April 2022 - NEST Users - NEST Initiative Mail

Assertion error during connection when using CopyModel and own neuron model
by Barna Zajzon 07 Oct '22

07 Oct '22

Dear all, I'm encountering the following error python: /home/zbarni/software/packages/nest/znest/nestkernel/model_manager.h:296: nest::Model* nest::ModelManager::get_node_model(nest::index) const: Assertion `m < node_models_.size()' failed. when using the following code: nest.SetKernelStatus({'total_num_virtual_procs':16, 'local_num_threads':16}) nest.Install('my_neuron_module') for iin range(16): nest.CopyModel('MyNeuron', f'MyNeuron_{i}') neurons = nest.Create('MyNeuron_0', 2) nest.Connect(neurons, neurons) The script uses a neuron model that I wrote in C++ and is loaded without errors. The error is thrown upon nest.Connect(), and goes away if I create the neurons using `MyNeuron` and not `MyNeuron_x` (copied) or if the #vp and #threads is 1. I've used the model with NEST 2.20.0 without problems, but I'd like to port the code to the latest version. Maybe I'm just missing something new functionality/API related to CopyModel and multiprocessing - have there been any critical changes in the model requirements? Any help would be greatly appreciated. Barni

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problems with step_current_generator parallelization
by Jan Střeleček 28 Apr '22

28 Apr '22

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

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

28 Apr '22

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

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

25 Apr '22

Dear NEST Users, As discussed a long time ago (see towards the end of the discussion in https://github.com/nest/nest-simulator/issues/329), the hh_cond_exp_traub model included in NEST is far from the model by Traub and Miles (1991) which inspired it. The model in NEST was implemented as part of the work on the Brette et al (2007) review paper. I am considering to create a pull request that will 1. rename the models to hh_brette_2007* in keeping with NEST naming guidelines for paper-specific models 2. change the threshold parameter V_T to be the actual threshold for spike emission (currently the criterium is V_m >= V_T + 30 and falling V_m) I was therefore wondering if anyone of you 1. uses the hh_cond_* models at all 2. would object to those changes? Depending on whether the models are being used or not, I'd either implement the renaming via deprecation or directly. Best, Hans Ekkehard -- Prof. Dr. Hans Ekkehard Plesser Head, Department of Data Science Faculty of Science and Technology Norwegian University of Life Sciences PO Box 5003, 1432 Aas, Norway Phone +47 6723 1560 Email hans.ekkehard.plesser(a)nmbu.no<mailto:hans.ekkehard.plesser@nmbu.no> Home http://arken.nmbu.no/~plesser

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

25 Apr '22

Dear NEST Users & Developers! I would like to invite you to our next fortnightly Open NEST Developer Video Conference, today Monday April 25, 11.30-12.30 CEST (UTC+2). Special feature today will be a discussion of the available, but maybe not so widely known astrocyte model implementation in NEST. Feel free to join the meeting also just to bring your own questions for direct discussion in the in-depth section. As usual, in the Project team round, a contact person of each team will give a short statement summarizing ongoing work in the team and cross-cutting points that need discussion among the teams. The remainder of the meeting we would go into a more in-depth discussion of topics that came up on the mailing list or that are suggested by the teams. Agenda * Welcome * Review of NEST User Mailing List * Project team round * In-depth discussion * Astrocyte models in NEST The agenda for this meeting is also available online, see https://github.com/nest/nest-simulator/wiki/2022-04-25-Open-NEST-Developer-… Looking forward to seeing you soon! Cheers, Dennis Terhorst ------------------ Log-in information ------------------ We use a virtual conference room provided by DFN (Deutsches Forschungsnetz). You can use the web client to connect. We however encourage everyone to use a headset for better audio quality or even a proper video conferencing system (see below) or software when available. Web client * Visit https://conf.dfn.de/webapp/conference/97938800 * Enter your name and allow your browser to use camera and microphone * The conference does not need a PIN to join, just click join and you're in. In case you see a dfnconf logo and the phrase "Auf den Meetingveranstalter warten", just be patient, the meeting host needs to join first (a voice will tell you). VC system/software How to log in with a video conferencing system, depends on you VC system or software. - Using the H.323 protocol (eg Polycom): vc.dfn.net##97938800 or 194.95.240.2##97938800 - Using the SIP protocol:97938800@vc.dfn.de - By telephone: +49-30-200-97938800 For those who do not have a video conference system or suitable software, Polycom provides a pretty good free app for iOS and Android, so you can join from your tablet (Polycom RealPresence Mobile, available from AppStore/PlayStore). Note that firewalls may interfere with videoconferencing in various and sometimes confusing ways. For more technical information on logging in from various VC systems, please see http://vcc.zih.tu-dresden.de/index.php?linkid=1.1.3.4

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Developer info: calibrate() is now called pre_run_hook()
by Hans Ekkehard Plesser 21 Apr '22

21 Apr '22

Dear NEST Developers! If you are just using NEST, you can ignore this message. If you are coding models at the C++ level, I just want to share this information to reduce the risk of confusion: The good old calibrate() method found in all neuron models has now been renamed to pre_run_hook(), see https://github.com/nest/nest-simulator/pull/2336. Thanks to Pooja for implementing this. I'd suggest that you merge the master branch into any open development branches to bring them up to date on this change. Best, Hans Ekkehard -- Prof. Dr. Hans Ekkehard Plesser Head, Department of Data Science Faculty of Science and Technology Norwegian University of Life Sciences PO Box 5003, 1432 Aas, Norway Phone +47 6723 1560 Email hans.ekkehard.plesser(a)nmbu.no<mailto:hans.ekkehard.plesser@nmbu.no> Home http://arken.nmbu.no/~plesser

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

19 Apr '22

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

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

13 Apr '22

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

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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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