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NEST Conference 2022 - registration is open
by Hans Ekkehard Plesser 17 Feb '22

17 Feb '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 particularly encourage young scientists to participate in the conference! This year's conference will again take place as a virtual event on Thursday/Friday 23/24 June 2022. 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 -- 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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Neuron models with NMDA channels
by cagnol＠ksvi.mff.cuni.cz 15 Feb '22

15 Feb '22

Hello, We would like to use neurons models with NMDA channels in our spiking neuron model. We're still unsure whether we will use a native neuron model in Nest or whether we will implement our own one in NESTML. My understanding is that the only model in Nest which does that is the Hill - Tononi model, which seems rather complex. How fast would you roughly expect a Hill - Tononi neuron network to run compared to a network made of aeif_cond_exp neurons? Do you know by any chance any example of adex NESTML models which implement NMDA and Gaba_B channels? Also, one last question not really related to the previous ones: Is there any way to model synaptic reliability in Nest? Thanks a lot, Remy,

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WOIV'22: Extended Deadline -- 6th International Workshop on In Situ Visualization
by Tom Vierjahn 14 Feb '22

14 Feb '22

Hi all, we have extended the submission deadline for WOIV’22 until March 7. And we have added a 3rd submission type: lightning presentations (2 to 4 pages, published via Zenodo). Please find the updated CfP below and on the webpage https://woiv.gitlab.io Cheers, Tom ----- # WOIV'22: 6th International Workshop on In Situ Visualization * Held in conjunction with ISC 2022 * Hamburg, Germany, June 2, 2022 ## Scope Large-scale HPC simulations with their inherent I/O bottleneck have made in situ visualization an essential approach for data analysis, although the idea of in situ visualization dates back to the golden era of coprocessing in the 1990s. In situ coupling of analysis and visualization to a live simulation circumvents writing raw data to disk for post-mortem analysis – an approach that is already inefficient for today’s very large simulation codes. Instead, with in situ visualization, data abstracts are generated that provide a much higher level of expressiveness per byte. Therefore, more details can be computed and stored for later analysis, providing more insight than traditional methods. We encourage contributed talks on methods and workflows that have been used for large-scale parallel visualization, with a particular focus on the in situ case. Presentations on codes that closely couple numerical methods and visualization are particularly welcome. Speakers should detail if and how the application drove abstractions or other kinds of data reductions and how these interacted with the expressiveness and flexibility of the visualization for exploratory analysis. Presentations on codes that closely couple numerical methods and visualization are particularly welcome. Speakers should detail frameworks used and data reductions applied. They should also indicate how these impacted the flexibility of the visualization for exploratory analysis. Of particular interest to WOIV and its attendees are recent developments for in situ libraries and software. Submissions documenting recent additions to existing in situ software or new in situ platforms are highly encouraged. WOIV is an excellent place to connect providers of in situ solutions with potential customers. For the submissions we are not only looking for success stories, but are also particularly interested in those experiments that started with a certain goal or idea in mind, but later got shattered by reality or insufficient hardware/software. Areas of interest for WOIV include, but are not limited to: * Techniques and paradigms for in situ visualization. * Algorithms relevant to in situ visualization. These could include algorithms empowered by in situ visualization or algorithms that overcome limitations of in situ visualization. * Systems and software implementing in situ visualization. These include both general purpose and bespoke implementations. This also includes updates to existing software as well as new software. * Workflow management. * Use of in situ visualization for application science or other examples of using in situ visualization. * Performance studies of in situ systems. Comparisons between in situ systems or techniques or comparisons between in situ and alternatives (such as post hoc) are particularly encouraged. * The impact of hardware changes on in situ visualization. * The online visualization of experimental data. * Reports of in situ visualization failures. * Emerging issues with in situ visualization. ## Submissions We accept submissions of short papers (6 to 8 pages), full papers (10 to 12 pages) and lightning presentations (2 to 4 pages) in Springer single column LNCS style. Please find LaTeX and Word templates at https://woiv.gitlab.io/woiv22/template. `Submissions are exclusively handled via EasyChair: https://woiv.gitlab.io/woiv22/submit. The review process is single or double blind, we leave it to the discretion of the authors whether they want to disclose their identity in their submissions. All submissions will be peer-reviewed by experts in the field, and will be evaluated according to relevance to the workshop theme, technical soundness, thoroughness of success/failure comparison, and impactfulness of method/results. Accepted short and full papers will appear as post-conference workshop proceedings in the Springer Lecture Notes in Computer Science (LNCS) series; lightning presentations will be published via Zenodo. The submitted versions will be made available to workshop participants during ISC. ## Important Dates * Submission deadline (extended): March 7, 2022, anywhere on earth * Notification of acceptance: April 15, 2022 * Final presentation slides due: May 10, 2012, anywhere on earth (subject to change) * Workshop: June 2, 2022 * Camera-ready version due: July 1, 2022 (subject to change, extrapolated from previous years) ## Chairs * Peter Messmer, NVIDIA * Tom Vierjahn, Westphalian University of Applied Sciences, Bocholt, Germany ## Steering Committee * Steffen Frey, University of Groningen, The Netherlands * Kenneth Moreland, Oak Ridge National Laboratory, USA * Thomas Theussl, KAUST, Saudi Arabia * Guido Reina, University of Stuttgart, Germany * Tom Vierjahn, Westphalian University of Applied Sciences, Bocholt, Germany ## Website, Venue, Registration * Website: https://woiv.gitlab.io * Submission system: https://woiv.gitlab.io/woiv22/submit * Template: https://woiv.gitlab.io/woiv22/template * Venue: https://www.isc-hpc.com (ISC 2022) * Workshop registration: https://woiv.gitlab.io/woiv22/register ## Contact E-Mail: woiv(a)googlegroups.com

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Open NEST Developer Video Conference Monday February 14 2022 11:30 CET (UTC+1)
by Dennis Terhorst 14 Feb '22

14 Feb '22

Dear NEST Users & Developers! I would like to invite you to our next fortnightly Open NEST Developer Video Conference, today Monday February 14, 11.30-12.30 CET (UTC+1). 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/2022-02-14-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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Webinar Invitation: ""Embodied Large Scale Spiking Neural Networks in the Neurorobotics Platform"
by Benedikt Feldotto 09 Feb '22

09 Feb '22

Dear all, NEST is a powerful tool to simulate biologically derived spiking Neural Networks. Besides the ever improving model details, learning paradigms and computational complexity, there are two complementary components necessary in order to simulate a (full) biologically plausible mammalian brain: Running simulations at large scale and embodying the brain simulation in a (virtual) body. In frame of the Fenix Infrastructure Webinar series I am going to present "Embodied large scale spiking neural networks in the Neurorobotics Platform" with a focus on the deployment on High Performance Computing Infrastructure next week Thursday. The presentation showcases the joint work of developers from NEST and the Neurorobotics Platform, the CSCS Swiss National Supercomputing centre and researchers in the RoboBrain project. Check out the details and registration at: https://fenix-ri.eu/events/14th-fenix-infrastructure-webinar-ebrains-servic… Looking forward to see you there, Benedikt -- Benedikt Feldotto M.Sc. Research Assistant Human Brain Project - Neurorobotics Technical University of Munich Department of Informatics Chair of Robotics, Artificial Intelligence and Real-Time Systems Room HB 2.02.20 Parkring 13 D-85748 Garching b. München Tel.: +49 89 289 17628 Mail: feldotto(a)in.tum.de https://www6.in.tum.de/en/people/benedikt-feldotto-msc/ www.neurorobotics.net

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Synapse labels and connection rules
by Barna Zajzon 02 Feb '22

02 Feb '22

Dear NEST community, When trying to pass a `synapse_label` parameter in the syn_spec dictionary, in conjunction with the `one_to_one` rule and node ids passed as arrays, I get the following error with NEST 3.0: File "/home/zbarni/code/projects/lif_sorn_seqlearn/lif-sorn-nest-implementation/remote/test_nestml_multith.py", line 29, in <module> nest.Connect([1], [2], conn_spec={'rule': 'one_to_one'}, syn_spec={'synapse_model': 'static_synapse_lbl', 'synapse_label': 1}) File "/home/zbarni/software/installed/miniconda3/envs/del-lif-sorn-nestml-check_py390/lib/python3.9/site-packages/nest/ll_api.py", line 228, in stack_checker_func return f(*args, **kwargs) File "/home/zbarni/software/installed/miniconda3/envs/del-lif-sorn-nestml-check_py390/lib/python3.9/site-packages/nest/lib/hl_api_connections.py", line 255, in Connect connect_arrays(pre, post, weights, delays, synapse_model, syn_param_keys, syn_param_values) File "pynestkernel.pyx", line 360, in pynestkernel.NESTEngine.connect_arrays nest.lib.hl_api_exceptions.TypeMismatch: TypeMismatch in SLI function connect_arrays It works when using the `all_to_all` rule. Is this the expected behavior or for some reason it's not possible to use synapse_label and the one_to_one rule (yet)? Thank you, Barna

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Open NEST Developer Video Conference Monday January 31 2022 11:30 CET (UTC+1)
by Dennis Terhorst 31 Jan '22

31 Jan '22

Dear NEST Users & Developers! I would like to invite you to our next fortnightly Open NEST Developer Video Conference, today Monday January 31, 11.30-12.30 CET (UTC+1). 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/2022-01-31-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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NMBU / Associate Professors in Machine Learning and Scientific Computing / Deadline 15 Feb 2022
by Hans Ekkehard Plesser 27 Jan '22

27 Jan '22

Dear Colleagues, The Department of Data Science at NMBU is currently looking for two full-time permanent associate professors in machine learning and scientific computing, respectively. We are also looking for adjunct professors (20%, 4 years) to cover ethical and legal aspects of data science and data security, respectively. I'd appreciate if you would pass this information on to colleagues who may be interested in any of the positions. As we currently are mostly male faculty members, we'd in particular appreciate applications by women. * Associate professor in Data Science (Machine Learning) - Deadline: Tuesday, February 15, 2022<https://www.jobbnorge.no/en/available-jobs/job/217579/associate-professor-i…> * Associate professor in Scientific Computing - Deadline: Tuesday, February 15, 2022<https://www.jobbnorge.no/en/available-jobs/job/217590/associate-professor-i…> * Professor II/Associate professor II in Ethics and Law of Data Science - Deadline: Tuesday, February 15, 2022<https://www.jobbnorge.no/en/available-jobs/job/217629/professor-ii-associat…> * Professor II/Associate professor II in Data Security - Deadline: Tuesday, February 15, 2022<https://www.jobbnorge.no/en/available-jobs/job/217607/professor-ii-associat…> 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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log data into data_path
by Benedikt Feldotto 21 Jan '22

21 Jan '22

Dear all, quick question about data logging to a specified folder: with nest.SetKernelStatus({"data_path": '/opt/data/log'}) I can specify the path, where data is logged to. If I do not specify a path, where does data get saved, or is it not saved to file if I do not specify 'data_path'? Thanks! Benedikt -- Benedikt Feldotto M.Sc. Research Assistant Human Brain Project - Neurorobotics Technical University of Munich Department of Informatics Chair of Robotics, Artificial Intelligence and Real-Time Systems Room HB 2.02.20 Parkring 13 D-85748 Garching b. München Tel.: +49 89 289 17628 Mail: feldotto(a)in.tum.de https://www6.in.tum.de/en/people/benedikt-feldotto-msc/ www.neurorobotics.net

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Open NEST Developer Video Conference Monday January 17 2021 11:30 CET (UTC+1)
by Dennis Terhorst 17 Jan '22

17 Jan '22

Dear NEST Users & Developers! I would like to invite you to our next fortnightly Open NEST Developer Video Conference, today Monday January 17, 11.30-12.30 CET (UTC+1). 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/2022-01-17-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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how do I record events emitted by "sinusoidal_poisson_generator"
by thierry nieus 03 Jan '22

03 Jan '22

Dear all, first of all, happy new year! I am using nest 2.2 (installed by conda) and I have set up a simple network of 20-100 neurons based on the ht_neuron model. I am delivering some noise to all neurons with the sinusoidal_poisson_generator (I can switch to another) and the simulation produces the results I am looking for. However I would like now to have a look at the spikes entering the network and therefore I need to access all events generated by the random generator. A sample of my code is: import nest receptors=nest.GetDefaults('ht_neuron')['receptor_types'] nest.CopyModel("sinusoidal_poisson_generator",'sin_pois',{'amplitude':50.,'rate':15.0 }) nest.CopyModel("static_synapse","AMPAnoise",{"receptor_type":receptors["AMPA"],"weight":10. }) neurons=nest.Create("ht_neuron",1) noise=nest.Create('sin_pois',1) g = nest.Create('sin_pois', 1) # current pulse dc_gen = nest.Create("dc_generator") nest.SetStatus(dc_gen, {"amplitude": 20., "start": 400, "stop": 1050}) nest.Connect(dc_gen, neurons, 'one_to_one') # recorders detect_noise = nest.Create('spike_detector', 1) nest.Connect(noise, neurons, 'one_to_one', syn_spec="AMPAnoise") nest.Connect(noise, detect_noise, 'one_to_one') ''' the latest does not work Creation of connection is not possible because: All outgoing connections from a device must use the same synapse type. ''' Is there a way to record those spikes ? Thanks in advance for any help Best

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Thank you for 2021!
by Hans Ekkehard Plesser 22 Dec '21

22 Dec '21

Dear NEST Users and Developers! I would like to thank you all for your engagement for high-quality computational neuroscience and research software in 2021. We have made some major steps forward with the release of NEST 3, NEST Desktop 3 and NESTML 4. A few days ago, PyNN 0.10 also brought support for NEST 3, nicely wrapping up the year of NEST 3. We also moved to quarterly releases with the release of NEST 3.0. If you wonder what happened to NEST 3.2 in that scheme of things don't worry, it will come in Januar. The combination of holiday season, new COVID restrictions and an important reporting deadline in the Human Brain Project—the major source of funding for NEST development in recent years—unfortunately left too little time to wrap everything up in time. 2022 promises to be an exciting year for NEST, including the deeper integration of NEST Desktop (so far mainly developed by Sebastian Spreizer) and NEST GPU (so far mainly developed by Bruno Golosio as NeuronGPU) into the NEST development process and community. Don't forget to block out 23/24 June in your calendars for the NEST Conference 2022 (this time on a Thursday and Friday)! On behalf of the NEST Initiative, I wish you happy holidays and all the best for 2022! 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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Call for Papers: WOIV'22: 6th International Workshop on In Situ Visualization
by Tom Vierjahn 20 Dec '21

20 Dec '21

Hi all, we will organise another edition of the in situ visualization workshop (https://woiv.gitlab.io) at ISC (https://isc-hpc.com). If you are working on visualizing results of neural simulations while these are still running, you might want to consider submitting your work to the workshop … Please find the CfP below. Cheers, Tom ----- # WOIV'22: 6th International Workshop on In Situ Visualization * Held in conjunction with ISC 2022 * Hamburg, Germany, June 2, 2022 ## Scope Large-scale HPC simulations with their inherent I/O bottleneck have made in situ visualization an essential approach for data analysis, although the idea of in situ visualization dates back to the golden era of coprocessing in the 1990s. In situ coupling of analysis and visualization to a live simulation circumvents writing raw data to disk for post-mortem analysis – an approach that is already inefficient for today’s very large simulation codes. Instead, with in situ visualization, data abstracts are generated that provide a much higher level of expressiveness per byte. Therefore, more details can be computed and stored for later analysis, providing more insight than traditional methods. We encourage contributed talks on methods and workflows that have been used for large-scale parallel visualization, with a particular focus on the in situ case. Presentations on codes that closely couple numerical methods and visualization are particularly welcome. Speakers should detail if and how the application drove abstractions or other kinds of data reductions and how these interacted with the expressiveness and flexibility of the visualization for exploratory analysis. Presentations on codes that closely couple numerical methods and visualization are particularly welcome. Speakers should detail frameworks used and data reductions applied. They should also indicate how these impacted the flexibility of the visualization for exploratory analysis. Of particular interest to WOIV and its attendees are recent developments for in situ libraries and software. Submissions documenting recent additions to existing in situ software or new in situ platforms are highly encouraged. WOIV is an excellent place to connect providers of in situ solutions with potential customers. For the submissions we are not only looking for success stories, but are also particularly interested in those experiments that started with a certain goal or idea in mind, but later got shattered by reality or insufficient hardware/software. Areas of interest for WOIV include, but are not limited to: * Techniques and paradigms for in situ visualization. * Algorithms relevant to in situ visualization. These could include algorithms empowered by in situ visualization or algorithms that overcome limitations of in situ visualization. * Systems and software implementing in situ visualization. These include both general purpose and bespoke implementations. This also includes updates to existing software as well as new software. * Workflow management. * Use of in situ visualization for application science or other examples of using in situ visualization. * Performance studies of in situ systems. Comparisons between in situ systems or techniques or comparisons between in situ and alternatives (such as post hoc) are particularly encouraged. * The impact of hardware changes on in situ visualization. * The online visualization of experimental data. * Reports of in situ visualization failures. * Emerging issues with in situ visualization. ## Submissions We accept submissions of short papers (6 to 8 pages) and full papers (10 to 12 pages) in Springer single column LNCS style. Please find LaTeX and Word templates at https://woiv.gitlab.io/woiv22/template. Submissions are exclusively handled via EasyChair: https://woiv.gitlab.io/woiv22/submit. The review process is single or double blind, we leave it to the discretion of the authors whether they want to disclose their identity in their submissions. All submissions will be peer-reviewed by experts in the field, and will be evaluated according to relevance to the workshop theme, technical soundness, thoroughness of success/failure comparison, and impactfulness of method/results. Accepted papers will appear as post-conference workshop proceedings in the Springer Lecture Notes in Computer Science (LNCS) series. The submitted versions will be made available to workshop participants during ISC. ## Important Dates * Submission deadline: February 13, 2022, anywhere on earth * Notification of acceptance: April 15, 2022 * Final presentation slides due: May 10, 2012, anywhere on earth (subject to change) * Workshop: June 2, 2022 * Camera-ready version due: July 1, 2022 (subject to change, extrapolated from previous years) ## Chairs * Peter Messmer, NVIDIA * Tom Vierjahn, Westphalian University of Applied Sciences, Bocholt, Germany ## Steering Committee * Steffen Frey, University of Groningen, The Netherlands * Kenneth Moreland, Sandia National Labs, USA * Thomas Theussl, KAUST, Saudi Arabia * Guido Reina, University of Stuttgart, Germany * Tom Vierjahn, Westphalian University of Applied Sciences, Bocholt, Germany ## Website, Venue, Registration * Website: https://woiv.gitlab.io * Submission system: https://woiv.gitlab.io/woiv22/submit * Template: https://woiv.gitlab.io/woiv22/template * Venue: https://www.isc-hpc.com (ISC 2022) * Workshop registration: https://woiv.gitlab.io/woiv22/register ## Contact E-Mail: woiv(a)googlegroups.com

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Open NEST Developer Video Conference Monday December 20 2021 11:30 CET (UTC+1)
by Jochen Martin Eppler 20 Dec '21

20 Dec '21

Dear NEST Users & Developers! I would like to invite you to our next fortnightly Open NEST Developer Video Conference, today Monday December 20, 11.30-12.30 CET (UTC+1). 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/2021-12-20-Open-NEST-Developer-… Looking forward to seeing you soon! Cheers, Jochen Martin Eppler! ------------------ 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 Phone: +49(2461)61-96653 ---------------------------------- Simulation Laboratory 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 Volker Rieke Geschaeftsfuehrung: Prof. Dr.-Ing. Wolfgang Marquardt (Vorsitzender), Karsten Beneke (stellv. Vorsitzender), Prof. Dr. Astrid Lambrecht, Prof. Dr. Frauke Melchior ------------------------------------------------------------------------------------------------ ------------------------------------------------------------------------------------------------

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NESTML: neuron/synapse model with differential dynamics for computing post synaptic currents
by barthelemy 16 Dec '21

16 Dec '21

Dear all, I am a new NEST user. I have a question concerning the range of neuron/synapses model possibilities of NEST. I would like to implement my own neuron/synapse model with NESTML, but I am unsure that it would be possible. Indeed, in my model, synaptic currents are not only relying on pre-synaptic spikes. To compute synaptic currents, the opening probability of pre-synaptic channel receptors are required. Those pre-synaptic channel receptors opening probabilities are evolving according to differential equations involving second order dynamics, with specific decays and taking into account the pre-synaptic spikes arrivals times at this specific synapse. Those differential equations for the opening probabilities are relying on different parameters, according to the neurotransmitter type (GABA A,GABA B, NMDA, AMPA ). Furthermore, additionally to the input spikes and the pre-synaptic channel receptors opening probabilities, the current membrane potential of the post-synaptic neuron is also required to compute the synaptic currents. Do you know if one of the NEST models implement similar dynamics? Is it possible to compute such synaptic dynamics with NESTML by creating a synapse or (and) a neuron model? Or is it not, due to specific limitations? Thank you, Best regards, JB

2 5

NEST Developers — Failing macOS checks solved
by Hans Ekkehard Plesser 08 Dec '21

08 Dec '21

Dear NEST Developers, You may have observed that Github checks failed on macOS in recent days. This is due to even more pedantic checking of standard compliance by the newest version of Clang. The issue is fixed in master now (#2231), so if you experience trouble with failing macOS tests, you should update your branch. 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

Set 'grng' seed
by Benedikt Feldotto 06 Dec '21

06 Dec '21

Dear all, in a previous version of NEST I used to set the RNG seeds like this: nest.SetKernelStatus({'grng_seed' : value_grngseed}) nest.SetKernelStatus({'rng_seeds' : value_rngseed)}) I already found in newer NEST versions I can set the RNG seed like: nest.rng_seed = value_rngseed Is there also a possibility to set the Global RNG seed 'grng' with newer NEST versions? Thanks! Benedikt -- Benedikt Feldotto M.Sc. Research Assistant Human Brain Project - Neurorobotics Technical University of Munich Department of Informatics Chair of Robotics, Artificial Intelligence and Real-Time Systems Room HB 2.02.20 Parkring 13 D-85748 Garching b. München Tel.: +49 89 289 17628 Mail: feldotto(a)in.tum.de https://www6.in.tum.de/en/people/benedikt-feldotto-msc/ www.neurorobotics.net

2 2

Open NEST Developer Video Conference Monday 6 December 2021 11:30 CET (UTC+1)
by Dennis Terhorst 06 Dec '21

06 Dec '21

Dear NEST Users & Developers! I would like to invite you to our next fortnightly Open NEST Developer Video Conference, today Monday 06 December, 11.30-12.30 CET (UTC+1). 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/2021-12-06-Open-NEST-Developer-… Looking forward to seeing you soon! best, Dennis Terhorst ------------------ Log-in information ------------------ We use a virtual conference room provided by DFN (Deutsches Forschungsnetz). You can use the web client to connect. We however encourage everyone to use a headset for better audio quality or even a proper video conferencing system (see below) or software when available. Web client * Visit https://conf.dfn.de/webapp/conference/97938800 * Enter your name and allow your browser to use camera and microphone * The conference does not need a PIN to join, just click join and you're in. In case you see a dfnconf logo and the phrase "Auf den Meetingveranstalter warten", just be patient, the meeting host needs to join first (a voice will tell you). VC system/software How to log in with a video conferencing system, depends on you VC system or software. - Using the H.323 protocol (eg Polycom): vc.dfn.net##97938800 or 194.95.240.2##97938800 - Using the SIP protocol:97938800@vc.dfn.de - By telephone: +49-30-200-97938800 For those who do not have a video conference system or suitable software, Polycom provides a pretty good free app for iOS and Android, so you can join from your tablet (Polycom RealPresence Mobile, available from AppStore/PlayStore). Note that firewalls may interfere with videoconferencing in various and sometimes confusing ways. For more technical information on logging in from various VC systems, please see http://vcc.zih.tu-dresden.de/index.php?linkid=1.1.3.4

1 0

NEST v3.1: Missing data for spike_recorder (ascii)
by Maryada Maryada 30 Nov '21

30 Nov '21

Dear NEST users, I am trying to debug my network and I found that my spike_recorder with *ascii* option isn't working as expected. I am simulating a network for a few milliseconds (say 1000. ms) and then do some structure changes and then re-run for another phase of a few ms (say 4000. ms) In the compact version, I am trying to see how this sample code would work. import nest nest.ResetKernel() nest.SetKernelStatus({ "overwrite_files": True, "data_path": './Debug-Log', "data_prefix": 'DEBUG-SPIKE-REC', }) noise_device = nest.Create("poisson_generator",params={'start': 0.,'rate' : 100.}) sd_params = { "record_to": 'ascii', "label": "Input_spike_recorder" } Input_SD = nest.Create("spike_recorder",1, params=sd_params) nest.Connect(noise_device,Input_SD) nest.Simulate(100.) # do something here nest.Simulate(100.) *Issue:* I only get the data recorded from 100th millisecond but for memory, I get all the data from 0-200 ms. This behavior is consistent for both overwrite_files as True and False. In the previous version (v2.20) I also used the same approach and had no issues. Is there a newer way to do such a simulation paradigm? I didn't find anything on this on the comparison page of NESTv2.x and NESTv3.x Am I missing something? It's really important for my work, I hope I could find a solution. -- Thanks and Regards *Maryada*

3 8

FitzHugh-Nagumo model in Nest simulator
by s.taffara92＠gmail.com 29 Nov '21

29 Nov '21

Hi, I visited the page 'https://nest-simulator.readthedocs.io/en/latest/models/' looking for the FitzHugh-Nagumo model keyword. I want to use it to create this kind of neuron in Nest. I can not find it. Can anyone help me? Thanks, Salvo

4 3

Random seed in NEST 3.0
by Maryada Maryada 26 Nov '21

26 Nov '21

Dear NEST users, As I understood from the documentation unless you set the seed using nest.rng_seed, nest.random.normal (for instance) should return the same value nest.ResetKernel() nest.rng_seed = 21#69696 v_m = nest.random.normal(mean=-51., std=10.) v_m.GetValue() In this code, I always receive the same v_m value for both cases, if the seed is set as 21 or 69696. The only time it changes is if I remove ResetKernel() call, which then is expected to return different values irrespective of rng_seed. With this code below, I also got the same results irrespective of rng_seed value nest.ResetKernel() nest.rng_seed = 3333#69696 for _ in range(10): v_m = nest.random.normal(mean=-51., std=10.) print(v_m.GetValue()) So, maybe rng_seed doesn't reflect on nest.random.normal distribution. However, then how can I make sure it draws a different set of values? -- Thanks and Regards *Maryada*

5 8

Izhikevich Simulation
by Allen Rabayda 22 Nov '21

22 Nov '21

Dear Nest Users, Has anyone used any NEST Synapse Models to create Gamma Rhythms during a simulation with the NEST Izhikevich Neuron model? My simulation, which uses the Stdp-Synapse model (additive type) does not appear to be converging into gamma rhythms (w/bi-model wt distribution) using super-threshold poisson point process (ref: Polychronization Computation With Spikes (Izhikevich, 2006), - DOI: 10.1162/089976606775093882 <https://doi.org/10.1162/089976606775093882>) - - - - Thanks for any suggestions, Best Regards, --Allen

2 2

Open NEST Developer Video Conference Monday 22 November 2021 11:30 CET (UTC+1)
by Dennis Terhorst 22 Nov '21

22 Nov '21

Dear NEST Users & Developers! I would like to invite you to our next fortnightly Open NEST Developer Video Conference, today Monday 22 November, 11.30-12.30 CET (UTC+1). 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/2021-11-22-Open-NEST-Developer-… Looking forward to seeing you soon! best, Dennis Terhorst ------------------ Log-in information ------------------ We use a virtual conference room provided by DFN (Deutsches Forschungsnetz). You can use the web client to connect. We however encourage everyone to use a headset for better audio quality or even a proper video conferencing system (see below) or software when available. Web client * Visit https://conf.dfn.de/webapp/conference/97938800 * Enter your name and allow your browser to use camera and microphone * The conference does not need a PIN to join, just click join and you're in. In case you see a dfnconf logo and the phrase "Auf den Meetingveranstalter warten", just be patient, the meeting host needs to join first (a voice will tell you). VC system/software How to log in with a video conferencing system, depends on you VC system or software. - Using the H.323 protocol (eg Polycom): vc.dfn.net##97938800 or 194.95.240.2##97938800 - Using the SIP protocol:97938800@vc.dfn.de - By telephone: +49-30-200-97938800 For those who do not have a video conference system or suitable software, Polycom provides a pretty good free app for iOS and Android, so you can join from your tablet (Polycom RealPresence Mobile, available from AppStore/PlayStore). Note that firewalls may interfere with videoconferencing in various and sometimes confusing ways. For more technical information on logging in from various VC systems, please see http://vcc.zih.tu-dresden.de/index.php?linkid=1.1.3.4

1 0

Call for Papers: Reproducibility in Neuroscience
by Alberto Antonietti 19 Nov '21

19 Nov '21

2 2

Installation procedure of NEST on M1 mac
by Julien Ballbé 18 Nov '21

18 Nov '21

Dear Madam, Dear Sir As a starting doctoral student in the field of computational neurosciences, I am particularly interested in using NEST in my research works. However, I am a bit confused about the procedure to install NEST on a M1 macbook pro, therefore, I prefer to ask you before doing anything. From what I understood from your website here are the steps that, I suppose, I should do to install NEST properly: - as I use a M1MAX Mac (MacOS 12.0) , I can't just install nest, I have to build it. To do so: - Download Miniforge for arm64 (from which I will be able to use Conda right?) - Install Python 3.9.4 for arm Mac macOS 64-bit universal2 installer <https://www.python.org/ftp/python/3.9.8/python-3.9.8-macos11.pkg> - Download the nest source code directly from github ( https://github.com/nest/nest-simulator) - Create a conda environment using the following command conda env create -f extras/conda-nest-simulator-dev.yml - Activate this environment ( conda activate...) - Create a build directory outside the NEST source and go into it - Install cmake package using conda ( conda install -c anaconda cmake) - Configure NEST by running: cmake -DCMAKE_INSTALL_PREFIX:PATH=<nest_install_dir> <nest_source_dir> - Once done I can run make. make install. make installcheck Here are my questions: - Is this installation procedure correct? - Once installed, how can I launch NEST from a python interpreter such as Spyder? Or is it only possible to launch it within a terminal window? - I am quite new to managing packages, so correct me if I am wrong, but have I to install everything using exclusively Conda ? - What is the purpose of creating a new environment to build NEST -Is there anything I missed or misunderstood? I realize how many questions I ask you, and I am very grateful for every advice you could give me. If it is more convenient for you, we can have a phone call when you want. -- *Julien BALLBÉ Y SABATÉ* *Étudiant en thèse - PhD student* *Neurophysiology of Visual Computation* Centre Giovanni Borelli - CNRS UMR 9010 Université de Paris 45 rue des Saint-Pères, 75006 Paris, France Tel: +33 6 79 03 40 35

4 12

[NEST 3.1] autapses/multapses switch for structural plasticity
by Aadhar Sharma 17 Nov '21

17 Nov '21

3 2

NESTML's versioning policy
by Robin Gilbert De Schepper 16 Nov '21

16 Nov '21

Hi all, I was wondering what NESTML's versioning scheme looks like, and what versions of NEST each NESTML version supports! e.g. can I generate code for multiple NEST versions with 1 NESTML version? Best regards, -- Robin De Schepper, MSc 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 network modelling? Discover our framework <https://github.com/dbbs-lab/bsb>: <https://github.com/dbbs-lab/bsb>

3 2

New Izhikevich neuron model; nest_names and synapse dynamics
by Nina Doorn 15 Nov '21

15 Nov '21

Good afternoon, I have adapted the current nest izhikevich neuron model in C++ to obtain a more general izhikevich neuron where more parameters can be set (for example voltage shifts and the membrane capacitance), and the b-parameter can change over time according to some condition, such that also thalamic neurons can be simulated. The new extension module works very well (with much thanks to all earlier help regarding installing extension modules). So hopefully people can eventually, with this model, obtain all the kinds of neurons that Izhikevich describes. As soon as everything is cleaned up and finished, I will upload the code to github. However, before I do that, I have two questions: 1. For the new parameters I added to the existing izhikevich model, I could only use parameter names that are in nest::names. However, for generality and to make it easy to use, I thought it would be better to use the same symbols that Izhikevich uses to describe his model. That way, people can easily replicate all the different types of neurons that Izhikevich describes. He uses these parameters: [image: image.png] Is it possible to include these parameters in the neuron model? Or is it better to just replace them with other parameter names that are already in the nest_names file? 2. The current izhikevich neuron model doesn't model realistic synapses. The membrane potential just jumps on each spike arrival. I would like to include different post-synaptic dynamics with different and preferably multiple timescales (like the beta_multisynapse). Someone mentioned before that a lot of the synaptic dynamics can be defined outside the neuron. So can I use beta synapses with the izhikevich neuron as it is now? Or should I somehow include these dynamics in the C++ file of my new module? I hope the questions are clear. Please let me know if I should provide any additional information. Thanks in advance and have a very nice weekend! Kind regards, Nina

2 1

Installing an extension module in tvb-nest docker
by Nina Doorn 11 Nov '21

11 Nov '21

Dear experts, To develop a spiking neuronal network model of the thalamus, I want to adapt the Izhikevich neuron model to account for the behavior of thalamocortical neurons. Before I do this, I wanted to test if it was possible to install an extension module in my setup. Therefore I followed these steps: https://nest-extension-module.readthedocs.io/en/latest/extension_modules.ht… to install this example nest-extension-module: https://github.com/nest/nest-extension-module . I am working with the tvb-multiscale docker container ( https://github.com/the-virtual-brain/tvb-multiscale/tree/master/tvb_multisc…) in VScode on windows. I've been working with this succesfully and easily managed to make thalamus models with the available aeIF neuron model of NEST. I'm using a python 3.7.3 interpreter and NEST 3. I've succesfully "made" the module with: > docker@84fabd16af99:~/mmb$ cmake > -Dwith-nest=/home/docker/env/neurosci/nest_build/bin/nest-config > ../nest-extension-module-master It gives me the message: > You can now build and install 'mymodule' using > make > make install > The library file libmymodule.so will be installed to > /home/docker/env/neurosci/nest_build/lib/nest/ > Help files will be installed to > /home/docker/env/neurosci/nest_build/share/doc/nest > The module can be loaded into NEST using > nest.Install('mymodule') (in PyNEST) > (mymodule) Install (in SLI > -- Configuring done > -- Generating done > -- Build files have been written to: /home/docker/mmb However, when I try to "make". I get a bunch of errors that I have added at the end of this email. My colleague tried to install exactly the same module in exactly the same way on his linux machine and it worked perfectly. But somehow for me, I get these weird errors that I haven't been able to resolve so far. Does anyone have an idea what the problem might be? It would be greatly appreciated. If you need any additional information please let me know. Thank you in advance and have a nice day! Kind regards, Nina Doorn Error message: docker@84fabd16af99:~/mmb$ make Scanning dependencies of target mymodule_module [ 10%] Building CXX object src/CMakeFiles/mymodule_module.dir/mymodule.cpp.o In file included from /home/docker/nest-extension-module-master/src/mymodule.cpp:30: /home/docker/nest-extension-module-master/src/pif_psc_alpha.h:92:1: error: expected class-name before ‘{’ token { ^ /home/docker/nest-extension-module-master/src/pif_psc_alpha.h:115:21: error: type ‘nest::Node’ is not a base type for type ‘mynest::pif_psc_alpha’ using nest::Node::handle; ^~~~~~ /home/docker/nest-extension-module-master/src/pif_psc_alpha.h:116:21: error: type ‘nest::Node’ is not a base type for type ‘mynest::pif_psc_alpha’ using nest::Node::handles_test_event; ^~~~~~~~~~~~~~~~~~ /home/docker/nest-extension-module-master/src/pif_psc_alpha.h:121:14: error: ‘nest::port mynest::pif_psc_alpha::send_test_event(nest::Node&, nest::port, nest::synindex, bool)’ marked ‘override’, but does not override nest::port send_test_event( nest::Node&, nest::port, nest::synindex, bool ) override; ^~~~~~~~~~~~~~~ /home/docker/nest-extension-module-master/src/pif_psc_alpha.h:129:8: error: ‘void mynest::pif_psc_alpha::handle(nest::SpikeEvent&)’ marked ‘override’, but does not override void handle( nest::SpikeEvent& ) override; //! accept spikes ^~~~~~ /home/docker/nest-extension-module-master/src/pif_psc_alpha.h:130:8: error: ‘void mynest::pif_psc_alpha::handle(nest::CurrentEvent&)’ marked ‘override’, but does not override void handle( nest::CurrentEvent& ) override; //! accept input current ^~~~~~ /home/docker/nest-extension-module-master/src/pif_psc_alpha.h:131:8: error: ‘void mynest::pif_psc_alpha::handle(nest::DataLoggingRequest&)’ marked ‘override’, but does not override void handle( nest::DataLoggingRequest& ) override; //! allow recording with multimeter ^~~~~~ /home/docker/nest-extension-module-master/src/pif_psc_alpha.h:133:14: error: ‘nest::port mynest::pif_psc_alpha::handles_test_event(nest::SpikeEvent&, nest::port)’ marked ‘override’, but does not override nest::port handles_test_event( nest::SpikeEvent&, nest::port ) override; ^~~~~~~~~~~~~~~~~~ /home/docker/nest-extension-module-master/src/pif_psc_alpha.h:134:14: error: ‘nest::port mynest::pif_psc_alpha::handles_test_event(nest::CurrentEvent&, nest::port)’ marked ‘override’, but does not override nest::port handles_test_event( nest::CurrentEvent&, nest::port ) override; ^~~~~~~~~~~~~~~~~~ /home/docker/nest-extension-module-master/src/pif_psc_alpha.h:135:14: error: ‘nest::port mynest::pif_psc_alpha::handles_test_event(nest::DataLoggingRequest&, nest::port)’ marked ‘override’, but does not override nest::port handles_test_event( nest::DataLoggingRequest&, nest::port ) override; ^~~~~~~~~~~~~~~~~~ /home/docker/nest-extension-module-master/src/pif_psc_alpha.h:138:8: error: ‘void mynest::pif_psc_alpha::get_status(DictionaryDatum&) const’ marked ‘override’, but does not override void get_status( DictionaryDatum& ) const override; ^~~~~~~~~~ /home/docker/nest-extension-module-master/src/pif_psc_alpha.h:139:8: error: ‘void mynest::pif_psc_alpha::set_status(const DictionaryDatum&)’ marked ‘override’, but does not override void set_status( const DictionaryDatum& ) override; ^~~~~~~~~~ /home/docker/nest-extension-module-master/src/pif_psc_alpha.h:143:8: error: ‘void mynest::pif_psc_alpha::init_buffers_()’ marked ‘override’, but does not override void init_buffers_() override; ^~~~~~~~~~~~~ /home/docker/nest-extension-module-master/src/pif_psc_alpha.h:146:8: error: ‘void mynest::pif_psc_alpha::calibrate()’ marked ‘override’, but does not override void calibrate() override; ^~~~~~~~~ /home/docker/nest-extension-module-master/src/pif_psc_alpha.h:149:8: error: ‘void mynest::pif_psc_alpha::update(const nest::Time&, long int, long int)’ marked ‘override’, but does not override void update( nest::Time const&, const long, const long ) override; ^~~~~~ /home/docker/nest-extension-module-master/src/pif_psc_alpha.h: In member function ‘nest::port mynest::pif_psc_alpha::send_test_event(nest::Node&, nest::port, nest::synindex, bool)’: /home/docker/nest-extension-module-master/src/pif_psc_alpha.h:324:23: error: no matching function for call to ‘nest::SpikeEvent::set_sender(mynest::pif_psc_alpha&)’ e.set_sender( *this ); ^ In file included from /home/docker/env/neurosci/nest_build/include/nest/connector_model.h:34, from /home/docker/env/neurosci/nest_build/include/nest/common_synapse_properties.h:27, from /home/docker/env/neurosci/nest_build/include/nest/connection.h:27, from /home/docker/nest-extension-module-master/src/drop_odd_spike_connection.h:27, from /home/docker/nest-extension-module-master/src/mymodule.cpp:29: /home/docker/env/neurosci/nest_build/include/nest/event.h:1288:1: note: candidate: ‘void nest::Event::set_sender(nest::Node&)’ Event::set_sender( Node& s ) ^~~~~ /home/docker/env/neurosci/nest_build/include/nest/event.h:1288:1: note: no known conversion for argument 1 from ‘mynest::pif_psc_alpha’ to ‘nest::Node&’ In file included from /home/docker/nest-extension-module-master/src/mymodule.cpp:30: /home/docker/nest-extension-module-master/src/pif_psc_alpha.h: In member function ‘nest::port mynest::pif_psc_alpha::handles_test_event(nest::SpikeEvent&, nest::port)’: /home/docker/nest-extension-module-master/src/pif_psc_alpha.h:337:53: error: ‘get_name’ was not declared in this scope throw nest::UnknownReceptorType( receptor_type, get_name() ); ^~~~~~~~ /home/docker/nest-extension-module-master/src/pif_psc_alpha.h:337:53: note: suggested alternative: ‘get_V_m_’ throw nest::UnknownReceptorType( receptor_type, get_name() ); ^~~~~~~~ get_V_m_ /home/docker/nest-extension-module-master/src/pif_psc_alpha.h: In member function ‘nest::port mynest::pif_psc_alpha::handles_test_event(nest::CurrentEvent&, nest::port)’: /home/docker/nest-extension-module-master/src/pif_psc_alpha.h:351:53: error: ‘get_name’ was not declared in this scope throw nest::UnknownReceptorType( receptor_type, get_name() ); ^~~~~~~~ /home/docker/nest-extension-module-master/src/pif_psc_alpha.h:351:53: note: suggested alternative: ‘get_V_m_’ throw nest::UnknownReceptorType( receptor_type, get_name() ); ^~~~~~~~ get_V_m_ /home/docker/nest-extension-module-master/src/pif_psc_alpha.h: In member function ‘nest::port mynest::pif_psc_alpha::handles_test_event(nest::DataLoggingRequest&, nest::port)’: /home/docker/nest-extension-module-master/src/pif_psc_alpha.h:366:53: error: ‘get_name’ was not declared in this scope throw nest::UnknownReceptorType( receptor_type, get_name() ); ^~~~~~~~ /home/docker/nest-extension-module-master/src/pif_psc_alpha.h:366:53: note: suggested alternative: ‘get_V_m_’ throw nest::UnknownReceptorType( receptor_type, get_name() ); ^~~~~~~~ get_V_m_ /home/docker/nest-extension-module-master/src/pif_psc_alpha.h: In member function ‘void mynest::pif_psc_alpha::get_status(DictionaryDatum&) const’: /home/docker/nest-extension-module-master/src/pif_psc_alpha.h:380:3: error: ‘ArchivingNode’ has not been declared ArchivingNode::get_status( d ); ^~~~~~~~~~~~~ /home/docker/nest-extension-module-master/src/pif_psc_alpha.h: In member function ‘void mynest::pif_psc_alpha::set_status(const DictionaryDatum&)’: /home/docker/nest-extension-module-master/src/pif_psc_alpha.h:397:3: error: ‘ArchivingNode’ has not been declared ArchivingNode::set_status( d ); ^~~~~~~~~~~~~ In file included from /home/docker/env/neurosci/nest_build/include/nest/connection_manager_impl.h:33, from /home/docker/nest-extension-module-master/src/mymodule.cpp:38: /home/docker/env/neurosci/nest_build/include/nest/conn_builder_factory.h: In instantiation of ‘nest::ConnBuilder* nest::ConnBuilderFactory<ConnBuilderType>::create(nest::NodeCollectionPTR, nest::NodeCollectionPTR, const DictionaryDatum&, const DictionaryDatum&) const [with ConnBuilderType = mynest::StepPatternBuilder; nest::NodeCollectionPTR = std::shared_ptr<nest::NodeCollection>; DictionaryDatum = lockPTRDatum<Dictionary, (& SLIInterpreter::Dictionarytype)>]’: /home/docker/env/neurosci/nest_build/include/nest/conn_builder_factory.h:67:3: required from here /home/docker/env/neurosci/nest_build/include/nest/conn_builder_factory.h:72:12: error: no matching function for call to ‘mynest::StepPatternBuilder::StepPatternBuilder(nest::NodeCollectionPTR&, nest::NodeCollectionPTR&, const DictionaryDatum&, const DictionaryDatum&)’ return new ConnBuilderType( sources, targets, conn_spec, syn_spec ); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /home/docker/nest-extension-module-master/src/mymodule.cpp:31: /home/docker/nest-extension-module-master/src/step_pattern_builder.h:35:3: note: candidate: ‘mynest::StepPatternBuilder::StepPatternBuilder(nest::NodeCollectionPTR, nest::NodeCollectionPTR, const DictionaryDatum&, const std::vector<lockPTRDatum<Dictionary, (& SLIInterpreter::Dictionarytype)> >&)’ StepPatternBuilder( const nest::NodeCollectionPTR sources, ^~~~~~~~~~~~~~~~~~ /home/docker/nest-extension-module-master/src/step_pattern_builder.h:35:3: note: no known conversion for argument 4 from ‘const DictionaryDatum’ {aka ‘const lockPTRDatum<Dictionary, (& SLIInterpreter::Dictionarytype)>’} to ‘const std::vector<lockPTRDatum<Dictionary, (& SLIInterpreter::Dictionarytype)> >&’ /home/docker/nest-extension-module-master/src/step_pattern_builder.h:32:7: note: candidate: ‘mynest::StepPatternBuilder::StepPatternBuilder(const mynest::StepPatternBuilder&)’ class StepPatternBuilder : public nest::ConnBuilder ^~~~~~~~~~~~~~~~~~ /home/docker/nest-extension-module-master/src/step_pattern_builder.h:32:7: note: candidate expects 1 argument, 4 provided /home/docker/nest-extension-module-master/src/step_pattern_builder.h:32:7: note: candidate: ‘mynest::StepPatternBuilder::StepPatternBuilder(mynest::StepPatternBuilder&&)’ /home/docker/nest-extension-module-master/src/step_pattern_builder.h:32:7: note: candidate expects 1 argument, 4 provided In file included from /home/docker/env/neurosci/nest_build/include/nest/model_manager.h:31, from /home/docker/env/neurosci/nest_build/include/nest/kernel_manager.h:31, from /home/docker/env/neurosci/nest_build/include/nest/connector_base_impl.h:26, from /home/docker/env/neurosci/nest_build/include/nest/connection.h:29, from /home/docker/nest-extension-module-master/src/drop_odd_spike_connection.h:27, from /home/docker/nest-extension-module-master/src/mymodule.cpp:29: /home/docker/env/neurosci/nest_build/include/nest/genericmodel.h: In instantiation of ‘bool nest::GenericModel<ElementT>::has_proxies() [with ElementT = mynest::pif_psc_alpha]’: /home/docker/env/neurosci/nest_build/include/nest/genericmodel.h:174:1: required from here /home/docker/env/neurosci/nest_build/include/nest/genericmodel.h:176:17: error: ‘class mynest::pif_psc_alpha’ has no member named ‘has_proxies’ return proto_.has_proxies(); ~~~~~~~^~~~~~~~~~~ /home/docker/env/neurosci/nest_build/include/nest/genericmodel.h: In instantiation of ‘bool nest::GenericModel<ElementT>::one_node_per_process() [with ElementT = mynest::pif_psc_alpha]’: /home/docker/env/neurosci/nest_build/include/nest/genericmodel.h:181:1: required from here /home/docker/env/neurosci/nest_build/include/nest/genericmodel.h:183:17: error: ‘class mynest::pif_psc_alpha’ has no member named ‘one_node_per_process’ return proto_.one_node_per_process(); ~~~~~~~^~~~~~~~~~~~~~~~~~~~ /home/docker/env/neurosci/nest_build/include/nest/genericmodel.h: In instantiation of ‘bool nest::GenericModel<ElementT>::is_off_grid() [with ElementT = mynest::pif_psc_alpha]’: /home/docker/env/neurosci/nest_build/include/nest/genericmodel.h:188:1: required from here /home/docker/env/neurosci/nest_build/include/nest/genericmodel.h:190:17: error: ‘class mynest::pif_psc_alpha’ has no member named ‘is_off_grid’ return proto_.is_off_grid(); ~~~~~~~^~~~~~~~~~~ /home/docker/env/neurosci/nest_build/include/nest/genericmodel.h: In instantiation of ‘void nest::GenericModel<ElementT>::calibrate_time(const nest::TimeConverter&) [with ElementT = mynest::pif_psc_alpha]’: /home/docker/env/neurosci/nest_build/include/nest/genericmodel.h:195:1: required from here /home/docker/env/neurosci/nest_build/include/nest/genericmodel.h:197:10: error: ‘class mynest::pif_psc_alpha’ has no member named ‘calibrate_time’; did you mean ‘calibrate’? proto_.calibrate_time( tc ); ~~~~~~~^~~~~~~~~~~~~~ calibrate /home/docker/env/neurosci/nest_build/include/nest/genericmodel.h: In instantiation of ‘void nest::GenericModel<ElementT>::sends_secondary_event(nest::GapJunctionEvent&) [with ElementT = mynest::pif_psc_alpha]’: /home/docker/env/neurosci/nest_build/include/nest/genericmodel.h:209:1: required from here /home/docker/env/neurosci/nest_build/include/nest/genericmodel.h:211:17: error: ‘class mynest::pif_psc_alpha’ has no member named ‘sends_secondary_event’; did you mean ‘send_test_event’? return proto_.sends_secondary_event( ge ); ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ send_test_event /home/docker/env/neurosci/nest_build/include/nest/genericmodel.h:211:43: error: return-statement with a value, in function returning ‘void’ [-fpermissive] return proto_.sends_secondary_event( ge ); ^ /home/docker/env/neurosci/nest_build/include/nest/genericmodel.h: In instantiation of ‘void nest::GenericModel<ElementT>::sends_secondary_event(nest::InstantaneousRateConnectionEvent&) [with ElementT = mynest::pif_psc_alpha]’: /home/docker/env/neurosci/nest_build/include/nest/genericmodel.h:216:1: required from here /home/docker/env/neurosci/nest_build/include/nest/genericmodel.h:218:17: error: ‘class mynest::pif_psc_alpha’ has no member named ‘sends_secondary_event’; did you mean ‘send_test_event’? return proto_.sends_secondary_event( re ); ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ send_test_event /home/docker/env/neurosci/nest_build/include/nest/genericmodel.h:218:43: error: return-statement with a value, in function returning ‘void’ [-fpermissive] return proto_.sends_secondary_event( re ); ^ /home/docker/env/neurosci/nest_build/include/nest/genericmodel.h: In instantiation of ‘void nest::GenericModel<ElementT>::sends_secondary_event(nest::DiffusionConnectionEvent&) [with ElementT = mynest::pif_psc_alpha]’: /home/docker/env/neurosci/nest_build/include/nest/genericmodel.h:223:1: required from here /home/docker/env/neurosci/nest_build/include/nest/genericmodel.h:225:17: error: ‘class mynest::pif_psc_alpha’ has no member named ‘sends_secondary_event’; did you mean ‘send_test_event’? return proto_.sends_secondary_event( de ); ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ send_test_event /home/docker/env/neurosci/nest_build/include/nest/genericmodel.h:225:43: error: return-statement with a value, in function returning ‘void’ [-fpermissive] return proto_.sends_secondary_event( de ); ^ /home/docker/env/neurosci/nest_build/include/nest/genericmodel.h: In instantiation of ‘void nest::GenericModel<ElementT>::sends_secondary_event(nest::DelayedRateConnectionEvent&) [with ElementT = mynest::pif_psc_alpha]’: /home/docker/env/neurosci/nest_build/include/nest/genericmodel.h:230:1: required from here /home/docker/env/neurosci/nest_build/include/nest/genericmodel.h:232:17: error: ‘class mynest::pif_psc_alpha’ has no member named ‘sends_secondary_event’; did you mean ‘send_test_event’? return proto_.sends_secondary_event( re ); ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ send_test_event /home/docker/env/neurosci/nest_build/include/nest/genericmodel.h:232:43: error: return-statement with a value, in function returning ‘void’ [-fpermissive] return proto_.sends_secondary_event( re ); ^ /home/docker/env/neurosci/nest_build/include/nest/genericmodel.h: In instantiation of ‘nest::SignalType nest::GenericModel<ElementT>::sends_signal() const [with ElementT = mynest::pif_psc_alpha]’: /home/docker/env/neurosci/nest_build/include/nest/genericmodel.h:237:1: required from here /home/docker/env/neurosci/nest_build/include/nest/genericmodel.h:239:17: error: ‘const class mynest::pif_psc_alpha’ has no member named ‘sends_signal’ return proto_.sends_signal(); ~~~~~~~^~~~~~~~~~~~ /home/docker/env/neurosci/nest_build/include/nest/genericmodel.h: In instantiation of ‘const nest::Node& nest::GenericModel<ElementT>::get_prototype() const [with ElementT = mynest::pif_psc_alpha]’: /home/docker/env/neurosci/nest_build/include/nest/genericmodel.h:267:1: required from here /home/docker/env/neurosci/nest_build/include/nest/genericmodel.h:269:10: error: invalid initialization of reference of type ‘const nest::Node&’ from expression of type ‘const mynest::pif_psc_alpha’ return proto_; ^~~~~~ /home/docker/env/neurosci/nest_build/include/nest/genericmodel.h: In instantiation of ‘void nest::GenericModel<ElementT>::set_model_id(int) [with ElementT = mynest::pif_psc_alpha]’: /home/docker/env/neurosci/nest_build/include/nest/genericmodel.h:274:1: required from here /home/docker/env/neurosci/nest_build/include/nest/genericmodel.h:276:10: error: ‘class mynest::pif_psc_alpha’ has no member named ‘set_model_id’ proto_.set_model_id( i ); ~~~~~~~^~~~~~~~~~~~ /home/docker/env/neurosci/nest_build/include/nest/genericmodel.h: In instantiation of ‘int nest::GenericModel<ElementT>::get_model_id() [with ElementT = mynest::pif_psc_alpha]’: /home/docker/env/neurosci/nest_build/include/nest/genericmodel.h:281:1: required from here /home/docker/env/neurosci/nest_build/include/nest/genericmodel.h:283:17: error: ‘class mynest::pif_psc_alpha’ has no member named ‘get_model_id’ return proto_.get_model_id(); ~~~~~~~^~~~~~~~~~~~ /home/docker/env/neurosci/nest_build/include/nest/genericmodel.h: In instantiation of ‘DictionaryDatum nest::GenericModel<ElementT>::get_status_() [with ElementT = mynest::pif_psc_alpha; DictionaryDatum = lockPTRDatum<Dictionary, (& SLIInterpreter::Dictionarytype)>]’: /home/docker/env/neurosci/nest_build/include/nest/genericmodel.h:251:1: required from here /home/docker/env/neurosci/nest_build/include/nest/genericmodel.h:253:30: error: ‘class mynest::pif_psc_alpha’ has no member named ‘get_status_base’; did you mean ‘get_status’? DictionaryDatum d = proto_.get_status_base(); ~~~~~~~^~~~~~~~~~~~~~~ get_status /home/docker/env/neurosci/nest_build/include/nest/genericmodel.h: In instantiation of ‘nest::Node* nest::GenericModel<ElementT>::allocate_(void*) [with ElementT = mynest::pif_psc_alpha]’: /home/docker/env/neurosci/nest_build/include/nest/genericmodel.h:159:1: required from here /home/docker/env/neurosci/nest_build/include/nest/genericmodel.h:161:9: error: cannot convert ‘mynest::pif_psc_alpha*’ to ‘nest::Node*’ in initialization Node* n = new ( adr ) ElementT( proto_ ); ^ make[2]: *** [src/CMakeFiles/mymodule_module.dir/build.make:63: src/CMakeFiles/mymodule_module.dir/mymodule.cpp.o] Error 1 make[1]: *** [CMakeFiles/Makefile2:125: src/CMakeFiles/mymodule_module.dir/all] Error 2 make: *** [Makefile:152: all] Error 2

5 18

Using NEST in Spyder/anaconda
by Julien Ballbé 10 Nov '21

10 Nov '21

Dear Sir, Dear Madam, I am currently trying to install NEST in order to be able to use it within an IDE, like Spyder. For the moment I am only able to do the following: open Terminal python3 import nest This works when I use it in the terminal of the computer, but when I open Spyder and execute the following: import nest neuron=nest.Create("iaf_psc_alpha") neuron.get() I get the following error message in the IPython console: runfile('/Users/julienballbe/NEST/untitled0.py', wdir='/Users/julienballbe/NEST') Traceback (most recent call last): File "/Users/julienballbe/NEST/untitled0.py", line 11, in <module> neuron=nest.Create("iaf_psc_alpha") AttributeError: module 'nest' has no attribute 'Create' I am using a Macbook pro M1Max, MacOS 12.0, Spyder 5.1.5, Python 3.9.7. I followed the instruction for building nest on your website ( https://nest-simulator.readthedocs.io/en/latest/installation/mac_install.ht…) and used your recommendation for M1 macs ( https://nest-simulator.readthedocs.io/en/latest/installation/conda_tips.html ). I build Nest following your instruction, the only error I got was when I ran : (nest-simulator-dev) julienballbe@pclnrs241 NEST % make installcheck NEST Testsuite Results ---------------------------------------------------------------------- Phase Tests Skipped Failures Errors Time ---------------------------------------------------------------------- 01 basetests 6 0 0 0 2.0 02 selftests 8 0 0 0 1.0 03 unittests 179 0 0 0 47.0 04 regressiontests 94 2 0 0 55.0 07 pynesttests 93 0 0 93 2.0 07 pynesttests nc 0 0 0 0 0.0 08 cpptests 30 0 0 0 0.0 ---------------------------------------------------------------------- Total 410 2 0 93 107.0 ---------------------------------------------------------------------- THE NEST TESTSUITE DISCOVERED PROBLEMS The following tests failed | .share.nest.testsuite.pytests.test_NodeCollection | .share.nest.testsuite.pytests.test_aeif_lsodar | .share.nest.testsuite.pytests.test_changing_tic_base | .share.nest.testsuite.pytests.test_clopath_synapse | .share.nest.testsuite.pytests.test_connect_all_to_all | .share.nest.testsuite.pytests.test_connect_array_fixed_indegree | .share.nest.testsuite.pytests.test_connect_array_fixed_outdegree | .share.nest.testsuite.pytests.test_connect_arrays | .share.nest.testsuite.pytests.test_connect_conngen | .share.nest.testsuite.pytests.test_connect_fixed_indegree | .share.nest.testsuite.pytests.test_connect_fixed_outdegree | .share.nest.testsuite.pytests.test_connect_fixed_total_number | .share.nest.testsuite.pytests.test_connect_one_to_one | .share.nest.testsuite.pytests.test_connect_pairwise_bernoulli | .share.nest.testsuite.pytests.test_connect_symmetric_pairwise_bernoulli | .share.nest.testsuite.pytests.test_create | .share.nest.testsuite.pytests.test_current_recording_generators | .share.nest.testsuite.pytests.test_erfc_neuron | .share.nest.testsuite.pytests.test_errors | .share.nest.testsuite.pytests.test_events | .share.nest.testsuite.pytests.test_facetshw_stdp | .share.nest.testsuite.pytests.test_get_set | .share.nest.testsuite.pytests.test_getconnections | .share.nest.testsuite.pytests.test_getnodes | .share.nest.testsuite.pytests.test_glif_cond | .share.nest.testsuite.pytests.test_glif_psc | .share.nest.testsuite.pytests.test_helper_functions | .share.nest.testsuite.pytests.test_jonke_synapse | .share.nest.testsuite.pytests.test_json | .share.nest.testsuite.pytests.test_labeled_synapses | .share.nest.testsuite.pytests.test_mc_neuron | .share.nest.testsuite.pytests.test_multiple_synapses | .share.nest.testsuite.pytests.test_nodeParametrization | .share.nest.testsuite.pytests.test_onetooneconnect | .share.nest.testsuite.pytests.test_parameter | .share.nest.testsuite.pytests.test_parrot_neuron | .share.nest.testsuite.pytests.test_parrot_neuron_ps | .share.nest.testsuite.pytests.test_poisson_generator_rate_change | .share.nest.testsuite.pytests.test_pp_psc_delta | .share.nest.testsuite.pytests.test_pp_psc_delta_stdp | .share.nest.testsuite.pytests.test_quantal_stp_synapse | .share.nest.testsuite.pytests.test_random123 | .share.nest.testsuite.pytests.test_random_parameter | .share.nest.testsuite.pytests.test_rate_copy_model | .share.nest.testsuite.pytests.test_rate_instantaneous_and_delayed | .share.nest.testsuite.pytests.test_rate_neuron | .share.nest.testsuite.pytests.test_rate_neuron_communication | .share.nest.testsuite.pytests.test_recording_backend_ascii | .share.nest.testsuite.pytests.test_recording_backend_memory | .share.nest.testsuite.pytests.test_recording_backends | .share.nest.testsuite.pytests.test_refractory | .share.nest.testsuite.pytests.test_regression_issue-1034 | .share.nest.testsuite.pytests.test_regression_issue-1409 | .share.nest.testsuite.pytests.test_regression_issue-2069 | .share.nest.testsuite.pytests.test_regression_issue-2125 | .share.nest.testsuite.pytests.test_siegert_neuron | .share.nest.testsuite.pytests.test_split_simulation | .share.nest.testsuite.pytests.test_stack | .share.nest.testsuite.pytests.test_status | .share.nest.testsuite.pytests.test_stdp_multiplicity | .share.nest.testsuite.pytests.test_stdp_nn_synapses | .share.nest.testsuite.pytests.test_stdp_synapse | .share.nest.testsuite.pytests.test_stdp_triplet_synapse | .share.nest.testsuite.pytests.test_step_rate_generator | .share.nest.testsuite.pytests.test_synapsecollection | .share.nest.testsuite.pytests.test_threads | .share.nest.testsuite.pytests.test_tsodyks2_synapse | .share.nest.testsuite.pytests.test_urbanczik_synapse | .share.nest.testsuite.pytests.test_visualization | .share.nest.testsuite.pytests.test_vogels_sprekeler_synapse | .share.nest.testsuite.pytests.test_weight_recorder | .share.nest.testsuite.pytests.test_weights_as_lists | .share.nest.testsuite.pytests.test_sp.test_conn_builder | .share.nest.testsuite.pytests.test_sp.test_disconnect | .share.nest.testsuite.pytests.test_sp.test_disconnect_multiple | .share.nest.testsuite.pytests.test_sp.test_enable_multithread | .share.nest.testsuite.pytests.test_sp.test_growth_curves | .share.nest.testsuite.pytests.test_sp.test_sp_manager | .share.nest.testsuite.pytests.test_sp.test_synaptic_elements | .share.nest.testsuite.pytests.test_sp.test_update_synaptic_elements | .share.nest.testsuite.pytests.test_spatial.test_SynapseCollection_distance | .share.nest.testsuite.pytests.test_spatial.test_basics | .share.nest.testsuite.pytests.test_spatial.test_connect_layers | .share.nest.testsuite.pytests.test_spatial.test_connect_sliced | .share.nest.testsuite.pytests.test_spatial.test_connection_with_elliptical_mask | .share.nest.testsuite.pytests.test_spatial.test_create_spatial | .share.nest.testsuite.pytests.test_spatial.test_dumping | .share.nest.testsuite.pytests.test_spatial.test_layerNodeCollection | .share.nest.testsuite.pytests.test_spatial.test_layer_GetStatus_SetStatus | .share.nest.testsuite.pytests.test_spatial.test_plotting | .share.nest.testsuite.pytests.test_spatial.test_rotated_rect_mask | .share.nest.testsuite.pytests.test_spatial.test_selection_function_and_elliptical_mask | .share.nest.testsuite.pytests.test_spatial.test_spatial_distributions Please report test failures by creating an issue at https://github.com/nest/nest_simulator/issues ---------------------------------------------------------------------- make[3]: *** [CMakeFiles/installcheck] Error 1 make[2]: *** [CMakeFiles/installcheck.dir/all] Error 2 make[1]: *** [CMakeFiles/installcheck.dir/rule] Error 2 make: *** [installcheck] Error 2 Can you please help me with this? I stay at your disposal for any further information. Thank you for your help, Best feelings, Julien Ballbé -- *Julien BALLBÉ Y SABATÉ* *Étudiant en thèse - PhD student* *Neurophysiology of Visual Computation* Centre Giovanni Borelli - CNRS UMR 9010 Université de Paris 45 rue des Saint-Pères, 75006 Paris, France Tel: +33 6 79 03 40 35

2 1

population specific structural plasticity switch
by Aadhar Sharma 10 Nov '21

10 Nov '21

2 2

NeuronUnit interface to NEST Adexp model.
by Russell J. Jarvis 10 Nov '21

10 Nov '21

Hi there NEST community, I am trying to build an interface between [NEST reduced cell models (Izhikevich/AdExp) and NeuronUnit](https://github.com/russelljjarvis/NESTNeuronUnit). For example here is one such [interface](https://github.com/russelljjarvis/NESTNeuronUnit/blob/master/nes… ) I find that if I run a single current injection experiment using the interface I get an expected number of spikes, but if I keep re-using the same interface in more and more experiments I get the same or similar number of spikes even with different current injection values. Its as if the initial conditions of the model are not re-setting properly. I wonder if there are any ideas of things I could check. This [simple file works okay](https://github.com/russelljjarvis/NESTNeuronUnit/blob/master/test_int…, but it only has one simulation run. Russell Jarvis (he,him) PhD Neuroscience [Personal Website](https://russelljjarvis.github.io/home/) I acknowledge the Dja Dja Wurrung and Taungurung Owners and Custodians of the lands on which I live and work and pay my respect to Elders past, present and future. phone: 61444576301 email: russelljarvis(a)protonmail.com Sent with [ProtonMail](https://protonmail.com/) Secure Email.

2 3

Get details of source and target from Connection list
by Maryada Maryada 09 Nov '21

09 Nov '21

Dear NEST users, In the past version, for debugging purposes I used to get information of my source and target using the GetStatus function. However, with NEST 3.0, I couldn't find a way to do so, mainly because I have to pass either a SynpaseCollection or NeuronCollection as a function argument to GetStatus. Is it possible to fetch node collection from neuron id? Or any easier way to get source and target properties. I referred document at link https://nest-simulator.readthedocs.io/en/v3.1/guides/connection_management.… I have attached the python file for the same. -- Thanks, *Maryada*

2 3

install nest-2.20.0
by Alberto 08 Nov '21

08 Nov '21

Dear experts, I'd like to install the Nest version 2.20.0 instead of the last 3.1. Is it still available for download? Thanks Alberto

4 8

Get details of source and target from Connection list
by Maryada Maryada 08 Nov '21

08 Nov '21

Dear NEST users, In the past version, for debugging purposes, I used to get information of my source and target using the GetStatus function. However, with NEST 3.0, I couldn't find a way to do so, mainly because I have to pass either a SynpaseCollection or NeuronCollection as a function argument to GetStatus. Is it possible to fetch node collection from neuron id? Or any easier way to get the source and target properties. I referred document at link https://nest-simulator.readthedocs.io/en/v3.1/guides/connection_management.… I have attached the python file for the same. -- Thanks and Regards *Maryada*

1 0

Open NEST Developer Video Conference Monday 8 November 2021 11:30 CET (UTC+1)
by Dennis Terhorst 08 Nov '21

08 Nov '21

Dear NEST Users & Developers! I would like to invite you to our next fortnightly Open NEST Developer Video Conference, today Monday 8 November, 11.30-12.30 CET (UTC+1). 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/2021-11-08-Open-NEST-Developer-… Looking forward to seeing you soon! best, Dennis Terhorst ------------------ Log-in information ------------------ We use a virtual conference room provided by DFN (Deutsches Forschungsnetz). You can use the web client to connect. We however encourage everyone to use a headset for better audio quality or even a proper video conferencing system (see below) or software when available. Web client * Visit https://conf.dfn.de/webapp/conference/97938800 * Enter your name and allow your browser to use camera and microphone * The conference does not need a PIN to join, just click join and you're in. In case you see a dfnconf logo and the phrase "Auf den Meetingveranstalter warten", just be patient, the meeting host needs to join first (a voice will tell you). VC system/software How to log in with a video conferencing system, depends on you VC system or software. - Using the H.323 protocol (eg Polycom): vc.dfn.net##97938800 or 194.95.240.2##97938800 - Using the SIP protocol:97938800@vc.dfn.de - By telephone: +49-30-200-97938800 For those who do not have a video conference system or suitable software, Polycom provides a pretty good free app for iOS and Android, so you can join from your tablet (Polycom RealPresence Mobile, available from AppStore/PlayStore). Note that firewalls may interfere with videoconferencing in various and sometimes confusing ways. For more technical information on logging in from various VC systems, please see http://vcc.zih.tu-dresden.de/index.php?linkid=1.1.3.4

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Requesting for workflow and analysis
by D S Jaswanth 04 Nov '21

04 Nov '21

Sir /madam I'm jaswanth , pursuing my master's degree in biochemistry @reva university Were I'm very much interested working with brain modelling by using neuroinformatical tools as part of my research project I request that please give me workflow for Analysing dataset and codes for analysis of dataset finally what types of datasets can be used for brain modelling by nest I hope for your consideration and guidance Thanks and regards

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NEST on macOS 12 Monterey
by Hans Ekkehard Plesser 04 Nov '21

04 Nov '21

Dear NEST Users, I would just like to let you know that I have successfully built, installed and tested NEST on macOS 12.0.1 (Monterey) on Apple Silicon, following the standard procedure for the Mac. Both Apple Clang 13.0 and G++ 11 work. Note that there have been some reports that upgrading to macOS Monterey can very thoroughly lock your machine, especially Intel-based machines (https://arstechnica.com/gadgets/2021/11/why-macos-updates-might-brick-your-…), so you may want to wait with upgrading until this is solved. 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: Adapt custom models from NEST 2.16 to NEST 3.
by Agnes Korcsak-Gorzo 28 Oct '21

28 Oct '21

Dear all, the request below from 20.10.2021 was successfully resolved. Best regards, Agnes """" Hello everyone, I want to adapt two custom models called "global_volume_transmitter" and "dopa_connection" from NEST 2.16 to NEST 3.1. The .cpp and .h files are attached to this email. Is it possible to have the models adapted to NEST 3.1? How could this be done? I hope someone can help me with that. Best regards, Daniel Todt """

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nest installment in Docker nestsim/nest container
by Nina Doorn 25 Oct '21

25 Oct '21

Dear experts, I have a question about using nest on docker/vscode on my windows PC. I hope this is the right place to ask since I couldn't answer my question using the troubleshooting session. I am using docker to use pyNEST on my windows computer. I have successfully installed NEST using the instructions mentioned here for installing on docker: https://nest-simulator.readthedocs.io/en/v2.20.1/installation/index.html. If I am in the container, I have python version 3.8.10. If I run python and then try to "import nest" it says there is no module named nest. Importing other python packages works perfectly in this way. But indeed, when I look at all the installed packages using pip list, there is no package called "nest". There is, however "nest-desktop 3.0.3" there. So I guess nest is not installed. However, I also don't know how to install it. If I use pip install nest, another package called nest is installed that is not the nest simulator (according to: #754 <https://github.com/nest/nest-simulator/issues/754>). Also, I don't know whether this problem is related or totally unrelated but it might give some insight: when I am in VScode in the nestsim/nest container and I click on python: select interpreter, nothing happens, I cannot select a python interpreter/no window opens. So maybe there is something wrong with the python installations or the used path? I hope the problem is clear. I've been trying different things for days so I would greatly appreciate any help you can offer me! Thanks in advance and have a nice day! Kind regards, Nina Doorn

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Open NEST Developer Video Conference Monday 11 October 2021 11:30 CEST (UTC+2)
by Dennis Terhorst 25 Oct '21

25 Oct '21

Dear NEST Users & Developers! I would like to invite you to our next fortnightly Open NEST Developer Video Conference, today Monday 25 October, 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/2021-10-25-Open-NEST-Developer-… Looking forward to seeing you soon! best, Dennis Terhorst ------------------ Log-in information ------------------ We use a virtual conference room provided by DFN (Deutsches Forschungsnetz). You can use the web client to connect. We however encourage everyone to use a headset for better audio quality or even a proper video conferencing system (see below) or software when available. Web client * Visit https://conf.dfn.de/webapp/conference/97938800 * Enter your name and allow your browser to use camera and microphone * The conference does not need a PIN to join, just click join and you're in. In case you see a dfnconf logo and the phrase "Auf den Meetingveranstalter warten", just be patient, the meeting host needs to join first (a voice will tell you). VC system/software How to log in with a video conferencing system, depends on you VC system or software. - Using the H.323 protocol (eg Polycom): vc.dfn.net##97938800 or 194.95.240.2##97938800 - Using the SIP protocol:97938800@vc.dfn.de - By telephone: +49-30-200-97938800 For those who do not have a video conference system or suitable software, Polycom provides a pretty good free app for iOS and Android, so you can join from your tablet (Polycom RealPresence Mobile, available from AppStore/PlayStore). Note that firewalls may interfere with videoconferencing in various and sometimes confusing ways. For more technical information on logging in from various VC systems, please see http://vcc.zih.tu-dresden.de/index.php?linkid=1.1.3.4

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HBP CodeJam#12
by Dennis Terhorst 21 Oct '21

21 Oct '21

Dear all, next month there will be another HBP CodeJam [1] coming up on Nov 23rd-26th and we think this might be an interesting occasion to meet and bring everyone up to the new possibilities now becoming available. The setup of models has become a lot simpler for example using NEST 3's object attribute access, and many models just need minor changes to make use of the powerful new syntax. Additionally the EBRAINS infrastructure has recently released very useful features that allow to combine different tools across the platform. While the CodeJam is mainly advertised for service providers, it would be extremely helpful to have interested power users in the discussion to get direct feed-back for which features to specially prioritize. As far as I know the event is open to anyone with an EBRAINS account for which you can quickly register [2]. We can set up discussion slots also for discussing your use-case, questions or comments, and the event is also suited to work on real code and boost your project. If you are interested for example to have a look into migrating your model to NEST 3, or if you have a particular topic you would like to discuss with NEST developers, or see what is possible on EBRAINS now, please register for the event and let me know! I'll try to gather the most productive set of people for those discussions. (In case you create a new EBRAINS account for this CodeJam let me know, so I can have your account linked to the workshop – need to check…) Looking forward! Best, Dennis [1]: https://www.humanbrainproject.eu/en/follow-hbp/events/ebrainshbp-codejam-co… [2]: https://ebrains.eu/register -- 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 ---------------------------------------------------------------------- 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.-Ing. Harald Bolt, Prof. Dr. Frauke Melchior ----------------------------------------------------------------------

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Connection management for huge network
by kusch lionel 20 Oct '21

20 Oct '21

Dear all, In my working group, we are working on the creation of the spiking neural network of human CA1 (4.8 million neurons). We are using a specific function for defining the connection between the neurons. This function gives us 30 billion pairwise connections. We would like to know what the most efficient for the creating the network in NEST 3 using this pairwise connectivity. Thank you in advance for your answer, Kusch Lionel

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Adapt custom models from NEST 2.16 to NEST 3.1
by Daniel Todt 20 Oct '21

20 Oct '21

Hello everyone, I want to adapt two custom models called "global_volume_transmitter" and "dopa_connection" from NEST 2.16 to NEST 3.1. The .cpp and .h files are attached to this email. Is it possible to have the models adapted to NEST 3.1? How could this be done? I hope someone can help me with that. Best regards, Daniel Todt -- Daniel Todt HPC in Neuroscience Jülich Supercomputing Centre (JSC) Forschungszentrum Jülich GmbH Tel.: +49 2461 61 85277 E-Mail: d.todt(a)fz-juelich.de ------------------------------------------------------------------------------------------------ ------------------------------------------------------------------------------------------------ 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), Dr. Astrid Lambrecht, Prof. Dr. Frauke Melchior ------------------------------------------------------------------------------------------------ ------------------------------------------------------------------------------------------------

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Dennis Asked
by Chris Huyck 12 Oct '21

12 Oct '21

I've recently downloaded a new version of NEST, and I'm trying to make a new synaptic model, but am breaking down in building their default MyModule model. The process onhttps://nest.github.io/nest-simulator/extension_modules<https://eur02.safelinks.protection.outlook.com/?url=https%3A%2F%2Fnest.gith…> says to run bootstrap.sh, but I can't find a bootstrap.sh. Do you have a version you could send me? If not, who can I contact for help (and how)? -Chris

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Open NEST Developer Video Conference Monday 11 October 2021 11:30 CEST (UTC+2)
by Dennis Terhorst 11 Oct '21

11 Oct '21

Dear NEST Users & Developers! I would like to invite you to our next fortnightly Open NEST Developer Video Conference, today Monday 11 October, 11.30-12.30 CEST (UTC+2). Today we again have two possible topics for the in-depth discussion that you may be interested in: * Plasticity models via NESTML, and * NEST wheels (Python package mechanism). 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/2021-10-11-Open-NEST-Developer-… Looking forward to seeing you soon! best, Dennis Terhorst ------------------ Log-in information ------------------ We use a virtual conference room provided by DFN (Deutsches Forschungsnetz). You can use the web client to connect. We however encourage everyone to use a headset for better audio quality or even a proper video conferencing system (see below) or software when available. Web client * Visit https://conf.dfn.de/webapp/conference/97938800 * Enter your name and allow your browser to use camera and microphone * The conference does not need a PIN to join, just click join and you're in. In case you see a dfnconf logo and the phrase "Auf den Meetingveranstalter warten", just be patient, the meeting host needs to join first (a voice will tell you). VC system/software How to log in with a video conferencing system, depends on you VC system or software. - Using the H.323 protocol (eg Polycom): vc.dfn.net##97938800 or 194.95.240.2##97938800 - Using the SIP protocol:97938800@vc.dfn.de - By telephone: +49-30-200-97938800 For those who do not have a video conference system or suitable software, Polycom provides a pretty good free app for iOS and Android, so you can join from your tablet (Polycom RealPresence Mobile, available from AppStore/PlayStore). Note that firewalls may interfere with videoconferencing in various and sometimes confusing ways. For more technical information on logging in from various VC systems, please see http://vcc.zih.tu-dresden.de/index.php?linkid=1.1.3.4

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Open NEST Developer Video Conference Monday 27 September 2021 11:30 CEST (UTC+2)
by Dennis Terhorst 27 Sep '21

27 Sep '21

Dear NEST Users & Developers! I would like to invite you to our next fortnightly Open NEST Developer Video Conference, today Monday 27 September, 11.30-12.30 CEST (UTC+2). 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/2021-09-27-Open-NEST-Developer-… Looking forward to seeing you soon! best, Dennis Terhorst ------------------ Log-in information ------------------ We use a virtual conference room provided by DFN (Deutsches Forschungsnetz). You can use the web client to connect. We however encourage everyone to use a headset for better audio quality or even a proper video conferencing system (see below) or software when available. Web client * Visit https://conf.dfn.de/webapp/conference/97938800 * Enter your name and allow your browser to use camera and microphone * The conference does not need a PIN to join, just click join and you're in. In case you see a dfnconf logo and the phrase "Auf den Meetingveranstalter warten", just be patient, the meeting host needs to join first (a voice will tell you). VC system/software How to log in with a video conferencing system, depends on you VC system or software. - Using the H.323 protocol (eg Polycom): vc.dfn.net##97938800 or 194.95.240.2##97938800 - Using the SIP protocol:97938800@vc.dfn.de - By telephone: +49-30-200-97938800 For those who do not have a video conference system or suitable software, Polycom provides a pretty good free app for iOS and Android, so you can join from your tablet (Polycom RealPresence Mobile, available from AppStore/PlayStore). Note that firewalls may interfere with videoconferencing in various and sometimes confusing ways. For more technical information on logging in from various VC systems, please see http://vcc.zih.tu-dresden.de/index.php?linkid=1.1.3.4

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NEST 3.1 is there!
by Dennis Terhorst 15 Sep '21

15 Sep '21

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Open NEST Developer Video Conference Monday 13 September 2021 11:30 CEST (UTC+2)
by Dennis Terhorst 13 Sep '21

13 Sep '21

Dear NEST Users & Developers! I would like to invite you to our next fortnightly Open NEST Developer Video Conference, today Monday 13 September, 11.30-12.30 CEST (UTC+2). Today we have two topics for the in-depth discussion that you may be interested in. 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 * Failing assertions #2101 <https://github.com/nest/nest-simulator/issues/2101> * Naming of modules (see nest-connplotter:#2 <https://github.com/nest/nest-connplotter/pull/2>) The agenda for this meeting is also available online, see https://github.com/nest/nest-simulator/wiki/2021-09-13-Open-NEST-Developer-… Looking forward to seeing you soon! best, Dennis Terhorst ------------------ Log-in information ------------------ We use a virtual conference room provided by DFN (Deutsches Forschungsnetz). You can use the web client to connect. We however encourage everyone to use a headset for better audio quality or even a proper video conferencing system (see below) or software when available. Web client * Visit https://conf.dfn.de/webapp/conference/97938800 * Enter your name and allow your browser to use camera and microphone * The conference does not need a PIN to join, just click join and you're in. In case you see a dfnconf logo and the phrase "Auf den Meetingveranstalter warten", just be patient, the meeting host needs to join first (a voice will tell you). VC system/software How to log in with a video conferencing system, depends on you VC system or software. - Using the H.323 protocol (eg Polycom): vc.dfn.net##97938800 or 194.95.240.2##97938800 - Using the SIP protocol:97938800@vc.dfn.de - By telephone: +49-30-200-97938800 For those who do not have a video conference system or suitable software, Polycom provides a pretty good free app for iOS and Android, so you can join from your tablet (Polycom RealPresence Mobile, available from AppStore/PlayStore). Note that firewalls may interfere with videoconferencing in various and sometimes confusing ways. For more technical information on logging in from various VC systems, please see http://vcc.zih.tu-dresden.de/index.php?linkid=1.1.3.4

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NEST 3.0: Plot weight matrices example ERROR
by Ing Jyh Tsang 31 Aug '21

31 Aug '21

I think there is an error in https://nest-simulator.readthedocs.io/en/stable/auto_examples/plot_weight_m… * min(E_neurons)and min(I_neurons) should be replace to * min(E_neurons.tolist()) and min(I_neurons.tolist())or some other way to get the right values Suggestion: The file plot_weight_matrices.py just contain a def plot_weight_matrices(E_neurons, I_neurons). If it had a complete code to create nodes, assign weights then plot the weight matrixes, the error could have been caught automatically (CI/CD)? Best, Inton

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