESTML model, how do I receive the spikes into the gating variable? If I am not wrong, I have to set the input as input: spikes real <- spike and then add them to the synaptic gating variable as a simple convolution: kernel G = delta(t) SS' = ((-SS/tau) + S_jump/N * convolve(G, spikes)) /s Note: the /s is because the equations in the paper are without units. Is this right? As kernel, I also tried exp(-t/tau), with the same tau as the one used for SS, but then it seemed to take forever to compute, so I left the delta... However, if the spikes themselves are Dirac deltas, I do not completely understand the meaning of this convolution... What is the correct way to get the spikes from the other neurons? thanks! gus.-

6 14

Open NEST Developer Video Conference Monday May 8 2023 11:30 CEST (UTC+2)
by Dennis Terhorst 08 May '23

08 May '23

Dear NEST Users & Developers! I would like to invite you to our next fortnightly Open NEST Developer Video Conference, today Monday May 8, 11.30-12.30 CEST (UTC+2). One point on the agenda is the recent burst of activity on refactoring of the test suite. Also 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 * Test suite refactoring The agenda for this meeting is also available online, see https://github.com/nest/nest-simulator/wiki/2023-05-08-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

NEST Conference 2023 — Abstract Submission Deadline Extended to 21 May
by Hans Ekkehard Plesser 04 May '23

04 May '23

Dear all, The abstract submission deadline for the NEST Conference 2023 has been extended to 21 May. We are looking forward to your contributions! [cid:image001.jpg@01D97E95.93B01E40] 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 15/16 June 2023. We are inviting contributions to the conference, including talks, "posters" and workshops on specific topics. For more information on how to submit your contribution, register and participate, please visit the conference website https://nest-simulator.org/conference Important dates 21 May 2023 — Deadline for submission of contributions 26 May 2023 — Notification of acceptance 5 June 2023 — Registration deadline 15 June 2023 — NEST Conference 2023 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

1 0

Can NEST handle data in batches?
by minervaliyin＠gmail.com 03 May '23

03 May '23

Hi all, I am currently using NEST to build a Liquid State Machine (LSM) as a preprocessing step for my work. I am setting the amplitude_times and amplitude_values of multiple step_current_generators as input, which is read from .npy files as batches of size 32. However, the issue is that the first dimension of the input data, which is 32 in this example, is not directly handled as the batch size in NEST. To work around this issue, I have implemented the following approach: I first get the shape of the input and determine the size of the first dimension, which in this case is 32. I then set up a for-loop that repeats 32 times. Within each repetition of the for-loop, I set the parameters of the step current generators as input, and then simulate for some time using the "Simulate" function (e.g. using "Simulate(3000)"). While this approach works, it is not ideal as it requires me to simulate each data sample individually. For example, if I have 100 batches, each with 32 data samples, I would need to simulate 100 x 32 x 3000ms to finish processing all the data samples. Therefore, I am wondering if there is a way to handle the input data directly in batches, as is typically done with tools like PyTorch. Thank you very much for your assistance! Best, Yin

1 0

Re: Custom input for neurons
by vivek sridhar 03 May '23

03 May '23

Hi all, I’m relatively new to NEST as well and would like to provide custom input to neurons over the course of the simulation. I’m trying to model a ring-attractor network that accepts continuously changing input (different neurons receive input over the course of the simulation). I specifically want to do this to update the neural inputs as I simulate animal movement in space (see https://www.pnas.org/doi/10.1073/pnas.2102157118 <https://www.pnas.org/doi/10.1073/pnas.2102157118> for details). Is there a way I can continuously change the neurons in the network that receive external input? Thank You. Vivek > On 3. May 2023, at 08:36, vivek sridhar <vivekhsridhar(a)yahoo.com> wrote: > > Hi all, > > I’m relatively new to NEST as well and would like to do something similar. I’m trying to model a ring-attractor network that accepts continuously changing input (different neurons receive input over the course of the simulation). I specifically want to do this to recursively update the neural inputs as I simulate animal movement (see https://www.pnas.org/doi/10.1073/pnas.2102157118 <https://www.pnas.org/doi/10.1073/pnas.2102157118> for details). Is there a way I can continuously change the neurons in the network that receive external input? > > Thank You. > > Vivek

1 0

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

1 0

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

2 1

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

1 0

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.-

5 8

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!!!

3 9

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.-

2 2

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?

3 6

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 ---------------------------------------------------------------------

1 0

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

1 0

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 >

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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/

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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

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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

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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

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