- NEST Users - NEST Initiative Mail

by Jochen Martin Eppler

Hi all! During an upgrade of the Mailman system today, some of you were affected by a small hick-up that caused your subscription to be suspended (not cancelled). Meanwhile, I've re-enabled all of you and you should be able to receive mails again just fine. Sorry for any confusion caused by this. Cheers, Jochen! -- 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), Dr. Astrid Lambrecht, Prof. Dr. Frauke Melchior ------------------------------------------------------------------------------------------------ ------------------------------------------------------------------------------------------------

3 years, 4 months

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test

by Jochen Martin Eppler

Please ignore -- 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), Dr. Astrid Lambrecht, Prof. Dr. Frauke Melchior ------------------------------------------------------------------------------------------------ ------------------------------------------------------------------------------------------------

3 years, 4 months

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Test

by Jochen Martin Eppler

Please ignore! -- 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), Dr. Astrid Lambrecht, Prof. Dr. Frauke Melchior ------------------------------------------------------------------------------------------------ ------------------------------------------------------------------------------------------------

3 years, 4 months

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Open NEST Developer Video Conference Monday 16 August 2021 11:30 CEST (UTC+2)

by Dennis Terhorst

Dear NEST Users & Developers! I would like to invite you to our next fortnightly Open NEST Developer Video Conference, today Monday 16 August, 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/2021-08-16-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

3 years, 4 months

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Re: libnestutil BlockVector Implementation

by Håkon Mørk

Hi Itaru, The problem we had with std::vector was how it allocates memory. When the memory allocated for a vector is full, its capacity is increased by allocating a bigger chunk of memory (commonly with double the capacity of the original vector), and all elements are moved to the new allocation. We observed that when connections are all put in one big vector, and the number of connections in the vector becomes large, memory consumption from vector growth becomes problematic. We therefore created a new container, BlockVector, to keep memory consumption under control and avoid moving the elements when increasing the capacity. The BlockVector achieves this by allocating an entire block of a fixed size every time the capacity has to be increased. The BlockVector therefore becomes a vector of vectors, where the entire size of each new block, which is a new vector in the vector of vectors, is allocated only once when the block is created. Some benchmarks were done during the review of the PR, https://github.com/nest/nest-simulator/pull/1047 You can find the benchmarks here: https://github.com/nest/nest-simulator/files/2505835/Bench_214_sq_db70dcc1e… Note that BlockVector was called "Seque" at the time. Best, Håkon ________________________________ From: Itaru Kitayama <itaru.kitayama(a)gmail.com> Sent: 10 August 2021 05:51 To: NEST User Mailing List <users(a)nest-simulator.org> Subject: [NEST Users] libnestutil BlockVector Implementation Hello Håkon, As you implemented, an instance of BlockVector is a vector of vectors but allows users to specify with one index. As I am having a few problems with mapping BlockVetors to the device memory, I am simply wondering as to why we can't just use std::vector< value_type >? If you guys observed significant performance improvements with BlockVectors in the past, would you mind pointing me to the papers or notes? Thanks, Itaru. _______________________________________________ NEST Users mailing list -- users(a)nest-simulator.org To unsubscribe send an email to users-leave(a)nest-simulator.org

3 years, 4 months

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Filip Blaštík - Noise generation after stimuation problem

by Filip Blastik

To whom it may concern, I am writing regarding the problem with giving my topology network noise after simulation with the signal. The network is oscillating with noise generator which is created as single layer which provides noise for other nodes (which consist of layers). I stimulate my network with stronger signal(another different layer) and after the simulation the Nodes stop reacting to the noise input and become stuck on refresh Voltage and its for longer periods than refractory period. The model is derivation of Hill-Tononi example network. The Nest is running on Ubuntu 20.04 , Conda/Spyder The nest is version v2.20.1 To visualize the problem here are the images which illustrate the problem [image: image.png] [image: image.png] Here is the snippet of the code with the connections and layer setups Best regards Bc. Filip Blaštík

3 years, 4 months

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NEST pool allocator

by Itaru Kitayama

Hi, If Tiziano who wrote the code could enlighten me on understanding further of the code that'd be great, but in case he left already could the Community can jump in?; The "chunks" are clearly dedicated to Nodes, but I wonder if there are cases chunks are used for other objects? Thanks, Itaru.

3 years, 5 months

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Open NEST Developer Video Conference Monday 19 July 2021 11:30 CEST (UTC+2)

by Dennis Terhorst

Dear NEST Users & Developers! I would like to invite you to our next fortnightly Open NEST Developer Video Conference, today Monday 19 July, 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: Running inside Docker on Piz Daint The agenda for this meeting is also available online, see https://github.com/nest/nest-simulator/wiki/2021-07-19-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

3 years, 5 months

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Open NEST Developer Video Conference Monday 5 July 2021 11:30 CEST (UTC+2)

by Dennis Terhorst

Dear NEST Users & Developers! I would like to invite you to our next fortnightly Open NEST Developer Video Conference, today Monday 5 July, 11.30-12.30 CEST (UTC+2). As there is the CNS Conference ongoing and many may be in a New York timezone we'll try to keep it short. 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/2021-07-05-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

3 years, 5 months

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Changing connection weight according to a function

by Ryan Rahy

Dear all, I am trying to build a network where one of the connection weights changes according to a given function. I'm specifically looking for a step function, such that the weight would stay constant at a negative value until a given time point, where it would suddenly change to positive value. As far as I can tell, the existing synaptic models with plasticity cannot do this. I'm trying to do this in order to model a rebound effect, where a neuron fires after being released form an inhibitory current. This effect takes place over a time scale of seconds in the circuit I'm studying, so using an existing model with built-in GABA-mediated rebound doesn't do the trick. So is there a way to manually change a connection weight during the simulation? If not, is there some other way I could achieve the same effect in NEST? Thanks in advance! Best, Ryan

3 years, 5 months

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