- NEST Users - NEST Initiative Mail

Sharing code that runs with an altered model of NEST
by Julia Gallinaro 14 Jun '21

14 Jun '21

Dear NEST Community, I have performed a small alteration on one model of NEST for a project I am working on (It is a minor alteration: I included a minimum hard bound for weights in the triplet STDP rule). I now want to share the code for this project, and would like to know what is the best approach for doing this. Should I provide my copy of the altered model file together with my project scripts? Or is there another way of doing it, which is more appropriate? I am sorry if that is a basic question, but it is the first time I change something on NEST code for a project. Best, Júlia

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NEST 3.0 Release Party (now!) 🥳
by Jochen Martin Eppler 11 Jun '21

11 Jun '21

Dear NEST users and developers! Finally, the wait is over: we have just created the NEST 3.0 release<https://doi.org/10.5281/zenodo.4739103>. Yay! A more formal announcement will follow tomorrow, but for now, it is time to party! Stop whatever you do right now, grab a drink and join us at https://conf.dfn.de/webapp/conference/97938800! Best regards, Jochen & Dennis (on behalf of the whole NEST team) -- 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.-Ing. Harald Bolt, Dr. Astrid Lambrecht, Prof. Dr. Frauke Melchior ------------------------------------------------------------------------------------------------ ------------------------------------------------------------------------------------------------

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Open NEST Developer Video Conference Monday 7 June 2021 11:30 CEST (UTC+2)
by Dennis Terhorst 07 Jun '21

07 Jun '21

Dear NEST Users & Developers! I would like to invite you to our next fortnightly Open NEST Developer Video Conference, today Monday 07 June, 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 The agenda for this meeting is also available online, see https://github.com/nest/nest-simulator/wiki/2021-06-07-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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Summary of changes to handling of Node collections
by Itaru Kitayama 27 May '21

27 May '21

Hi, Can someone point me to the summary of changes other than git log so I can understand better the changes introduced for the NEST-3 releases? Thanks, Itaru.

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NEST Conference 2021 abstract submission deadline extended
by Anne Elfgen 17 May '21

17 May '21

Dear all, The *abstract submission deadline* for the (virtual) *NEST Conference 2021 **has been extended* to Wednesday, *26 May*. We are still looking forward to your contributions! The NEST Conference provides an opportunity for the NEST Community to meet, exchange success stories, swap advice, learn about current developments in and around NEST spiking network simulation and its application. This year's conference will again take place as a *virtual conference* on *Monday/Tuesday 28/29 June 2021*followed by a virtual NEST User Hackathon until Friday 2 July. We are inviting contributions to the conference, including plenary talks, "posters", breakout sessions and workshops on specific topics. *Important dates* *16 May*2021 — Deadline for NEST Initiative Membership applications *26 May*2021 — Deadline for submission of contributions *08 June*2021 — Notification of acceptance *21 June*2021 — Registration deadline *28 June*2021 — NEST Conference 2021 starts For more information on how to submit your contribution, register and participate, please visit the conference website *https://nest-simulator.org/conference* <https://nest-simulator.org/conference> We are looking forward to seeing you all in June! Hans Ekkehard Plesser, Dennis Terhorst, Anne Elfgen & many more --------------------- * Registration fee for non-members: 50 CHF Registration fee for NEST Initiative members: 20 CHF Annual NI membership fee: 25 CHF

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Re: Stop hanging simulations
by Hans Ekkehard Plesser 10 May '21

10 May '21

Hi Tom, As a DIY workaround, you can use the RunManager context to simulate in small steps and break if it gets too slow. I haven't tested the code, just sketching from memory. Instead of calling nest.Simulate(1000), use with nest.RunManager(): for _ in range(100): t = time.time() nest.Run(10) if time.time() - t > 5: break The logic is as follows: You split the 1000 ms into 100 times 10 ms. This is fast with Run() within the RunManager(). You then use Python's time to see how long it takes to simulate 10 ms and break if it takes too long, here a 5 s limit. You can then use GetKernelStatus to get the current time in the simulation. It would be interesting to add this as a kernel feature. Let me know if it works! 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 On 06/05/2021, 16:08, "TOM BUGNON" <bugnon(a)wisc.edu<mailto:bugnon@wisc.edu>> wrote: Hi all, Under some circumstances simulations can slow down up to the point where the nest.Simulate() does not advance anymore and stays stuck at a given virtual time, with a "realtime factor" of 0. I suppose this can happen for instance when a network falls into a regime of runaway excitation in which a massive number of spikes are being exchanged. I'm looking for a way to stop the simulation in such a case, (say when the realtime factor goes below a set threshold, or when the output files are not updated for a certain duration), ideally in such a way that the program can continue running rather than crashing. If anyone has a suggestion about how to go around this issue I'd be happy to hear it. Thanks in advance! Best, Tom

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Open NEST Developer Video Conference Monday 10 May 2021 11:30 CEST (UTC+2)
by Dennis Terhorst 10 May '21

10 May '21

Dear NEST Users & Developers! I would like to invite you to our next fortnightly Open NEST Developer Video Conference, today Monday 10 May, 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. Today we would have a deeper look on CI/testing in the current GitHub-Actions context and STDP models in particular. Agenda Welcome Review of NEST User Mailing List Project team round In-depth discussion * Interactively debugging GitHub Actions <https://github.com/nest/nest-simulator/actions> failures * Discussion of STDP synapse unit testing #1840 <https://github.com/nest/nest-simulator/pull/1840> The agenda for this meeting is also available online, see https://github.com/nest/nest-simulator/wiki/2021-05-10-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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Profiling PyNEST—easier than you think and some interesting results
by Hans Ekkehard Plesser 07 May '21

07 May '21

Hi everyone! I realized today that profiling PyNEST is easier than I thought. In iPython, you can just run run -p -s cumulative -D srn.prof ../src/pynest/examples/store_restore_network.py which will run the script, present a summary sorted by cumulative time and write binary profiling data (pstats format) to file srn.prof. Then run (gprof2dot available from, e.g., PiPy) gprof2dot -f pstats -o srn.dot srn.prof and finally dot -Tpdf srn.dot Both tools have lot's of options. In my case (an older version of the script above, currently under review in #1919, not yet in master), the attached PDF resulted, showing that getting connection properties indeed takes a lot of time. Note that the graph only resolves time spent in Python code, time spent in C++ code is hiding behind "run()". Below some more timing results from a network of 1000 neurons with 100,000 connections: In [16]: %time c = nest.GetConnections() CPU times: user 66.5 ms, sys: 8.09 ms, total: 74.6 ms Wall time: 75.7 ms In [17]: %time c = nest.GetConnections().weight CPU times: user 869 ms, sys: 75.3 ms, total: 944 ms Wall time: 955 ms In [18]: %time c = nest.GetConnections().get("weight", output="pandas") CPU times: user 1.69 s, sys: 186 ms, total: 1.88 s Wall time: 1.9 s Clearly, GetConnections() is quite fast, while reading out the weights costs. What maybe surprised me most is that turning the data as a Pandas DataFrame costs a whole second extra—I wonder if we do something suboptimal here. 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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Stop hanging simulations
by TOM BUGNON 06 May '21

06 May '21

Hi all, Under some circumstances simulations can slow down up to the point where the nest.Simulate() does not advance anymore and stays stuck at a given virtual time, with a "realtime factor" of 0. I suppose this can happen for instance when a network falls into a regime of runaway excitation in which a massive number of spikes are being exchanged. I'm looking for a way to stop the simulation in such a case, (say when the realtime factor goes below a set threshold, or when the output files are not updated for a certain duration), ideally in such a way that the program can continue running rather than crashing. If anyone has a suggestion about how to go around this issue I'd be happy to hear it. Thanks in advance! Best, Tom

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Apologies for spam via NEST Users
by Hans Ekkehard Plesser 27 Apr '21

27 Apr '21

Dear NEST Users subscribers, In the last 24 hours, you unfortunately received two spam emails via NEST Users. This happened as someone exploited our approach of managing NEST Users based on trust. So far, we allow all registered subscribers to send mails to the list without further control, and we generally accept all subscription requests without double-checking that the requests really come from a person with a genuine interest in NEST. This time, someone exploited our trust to spread spam. We will review our policies to avoid undue spamming, but I do hope we will be able to continue in the spirit of trust that has so far been a hallmark of the NEST Community. Let me close with a bit of advertising of my own: Do not forget to submit your abstract to the NEST Conference 2021 at https://www.nest-simulator.org/conference! 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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