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Re: libnestutil BlockVector Implementation
by Håkon Mørk 10 Aug '21

10 Aug '21

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

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Re: Filip Blaštík - Noise generation after stimuation problem
by Hans Ekkehard Plesser 10 Aug '21

10 Aug '21

Hello Filip, I am not quite sure I understand your problem description. You write that "... after the simulation the Nodes top reacting to the noise input and become stuck on the refresh Voltage ...". But in the figure you show, the neurons have V_M ≈ -75 mV ≈ E_L for the first 30 ms, which would correspond to neurons only receiving noise input during this time and afterward seem to spike at roughly 20 ms intervals. It does seem curious that they seem to have a more or less constant membrane potential of ≈ -65 mV between the phases with spiking. So one question is what happens around 30 ms? The other question is why the "locking" to -65 mV. Could you send the full simulation script leading to the figure you included? Or even better, a minimal version of it, i.e., a complete, runnable script producing a figure with the effect you showed, but with as few layers and as few neurons per layer as possible? Best regards, Hans Ekkehard -- Prof. Dr. Hans Ekkehard Plesser Head, Department of Data Science Faculty of Science and Technology Norwegian University of Life Sciences PO Box 5003, 1432 Aas, Norway Phone +47 6723 1560 Email hans.ekkehard.plesser(a)nmbu.no<mailto:hans.ekkehard.plesser@nmbu.no> Home http://arken.nmbu.no/~plesser On 26/07/2021, 14:28, "Filip Blastik" <filipblastik(a)gmail.com<mailto:filipblastik@gmail.com>> wrote: 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 [cid:image001.png@01D78DC3.D2D6F180] [cid:image002.png@01D78DC3.D2D6F180] Here is the snippet of the code with the connections and layer setups Best regards Bc. Filip Blaštík

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NEST pool allocator
by Itaru Kitayama 20 Jul '21

20 Jul '21

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.

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Open NEST Developer Video Conference Monday 19 July 2021 11:30 CEST (UTC+2)
by Dennis Terhorst 19 Jul '21

19 Jul '21

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

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Open NEST Developer Video Conference Monday 5 July 2021 11:30 CEST (UTC+2)
by Dennis Terhorst 05 Jul '21

05 Jul '21

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

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Changing connection weight according to a function
by Ryan Rahy 28 Jun '21

28 Jun '21

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

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

21 Jun '21

Dear NEST Users & Developers! I would like to invite you to our next fortnightly Open NEST Developer Video Conference, today Monday 21 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/2021-06-21-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 wheels
by Robin Gilbert De Schepper 15 Jun '21

15 Jun '21

Hi all! NEST is pip installable! I'd like to collect some feedback on #2073 <https://github.com/nest/nest-simulator/pull/2073> so anyone that is interested to try out a (temporary) pip installed NEST can try `pip install nest-on-square-wheels`. It takes as long as a regular NEST install so it can take a while to finish. In case of errors the error message is usually buried in quite a big red blob of pip mumbo jumbo, but other than that it should be a nice hands-off experience :) You can build with MPI: > pip install nest-on-square-wheels --install-option="--mpi=ON" and control the amount of CMake jobs if it makes your machine stall: > pip install nest-on-square-wheels --install-option="--mpi=ON" --install-option="--jobs=2" All feedback is welcome on the PR, these temporary `nest-on-square-wheels` will be removed in the near future so obviously don't count on them in any scripts or package lists. -- 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>

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NEST Conference 2021 - register by June 21!
by Anne Elfgen 14 Jun '21

14 Jun '21

Dear all, Just a little reminder that the registration deadline for the NEST Conference 2021 is on Monday next week, June 21. More information on the programme and how to register can be found on the conference website https://nest-simulator.org/conference 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. 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 are looking forward to seeing you all! Hans Ekkehard Plesser & many more --------------------- * Registration fee for non-members: 50 CHF Registration fee for NEST Initiative members: 20 CHF Annual NI membership fee: 25 CHF ------------------------------------------------------------------------------------------------ ------------------------------------------------------------------------------------------------ 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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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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