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

19 Apr '22

Hello Rachael, Could you post a minimal script or Jupyter notebook reproducing the problem? Does the problem only occur on the Neurorobotics platform or can you reproduce it locally on your computer as well? Best regards, Hans Ekkehard -- Prof. Dr. Hans Ekkehard Plesser Head, Department of Data Science Faculty of Science and Technology Norwegian University of Life Sciences PO Box 5003, 1432 Aas, Norway Phone +47 6723 1560 Email hans.ekkehard.plesser(a)nmbu.no<mailto:hans.ekkehard.plesser@nmbu.no> Home http://arken.nmbu.no/~plesser On 13/04/2022, 13:20, "Rachael Stentiford" <rachael.stentiford(a)brl.ac.uk<mailto:rachael.stentiford@brl.ac.uk>> wrote: Some people who received this message don't often get email from rachael.stentiford(a)brl.ac.uk. Learn why this is important<http://aka.ms/LearnAboutSenderIdentification> Apologies for so many emails. Looks like i jumped the gun a little and i am still having this issue. So if anyone does have any ideas, I would welcome the help. Cheers, Rachael ________________________________ From: Rachael Stentiford <rachael.stentiford(a)brl.ac.uk> Sent: Wednesday, April 13, 2022 11:46 AM To: users(a)nest-simulator.org <users(a)nest-simulator.org> Subject: Re: Kernel death when recording from 300+ cells for 2mins+ Looks like i have solved this issue now. For those interested in the solution, i have switched from using the efficient method for splitting a simulation into multiple intervals described in the docs, which has the clean up functions outside of the loop, to just using nest.Simulate() in the loop so the clean up functions are called each time. Cheers, Rachael ________________________________ From: Rachael Stentiford <rachael.stentiford(a)brl.ac.uk> Sent: Tuesday, April 12, 2022 6:32 PM To: users(a)nest-simulator.org <users(a)nest-simulator.org> Subject: [NEST Users] Kernel death when recording from 300+ cells for 2mins+ Dear all, I hope you are doing well. I am having an issue using pyNEST which i haven't come across before and have been unable to find answer to elsewhere. I am working with Python 3.8 and Nest 2.18 (which is the version currently used by the Neurorobotics platform). I have a network of 6 x 360 neurons, and i am trying to record spikes from 360 of these. However, I am finding that if i try to simulate for more than ~2 mins i run into problems. In jupyter notebooks I get a kernel death error, but even just running a standard python script NEST dies. I can simulate for longer if i only record from a single neuron. Previously I have used networks of 4 x 180 neurons and recorded from 180 for 10+ minutes without an issue. I have tried splitting up the simulation into multiple intervals, as explained in the docs, and saving spikes in between. This would mean there are fewer spikes to save each time, but this doesn't appear to help. Ideally i would like to record from 360 cells for around 30 mins. Have any of you come across a similar issue in the past, or have any suggestions for how I could fix this issue? Thanks for your help! Rachael ------------------------- Dr Rachael Stentiford (she/her) Research Associate in Neurobotics Bristol Robotics Laboratory University of the West of England Bristol BS16 1QY

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

13 Apr '22

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

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Nest 3.0 conda installation issue using source code
by Maryada Maryada 13 Apr '22

13 Apr '22

Dear NEST users, After trying multiple ideas, I am still facing the issue where my installation is successful with an error message: -- Configuring done CMake Warning at cmake/UseCython.cmake:100 (add_library): Cannot generate a safe runtime search path for target pynestkernel because files in some directories may conflict with libraries in implicit directories: runtime library [libgomp.so.1] in /usr/lib/gcc/x86_64-linux-gnu/9 may be hidden by files in: /home/<user>/miniconda3/envs/nestConda/lib Some of these libraries may not be found correctly. Call Stack (most recent call first): cmake/UseCython.cmake:283 (python_add_module) pynest/CMakeLists.txt:28 (cython_add_module) ------------------------------------------------------------------------------------------------ This leads to the failure of multiple tests. The summary of the tests and logs for the failed tests is attached. I must mention that I tested the installation by creating a neuron and it works fine. It would be nice to get rid of the error, please see error_msg file to see where it fails. -- Thanks and Regards *Maryada*

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Open NEST Developer Video Conference Monday April 11 11:30 CEST (UTC+2 !!!)
by Jessica Mitchell 11 Apr '22

11 Apr '22

Dear NEST Users & Developers! I would like to invite you to our next fortnightly Open NEST Developer Video Conference, today Monday April 11, 11.30-12.30 CEST (UTC+2). Feel free to join the meeting also just to bring your own questions for direct discussion in the in-depth section. As usual, in the Project team round, a contact person of each team will give a short statement summarizing ongoing work in the team and cross-cutting points that need discussion among the teams. The remainder of the meeting we would go into a more in-depth discussion of topics that came up on the mailing list or that are suggested by the teams. Agenda * Welcome * Review of NEST User Mailing List * Project team round * In-depth discussion The agenda for this meeting is also available online, see https://github.com/nest/nest-simulator/wiki/2022-04-11-Open-NEST-Developer-… Looking forward to seeing you soon! Cheers, Jessica Mitchell 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 ------------------------------------------------------------------------------------------------ ------------------------------------------------------------------------------------------------ Forschungszentrum Juelich GmbH 52425 Juelich Sitz der Gesellschaft: Juelich Eingetragen im Handelsregister des Amtsgerichts Dueren Nr. HR B 3498 Vorsitzender des Aufsichtsrats: MinDir Volker Rieke Geschaeftsfuehrung: Prof. Dr.-Ing. Wolfgang Marquardt (Vorsitzender), Karsten Beneke (stellv. Vorsitzender), Prof. Dr. Astrid Lambrecht, Prof. Dr. Frauke Melchior ------------------------------------------------------------------------------------------------ ------------------------------------------------------------------------------------------------ Neugierige sind herzlich willkommen am Sonntag, den 21. August 2022, von 10:00 bis 17:00 Uhr. Mehr unter: https://www.tagderneugier.de

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NEST Conference 2022 - call for contributions is open
by Hans Ekkehard Plesser 07 Apr '22

07 Apr '22

Dear Colleagues, The NEST Initiative is excited to invite everyone interested in Neural Simulation Technology and the NEST Simulator to the NEST Conference 2022. The NEST Conference provides an opportunity for the NEST Community to meet, exchange success stories, swap advice, learn about current developments in and around NEST spiking network simulation and its application. We explicitly encourage young scientists to participate in the conference! This year's conference will again take place as a virtual conference on Thursday/Friday 23/24 June 2022. Submission of contributions is now open! We are inviting contributions to the conference, including talks, "posters" and workshops on specific topics. Please register and submit your contribution(s) via the conference website https://nest-simulator.org/conference. Important dates 30 April 2022 - Deadline for NEST Initiative membership applications eligible for fee reduction 11 May 2022 - Deadline for submission of contributions 03 June 2022 - Notification of acceptance 17 June 2022 - Registration deadline 23 June 2022 - NEST Conference 2022 starts We are looking forward to seeing you all in June! Hans Ekkehard Plesser and the conference organizing committee -- Prof. Dr. Hans Ekkehard Plesser Head, Department of Data Science Faculty of Science and Technology Norwegian University of Life Sciences PO Box 5003, 1432 Aas, Norway Phone +47 6723 1560 Email hans.ekkehard.plesser(a)nmbu.no<mailto:hans.ekkehard.plesser@nmbu.no> Home http://arken.nmbu.no/~plesser

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Reproducing "Synchrony generation in recurrent networks with frequency-dependent synapses"
by Sebastian Schmitt 07 Apr '22

07 Apr '22

Dear NEST users! I've found an implementation of "Synchrony generation in recurrent networks with frequency-dependent synapses" Tsodyks, Uziel, Markram 2000 in https://github.com/uahic/Nest_2_10_release/blob/d3a7b0b8105622b40ef87d8a5ba… but it's missing in the latest versions of NEST. Is there a comparable implementation in a recent NEST release? Preferably in Python? Thanks in advance, Sebastian

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Position as NEST Developer at NMBU / Deadline 26 April 2022
by Hans Ekkehard Plesser 05 Apr '22

05 Apr '22

Dear colleagues, We are looking for a new NEST developer to join the NEST team at NMBU in Ås, Norway, as head engineer or senior engineer. The position is funded by the Human Brain Project, available immediately and limited to 30 September 2023. Application deadline is 26 April 2023. For details, please see https://www.jobbnorge.no/en/available-jobs/job/224028/head-engineer-senior-… or get in touch with me. 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

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Open NEST Developer Video Conference Monday March 28 2022 11:30 CEST (UTC+2 !!!)
by Dennis Terhorst 28 Mar '22

28 Mar '22

Dear NEST Users & Developers! I would like to invite you to our next fortnightly Open NEST Developer Video Conference, today Monday March 14, 11.30-12.30 CEST (UTC+2). /Note/ that we changed to daylight savings time (aka "summer time") and are now UTC+2. Feel free to join the meeting also just to bring your own questions for direct discussion in the in-depth section. As usual, in the Project team round, a contact person of each team will give a short statement summarizing ongoing work in the team and cross-cutting points that need discussion among the teams. The remainder of the meeting we would go into a more in-depth discussion of topics that came up on the mailing list or that are suggested by the teams. Agenda * Welcome * Review of NEST User Mailing List * Project team round * In-depth discussion * Inclusion of NEST-GPU by Golosio et al. The agenda for this meeting is also available online, see https://github.com/nest/nest-simulator/wiki/2022-03-28-Open-NEST-Developer-… Looking forward to seeing you soon! Cheers, Dennis Terhorst ------------------ Log-in information ------------------ We use a virtual conference room provided by DFN (Deutsches Forschungsnetz). You can use the web client to connect. We however encourage everyone to use a headset for better audio quality or even a proper video conferencing system (see below) or software when available. Web client * Visit https://conf.dfn.de/webapp/conference/97938800 * Enter your name and allow your browser to use camera and microphone * The conference does not need a PIN to join, just click join and you're in. In case you see a dfnconf logo and the phrase "Auf den Meetingveranstalter warten", just be patient, the meeting host needs to join first (a voice will tell you). VC system/software How to log in with a video conferencing system, depends on you VC system or software. - Using the H.323 protocol (eg Polycom): vc.dfn.net##97938800 or 194.95.240.2##97938800 - Using the SIP protocol:97938800@vc.dfn.de - By telephone: +49-30-200-97938800 For those who do not have a video conference system or suitable software, Polycom provides a pretty good free app for iOS and Android, so you can join from your tablet (Polycom RealPresence Mobile, available from AppStore/PlayStore). Note that firewalls may interfere with videoconferencing in various and sometimes confusing ways. For more technical information on logging in from various VC systems, please see http://vcc.zih.tu-dresden.de/index.php?linkid=1.1.3.4

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Creating a new NodeCollection from Mask or by global_ids
by Kempter, Miriam 22 Mar '22

22 Mar '22

Dear Nest Team, working with Python 3.8 and Nest 3.2 my goal is, after creating a spatial NodeCollection "neurons", to create a new NodeCollection containing a selection of the node from "neurons". To achieve this I tried two different approaches: 1. Create a Mask object and use nest.SelectNodesByMask() nodes_in_mask = nest.SelectNodesByMask(neurons, ctr_position, mask_obj) 2. Transform the NodeCollection into a list of node ids, pick 3 random ids, and create a new NodeCollection containing those 3 Nodes neurons_list = neurons.tolist() for x in range(0, 3): center = random.choice(neurons_list) node_ids.append(center) node_ids.sort() new_collection = nest.NodeCollection(node_ids) But with both approaches I get the same problems that some Information (of the positions) seems to go missing. This shows in different ways. First the new NodeCollections are no longer spatial (nodes_in_mask.spatial and new_collection.spatial return none). Second trying to get the node Positions results in an Error: nest.GetPosition(nodes_in_mask) -> Error #1 nest.lib.hl_api_exceptions.LayerExpected: LayerExpected in SLI function GetPosition_g: And last, trying to Plot the Layer also results in an Error: fig = nest.PlotLayer(nodes_in_mask) -> Error #2 TypeError: 'NoneType' object is not subscriptable I attached a .txt file containing py code showing the problems. Why do those Problems occur and what can I do to solve them? Is there a way to create an empty NodeCollection s.t. I can add the wished nodes one by one? What exactly does the metadata of a Nodecollection represent? Is there a way to set it manually for example to spatial? Thank you in advance for your Answers, Miriam

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NESTML, 'UnknownNode' model
by Alexander Kozlov 14 Mar '22

14 Mar '22

Hi, Any neuron model built with NESTML and installed via nest.Install('mymodule') receives 'UnknownNode' as the value for 'model': > nrn.get('model') > 'UnknownNode' Can this be ignored by users? Is it possible to set the value in .nestml file for compatibility with standard models? Best regards, Alex.

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