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Open NEST Developer Video Conference Monday 1 March 2021 11:30 CET (UTC+1)
by Dennis Terhorst 01 Mar '21

01 Mar '21

Dear NEST Users & Developers! I would like to invite you to our next fortnightly Open NEST Developer Video Conference, today Monday 1 March, 11.30-12.30 CET (UTC+1). 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 this would for example be a discussion about changing the minimum required Python version. Agenda Welcome Review of NEST User Mailing List Project team round In-depth discussion Raise minimal Python version required: hike to 3.7 or 3.8 (see #1932 <https://github.com/nest/nest-simulator/pull/1932#issuecomment-782710952>)? The agenda for this meeting is also available online, see https://github.com/nest/nest-simulator/wiki/2021-03-01-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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Error when plotting masks with azimuthal angle
by Arturo del Cerro Vergara 26 Feb '21

26 Feb '21

Hello, my name is Arturo and I think I found a bug when calling PlotTargets using the mask plot option with an azimuthal angle > 0. Below I give an example very easy to follow that shows that although the targets are plotted correctly, the mask is not. Correct me if I am doing anything wrong please. I attach an image of the results also. Thank you, Arturo. Code: l = topo.CreateLayer({'rows': 21, 'columns': 21, 'elements': 'iaf_psc_alpha'}) conndict = {'connection_type': 'divergent', 'mask': {'rectangular': {'lower_left': [-0.3, -0.12], 'upper_right': [-0.05, 0.12], 'azimuth_angle': 45.}}, 'kernel': 1.0} topo.ConnectLayers(l, l, conndict) fig = topo.PlotLayer(l, nodesize=40) ctr = topo.FindCenterElement(l) topo.PlotTargets(ctr, l, fig=fig, mask=conndict['mask'], src_size=250, tgt_color='red', tgt_size=20) [image: Captura.PNG]

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NEST Developers / Github Checks: Please merge master into open PRs/branches
by Hans Ekkehard Plesser 25 Feb '21

25 Feb '21

Dear NEST Developers! Thanks to Lekshmi's great work, we can now use Github checks for continuous integration testing. Please merge master into your open PRs/branches to make sure your contributions run the Github checks. We will run Github checks and Travis checks in parallel for now. 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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Help on models from the command line?
by Hans Ekkehard Plesser 24 Feb '21

24 Feb '21

Hi! Just a question, I may have ovelooked something. If I use NEST help to get information about a neuron model, I get the message that there is no help: In [28]: nest.help('iaf_psc_alpha') Sorry, there is no help for 'iaf_psc_alpha'. But we have all the nice model documentation. Have I overlooked something or do we need to upgrade help()? 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: Nest on parallel computer
by Hans Ekkehard Plesser 20 Feb '21

20 Feb '21

Dear Johan, You do not tell us what the “result” number is that you print out. But I notice that the value you get when running with 10 MPI processes on PDC, is about 10 times smaller than the value you see with one process on your PC. I’ll venture a guess and assume you have a network of N neurons which you connect to one spike detector. You simulate, read out the number of spikes and convert it into a firing rate, dividing number of spikes by N * simtime. In an MPI-parallel simulation, the spike detector on each MPI process only gets the spikes of neurons simulated on that MPI process. If you still divide by the full number of neurons to compute the rate, one would expect exactly the behavior you observe. In the future, please provide more details about what you are doing, so we can provide more pointed advice. 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 19/02/2021, 22:20, "JOHAN LILJEFORS" <JOHAN(a)liljefors.eu<mailto:JOHAN@liljefors.eu>> wrote: Dear Nest users, I am fairly new to Nest having used it only for a few months and it has been working without any problems on my PC running Linux. Recently I was given access to a PDC where I have been submitting jobs but I am encountering a problem with my model. I'm running Python 3.7.3 and Nest 2.18. On both my PC and on the PDC, I run the following python script: ------------------------------ import Nest For counter in range(0,10): nest.resetkernel() ___run___script print(result) ------------------------------ I execute this with "srun -n=1 python3 run.py" This outputs 10 numbers, ranging from 0.35-0.4. On the PDC, i run the same scripts but without the for loop: ------------------------------ import Nest nest.resetkernel() ___run___script print(result) ------------------------------ I execute this with "srun -n=10 python3 run.py" this outputs 10 numbers, but this time much smaller around 0.04. I am not doing any file operations, nor any MPI communication between the tasks and I am genuinely confused as to how submitting multiple tasks can yield a different result than a single task. Has anyone encountered anything similar? Regards Johan Liljefors

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Nest on parallel computer
by JOHAN LILJEFORS 19 Feb '21

19 Feb '21

Dear Nest users, I am fairly new to Nest having used it only for a few months and it has been working without any problems on my PC running Linux. Recently I was given access to a PDC where I have been submitting jobs but I am encountering a problem with my model. I'm running Python 3.7.3 and Nest 2.18. On both my PC and on the PDC, I run the following python script: ------------------------------ import Nest For counter in range(0,10): nest.resetkernel() ___run___script print(result) ------------------------------ I execute this with "srun -n=1 python3 run.py" This outputs 10 numbers, ranging from 0.35-0.4. On the PDC, i run the same scripts but without the for loop: ------------------------------ import Nest nest.resetkernel() ___run___script print(result) ------------------------------ I execute this with "srun -n=10 python3 run.py" this outputs 10 numbers, but this time much smaller around 0.04. I am not doing any file operations, nor any MPI communication between the tasks and I am genuinely confused as to how submitting multiple tasks can yield a different result than a single task. Has anyone encountered anything similar? Regards Johan Liljefors

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SAVE THE DATE for the virtual NEST Conference 2021
by Anne Elfgen 18 Feb '21

18 Feb '21

Dear Colleagues, The NEST Initiative is excited to invite everyone interested in Neural Simulation Technology and the NEST Simulator to the NEST Conference 2021! 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 willagaintake place as a *virtual conference*on Monday/Tuesday *28**/**29 June **2021*followed by a virtual NESTUserHackathon until Friday 2 July, whichoffers the opportunity to deep-dive your own code with expert developers at your fingertips. For more information 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 EkkehardPlesser, Dennis Terhorst & Anne Elfgen

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Nest compile on Piz-Daint
by Sergio Solinas 17 Feb '21

17 Feb '21

Dear NEST Users, I'm trying to get NEST up and running on Piz-Daint. I could manage to have it fully compiled and installed with python bindings, MPI, GSL and Boost. However, simulations start but get killed returning a std::bad_alloc. make installcheck also fails. Did anyone managed to have it installed on this HPC? Best regards, Sergio MG Solinas Dip. di Scienze Biomediche Università di Sassari Viale San Pietro 23 07100 - Sassari The NEURON School <https://www.neuronschool.org/> -- -- *Dona il 5x1000* all'Università degli Studi di Sassaricodice fiscale: 00196350904

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neuron parameter as array?
by Cristiano Alessandro 16 Feb '21

16 Feb '21

Hi all, I am writing a new neuron model using nestml and then I modify the C++ code. I am having a hard time defining an input parameter of the neuron as an array of numbers. Is this even possible? Thanks. Regards Cristiano

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Open NEST Developer Video Conference Monday 1 February 2021 11:30 CET (UTC+1)
by Dennis Terhorst 15 Feb '21

15 Feb '21

Alaaf!¹ Dear NEST Users & Developers! I would like to invite you to our next fortnightly Open NEST Developer Video Conference, today Monday 15 February, 11.30-12.30 CET (UTC+1). 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/2021-02-15-Open-NEST-Developer-… Looking forward to seeing you soon! best, Dennis Terhorst ¹) "Alaaf" is the traditional chant in this particular southern region of the Rheinland for this particular day. See https://en.wikipedia.org/wiki/Rosenmontag ------------------ 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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Master branch Doxygen location
by Itaru Kitayama 08 Feb '21

08 Feb '21

Hi, The NEST "Read the Docs" tells us how to invoke doxygen, but I am wondering if the community continuously builds Doxygen db every time a series is committed to master and put it somewhere.

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Registration to the mailing list
by Vittorio De Falco 04 Feb '21

04 Feb '21

Dear NEST users, I tried to inscribe to the mailing list with this e-mail account deltafi.mat(a)live.it. I completed the registration, but I did not receive any link. Could you please help me? Thanks for your support. Best, Vittorio *************************************************************** * Postdoctoral Researcher in Mathematics * University of Naples "Federico II" * Department of Mathematics and Application "R. Caccioppoli" * Via Cintia, IT-80126 Naples, Italy * CELL: +39 340 544 70 15 ****************************************************************

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Spike Event Multiplicity
by Benedikt Feldotto 04 Feb '21

04 Feb '21

Dear all, I realized that spikes that pass synapses (e.g. stdp_connection) are not processing a "multiplicity" value. However, some other nodes e.g. spikes delivered from the volume_transmitter into the stdp_dopa_connection include such a value. Does this mean, the multiplicity for spike events that pass a synapse is always equal to 1? Thanks! Best Regards, 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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Turn Off NEST Warnings
by Benedikt Feldotto 03 Feb '21

03 Feb '21

Dear all, is there a possibility to turn off NEST warnings such as: It does not influence my experiments per se, but we are currently recording videos for our review and it just doesnt make a good impression to have warnings popping up :) 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 1 February 2021 11:30 CET (UTC+1)
by Dennis Terhorst 01 Feb '21

01 Feb '21

Dear NEST Users & Developers! I would like to invite you to our next fortnightly Open NEST Developer Video Conference, today Monday 1 February, 11.30-12.30 CET (UTC+1). 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/2021-02-01-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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CBD Online
by brielleyoung31＠gmail.com 20 Jan '21

20 Jan '21

If you are thinking of starting a CBD product business, then you should get to know the different CBD products on the market. Cannabidiol, also called cannabidiol, is a powerful phytochemical found in nature. It's one of only 47 known compounds that produce delta-9-tetrahydrocannabinol (THC) in plants. The good news is that scientists have successfully bred several strains of plants that contain cannabidiol and made it usable as a food supplement. Some of these strains are even available online, which makes it easier for people to try out new products that they haven't tried before. Unfortunately, not every CBD product is created equal. It's important to understand the differences between these strains so that you can get a better understanding of which ones will be the most effective when used as dietary supplements. Take some time to learn more about these CBD products, because there is an abundance of information available at https://goldbee.com/. A good way to start is by looking at the ingredients. Most of the CBD products available today are derived from a variety of different sources. Some sources include hemp, the leaves of hemp, and other plants. Other sources are not as reliable, such as hemp seed oil, hemp hurd, and other plant parts. Take the time to learn about the various components of each CBD product so that you can make a more informed decision. One of the best natural compounds found in CBD products is cannabidiol. This substance is often used interchangeably with cannabigerol. While cannabidiol has been shown to have a number of health benefits, it has also been shown to produce some of the same side effects as other substances. In some instances, it has been shown to cause depression, and it has also been linked to memory loss and muscle weakness. This substance has also been banned in several countries because of its possible side effects. It's important to note that some clinical trials have shown positive results with this compound. However, there are still many questions surrounding this herb. It's important that you understand why it is important to have clinical trials conducted on CBD products. If the medical community is able to determine the full potential for CBD, then it will help them come up with better medications. There may come a time when it will be possible to develop a CBD pill that produces the same positive results without the dangerous side effects. With that said, it's important that you research different CBD products so that you're ready to enter the world of natural medicine. There are a lot of different options out there that offer great products that can help you combat a wide range of conditions. Take some time to get familiar with all of your options, and then you will be ready to get started.

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CBD Products Online
by brielleyoung31＠gmail.com 20 Jan '21

20 Jan '21

If you are thinking of starting a CBD product business, then you should get to know the different CBD products on the market. Cannabidiol, also called cannabidiol, is a powerful phytochemical found in nature. It's one of only 47 known compounds that produce delta-9-tetrahydrocannabinol (THC) in plants. The good news is that scientists have successfully bred several strains of plants that contain cannabidiol and made it usable as a food supplement. Some of these strains are even available online, which makes it easier for people to try out new products that they haven't tried before. Unfortunately, not every CBD product is created equal. It's important to understand the differences between these strains so that you can get a better understanding of which ones will be the most effective when used as dietary supplements. Take some time to learn more about these CBD products, because there is an abundance of information available. A good way to start is by looking at the ingredients. Most of the CBD products available today are derived from a variety of different sources. Some sources include hemp, the leaves of hemp, and other plants. Other sources are not as reliable, such as hemp seed oil, hemp hurd, and other plant parts. Take the time to learn about the various components of each CBD product so that you can make a more informed decision. One of the best natural compounds found in CBD products is cannabidiol. This substance is often used interchangeably with cannabidiol. While cannabidiol has been shown to have a number of health benefits, it has also been shown to produce some of the same side effects as other substances. In some instances, it has been shown to cause depression, and it has also been linked to memory loss and muscle weakness. This substance has also been banned in several countries because of its possible side effects. It's important to note that some clinical trials have shown positive results with this compound. However, there are still many questions surrounding this herb. It's important that you understand why it is important to have clinical trials conducted on CBD products. If the medical community is able to determine the full potential for CBD, then it will help them come up with better medications. There may come a time when it will be possible to develop a CBD pill that produces the same positive results without the dangerous side effects. With that said, it's important that you research different CBD products so that you're ready to enter the world of natural medicine. There are a lot of different options out there that offer great products that can help you combat a wide range of conditions. Take some time to get familiar with all of your options, and then you will be ready to get started.

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Plot weight matrices example
by Ing Jyh Tsang 19 Jan '21

19 Jan '21

HI, I may be mistaken, but isn't the EI and IE index switched (https://nest-simulator.readthedocs.io/en/stable/auto_examples/plot_weight_m…) ? a_EI = nest.GetConnections(I_neurons, E_neurons) c_EI = nest.GetStatus(a_EI, keys='weight') a_IE = nest.GetConnections(E_neurons, I_neurons) c_IE = nest.GetStatus(a_IE, keys='weight') for idx, n in enumerate(a_EI): W_EI[n[0] - min(I_neurons), n[1] - min(E_neurons)] += c_EI[idx] for idx, n in enumerate(a_IE): W_IE[n[0] - min(E_neurons), n[1] - min(I_neurons)] += c_IE[idx] Thanks,

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Re: NEST installation error on Mac
by Hans Ekkehard Plesser 18 Jan '21

18 Jan '21

Hi Pooja, Over the weekend, I did a brief test on a Mac with Big Sur an built NEST successfully. Below is a detailed description of my setup and steps I have taken. I hope this helps. Best, Hans Ekkehard System: Mac Book Air with INTEL CPU, Big Sur 11.1 Apple Command Line Tools % xcode-select --print-path /Library/Developer/CommandLineTools Homebrew packages (explicitly installed; see below for full list) % brew leaves boost cmake git gsl imagemagick open-mpi scipy wget Conda packages (base installation is miniconda3; this shows only explicitly installed packages, full list below) % conda create -n nest_dev nomkl numpy scipy matplotlib ipython cython nose % conda activate nest_dev % pip install junitparser % conda export --from-history name: nest_dev channels: - defaults dependencies: - nomkl - numpy - nose - matplotlib - cython - ipython - scipy Additionally via pip: junitparser CMake invocation and report % cmake -DCMAKE_INSTALL_PREFIX:PATH=`pwd`/install -Dwith-mpi=ON ../src -- NEST version: master@0e6cd2819 -------------------------------------------------------------------------------- NEST Configuration Summary -------------------------------------------------------------------------------- Build type : Target System : Darwin Cross Compiling : FALSE C compiler : AppleClang 12.0.0.12000032 (/Library/Developer/CommandLineTools/usr/bin/cc) C compiler flags : -O2 -Wall -Xclang -fopenmp C++ compiler : AppleClang 12.0.0.12000032 (/Library/Developer/CommandLineTools/usr/bin/c++) C++ compiler flags : -std=c++11 -O2 -Wall -Xclang -fopenmp Build dynamic : ON Built-in modules : models User modules : None Python bindings : Yes (Python 3.8.5: /Users/hep/opt/miniconda3/envs/nest_dev/bin/python3) Includes : /Users/hep/opt/miniconda3/envs/nest_dev/include/python3.8 Libraries : /Users/hep/opt/miniconda3/envs/nest_dev/lib/libpython3.8.dylib Cython bindings : Yes (Cython 0.29.21: /Users/hep/opt/miniconda3/envs/nest_dev/bin/cython) MPI4PY header : NO Use threading : Yes (OpenMP: -Xclang -fopenmp) Use GSL : Yes (GSL 2.6) Includes : /usr/local/Cellar/gsl/2.6/include Libraries : /usr/local/Cellar/gsl/2.6/lib/libgsl.dylib;/usr/local/Cellar/gsl/2.6/lib/libgslcblas.dylib Use Readline : No Use libltdl : Yes (LTDL 2.4.6) Includes : /usr/local/include Libraries : /usr/local/lib/libltdl.dylib Use doxygen : No Use MPI : Yes (MPI: /usr/local/bin/mpicxx) FLAGS : Includes : /usr/local/Cellar/open-mpi/4.0.5/include Link Flags : -L/usr/local/Cellar/libevent/2.1.12/lib Libraries : /usr/local/Cellar/open-mpi/4.0.5/lib/libmpi.dylib Use MUSIC : No Use libneurosim : No Use Boost : Yes (Boost 1.75.0) Includes : /usr/local/include Libraries : Use recording backend Arbor : No Use SIONlib : No ———————————————————————————————————————— Results from testsuite % make -j4 install % make installcheck ---------------------------------------------------------------------- NEST Testsuite Results ---------------------------------------------------------------------- Phase Tests Skipped Failures Errors Time ---------------------------------------------------------------------- 01 basetests 6 0 0 0 12.0 02 selftests 8 4 0 0 24.0 03 unittests 185 1 0 0 208.0 04 regressiontests 94 7 0 0 142.0 05 mpitests 79 0 0 0 258.0 07 pynesttests 796 11 0 0 144.2 08 cpptests 29 0 0 0 0.0 ---------------------------------------------------------------------- Total 1197 23 0 0 788.2 ---------------------------------------------------------------------- Complete list of Brew packages % brew list aom 2.0.1 boost 1.75.0_1 cmake 3.19.3 docbook 5.1_1 docbook-xsl 1.79.2_1 freetype 2.10.4 gcc 10.2.0_2 gdbm 1.18.1_1 gettext 0.21 ghostscript 9.53.3_1 git 2.30.0 glib 2.66.4_1 gmp 6.2.1 gnu-getopt 2.36.1 gsl 2.6 hwloc 2.4.0 icu4c 67.1 ilmbase 2.5.4 imagemagick 7.0.10-57 isl 0.23 jpeg 9d libde265 1.0.8 libevent 2.1.12 libffi 3.3_2 libheif 1.10.0 libidn2 2.3.0 liblqr 0.4.2_1 libmpc 1.2.1 libomp 11.0.1 libpng 1.6.37 libtiff 4.2.0 libtool 2.4.6_2 libunistring 0.9.10 little-cms2 2.11 mpfr 4.1.0 numpy 1.19.5 open-mpi 4.0.5 openblas 0.3.13 openexr 2.5.4 openjpeg 2.3.1 openssl(a)1.1<mailto:openssl@1.1> 1.1.1i pcre 8.44 pcre2 10.36 pybind11 2.6.1_1 python(a)3.8<mailto:python@3.8> 3.8.7 python(a)3.9<mailto:python@3.9> 3.9.1_6 readline 8.1 scipy 1.6.0 shared-mime-info 2.1 sqlite 3.34.0 tcl-tk 8.6.11 webp 1.1.0 wget 1.21 x265 3.4_2 xmlto 0.0.28 xz 5.2.5 Complete list of Conda packages in nest_dev % conda activate nest_dev % conda env export name: nest_dev channels: - defaults dependencies: - appnope=0.1.2=py38hecd8cb5_1001 - backcall=0.2.0=py_0 - blas=1.0=openblas - ca-certificates=2020.12.8=hecd8cb5_0 - certifi=2020.12.5=py38hecd8cb5_0 - cycler=0.10.0=py38_0 - cython=0.29.21=py38h23ab428_0 - decorator=4.4.2=py_0 - freetype=2.10.4=ha233b18_0 - ipython=7.19.0=py38h01d92e1_1 - ipython_genutils=0.2.0=pyhd3eb1b0_1 - jedi=0.17.2=py38hecd8cb5_1 - jpeg=9b=he5867d9_2 - kiwisolver=1.3.0=py38h23ab428_0 - lcms2=2.11=h92f6f08_0 - libcxx=10.0.0=1 - libedit=3.1.20191231=h1de35cc_1 - libffi=3.3=hb1e8313_2 - libgfortran=3.0.1=h93005f0_2 - libopenblas=0.3.10=h0794777_0 - libpng=1.6.37=ha441bb4_0 - libtiff=4.1.0=hcb84e12_1 - lz4-c=1.9.2=h79c402e_3 - matplotlib=3.3.2=hecd8cb5_0 - matplotlib-base=3.3.2=py38h181983e_0 - ncurses=6.2=h0a44026_1 - nomkl=3.0=0 - nose=1.3.7=pyhd3eb1b0_1006 - numpy=1.19.2=py38h63973fd_0 - numpy-base=1.19.2=py38h68fea81_0 - olefile=0.46=py_0 - openssl=1.1.1i=h9ed2024_0 - parso=0.7.0=py_0 - pexpect=4.8.0=pyhd3eb1b0_3 - pickleshare=0.7.5=pyhd3eb1b0_1003 - pillow=8.1.0=py38h5270095_0 - pip=20.3.3=py38hecd8cb5_0 - prompt-toolkit=3.0.8=py_0 - ptyprocess=0.7.0=pyhd3eb1b0_2 - pygments=2.7.4=pyhd3eb1b0_0 - pyparsing=2.4.7=py_0 - python=3.8.5=h26836e1_1 - python-dateutil=2.8.1=py_0 - readline=8.0=h1de35cc_0 - scipy=1.5.2=py38h4420a3a_0 - setuptools=51.1.2=py38hecd8cb5_4 - six=1.15.0=py38hecd8cb5_0 - sqlite=3.33.0=hffcf06c_0 - tk=8.6.10=hb0a8c7a_0 - tornado=6.1=py38h9ed2024_0 - traitlets=5.0.5=py_0 - wcwidth=0.2.5=py_0 - wheel=0.36.2=pyhd3eb1b0_0 - xz=5.2.5=h1de35cc_0 - zlib=1.2.11=h1de35cc_3 - zstd=1.4.5=h41d2c2f_0 - pip: - future==0.18.2 - junitparser==1.6.2 -- 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 15/01/2021, 15:48, "Babu, Pooja" <p.babu(a)fz-juelich.de<mailto:p.babu@fz-juelich.de>> wrote: Hello everyone, I have a Mac with Big Sur and I tried installing NEST with a Conda environment as mentioned here<https://www.nest-initiative.org/mailinglist/hyperkitty/list/users@nest-simu…> by pulling in the latest code from Github. My commands look like this conda create -n nestml_dev nomkl numpy scipy matplotlib ipython cython nose pytest conda activate nestml_dev <Pull the latest code from github> mkdir nest-simulator-build cd nest-simulator-build cmake -DCMAKE_INSTALL_PREFIX:PATH=<nest_path> -DCMAKE_C_COMPILER=gcc-10 -DCMAKE_CXX_COMPILER=g++-10 <nest_src> make -j4 make install After this, if I try to import nest in python or run nest from the command line, I get the following error OMP: Error #13: Assertion failure at kmp_csupport.cpp(590). OMP: Hint Please submit a bug report with this message, compile and run commands used, and machine configuration info including native compiler and operating system versions. Faster response will be obtained by including all program sources. For information on submitting this issue, please see http://www.intel.com/software/products/support/. Abort trap: 6 Has anyone else seen this error? Any pointers on this would be helpful. Thank you, Pooja ------------------------------------------------------------------------------------------------ ------------------------------------------------------------------------------------------------ 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 ------------------------------------------------------------------------------------------------ ------------------------------------------------------------------------------------------------

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V_act_NMDA and S_act_NMDA parameter in ht_neuron
by Maryada Maryada 18 Jan '21

18 Jan '21

Dear all, I am looking for the details of ht_neuron model and referred to DOI: https://doi.org/10.1152/jn.00915.2004 for details. However, I couldn't find information on V_act_NMDA and S_act_NMDA. Can anyone please point me in the specific paragraph/table in the paper or share a one line explanation. I have attached a screenshot of the equation from the example notebook and also the complete notebook for quick reference -- Thanks and Regards *Maryada*

2 3

Open NEST Developer Video Conference Monday 18 January 2021 11:30 CET (UTC+1)
by Dennis Terhorst 18 Jan '21

18 Jan '21

Dear NEST Users & Developers! I would like to invite you to our next fortnightly Open NEST Developer Video Conference, today Monday 18 January, 11.30-12.30 CET (UTC+1). 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/2021-01-18-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 installation error on Mac
by Babu, Pooja 15 Jan '21

15 Jan '21

Hello everyone, I have a Mac with Big Sur and I tried installing NEST with a Conda environment as mentioned here<https://www.nest-initiative.org/mailinglist/hyperkitty/list/users@nest-simu…> by pulling in the latest code from Github. My commands look like this conda create -n nestml_dev nomkl numpy scipy matplotlib ipython cython nose pytest conda activate nestml_dev <Pull the latest code from github> mkdir nest-simulator-build cd nest-simulator-build cmake -DCMAKE_INSTALL_PREFIX:PATH=<nest_path> -DCMAKE_C_COMPILER=gcc-10 -DCMAKE_CXX_COMPILER=g++-10 <nest_src> make -j4 make install After this, if I try to import nest in python or run nest from the command line, I get the following error OMP: Error #13: Assertion failure at kmp_csupport.cpp(590). OMP: Hint Please submit a bug report with this message, compile and run commands used, and machine configuration info including native compiler and operating system versions. Faster response will be obtained by including all program sources. For information on submitting this issue, please see http://www.intel.com/software/products/support/. Abort trap: 6 Has anyone else seen this error? Any pointers on this would be helpful. Thank you, Pooja ------------------------------------------------------------------------------------------------ ------------------------------------------------------------------------------------------------ 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 ------------------------------------------------------------------------------------------------ ------------------------------------------------------------------------------------------------

1 0

Error in Simulate
by Petia Koprinkova 15 Jan '21

15 Jan '21

We have encountered the following error: Traceback (most recent call last): File "all_v2.py", line 364, in <module> nest.Simulate(sim_time) File"/opt/soft/nest-2.18.0/lib64/python3.6/site-packages/nest/ll_api.py",line 246, in stack_checker_func return f(*args, **kwargs) File"/opt/soft/nest-2.18.0/lib64/python3.6/site-packages/nest/lib/hl_api_simulation.py",line 66, in Simulate sr('ms Simulate') File"/opt/soft/nest-2.18.0/lib64/python3.6/site-packages/nest/ll_api.py",line 132, in catching_sli_run raise exceptionCls(commandname, message) nest.ll_api.C++Exception: ('C++Exception in Simulate_d:std::bad_alloc', 'C++Exception', <SLILiteral: Simulate_d>, ':std::bad_alloc') Could you help to resolve it? Best regards,Petia Koprinkova-Hristova

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Trouble about the spiking time will increase and get so bigger with the simulation epoch increasing.
by enguang zhou 13 Jan '21

13 Jan '21

Deal all, I am recording the spiking time of neurons after every simulation, and I find that the time beginning of every simulation isn't all 0 except the first simulation. So how can I set to recording spiking time beginning from 0 during all simulations? By now I am processing that for every simulation spiking time recording by deleting all the time used before a specific simulation epoch. Hope for your answer,thanks! Enguang

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Problems with installation of NEST on MAC
by Vittorio De Falco 12 Jan '21

12 Jan '21

Dear Users of NEST, I have downloaded and installed nest on my MAC. I was able to configure it. When I launch make I receive the following error Undefined symbols for architecture x86_64: "___kmpc_critical", referenced from: SLIInterpreter::message(int, char const*, char const*, char const*) const in interpret.cc.o "___kmpc_end_critical", referenced from: SLIInterpreter::message(int, char const*, char const*, char const*) const in interpret.cc.o "___kmpc_global_thread_num", referenced from: SLIInterpreter::message(int, char const*, char const*, char const*) const in interpret.cc.o "_omp_in_parallel", referenced from: Name::insert(std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> > const&) in name.cc.o ld: symbol(s) not found for architecture x86_64 clang: error: linker command failed with exit code 1 (use -v to see invocation) make[2]: *** [sli/libsli.dylib] Error 1 make[1]: *** [sli/CMakeFiles/sli_lib.dir/all] Error 2 make: *** [all] Error 2 I have already installed it successfully the previous week, but for example I have problem when I launch an example code from NEST (one_neuron.py), because import nest is recognised, while "import nest.voltage_trace" is not found ModuleNotFoundError: No module named 'nest.voltage_trace' Sorry I am a little bit confused. When I try to launch a code in a folder different from the nest-simulator folder "import nest" is not recognised. Could you please explain me better how to solve such an issue? Thank you very much for your support. Best, Vittorio *************************************************************** * Postdoctoral Researcher in Mathematics * University of Naples "Federico II" * Department of Mathematics and Application "R. Caccioppoli" * Via Cintia, IT-80126 Naples, Italy * CELL: +39 340 544 70 15 ****************************************************************

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spatiotemporal Poisson generator
by Abolfazl Ziaeemehr 08 Jan '21

08 Jan '21

Hello everyone, Is it possible to include a *spatiotemporal poisson generator* in the simulation? I am trying to apply a current to a population of neurons which is something like this? [image: Selection_001.png] where `i` is the index of the neuron and `t` is the current time of the simulation. Thank you for any guidance. best, -- Abolfazl Ziaeemehr PhD in Computational Neuroscience Institute for Advanced Studies in Basic Sciences (IASBS) Page: iasbs.ac.ir/~a.ziaeemehr https://github.com/Ziaeemehr

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I want to know the derivative equation of iaf_psc_alpha neuron model to design some algorithms for neural network
by enguang zhou 06 Jan '21

06 Jan '21

Hi everyone, I have a very big problem now again for the iaf neuron(such as iaf_psc_alpha), which is I don't know know differential equation for the neuron model, so I can't get the derivative of voltage about some other variable, such as derivative of voltage versus synapse weight. The point is I do need to know the derivative equation of iaf_psc_alpha neuron model to design some algorithm for neural network. For the paper mentioned below, I still can't figure out the exact derivative equation of voltage or voltage state equation. https://link.springer.com/article/10.1007/s004220050570 By the way, At last meeting, I wanted to ask that but my device had trouble when host asked, so awkward. Hope for your answer. Thank you. Enguang

2 2

How does the synapse weight influence 'iaf_psc_alpha' neuron(or any other neuron you know) to send a spike?
by enguang zhou 04 Jan '21

04 Jan '21

Hello everyone, As the title says, can someone help me answer this? I am really confused about this. Because I need to know how to control the neuron spiking from the mathematical formula, and I check out the iaf_psc_alpha.cpp and its .h file, and I can't get a clue how does the synapse weight value influence the neuron spiking. I would be appreciate if you can tell me how to check out the code in nest_simualator. Thank you. Enguang

2 5

Open NEST Developer Video Conference Monday 4 January 2021 11:30 CET (UTC+1)
by Dennis Terhorst 04 Jan '21

04 Jan '21

Dear NEST Users & Developers! I would like to wish you all a Happy New Year and invite you to our first fortnightly Open NEST Developer Video Conference of this year, today Monday 4 January, 11.30-12.30 CET (UTC+1). Today we have a special feature discussion on * Python module installation Additionally, 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 Python module installation The agenda for this meeting is also available online, see https://github.com/nest/nest-simulator/wiki/2021-01-04-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

Thank you for 2020
by Hans Ekkehard Plesser 23 Dec '20

23 Dec '20

Dear NEST Users! I would like to thank all of you in the NEST Community for you efforts and interest in NEST in 2020, which has been a special year for us all. We have achieved a lot and I am very confident that 2021 will finally see the official release of NEST 3 as the culmination of several years work with significant benefits for users. After the good experiences with the virtual NEST conference this year, the NEST Initiative has decided to hold the conference as a digital conference also in 2021, as this allows a much wider range of users to participate. The conference will take place at its usual time in the end of June. I wish you all happy holidays and all the best for 2021! Hans Ekkehard Plesser President, The NEST Initiative -- Prof. Dr. Hans Ekkehard Plesser Head, Department of Data Science Faculty of Science and Technology Norwegian University of Life Sciences PO Box 5003, 1432 Aas, Norway Phone +47 6723 1560 Email hans.ekkehard.plesser(a)nmbu.no<mailto:hans.ekkehard.plesser@nmbu.no> Home http://arken.nmbu.no/~plesser

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Open NEST Developer Video Conference Monday 21 December 2020 11:30 CET (UTC+1)
by Dennis Terhorst 21 Dec '20

21 Dec '20

Dear NEST Users & Developers! I would like to invite you to our last fortnightly Open NEST Developer Video Conference of this year, today Monday 21 December, 11.30-12.30 CET (UTC+1). Today we have a special feature discussion on *NeuronGPU *by Bruno Golosio, bringing GPU acceleration to spiking neural networks. Additionally, 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 NeuronGPU The agenda for this meeting is also available online, see https://github.com/nest/nest-simulator/wiki/2020-12-21-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

1 0

Multi-node parallel simulation error
by jiadu xie 17 Dec '20

17 Dec '20

I want to run neuron simulations in parallel on multiple servers in OpenMPI. I've installed Nest through conda: conda install -c conda-forge nest-simulator. multi_test.pycode show as below： from nest import * SetKernelStatus({"total_num_virtual_procs": 4}) pg = Create("poisson_generator", params={"rate": 50000.0}) n = Create("iaf_psc_alpha", 4) sd = Create("spike_detector", params={"to_file": True}) print("work01,My Rank is :{}".format(Rank())) #print("Processes Number is :{}".format(NumProcesses()) #print("Processor Name is :{}".format(ProcessorName()) Connect(pg, [n[0]], syn_spec={'weight': 1000.0, 'delay': 1.0}) Connect([n[0]], [n[1]], syn_spec={'weight': 1000.0, 'delay': 1.0}) Connect([n[1]], [n[2]], syn_spec={'weight': 1000.0, 'delay': 1.0}) Connect([n[2]], [n[3]], syn_spec={'weight': 1000.0, 'delay': 1.0}) Connect(n, sd) Simulate(100.0) To Reproduce Steps to reproduce the behavior: (pynest) work@work01:~/xiejiadu/nest_multi_test$ /home/work/anaconda3/envs/pynest/bin/mpirun -np 2 -host work01:1,work02:1 /home/work/anaconda3/envs/pynest/bin/python3 /home/work/xiejiadu/nest_multi_test/multi_test.py [INFO] [2020.11.23 3:57:6 /home/conda/feedstock_root/build_artifacts/nest-simulator_1580129123254/work/nestkernel/rng_manager.cpp:217 @ Network::create_rngs_] : Creating default RNGs [INFO] [2020.11.23 3:57:6 /home/conda/feedstock_root/build_artifacts/nest-simulator_1580129123254/work/nestkernel/rng_manager.cpp:260 @ Network::create_grng_] : Creating new default global RNG [INFO] [2020.11.23 3:57:6 /home/conda/feedstock_root/build_artifacts/nest-simulator_1580129123254/work/nestkernel/rng_manager.cpp:217 @ Network::create_rngs_] : Creating default RNGs [INFO] [2020.11.23 3:57:6 /home/conda/feedstock_root/build_artifacts/nest-simulator_1580129123254/work/nestkernel/rng_manager.cpp:260 @ Network::create_grng_] : Creating new default global RNG python3: /home/conda/feedstock_root/build_artifacts/nest-simulator_1580129123254/work/sli/scanner.cc:581: bool Scanner::operator()(Token&): Assertion `in->good()' failed. [work02:95945] *** Process received signal *** [work02:95945] Signal: Aborted (6) [work02:95945] Signal code: (-6) [work02:95945] [ 0] /lib/x86_64-linux-gnu/libpthread.so.0(+0x12730)[0x7fc94a207730] [work02:95945] [ 1] /lib/x86_64-linux-gnu/libc.so.6(gsignal+0x10b)[0x7fc94a0697bb] [work02:95945] [ 2] /lib/x86_64-linux-gnu/libc.so.6(abort+0x121)[0x7fc94a054535] [work02:95945] [ 3] /lib/x86_64-linux-gnu/libc.so.6(+0x2240f)[0x7fc94a05440f] [work02:95945] [ 4] /lib/x86_64-linux-gnu/libc.so.6(+0x30102)[0x7fc94a062102] [work02:95945] [ 5] /home/work/anaconda3/envs/pynest/lib/python3.8/site-packages/nest/../../../libsli.so(_ZN7ScannerclER5Token+0x1489)[0x7fc93cf3ceb9] [work02:95945] [ 6] /home/work/anaconda3/envs/pynest/lib/python3.8/site-packages/nest/../../../libsli.so(_ZN6ParserclER5Token+0x49)[0x7fc93cf2f229] [work02:95945] [ 7] /home/work/anaconda3/envs/pynest/lib/python3.8/site-packages/nest/../../../libsli.so(_ZNK14IparseFunction7executeEP14SLIInterpreter+0x96)[0x7fc93cf66666] [work02:95945] [ 8] /home/work/anaconda3/envs/pynest/lib/python3.8/site-packages/nest/../../../libsli.so(+0x74193)[0x7fc93cf25193] [work02:95945] [ 9] /home/work/anaconda3/envs/pynest/lib/python3.8/site-packages/nest/../../../libsli.so(_ZN14SLIInterpreter8execute_Em+0x222)[0x7fc93cf29a32] [work02:95945] [10] /home/work/anaconda3/envs/pynest/lib/python3.8/site-packages/nest/../../../libsli.so(_ZN14SLIInterpreter7startupEv+0x27)[0x7fc93cf29e57] [work02:95945] [11] /home/work/anaconda3/envs/pynest/lib/python3.8/site-packages/nest/../../../libnest.so(_Z11neststartupPiPPPcR14SLIInterpreterNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEE+0x1ea0)[0x7fc93d97ba40] [work02:95945] [12] /home/work/anaconda3/envs/pynest/lib/python3.8/site-packages/nest/pynestkernel.so(+0x444dc)[0x7fc93dd774dc] [work02:95945] [13] /home/work/anaconda3/envs/pynest/bin/python3(+0x1b4924)[0x55e5ae205924] [work02:95945] [14] /home/work/anaconda3/envs/pynest/bin/python3(_PyEval_EvalFrameDefault+0x4bf)[0x55e5ae22dbcf] [work02:95945] [15] /home/work/anaconda3/envs/pynest/bin/python3(_PyFunction_Vectorcall+0x1b7)[0x55e5ae21a637] [work02:95945] [16] /home/work/anaconda3/envs/pynest/bin/python3(_PyEval_EvalFrameDefault+0x71a)[0x55e5ae22de2a] [work02:95945] [17] /home/work/anaconda3/envs/pynest/bin/python3(_PyEval_EvalCodeWithName+0x260)[0x55e5ae219490] [work02:95945] [18] /home/work/anaconda3/envs/pynest/bin/python3(+0x1f6bb9)[0x55e5ae247bb9] [work02:95945] [19] /home/work/anaconda3/envs/pynest/bin/python3(+0x13a23d)[0x55e5ae18b23d] [work02:95945] [20] /home/work/anaconda3/envs/pynest/bin/python3(PyVectorcall_Call+0x6f)[0x55e5ae1aef2f] [work02:95945] [21] /home/work/anaconda3/envs/pynest/bin/python3(_PyEval_EvalFrameDefault+0x5fc1)[0x55e5ae2336d1] [work02:95945] [22] /home/work/anaconda3/envs/pynest/bin/python3(_PyEval_EvalCodeWithName+0x260)[0x55e5ae219490] [work02:95945] [23] /home/work/anaconda3/envs/pynest/bin/python3(_PyFunction_Vectorcall+0x594)[0x55e5ae21aa14] [work02:95945] [24] /home/work/anaconda3/envs/pynest/bin/python3(_PyEval_EvalFrameDefault+0x4e73)[0x55e5ae232583] [work02:95945] [25] /home/work/anaconda3/envs/pynest/bin/python3(_PyFunction_Vectorcall+0x1b7)[0x55e5ae21a637] [work02:95945] [26] /home/work/anaconda3/envs/pynest/bin/python3(_PyEval_EvalFrameDefault+0x4bf)[0x55e5ae22dbcf] [work02:95945] [27] /home/work/anaconda3/envs/pynest/bin/python3(_PyFunction_Vectorcall+0x1b7)[0x55e5ae21a637] [work02:95945] [28] /home/work/anaconda3/envs/pynest/bin/python3(_PyEval_EvalFrameDefault+0x71a)[0x55e5ae22de2a] [work02:95945] [29] /home/work/anaconda3/envs/pynest/bin/python3(_PyFunction_Vectorcall+0x1b7)[0x55e5ae21a637] [work02:95945] *** End of error message *** -------------------------------------------------------------------------- Primary job terminated normally, but 1 process returned a non-zero exit code. Per user-direction, the job has been aborted. -------------------------------------------------------------------------- -------------------------------------------------------------------------- WARNING: Open MPI failed to TCP connect to a peer MPI process. This should not happen. Your Open MPI job may now hang or fail. Local host: work01 PID: 114620 Message: connect() to 192.168.204.122:1024 failed Error: Operation now in progress (115) -------------------------------------------------------------------------- [work01:114615] PMIX ERROR: UNREACHABLE in file server/pmix_server.c at line 2193 -- N E S T -- Copyright (C) 2004 The NEST Initiative Version: nest-2.18.0 Built: Jan 27 2020 12:49:17 This program is provided AS IS and comes with NO WARRANTY. See the file LICENSE for details. Problems or suggestions? Visit https://www.nest-simulator.org Type 'nest.help()' to find out more about NEST. Nov 23 03:57:06 ModelManager::clear_models_ [Info]: Models will be cleared and parameters reset. Nov 23 03:57:06 Network::create_rngs_ [Info]: Deleting existing random number generators Nov 23 03:57:06 Network::create_rngs_ [Info]: Creating default RNGs Nov 23 03:57:06 Network::create_grng_ [Info]: Creating new default global RNG Nov 23 03:57:06 RecordingDevice::set_status [Info]: Data will be recorded to file and to memory. work01,My Rank is :0 -------------------------------------------------------------------------- mpirun noticed that process rank 1 with PID 95945 on node work02 exited on signal 6 (Aborted). -------------------------------------------------------------------------- Command to run /home/work/anaconda3/envs/pynest/bin/mpirun -np 2 -host work01:1,work02:1 /home/work/anaconda3/envs/pynest/bin/python3 /home/work/xiejiadu/nest_multi_test/multi_test.py Expected behavior A clear and concise description of what you expected to happen. Screenshots If applicable, add screenshots to help explain your problem. Desktop/Environment: OS: Debain-10.0 Shell: conda4.8.3 Python-Version: Python 3.8.6 NEST-Version: nest-2.18 Installation:conda packet, with MPI Best jiaduxie

2 2

NEST Spack package maintainers
by itaru.kitayama＠gmail.com 15 Dec '20

15 Dec '20

I am updating the package.py script a bit so that it can build; though I wonder who are the maintainers of the Spack package currently?

1 1

NEST developer documentation
by Cristiano Alessandro 11 Dec '20

11 Dec '20

Dear all, I am new to developing NEST neuron models. I am aware I should use NEST-ML and I started that way, but I now need to modify the (successfully) generated C++ code. To do so, I would like to understand the details of the C++ implementation, including the overall logic of the class NEST-ML created (what is the functionality of the methods and attributes). Where can I find documentation about this? I would also like to take a look at the description of the NEST C++ developers library. I could not find these aspects in the Nest Developer Space. Thank you in advance. Best Cristiano

3 3

NEST developer documentation
by Cristiano Alessandro 11 Dec '20

11 Dec '20

Dear all, I am new to developing NEST neuron models. I am aware I should use NEST-ML and I started that way, but I now need to modify the (successfully) generated C++ code. To do so, I would like to understand the details of the C++ implementation, including the overall logic of the class NEST-ML created (what is the functionality of the methods and attributes). Where can I find documentation about this? I would also like to take a look at the description of the NEST C++ developers library. I could not find these aspects in the Nest Developer Space. Thank you in advance. Best Cristiano

1 0

Open NEST Developer Video Conference Monday 07 December 2020 11:30 CET (UTC+1)
by Dennis Terhorst 07 Dec '20

07 Dec '20

Dear NEST Users & Developers! I would like to invite you to our next fortnightly Open NEST Developer Video Conference today Monday 07 December, 11.30-12.30 CET (UTC+1). 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 To squash, or not to squash The agenda for this meeting is also available online, see https://github.com/nest/nest-simulator/wiki/2020-12-07-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

1 0

Combining neuron model features
by d.standage＠bham.ac.uk 03 Dec '20

03 Dec '20

Hi all - I'm aiming to run simulations using Izhikevich's neuron model (or another efficient model with spike generation), two dendritic compartments, two glutamate receptor subtypes, and temporal synaptic dynamics. My understanding is that Nest supports the Izhikevich neuron model with instantaneous current injection (i.e. no synaptic dynamics), the iaf_cond_alpha_mc neuron model for multiple compartments, the aeif_cond_alpha_multisynapse model for multiple receptor subtypes, and any of the _psc_ or _cond_ neuron models for synaptic dynamics. Am I looking at multiple choice here? I.e. I can't use a single neuron model with all of these features? If so, does anyone know of any Nest add-ons that efficiently handle all the features above? I'd be grateful for any advice. Best Dominic

3 2

Technical Editor – European Research Infrastructures for Neuroscience (EBRAINS)
by Hans Ekkehard Plesser 03 Dec '20

03 Dec '20

Dear colleagues, The Computational Neuroscience Group at the Norwegian University of Life Sciences (www.nmbu.no<http://www.nmbu.no/>) aims to recruit a technical editor in a senior engineer position. The position is part of our contribution to the Human Brain Project (www.humanbrainproject.eu<http://www.humanbrainproject.eu/>) in building the European EBRAINS research infrastructures for neuroscience. This full-time position is available immediately and limited until 31 March 2023. As technical editor, you will be part of the EBRAINS High-Level Service Team and be responsible for coordinating and supervising the production and provision of documentation and tutorial materials for EBRAINS service offerings with the pertaining EBRAINS partners. We are looking for applicants with a master's, preferably a doctoral, degree in a STEM discipline, ideally with experience in technical writing, documentation generation systems, and neuroscience. Closing date for applications is 4 January 2021. For more information about the position and to submit your application, please see https://www.jobbnorge.no/en/available-jobs/job/196909/technical-editor-seni… Please contact Prof Hans Ekkehard Plesser (hans.ekkehard.plesser(a)nmbu.no<mailto:hans.ekkehard.plesser@nmbu.no>) if you have any questions concerning the position. 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

1 0

Reset Spike Detector
by feldotto 03 Dec '20

03 Dec '20

Dear all,I am running a large simulation where I need to evaluate the spike frequency of large populations in several elapsed time frames. In order to keep this procedure efficient and memory efficient, is it possible to reset the spikeDetector (delete all events)?Thanks in advance!Best,Benedikt

3 2

Getting single neuron spiking
by nosratullah mohammadi 30 Nov '20

30 Nov '20

Dear NEST Users, I wonder how to get single neuron spikes out of spike detector that record all of the neurons in the network. Best, Nosratullah Mohammadi (Mr.)

2 1

Open NEST Developer Video Conference Monday 23 November 2020 11:30 CET (UTC+1)
by Dennis Terhorst 23 Nov '20

23 Nov '20

Dear NEST Users & Developers! I would like to invite you to our next fortnightly Open NEST Developer Video Conference today Monday 23 November, 11.30-12.30 CET (UTC+1). 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 For the in-depth discussion the topic of "/Compiler variants vs. MPI implementations/" was proposed, as this is recently causing headache on some setups. The agenda for this meeting is also available online, see https://github.com/nest/nest-simulator/wiki/2020-11-23-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 network object
by alehr 20 Nov '20

20 Nov '20

Dear NEST developer, I would like to initialize a network with neurons and connections and then run many simulations with it. It would be great if I could build the network one time and then deepcopy (or something similar) for each simulation. Is something like this possible? Thanks, Andrew Lehr

7 13

Microcircuit example, segmentation fault
by d.standage＠bham.ac.uk 17 Nov '20

17 Nov '20

Hi all - I'm running NEST on Ubuntu 18.04, installed with Conda. I can run the example networks in the user documentation, except the Microcircuit Example (having downloaded all the files). It causes a segmentation fault during the call to Simulate( ). I can provide the full error message, but in the interest of brevity - Signal: Segmentation fault (11) Signal code: Address not mapped (1) ... [ 0] /lib/x86_64-linux-gnu/libpthread.so.0(+0x128a0)[0x7feb38d5f8a0] ... Segmentation fault (core dumped) Has anyone else had this issue? I'd be grateful for any help you can provide. Best Dominic

3 3

Re: NEST on macOS 11 Big Sur
by Joris Dolderer 14 Nov '20

14 Nov '20

Thank you for your very useful e-mail! You wrote a lot, but you also had something to say. On Sat, 14 Nov 2020, 13:35 Hans Ekkehard Plesser, < hans.ekkehard.plesser(a)nmbu.no> wrote: > > Dear all, > > I am happy to report that NEST seems to work find under macOS 11 Big Sur. > So far, I have only tested on Intel hardware, a system with the Apple M1 > chip is on its way. > > Specifcially, I proceeded as follows: > > 1. After upgrading to Big Sur, run "brew doctor" and follow the > instructions to update the Apple Command Line Tools. If you encounter > problems, see > https://stackoverflow.com/questions/64821648/homebrew-fails-on-macos-big-sur > > 2. Run "brew update" and "brew upgrade". > > 3. For safety's sake, I then ran "brew uninstall nest" and then "brew > install nest". This gave me a working NEST 2.20.0 installation. > > > To build NEST myself, I first performed steps 1 and 2 above and then > > 3. conda update conda > conda create -n nest_dev nomkl numpy scipy matplotlib ipython cython > nose > conda activate nest_dev > pip install junitparser > > The nomkl package ensures that NumPy does not use Intel's MKL, which can > lead to conflicting OpenMP libraries. > Junitparser is needed to handle testsuite results and is only available > from PyPI. > > 4. Pull latest sources from NEST master branch to src > > 5. mkdir bld > cd bld > cmake -DCMAKE_INSTALL_PREFIX:PATH=<install path> -Dwith-mpi=ON ../src > make -j4 install && make installcheck > > All tests pass. If many MPI tests fail, you may need to add > --oversubscribe to the mpirun command in your .nestrc file. C++ tests will > only run if you have installed boost, e.g., with "brew install boost". > > 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 > Home http://arken.nmbu.no/~plesser > > > _______________________________________________ > NEST Users mailing list -- users(a)nest-simulator.org > To unsubscribe send an email to users-leave(a)nest-simulator.org > > > > ------------------------------------------------------------------------------------------------ > > ------------------------------------------------------------------------------------------------ > 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 > > ------------------------------------------------------------------------------------------------ > > ------------------------------------------------------------------------------------------------ > >

1 0

NEST on macOS 11 Big Sur
by Hans Ekkehard Plesser 14 Nov '20

14 Nov '20

Dear all, I am happy to report that NEST seems to work find under macOS 11 Big Sur. So far, I have only tested on Intel hardware, a system with the Apple M1 chip is on its way. Specifcially, I proceeded as follows: 1. After upgrading to Big Sur, run "brew doctor" and follow the instructions to update the Apple Command Line Tools. If you encounter problems, see https://stackoverflow.com/questions/64821648/homebrew-fails-on-macos-big-sur 2. Run "brew update" and "brew upgrade". 3. For safety's sake, I then ran "brew uninstall nest" and then "brew install nest". This gave me a working NEST 2.20.0 installation. To build NEST myself, I first performed steps 1 and 2 above and then 3. conda update conda conda create -n nest_dev nomkl numpy scipy matplotlib ipython cython nose conda activate nest_dev pip install junitparser The nomkl package ensures that NumPy does not use Intel's MKL, which can lead to conflicting OpenMP libraries. Junitparser is needed to handle testsuite results and is only available from PyPI. 4. Pull latest sources from NEST master branch to src 5. mkdir bld cd bld cmake -DCMAKE_INSTALL_PREFIX:PATH=<install path> -Dwith-mpi=ON ../src make -j4 install && make installcheck All tests pass. If many MPI tests fail, you may need to add --oversubscribe to the mpirun command in your .nestrc file. C++ tests will only run if you have installed boost, e.g., with "brew install boost". 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 Home http://arken.nmbu.no/~plesser

1 0

Open NEST Developer Video Conference Monday 9 November 2020 11:30 CET (UTC+1)
by Dennis Terhorst 09 Nov '20

09 Nov '20

Dear NEST Users & Developers! I would like to invite you to our next fortnightly Open NEST Developer Video Conference today Monday 9 November, 11.30-12.30 CET (UTC+1). 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/2020-11-09-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

Configuration of multi-node parallel environment
by 1323504842＠qq.com 05 Nov '20

05 Nov '20

Hi,I am now simulating a small network for testing on two machines, and run it with the following command. It seems that the two machines run by themselves without interaction,running your own. mpirun -np 2 -host work0,work1 python ./multi_test.py Can nest simulate a network in a multi-node cluster environment? If yes, how do the nodes exchange data? Do you know about the configuration of a parallel cluster environment? I installed NEST under ANCCONDA? Can anyone share some experience?

2 1

Data-handling with NEST-MPI
by swathi anil 03 Nov '20

03 Nov '20

Hello all, I use NEST with OpenMPI on a high performance cluster to run plasticity related network simulations. So far I have divided my whole job into: phase 1: data collection (data collected: senders, times, sources, targets for each time point) phase 2: data anaylsis (refers to spike count and connectivity calculation) I face an issue with data-handling. In phase 1, the data pertaining to each of the four variables is saved in X different files (X = number of virtual processes), rank-wise. This means that the total number of files generated goes [ n(time-points)*X*4 ], which surpasses the chunk file storage limit, per user for the cluster. Each file here is an ndarray saved as a *.npy file. I wonder if there is a way to retrieve the data from each of the X processes while collecting data, concatenating and then saving them? So instead of X number of files, I can save the concatenated version. This probably involves recruiting a single VP to collect and concatenate and save the datapoints, but i am not quite sure how to execute this using NEST. Any help would be highly appreciated! Thanks in advance! Best, Swathi

3 2

because of the spike time stored in unordered time, so I get problem ablout the use of stdp_synapse.
by 1240288839＠qq.com 27 Oct '20

27 Oct '20

Dear all! I want to know how to use stdp_synapse correctly but I noticed there is a sentence 'Another important point is that spikes do NOT pass the Connection object in correct order of biological arrival time—they are unordered in time' about the overview of stdp_synapse; it's the last part of spike handling at website https://nest.github.io/nest-simulator/synapses_overview. So if these spike time are unordered, whether the stdp_synapse function would mimic properly.

3 4

Open NEST Developer Video Conference Monday 26 October 2020 11:30 CET (UTC+1)
by Dennis Terhorst 26 Oct '20

26 Oct '20

Dear NEST Users & Developers! I would like to invite you to our next fortnightly Open NEST Developer Video Conference today Monday 26 October, 11.30-12.30 CET (UTC+1). Please note that we changed to winter time (UTC+1). 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 We will continue discussion on some of the topics of last time: * Issue #1773 <https://github.com/nest/nest-simulator/issues/1773>: wrapper around |Prepare| and |Run| (postponed from last time) * organizing HBP CodeJam#11 activities <https://www.humanbrainproject.eu/en/education/participatecollaborate/infras…> The agenda for this meeting is also available online, see https://github.com/nest/nest-simulator/wiki/2020-10-26-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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V_th Issue in Izhikevich Neuron Model
by Allen Rabayda 17 Oct '20

17 Oct '20

Dear Nest Community, When trying to reproduce Izhikevich's Simple Neuron Model with NEST Izhikevich Neuron Model, it is spiking before reaching my V_th potential threshold setting of 30 mV, producing results inconsistent with the publication. Would anybody have insight as to why the neuron is spiking early? Did I perhaps not include a relevant NEST setting? I compared it to an explicit implementation of the ODEs, attached, for your reference of expected neuron response. Thank you for any suggestions. Best Regards, --Allen

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test failures on nest master@6997cae6c on Fedora 32 with Intel Prallel Studio XE 2020 update 2
by Nilton Liuji Kamiji 16 Oct '20

16 Oct '20

Dear all, I have compiled NEST master@6997cae6c onFedora 32 with both, 1- gcc (10.2.1) and OpenMPI (4.0.4): the default on this distro 2 - Intel Parallel Studio XE update 2 with GSL compiled from source using the same compiler using same configuration (-Dwith-mpi=ON, -Dwith-boost=ON) . On Intel, -Dwith-gsl=${GSL_DIR} was added to point to the GSL built with the Intel Compiler. On the gcc configuration, all tests worked fine (I defined OMPI_MCA_rmaps_base_oversubscribe=1 to avoid oversubscription error as reported in issue #1758). On the other hand, on the Intel configuration, several MPI tests have failed as described in the attached files. (To allow oversubscription the following variables were defined: I_MPI_WAIT_MODE=1 and I_MPI_THREAD_YIELD=3) I report it here as it is probably not directly a NEST code issue, but hope that someone in the community could have the answer. If I should submit it as an issue on GitHub, please let me know. Attached files: cmake_command_summary.txt : cmake command invocation and summary installcheck.log : make installcheck log reports.tar.gz : reports folder created by make installcheck; it also contains the instalcheck.log file above Best, Nilton -- Nilton Liuji Kamiji University of Sao Paulo Department of Physics, FFCLRP Laboratory of Neural Systems Phone: +55 16 3315 3859

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Running NEST with SIONlib
by Itaru Kitayama 14 Oct '20

14 Oct '20

Hi, Has anyone explored the external library support? I am on Fugaku and the jobs can create casually tens of thousands of files in a single directory; this aborts jobs. Itaru.

2 5

Open NEST Developer Video Conference Monday 12 October 2020 11:30 CEST (UTC+2)
by Dennis Terhorst 12 Oct '20

12 Oct '20

Dear NEST Users & Developers! I would like to invite you to our next fortnightly Open NEST Developer Video Conference today Monday 12 October, 11.30-12.30 CEST (UTC+2). 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 * HBP CodeJam #11 <https://www.humanbrainproject.eu/en/education/participatecollaborate/infras…> * Extension Module System <https://github.com/nest/nest-simulator/projects/22> * Issue #1773 <https://github.com/nest/nest-simulator/issues/1773>: wrapper around |Prepare| and |Run| The agenda for this meeting is also available online, see https://github.com/nest/nest-simulator/wiki/2020-10-12-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 28 September 2020 11:30 CEST (UTC+2)
by Dennis Terhorst 28 Sep '20

28 Sep '20

Dear NEST Users & Developers! I would like to invite you to our next fortnightly Open NEST Developer Video Conference today Monday 28 September, 11.30-12.30 CEST (UTC+2). 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 Benchmarking setups for CoSim and the NRP-NEST coupling. Special guests will be Kim Sontheimer and Cristian Jimenez-Romero of the SimLab Neuroscience The agenda for this meeting is also available online, see https://github.com/nest/nest-simulator/wiki/2020-09-28-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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Is there a developer meeting soon?
by Robin Gilbert De Schepper 23 Sep '20

23 Sep '20

Hi! It seems to have been a while since an invitation to the bi-weekly meeting has been sent out. Will they resume soon? I would like to discuss the topic of extension modules and feel like the meeting is great place to get informed. 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/

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Open NEST Developer Video Conference Monday 14 September 2020 11:30 CEST (UTC+2)
by Dennis Terhorst 14 Sep '20

14 Sep '20

Dear NEST Users & Developers! I would like to invite you to our next fortnightly Open NEST Developer Video Conference today Monday 14 September, 11.30-12.30 CEST (UTC+2). 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. The ongoing hackathon this week will be one of the topics and a quick overview will be discussed. 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/2020-09-14-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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error when making
by Carlos Gutierrez 05 Sep '20

05 Sep '20

Dear All, I get the following error when making NEST 2.20 on my desktop, any idea where is the problem?. Thanks, Carlos. [ 99%] Building CXX object pynest/CMakeFiles/pynestkernel.dir/pynestkernel.cxx.o [100%] Linking CXX shared module pynestkernel.so /usr/bin/ld: /usr/local/lib/libpython3.8.a(abstract.o): relocation R_X86_64_PC32 against symbol `_Py_NotImplementedStruct' can not be used when making a shared object; recompile with -fPIC /usr/bin/ld: final link failed: bad value collect2: error: ld returned 1 exit status make[2]: *** [pynest/CMakeFiles/pynestkernel.dir/build.make:103: pynest/pynestkernel.so] Error 1 make[1]: *** [CMakeFiles/Makefile2:1030: pynest/CMakeFiles/pynestkernel.dir/all] Error 2 make: *** [Makefile:141: all] Error 2 ######## -------------------------------------------------------------------------------- NEST Configuration Summary -------------------------------------------------------------------------------- Build type : Target System : Linux Cross Compiling : FALSE C compiler : GNU 9.3.0 (/usr/bin/cc) C compiler flags : -fPIC -fopenmp -pthread -fdiagnostics-color=auto C++ compiler : GNU 9.3.0 (/usr/bin/c++) C++ compiler flags : -std=c++11 -fPIC -fopenmp -pthread -fdiagnostics-color=auto Build dynamic : ON Built-in modules : models;precise;topology User modules : None Python bindings : Yes (Python 3.8: /usr/local/bin/python3) Includes : /usr/local/include/python3.8 Libraries : /usr/local/lib/libpython3.8.a Cython bindings : Yes (Cython 0.29.21: /usr/local/bin/cython) Use threading : Yes (OpenMP: -fopenmp) Use GSL : Yes (GSL 2.5) Includes : /usr/include Libraries : /usr/lib/x86_64-linux-gnu/libgsl.so;/usr/lib/x86_64-linux-gnu/libgslcblas.so Use Readline : Yes (GNU Readline 8.0) Includes : /usr/include Libraries : /usr/lib/x86_64-linux-gnu/libreadline.so;/usr/lib/x86_64-linux-gnu/libncurses.so Use libltdl : Yes (LTDL ) Includes : /usr/include Libraries : /usr/lib/x86_64-linux-gnu/libltdl.so Use doxygen : No Use MPI : Yes (MPI: /usr/bin/mpicxx) FLAGS : -pthread Includes : /usr/lib/x86_64-linux-gnu/openmpi/include/openmpi;/usr/lib/x86_64-linux-gnu/openmpi/include Link Flags : -pthread Libraries : /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi_cxx.so;/usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so Use MUSIC : No Use libneurosim : No Use Boost : No --------------------------------------------------------------------------------

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Open NEST Developer Video Conference Monday 31 August 2020 11:30 CEST (UTC+2)
by Dennis Terhorst 31 Aug '20

31 Aug '20

Dear NEST Users & Developers! I would like to invite you to our next fortnightly Open NEST Developer Video Conference today Monday 31 August, 11.30-12.30 CEST (UTC+2). 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/2020-08-31-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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Re: Issue with NEST Live Media 2.20
by Steffen Graber 27 Aug '20

27 Aug '20

Hi Maryada I just tested the VM with Windows 10 Home (Version 1903) and with Virtualbox 6.12. No problems at startup. The network does not seem to start in your installation. If not done yet I would first delete the VM completely and reinstall it. Then deactivate the network in the settings of the VM and restart it again. Hope this helps. Best Steffen Am 26.08.20 um 11:08 schrieb Maryada Maryada: > Sorry for the late reply. > Here you go. I hope this helps. > > On Tue, Aug 25, 2020 at 2:16 PM Steffen Graber <s.graber(a)fz-juelich.de > <mailto:s.graber@fz-juelich.de>> wrote: > > Hi, > > That's ok. Could you send me the log of the VM? > Highlight the VM in the manager and press CTRL+L. > > Best > > Steffen > > Am 25.08.20 um 13:01 schrieb Maryada Maryada: > > Hey, > > The latest one, 6.1.12 > > > > On Tue, Aug 25, 2020 at 12:52 PM Steffen Graber > <s.graber(a)fz-juelich.de <mailto:s.graber@fz-juelich.de> > > <mailto:s.graber@fz-juelich.de <mailto:s.graber@fz-juelich.de>>> > wrote: > > > > Hi, > > > > Do you have the ExtensionPack installed? In which version? > > > > Best > > > > Steffen > > > > Am 25.08.20 um 12:39 schrieb Maryada Maryada: > > > Hi Steffen, > > > I am using Windows 10 as my host OS and Oracle Virtual Box 6.1 > > > > > > On Tue, Aug 25, 2020 at 12:34 PM Steffen Graber > > <s.graber(a)fz-juelich.de <mailto:s.graber@fz-juelich.de> > <mailto:s.graber@fz-juelich.de <mailto:s.graber@fz-juelich.de>> > > > <mailto:s.graber@fz-juelich.de > <mailto:s.graber@fz-juelich.de> <mailto:s.graber@fz-juelich.de > <mailto:s.graber@fz-juelich.de>>>> > > wrote: > > > > > > Hi Maryada, > > > > > > Just tried Live Media 2.20 under Ubuntu 20.04 with > Virtualbox 6.1. > > > Starting the VM worked fine for me. > > > > > > Which operating system and which version of Virtualbox > do you use? > > > > > > Best > > > > > > Steffen > > > > > > Am 25.08.20 um 11:40 schrieb Maryada Maryada: > > > > Hi, > > > > I am trying to import Live Media 2.20 however the VM > > virtualbox is > > > > always get stuck immediately > > > > as it starts (see attachment). I also tried to import the > > 2.18 version > > > > just to be sure if it's an issue on my side. However, > that's > > working > > > > perfectly fine. > > > > > > > > Is there an additional requirement that I might be > missing? > > > > -- > > > > Thanks and Regards > > > > > > > > *Maryada* > > > > > > > > > > > > _______________________________________________ > > > > NEST Users mailing list -- users(a)nest-simulator.org > <mailto:users@nest-simulator.org> > > <mailto:users@nest-simulator.org > <mailto:users@nest-simulator.org>> > > > <mailto:users@nest-simulator.org > <mailto:users@nest-simulator.org> > > <mailto:users@nest-simulator.org > <mailto:users@nest-simulator.org>>> > > > > To unsubscribe send an email to > > users-leave(a)nest-simulator.org > <mailto:users-leave@nest-simulator.org> > <mailto:users-leave@nest-simulator.org > <mailto:users-leave@nest-simulator.org>> > > > <mailto:users-leave@nest-simulator.org > <mailto:users-leave@nest-simulator.org> > > <mailto:users-leave@nest-simulator.org > <mailto:users-leave@nest-simulator.org>>> > > > > > > > > > > -- > > > > > > ------------------------------------------------------------------------------------- > > > Steffen Graber > > > SimLab Neuroscience > > > Division HPC in Neuroscience > > > Jülich Supercomputing Centre > > > Institute for Advanced Simulation > > > Forschungszentrum Jülich GmbH > > > E-mail: s.graber(a)fz-juelich.de > <mailto:s.graber@fz-juelich.de> <mailto:s.graber@fz-juelich.de > <mailto:s.graber@fz-juelich.de>> > > <mailto:s.graber@fz-juelich.de <mailto:s.graber@fz-juelich.de> > <mailto:s.graber@fz-juelich.de <mailto:s.graber@fz-juelich.de>>> > > > Phone: +49 2461 61 85457 > > > http://www.fz-juelich.de/ias/jsc > > > > > > Institute of Neuroscience and Medicine (INM-6) > > > Computational and Systems Neuroscience & > > > Institute for Advanced Simulation (IAS-6) > > > Theoretical Neuroscience & > > > JARA Institute Brain Structure-Function Relationships > (INM-10) > > > Forschungszentrum Jülich GmbH > > > http://www.csn.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 > > > > > > ------------------------------------------------------------------------------------- > > > > > > > > > > > > -- > > > Thanks and Regards > > > > > > *Maryada* > > > > > > > > > _______________________________________________ > > > NEST Users mailing list -- users(a)nest-simulator.org > <mailto:users@nest-simulator.org> > > <mailto:users@nest-simulator.org > <mailto:users@nest-simulator.org>> > > > To unsubscribe send an email to > users-leave(a)nest-simulator.org <mailto:users-leave@nest-simulator.org> > > <mailto:users-leave@nest-simulator.org > <mailto:users-leave@nest-simulator.org>> > > > > > > > -- > > > ------------------------------------------------------------------------------------- > > Steffen Graber > > SimLab Neuroscience > > Division HPC in Neuroscience > > Jülich Supercomputing Centre > > Institute for Advanced Simulation > > Forschungszentrum Jülich GmbH > > E-mail: s.graber(a)fz-juelich.de <mailto:s.graber@fz-juelich.de> > <mailto:s.graber@fz-juelich.de <mailto:s.graber@fz-juelich.de>> > > Phone: +49 2461 61 85457 > > http://www.fz-juelich.de/ias/jsc > > > > Institute of Neuroscience and Medicine (INM-6) > > Computational and Systems Neuroscience & > > Institute for Advanced Simulation (IAS-6) > > Theoretical Neuroscience & > > JARA Institute Brain Structure-Function Relationships (INM-10) > > Forschungszentrum Jülich GmbH > > http://www.csn.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 > > > ------------------------------------------------------------------------------------- > > > > > > > > -- > > Thanks and Regards > > > > *Maryada* > > > > -- > ------------------------------------------------------------------------------------- > Steffen Graber > SimLab Neuroscience > Division HPC in Neuroscience > Jülich Supercomputing Centre > Institute for Advanced Simulation > Forschungszentrum Jülich GmbH > E-mail: s.graber(a)fz-juelich.de <mailto:s.graber@fz-juelich.de> > Phone: +49 2461 61 85457 > http://www.fz-juelich.de/ias/jsc > > Institute of Neuroscience and Medicine (INM-6) > Computational and Systems Neuroscience & > Institute for Advanced Simulation (IAS-6) > Theoretical Neuroscience & > JARA Institute Brain Structure-Function Relationships (INM-10) > Forschungszentrum Jülich GmbH > http://www.csn.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 > ------------------------------------------------------------------------------------- > > > > -- > Thanks and Regards > > *Maryada* > -- ------------------------------------------------------------------------------------- Steffen Graber SimLab Neuroscience Division HPC in Neuroscience Jülich Supercomputing Centre Institute for Advanced Simulation Forschungszentrum Jülich GmbH E-mail: s.graber(a)fz-juelich.de Phone: +49 2461 61 85457 http://www.fz-juelich.de/ias/jsc Institute of Neuroscience and Medicine (INM-6) Computational and Systems Neuroscience & Institute for Advanced Simulation (IAS-6) Theoretical Neuroscience & JARA Institute Brain Structure-Function Relationships (INM-10) Forschungszentrum Jülich GmbH http://www.csn.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 -------------------------------------------------------------------------------------

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Issue with NEST Live Media 2.20
by Maryada Maryada 25 Aug '20

25 Aug '20

Hi, I am trying to import Live Media 2.20 however the VM virtualbox is always get stuck immediately as it starts (see attachment). I also tried to import the 2.18 version just to be sure if it's an issue on my side. However, that's working perfectly fine. Is there an additional requirement that I might be missing? -- Thanks and Regards *Maryada*

2 5

Random refractory period
by giovannidisarra 18 Aug '20

18 Aug '20

How can I set a random refractory period (different for every neuron) in a population with SetDefaults()?

2 1

Open NEST Developer Video Conference Monday 17 August 2020 11:30 CEST (UTC+2)
by Dennis Terhorst 17 Aug '20

17 Aug '20

Dear NEST Users & Developers! I would like to invite you to our next fortnightly Open NEST Developer Video Conference today Monday 17 August, 11.30-12.30 CEST (UTC+2). 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/2020-08-17-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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Saving and loading entire network
by LOW, SOCK CHING 05 Aug '20

05 Aug '20

Hi, I am new to pynest and am using it to implement a liquid state machine. It works marvelously for generating the network. My workflow is as follows: - Initialise kernel - Get stimulation episodes - Create neurons (including spike generators) - Connect neurons - nest.Simulate() - nest.GetStatus(recording_neurons) for readout at relevant timepoints I would like to save the network so I can run nest.Simulate() on other episodes in a real-time application, is there a straight-forward way to do so? I have tried pickling conn = nest.GetConnections() but to my knowledge that does not include a lot of details about the connection, like the weight. It also does not return where there is *no* connections, which means simply using nest.SetConnections(conn) prior to nest.Simulate() will not work to reproduce the previously generated network even if I initialise with all the same variables. I have found the functions GetNetwork() and GetNodes() but I'm not sure how I can use them, or if they are even useful for what I need. Cheers, Sock Ching

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Open NEST Developer Video Conference Monday 3 August 2020 11:30 CEST (UTC+2)
by Dennis Terhorst 03 Aug '20

03 Aug '20

Dear NEST Users & Developers! I would like to invite you to our next fortnightly Open NEST Developer Video Conference today Monday 3 August, 11.30-12.30 CEST (UTC+2). 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/2020-08-03-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 20 July 2020 11:30 CEST (UTC+2)
by Dennis Terhorst 20 Jul '20

20 Jul '20

Dear NEST Users & Developers! I would like to invite you to our next fortnightly Open NEST Developer Video Conference today Monday 20 July, 11.30-12.30 CEST (UTC+2). 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/2020-07-20-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 6 July 2020 11:30 CEST (UTC+2)
by Dennis Terhorst 06 Jul '20

06 Jul '20

Dear NEST Users & Developers! I would like to invite you to our next fortnightly Open NEST Developer Video Conference today Monday 6 July, 11.30-12.30 CEST (UTC+2). 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: Hackathon Wrap-up The agenda for this meeting is also available online, see https://github.com/nest/nest-simulator/wiki/2020-07-06-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

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How to normalize incoming/outgoing synaptic weights
by Keiko Fujii 29 Jun '20

29 Jun '20

Hello everyone, I would like to ask how to normalize synaptic weights during STDP learning. What I want to do is keeping the total amount of synaptic weights to/from each neuron constant. I try to describe my goal a bit more precisely: i: The index of a pre-synaptic neuron. j: The index of a post-synaptic neuron. w_ij(t): The synaptic weight from i-th neuron to j-th neuron at time=t. s_i(t): the sum of all incoming synaptic weights to i-th neuron at time=t. i.e. the sum of w_ij(t) over j. The goal is to set the sum of incoming weights (s_i(*)) to 1 by normalization (1 is just for simplicity). By STDP, we can get updated synaptic weight matrix w_ij(t+1), and the sum s_i(t+1) is not necessarily 1. So, I want to set w_ij(t+1) <- w_ij(t+1) / s_i(t+1) I briefly read the documentation for synaptic models( https://nest-simulator.readthedocs.io/en/stable/models/synapses.html). I am not very confident if my understanding is correct, but it seems that existing synaptic models handle only one synaptic weight. How can I gather data of all incoming(or outgoing as well) weights to a neuron and use the summation value inside of the STDP synapse model? Best regards, Keiko Fujii

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Error: UnknownModelName
by Allen Rabayda 27 Jun '20

27 Jun '20

Dear Nest Community, Would anyone have insight into why I'm getting an UnknownModelName error? I'm new to Nest and am using Nest 18.0 on Lubuntu Virtual Box (Windows 10 OS). Thanks for any help. Best Regards, --Allen **** Error Message--additional details attached ****** raise exceptionCls(commandname, message) nest.ll_api.UnknownModelName: ('UnknownModelName in CopyModel_l_l_D: /stdp_izh_bitwise_correct_connection is not a known model name. Please check the modeldict for a list of available models.', 'UnknownModelName', <SLILiteral: CopyModel_l_l_D>, ': /stdp_izh_bitwise_correct_connection is not a known model name. Please check the modeldict for a list of available models.') ********************************************************

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Install nest via homebrew
by Tammo Ippen 22 Jun '20

22 Jun '20

Hello nest users with a mac, From now on, it is possible to install nest via homebrew from the default homebrew-core tap: https://formulae.brew.sh/formula/nest#default [1] You get nest 2.20.0 with OpenMP and PyNEST bindings with python 3.8 delivered as a 'bottle' (prebuild binary package) in a couple of seconds - with all dependencies. Go to https://brew.sh/ [2] and follow the installation of homebrew. When brew is installed, just type: brew install nest And you should see something like: $ brew install nest ==> Downloading https://homebrew.bintray.com/bottles/nest-2.20.0_1.catalina.bottle.tar.gz ==> Downloading from https://akamai.bintray.com/38/38bfd492f381cd059a495122d1c3342e8fb5095501c04… ######################################################################## 100.0% ==> Pouring nest-2.20.0_1.catalina.bottle.tar.gz Warning: nest dependency gcc was built with a different C++ standard library (libstdc++ from clang). This may cause problems at runtime. ==> Caveats The PyNEST bindings and its dependencies are installed with the python(a)3.8 formula. If you want to use PyNEST, use the Python interpreter from this path: /usr/local/opt/python(a)3.8/bin You may want to add this to your PATH. ==> Summary 🍺 /usr/local/Cellar/nest/2.20.0_1: 1,290 files, 21.2MB Now you can run nest like: $ nest -- N E S T -- Copyright (C) 2004 The NEST Initiative Version: nest-2.20.0 Built: Jun 22 2020 13:38:00 This program is provided AS IS and comes with NO WARRANTY. See the file LICENSE for details. Problems or suggestions? Visit https://www.nest-simulator.org Type 'help' to get more information. Type 'quit' or press CTRL-D to quit. SLI ] If you want to use PyNEST, you have to use the python(a)3.8 formula python - the dependencies numpy, scipy, etc. are also delivered via homebrew and they are build with the python(a)3.8 formula, which is keg-only [3]. Add the opt-bin path to your PATH variable like: export PATH=/usr/local/opt/python@3.8/bin:$PATH and you can start with: $ python3.8 -c 'import nest' -- N E S T -- Copyright (C) 2004 The NEST Initiative Version: nest-2.20.0 Built: Jun 22 2020 13:38:00 This program is provided AS IS and comes with NO WARRANTY. See the file LICENSE for details. Problems or suggestions? Visit https://www.nest-simulator.org Type 'nest.help()' to find out more about NEST. Best, Tammo Links: ------ [1] https://formulae.brew.sh/formula/nest#default [2] https://brew.sh/ [3] https://docs.brew.sh/How-to-Build-Software-Outside-Homebrew-with-Homebrew-k…

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Feature discussion: STDP and delays
by Dennis Terhorst 22 Jun '20

22 Jun '20

Dear NEST enthusiasts! In the NEST Meeting on May 25th <https://github.com/nest/nest-simulator/wiki/2020-05-25-Open-NEST-Developer-…> [1] there was a very interesting discussion of handling of delays in networks with STDP in NEST. It became obvious, that this topic requires a more in-depth discussion and it was decided to do a separate VC for this discussion, which will happen this week on * Thursday, June 25, 2020 - 13:30 CEST with the connection details <https://github.com/nest/nest-simulator/wiki/Connection-Details> [2] as usual. Best, Dennis [1]: https://github.com/nest/nest-simulator/wiki/2020-05-25-Open-NEST-Developer-… [2]: https://github.com/nest/nest-simulator/wiki/Connection-Details i.e. https://conf.dfn.de/webapp/conference/97938800 -- 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 -------------------------------------------------------------------------------------

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Open NEST Developer Video Conference Monday 22 June 2020 11:30 CEST (UTC+2)
by Dennis Terhorst 22 Jun '20

22 Jun '20

Dear NEST Users & Developers! I would like to invite you to our next fortnightly Open NEST Developer Video Conference on Monday 22 June, 11.30-12.30 CEST (UTC+2). 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/2020-06-22-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

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Installation on supercomputer failed
by Petia Koprinkova 19 Jun '20

19 Jun '20

Hi, We are trying to install NEST on supercomputer Ahitohol but we were unable to manage with some errors. Here attached is a screenshot with last reported errors. Could you help to resolve it?Regards,Petia

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LIF neuron with both current based and conductance based synapses
by Hartmut Schmidt 18 Jun '20

18 Jun '20

Dear all, I am trying to implement a network consisting of LIF neurons with mixed current based and conductance based synaptic connections. Eg. one LIF neuron which gets two inputs from which one is treated as current input and the other as conductance input. That means, how to treat the input should be encoded in the synapse and not in the type of the postsynaptic neuron. Is such a neuron model already implemented or is there a way to implement this? Thanks for your help. Best, Hartmut

3 2

pipnest
by Robin Gilbert De Schepper 17 Jun '20

17 Jun '20

Hi, I created a little tool that provides packaging for NEST extension modules into python packages that can be `pip installed` on the target machine. https://pip-nest.readthedocs.io/en/latest/ First off, is this interesting to the community? It certainly seems easier to `pip install some-module` than to provide installation instructions, and I can now specify my modules as dependencies in code I distribute. Secondly, there are some shortcomings based on the fact that the pip install only reliably produces the build artifacts into python's site-packages and nest doesn't look for them there. This can probably only be elegantly solved by adding an `entry_point` to the nest python module so that these pip nest modules can announce themselves there? -- 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/

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NEST Conference 2020 Program — Registration Deadline Monday 22 June 2020
by Hans Ekkehard Plesser 16 Jun '20

16 Jun '20

Dear Colleagues! The virtual NEST Conference 2020 on 29/30 June is less than two weeks away and we are happy to invite you to an exciting program of presentations and workshops, which you will find below. The conference will be single track to facilitate interactions and include virtual coffee breakouts to mix and mingle. Please don't forget to register by MONDAY, 22 June 2020 at https://www.nest-simulator.org/conference. Please note that we now also accept PayPal as a payment method. See you at the NEST Conference 2020! Hans Ekkehard Plesser & Susanne Kunkel Monday 29 June, 2020 (all times are CEST) * 09:00 — Welcome & Introduction (Susanne Kunkel) * 09:15 — NEST user-level documentation: Why, how and what’s next? (Sara Konradi) * 09:35 — Exploring new Fenix resources using NEST (Alexander Patronis) * 09:55 — Minibreak * 10:00 — Toward a possible integration of NeuronGPU in NEST (Bruno Golosio) * 10:45 — Coffee breakout * 11:15 — Workshop: NEST multiscale co-simulation (Wouter Klijn) * 12:15 — Lunch break * 13:15 — Thalamo-cortical spiking model of incremental learning combining perception, context and NREM-sleep-mediated noise-resilience (Chiara De Luca) * 14:00 — Minibreak * 14:05 — An Integrated Model of Visual Perception and Reinforcement(Petia Koprinkova-Hristova) * 14:25 — Partial Information Decomposition Contextual Neurons in NEST(Sepehr Mahmoudian) * 14:45 — Coffee breakout * 15:15 — deNEST: a declarative frontend for specifying networks and running simulations in NEST (Tom Bugnon) * 15:35 — Primate perisylvian cortex in NEST: from reflex to small world (Harry Howard) * 15:55 — Minibreak * 16:00 — Modeling robust and efficient coding in the mouse primary visual cortex using computational perturbations (Stefan Mihalas) * 16:45 — Wrap-up (Hans Ekkehard Plesser) * 17:00 — Mingle Tuesday 30 June, 2020 (all times are CEST) * 09:00 — A spiking neural network builder for systematic data-to-model workflow(Carlos E Gutierrez) * 09:20 — Insite: A Generalized Pipeline for In-transit Visualization and Analysis(Simon Oehrl) * 09:40 — Minibreak * 09:45 — NEST Component for Modeling Spiking Neuron-Astrocyte Networks(Jugoslava Aćimović) * 10:30 — Coffee breakout * 11:00 — Atlas-mapped reconstruction and simulation of the cerebellar Lingula in NEST (Alice Geminiani) * 11:20 — Cerebro-cerebellar loops for sensorimotor adaptation (Alberto Antonietti) * 11:40 — Minibreak * 11:45 — Modeling plasticity inducing stimulation protocols in recurrent neuronal networks with homeostatic structural plasticity (Swathi Anil) * 12:30 — Lunch break * 13:30 — Dendrites in NEST (Willem Wybo) * 13:50 — Just-in-time compilation for NESTML models in NEST Simulator (Charl Linssen) * 14:10 — NEST Desktop: A web-based GUI for the NEST Simulator (Sebastian Spreizer) * 14:30 — Minibreak * 14:40 — Evolving interpretable plasticity rules using NEST (Jakob Jordan) * 15:25 — Coffee breakout * 15:45 — Workshop: deNEST: a declarative frontend for specifying networks and running simulations in NEST (Tom Bugnon & William Mayner) * 16:45 — Closing Remarks -- Prof. Dr. Hans Ekkehard Plesser Head, Data Science Section 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 Home http://arken.nmbu.no/~plesser

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Training SNNs with PyNEST
by s.kraemer96＠gmx.net 15 Jun '20

15 Jun '20

Dear all, I´m writing a master thesis on spiking neural networks and how transparent they are. For that I need to implement a SNN network and train it. So I started with Brian but that is much to complex and I don´t need something special. So I decided to use PyNest. I did all the tutorials but I´m missing a tutorial how to train the network. I don´t know how to put in a dataset to train the model. I haven´t found anything to this topic. So my questions are: 1. Can PyNest train set up a SNN and train it trough data and if not is there another simulator who can do this? 2. How do I do it? Is there anything I missed to read or can someone send me an example? This would be very helpful. Thanks for your help. Best, Sonja

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Open NEST Developer Video Conference Monday 8 June 2020 11:30 CEST (UTC+2)
by Dennis Terhorst 08 Jun '20

08 Jun '20

Dear NEST Users & Developers! I would like to invite you to our next fortnightly Open NEST Developer Video Conference on Monday 8 June, 11.30-12.30 CEST (UTC+2). 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 suggested from the teams. In-depth discussions will cover updates on the ongoing discussion around #1604 (STDP and delays) and proposed refactoring of the testing framework. 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/2020-06-08-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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[NEST users] Docker container with NEST3 and music
by Benjamin Staude 05 Jun '20

05 Jun '20

Hi NEST users, Does anyone know if there is a Docker container available that has NEST3 and the MUSIC interface installed? Best regards, Benjamin -- -- -- Dr. Benjamin Staude | Paul-Lincke-Ufer 7 | 10999 Berlin | benjamin.staude(a)gmail.com

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NEST Conference 2020 Registration now open
by Dennis Terhorst 04 Jun '20

04 Jun '20

The NEST Conference organization team would like to share the following exciting news: Dear Colleagues! The NEST Conference Website is open again on https://nest-simulator.org/conference and we have now opened for registration as well. Registration by 22 June 2020 is required for attendance. Only registered users will receive log-in information for the conference. Registration to the conference is * free of charge for members of the NEST Initiative * 35 CHF for non-members To qualify for the member rate, you must apply for membership in the NEST Initiative by 10 June. See http://www.nest-initiative.org/membership/ for information on how to join. Membership is currently free of charge for students, including PhD students, and 25 CHF annually for everyone else. We are looking forward to seeing you on 29/30 June! Hans Ekkehard -- Prof. Dr. Hans Ekkehard Plesser Head, Data Science Section 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 Home http://arken.nmbu.no/~plesser

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NEST Conference 2020 Registration now open
by Hans Ekkehard Plesser 03 Jun '20

03 Jun '20

Dear Colleagues! The NEST Conference Website is open again on https://nest-simulator.org/conference and we have now opened for registration as well. Registration by 22 June 2020 is required for attendance. Only registered users will receive log-in information for the conference. Registration to the conference is * free of charge for members of the NEST Initiative * 35 CHF for non-members To qualify for the member rate, you must apply for membership in the NEST Initiative by 10 June. See http://www.nest-initiative.org/membership/ for information on how to join. Membership is currently free of charge for students, including PhD students, and 25 CHF annually for everyone else. We are looking forward to seeing you on 29/30 June! Hans Ekkehard -- Prof. Dr. Hans Ekkehard Plesser Head, Data Science Section 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 Home http://arken.nmbu.no/~plesser

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NEST Conference Abstract Submission via EMAIL
by Hans Ekkehard Plesser 02 Jun '20

02 Jun '20

Dear Colleagues, Regrettably, the website for the NEST Conference 2020 became unavailable shortly before the abstract submission deadline. We are currently working to restore the website. In the meantime, please submit your abstract BY EMAIL to conference(a)nest-initiative.org using the attached template (DOCX). Please also find an example abstract with detailed instructions attached. We extend the deadline to 2 June 2020. Best regards, Hans Ekkehard

2 1

NEST 2.20.1
by Ing Jyh Tsang 02 Jun '20

02 Jun '20

Hi, Is NEST 2.20.1<https://github.com/nest/nest-simulator/milestone/8> the installed version (when following https://nest-simulator.readthedocs.io/en/stable/installation/index.html), since it solves issue #1394<https://github.com/nest/nest-simulator/issues/1394>? it seems it is completed. If this is not, when will this happen? Thanks a lot Ing Jyh Tsang

1 0

send() function
by Itaru Kitayama 01 Jun '20

01 Jun '20

Hi, How do I check where send() function implemented in connector_base.h is generated and stored in which object file? Itaru.

1 1

NEST Conference website not reachable
by Bruno Golosio 30 May '20

30 May '20

Hello, the deadline for submission of contributions is approaching and the NEST Conference website is down since yesterday. Is there an alternative way to submit contributions? Bruno -- Bruno Golosio, PhD Associate Professor of Applied Physics Coordinator of the School of Medical Physics Department of Physics University of Cagliari (Italy) [image: image.gif]

1 0

Finding the right parameters for the balanced network
by nosratullah mohammadi 26 May '20

26 May '20

Dear Nest Users, I hope all of you be in health during these times. I want to create a balanced network as it’s the first step of my master thesis. The model I want to use is “iaf_cond_exp” which is a must for later purposes. There’s an example in Pynest folder of a balanced network, unless it’s using “iaf_psc_alpha” and it doesn’t fit my goals. When I try to change the model, and run the program, the network doesn’t get active and there’s nothing to record. I divided my question into two part: - Does anyone have a balanced network with “iaf_cond_exp” neurons and all of its necessary parameters to run? - In general, how do people find or calculate their network parameters to fit the neuron model they use and don’t get lost in the massive number of parameters. Note: I also tried to use the example of “brunel_alpha_evolution_strategies.py” example which is a genetic algorithm to find the best parameter, although it finds the parameters after 50 generation, I use those parameters afterwards. It just doesn’t work! Kind regards, Nosratullah Mohammadi

2 2

NEST Conference 2020 — Submission deadline 1 June 2020
by Anne Elfgen 26 May '20

26 May '20

Dear all, Just a little reminder that the submission deadline for the (virtual) NEST Conference 2020 is *this Monday, June 1st. *We are 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 take place as a *virtual conference* on *Monday/Tuesday 29/30 June 2020*. We are inviting contributions to the conference, including plenary talks, "posters" and breakout sessions on specific topics. *Important dates* *01 June 2020* — Deadline for submission of contributions *08 June 2020* — Notification of acceptance *10 June 2020* — Deadline for NEST Initiative Membership applications (registration is free for members in 2020) *22 June 2020* — Registration deadline *29 June 2020* — NEST Conference 2020 starts For more information on how to submit your contribution, register and participate, please visit the conference website *https://nest-simulator.org/conference* We are looking forward to seeing you all in June! Hans Ekkehard Plesser, Susanne Kunkel, Dennis Terhorst, Anne Elfgen & many more

1 0

Open NEST Developer Video Conference Monday 25 May 2020 11:30 CEST (UTC+2)
by Dennis Terhorst 25 May '20

25 May '20

Dear NEST Users & Developers! I would like to invite you to our next fortnightly Open NEST Developer Video Conference on Monday 25 May, 11.30-12.30 CEST (UTC+2). 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 suggested from 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/2020-05-25-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

1 0

Reset Kernel + STDP Performance
by Benedikt S. Vogler 22 May '20

22 May '20

Hello everyone! I am writing to you regarding two matters: Reset Network/Kernel in nest2->nest 3 In the last developer conference, Daphne Cornelisse talked about that she used ResetNetwork() to solve her problem. ResetNetwork() is marked as deprecated. No one said anything, so I got confused why this is apparently the recommended way or at least approved. She showed me, that it works (in her case). It is deprecated, so there is probably some good reasoning behind it. The documentation says: "ResetNetwork is deprecated and will be removed in NEST 3, because this function is not fully able to reset network and simulator state. What are the edge cases where the use causes problems? In this ticket, it is stated that the feature is just removed with any replacement. https://github.com/nest/nest-simulator/issues/525 Thus, in nest3 there is only ResetKernel(). This means that you have to rebuild the network for any application where you do multiple simulations with different input or parameter changes. I am using nest3 for reinforcement learning and in each training episode, I have to extract all the weights and save them, reset the kernel, reconstruct the net, then load all the weights. This adds a lot of overhead in performance and bloats my code. I basically have another front-end storing the net and talking to the nest back-end. Therefore, the update to nest3 is a downgrade for many applications. I don’t have a solution for this issue, but I want to spark some discussion as I learned that I am not the only nest user to stumble into this issue. STDP Performance boost by manual computation in python In the paper "Demonstrating Advantages of Neuromorphic Computation: A Pilot Study“ by Wunderlich et al. (https://www.frontiersin.org/articles/10.3389/fnins.2019.00260/full) some performance improvement on STDP was reported. "The synaptic weight updates in each iteration were restricted to those synapses which transmitted spikes, i.e., the synapses from the active input unit to all output units (32 out of the 1,024 synapses), as the correlation a+ of all other synapses is zero in a perfect simulation without fixed-pattern noise. This has the effect of reducing the overall time required to simulate one iteration[…]“ The provided source code (https://github.com/electronicvisions/model-sw-pong/blob/976e0778ca05cfd96c4… <https://github.com/electronicvisions/model-sw-pong/blob/976e0778ca05cfd96c4…>) indeed contains a manual computation of STDP. When using the nest library I don’t expect to do some computation in python to be faster. It appears to me that the nest implementation is computing STDP every time, even without spikes? Maybe someone can comment on this whether this can be improved in nest? Kind regards, Benedikt S. Vogler -- Benedikt S. Vogler benedikt.s.vogler(a)tum.de Student M.Sc. Robotics, Cognition, Intelligence

3 3

Inhibitory plasticity with current based neurons
by Julia Gallinaro 11 May '20

11 May '20

Dear all, I would like to simulate a network of current based LIF ('iaf_psc_delta') with inhibitory plasticity. I tried using the model vogels_sprekeler_synapse, but the resulting weights are positive (and they increase when firing rate is high). I guess it is because when used with conductance based neurons, the resulting weights would be multiplied by a gI<0? And with current based neurons, this is not the case. The weight is directly used as the synaptic weight. Do I understand it right? Is there a way to implement inhibitory plasticity using the vogels_sprekeler_synapse and current based LIF? Best, Júlia

3 5

Open NEST Developer Video Conference Monday 27 April 2020 11:30 CEST (UTC+2)
by Dennis Terhorst 11 May '20

11 May '20

Dear NEST Users & Developers! I would like to invite you to our next fortnightly Open NEST Developer Video Conference on Monday 11 May, 11.30-12.30 CEST (UTC+2). 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 suggested from 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/2020-05-11-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

2 2

Spike Train Frequencies Inspection
by Benedikt Feldotto 08 May '20

08 May '20

Dear all, I am working with frequency encoded spike trains and therefore like to observe the changing spike frequencies between different individual connections in my network (if possible in real time). While I can record the spike events with time using 'spike_detector' units, I couldn't find a direct method to calculate the frequency. Is there any method implemented or a preferred way to calculate frequencies from spike trains over time or would this calculation be up to the user? I am also thinking about using an indirect way by attaching a leaky integrate and fire neuron with infinite threshold. Thanks! Best, 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

Control over the synaptic weight and synaptic decay time
by Nosratullah M 08 May '20

08 May '20

Dear all, I hope you are in staying safe. I'm working on a balanced network consisting of "iaf_cond_exp" neurone model. I want to have the control over these parameters at the same time: - increasing the synaptic decay time. - reducing the synaptic weight. The goal is to make the area under the synaptic current, constant. So that we know that the only parameter that is affecting on the network, is synaptic delay. I wonder if you know of any furmula in mathematics or any algorithm, that can help me, making this process automatic. And keeping the area under the curve, a constant value. Best wishes, Nosratullah

3 3

local_num_threads, multiprocessing and topology.ConnectLayers
by Juan Manuel Vicente 06 May '20

06 May '20

Hi all, I'm trying to understand some inner workings of Nest. Rigth now I'm running simulations with close half millons elements, using mpirun in a cluster with 25 nodes. The problem I am having is that the "setup" (layer creation and connections) phase takes close to 8min and the simulation only takes 1min. So I tried to use python's multiprocessing package to speed it up, with the following code: nest.ResetKernel() nest.SetKernelStatus({"local_num_threads": 1}) #... connections = [ (layer1, layer1, conn_ee_dict, 1), (layer1, layer2, conn_ee_dict, 2), (layer2, layer2, conn_ee_dict, 3), (layer2, layer1, conn_ee_dict, 4) ] # Process the connections. def parallel_topology_connect(parameters): [pre, post, projection, number] = parameters print(f"Connection number: {number}") topology.ConnectLayers(pre, post, projection) pool = multiprocessing.Pool(processes=4) pool.map(parallel_topology_connect, connections) The above example takes around 0.9s, but if the last two to lines are changed for a sequential call, it takes 2.1s: for [pre, post, projection, number] in connections: print(f"Connection number: {number}") topology.ConnectLayers(pre, post, projection) So far the multiprocessing works great, the problem comes when the "local_num_threads" parameters is changed from 1 to 2 or more, in the cluster it could be 32. The code gets stuck in the topology.Connect without any error, after a while I just stopped it. Also I realised that the tolopoly.ConnectLayers just spawn one thread to connects layers despite the local_num_threads is setted more than one. Any idea what is going on? Thanks in advance Juan Manuel PD: The full example code is attached (60 lines of code). The local_num_threads and multiprocessing_flag variables change the behaviors of the code.

4 5

Implementing Synaptic Failure Rate
by Joshua Stern 04 May '20

04 May '20

Hello, I hope everyone is well. I am working on replicating some results from Teremae et al 2012 <https://www.nature.com/articles/srep00485#Sec4> and have run into an area of uncertainty. The paper calls for there to be a synaptic weight-dependent failure rate of synaptic transmission: [image: image.png] Is there any way to implement this in Nest? If it would help, I am working on a custom neuron model built in Nestml. I can also write some C++ if it seems that there would be an easy way to add this functionality with a short function. Alternatively, are there canonical ways to alter network structure to account for such a failure rate if it cannot be implemented in Nest? Thank you and best wishes, Josh Stern

2 2

NEST3 / Some thoughts on NodeCollections and Connect
by Hans Ekkehard Plesser 01 May '20

01 May '20

Dear Colleagues, This mail is mostly relevant for developers, but I would also like interested users to take a look and comment. In https://github.com/nest/nest-simulator/issues/1570#issuecomment-622380622 I have attempted to summarize a number of thoughts about the details of node representation and Connect() semantics. While a lot is in place, we still need to clarify some details in the near future, before we can release NEST 3. Your input is therefore welcome! If you haven't looked at NEST 3 yet, you may want to take a look at https://nest-simulator.readthedocs.io/en/latest/guides/nest2_to_nest3/nest2… first. Best regards, Hans Ekkehard -- Prof. Dr. Hans Ekkehard Plesser Head, Data Science Section 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 Home http://arken.nmbu.no/~plesser

1 0

NEST Conference 2020 goes virtual — Call for Contributions
by Anne Elfgen 30 Apr '20

30 Apr '20

Dear all, The NEST Initiative is excited to invite everyone interested in Neural Simulation Technology and the NEST Simulator to the NEST Conference 2020. 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 take place as a *virtual conference* on *Monday/Tuesday 29/30 June 2020*. We are now inviting contributions to the conference, including plenary talks, "posters" and breakout sessions on specific topics. *Important dates* *01 June 2020* — Deadline for submission of contributions *08 June 2020* — Notification of acceptance *10 June 2020* — Deadline for NEST Initiative Membership applications (registration is free for members in 2020) *22 June 2020* — Registration deadline *29 June 2020* — NEST Conference 2020 starts For more information on how to submit your contribution, register and participate, please visit the conference website *https://nest-simulator.org/conference* We are looking forward to seeing you all in June! Hans Ekkehard Plesser, Susanne Kunkel, Dennis Terhorst, Anne Elfgen & many more

1 0

error at installing nest2.20 from source code
by Abolfazl Ziaeemehr 29 Apr '20

29 Apr '20

Hello everyone, I used the source code to install nest simulator 2.20 from here <https://nest-simulator.readthedocs.io/en/stable/installation/linux_install.…> and did the following steps (I used to do the same steps for version 2.18 without error.) cmake -Dwith-python=3 -DCMAKE_INSTALL_PREFIX:PATH=</install/path> </path/to/NEST/src> make make install make installcheck I got this error from "make installcheck": Phase 1: Testing if SLI can execute scripts and report errors ------------------------------------------------------------- Running test 'selftests/test_pass.sli'... Running Apr 21 19:46:31 SLIStartup [Error]: NEST_DATA_DIR is not usable: Apr 21 19:46:31 SLIStartup [Error]: Directory '/usr/share/nest' does not exist. Apr 21 19:46:31 SLIStartup [Error]: I'm using the default: /home/abolfazl/prog/install-dir/nest-simulator-2.20.0_build/share/nest Apr 21 19:46:31 SLIStartup [Error]: NEST_DOC_DIR is not usable: Apr 21 19:46:31 SLIStartup [Error]: Directory '/usr/share/doc/nest' does not exist. Apr 21 19:46:31 SLIStartup [Error]: I'm using the default: /home/abolfazl/prog/install-dir/nest-simulator-2.20.0_build/share/doc/nest /usr/bin//bin/nest /usr/share/doc/nest/selftests/test_pass.sli /home/abolfazl/prog/install-dir/nest-simulator-2.20.0_build/bin/nest_serial: 20: /home/abolfazl/prog/install-dir/nest-simulator-2.20.0_build/bin/nest_serial: Apr: not found Failed: unexpected exit code 127 Running Apr 21 19:46:31 SLIStartup [Error]: NEST_DATA_DIR is not usable: Apr 21 19:46:31 SLIStartup [Error]: Directory '/usr/share/nest' does not exist. Apr 21 19:46:31 SLIStartup [Error]: I'm using the default: /home/abolfazl/prog/install-dir/nest-simulator-2.20.0_build/share/nest Apr 21 19:46:31 SLIStartup [Error]: NEST_DOC_DIR is not usable: Apr 21 19:46:31 SLIStartup [Error]: Directory '/usr/share/doc/nest' does not exist. Apr 21 19:46:31 SLIStartup [Error]: I'm using the default: /home/abolfazl/prog/install-dir/nest-simulator-2.20.0_build/share/doc/nest /usr/bin//bin/nest /usr/share/doc/nest/selftests/test_pass.sli /home/abolfazl/prog/install-dir/nest-simulator-2.20.0_build/bin/nest_serial: 20: /home/abolfazl/prog/install-dir/nest-simulator-2.20.0_build/bin/nest_serial: Apr: not found *** *** An unexpected exit code usually hints at a bug in the test suite! *** *** Please report the problem at *** https://github.com/nest/nest-simulator/issues *** *** To help us diagnose the problem, please attach the archived content *** of these directories to the issue: *** - '/home/abolfazl/prog/install-dir/nest-simulator-2.20.0_build/reports' *** - '/home/abolfazl/prog/install-dir/nest-simulator-2.20.0_build/reports/nest.CgbAi' *** CMakeFiles/installcheck.dir/build.make:57: recipe for target 'CMakeFiles/installcheck' failed make[3]: *** [CMakeFiles/installcheck] Error 2 CMakeFiles/Makefile2:99: recipe for target 'CMakeFiles/installcheck.dir/all' failed make[2]: *** [CMakeFiles/installcheck.dir/all] Error 2 CMakeFiles/Makefile2:106: recipe for target 'CMakeFiles/installcheck.dir/rule' failed make[1]: *** [CMakeFiles/installcheck.dir/rule] Error 2 Makefile:188: recipe for target 'installcheck' failed make: *** [installcheck] Error 2 -- regards, Abolfazl Ziaeemehr Department of Physics, PhD student in Computational Physics Institute for Advanced Studies in Basic Sciences (IASBS) Tel: 0919 607 4296 Page: iasbs.ac.ir/~a.ziaeemehr

3 11

Reset while keeping network connections
by Daphne Cornelisse 27 Apr '20

27 Apr '20

Dear Nest community, I have a network of LIF neurons ('iaf_cond_alpha') and I would like to implement STDP synapses, rather than the standard 'static_synapse'. I would like to be able to set a subset of the network to STDP synapses (e.g. all excitatory ones) and leave the rest static. This is how have implemented that currently (see code). I am using a for loop because I want to see how STDP changes the activity over time (over many iterations), which leaves me with the following two questions: *1. Is this a correct way to implement STDP in nest? * *2. Is there a way to reset the network such that the connections are not lost? *ResetNetwork() and ResetKernel() both seem to destroy all the network connections. While I would like to keep them, so that the network becomes less and less randomly connected per simulation. Thank you! Best, Daphne *CODE* # define network connectivity conn_dict = {'rule': 'pairwise_bernoulli', 'p': 0.1} # define dicts for static synapses static_ex_params = {'model':'static_synapse','weight': 6.0, 'delay': 1.5} static_in_params = {'model':'static_synapse','weight': -96.0, 'delay': 1.5} if self.STDP == 'ALL': # all synapses should be stdp ones, make connections between the two populations: # from exc neurons to all neurons nest.Connect(neurons_all[:self.NE], neurons_all, conn_dict, self.syn_params_ex) # from interneurons to all neurons nest.Connect(neurons_all[self.NE:], neurons_all, conn_dict, self.syn_params_in) elif self.STDP == 'EXC': # keep the inhibitory synapses static # connections from exc neurons to all neurons nest.Connect(neurons_all[:self.NE], neurons_all, conn_dict, self.syn_params_ex) # connections from interneurons to all neurons nest.Connect(neurons_all[self.NE:], neurons_all, conn_dict, static_in_params) where synapse_params_in = { 'model':'stdp_synapse', 'lambda': 0.01, 'alpha': 1.0, 'delay': 1.5, 'weight':-95.0 }

3 2

Open NEST Video Conference Satellite Event: A declarative front-end for network and simulation specifications
by Dennis Terhorst 24 Apr '20

24 Apr '20

Dear NEST Users & Developers! Additionally to the Open NEST Developers VC on Monday, we would like to announce a user contributed presentation of *A declarative front-end for network and simulation specifications* by /Tom Bugnon/ (Paris) and /Will Mayner/ (Wisconsin). on Monday 27 April, 16.00-17.00 CEST (UTC+2) / 9.00am CDT (UTC-5). This frontend to NEST allows to define the structure of more-or-less arbitrary simulations in a set of parameter files. Those let the user define network parameters (layers, neuron/synapse models, connections and nest.Topo "connection models", "input" layers etc.) and simulation parameters (set-up recorders, set-up "sessions", or units of simulations, for which the user can define specific inputs, changes in the state of some units, etc). This approach makes it easier to version-control the network and simulation specifications, share parameter files, perform parameter exploration, or run the same network in different conditions. We will meet in the same VC room, but due to the timezone difference of the presenters this had to be detached from the meeting in the morning. Connection details are given below. 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 -- 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 -------------------------------------------------------------------------------------

1 0

Open NEST Developer Video Conference Monday 27 April 2020 11:30 CEST (UTC+2)
by Dennis Terhorst 24 Apr '20

24 Apr '20

Dear NEST Users & Developers! I would like to invite you to our next fortnightly Open NEST Developer Video Conference on Monday 27 April, 11.30-12.30 CEST (UTC+2). This VC will be in the updated format and we may do some more explanation than I'd expect in future meetings. 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 suggested from the teams. Agenda Welcome Review of NEST User Mailing List Short introduction to Github project usage Project team round In-depth discussion The agenda for this meeting is also available online, see https://github.com/nest/nest-simulator/wiki/2020-04-27-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

1 0

Re: SARS-CoV face mask sanitizing gels
by ywjingqing 23 Apr '20

23 Apr '20

1 0

Question about MPI and multithreading
by kusch lionel 15 Apr '20

15 Apr '20

Dear all, I am actually working on the I/O for Nest with MPI. I am not aware of the solution of Nest for managing the communication between process and thread. I would like to learn more about it for adapting the interface with the actual solution. If someone can answer some of my questions : 1) By looking at the initialization of the MPI, I saw Nest use the /MPI_THREAD_FUNNELED /for the level of thread support. What is the reason for it? 2) This level of thread support surprise me because I suppose that it will overload one thread with all the MPI calls. Why do you do not choose the level /MPI_THREAD_SERIALIZED/? 3) I would like to have different levels for thread support. Do you think it's possible ? Thank you in advance for your answer, Kusch Lionel PS: The reference to the different MPI thread support : http://mpi.deino.net/mpi_functions/MPI_Init_thread.html

2 1

GitHub Projects
by Dennis Terhorst 14 Apr '20

14 Apr '20

Dear NEST users and developers, some of you may already have noticed, that we recently updated a lot of issues and pull-requests in our repository. The changes are completely organizational and aim to provide a better overview and service to our community. In particular, we removed the "C:" category labels (Model, Kernel, PyNEST, Documentation, ...) and instead now make use of corresponding GitHub projects. There, issues and pull-requests are represented as "cards" on a Kanban-like board, which gives a comprehensive view on the current topics and enables dedicated discussions to focus more easily. For each project we assigned a contact person that will take care of organizing work for that subset of cards. You notice that also the "P:" progress labels have mostly been removed (except "blocked" and "won't fix"), as this is automatically tracked in the columns of the projects and is much easier to manage there. The change to GitHub projects enables us to discuss topics in a more focused fashion than detailed issue-by-issue, which will also be reflected in the Open NEST Developer Video Conference. Projects will give a general status update and can raise overarching questions into the discussion. The detailed issue-by-issue work on the other hand, is organized by the project groups separately and each group may decide to do separate meetings to discuss details. Besides the long-running projects corresponding to the category labels, larger short/mid-term activities are organized in "Feature-Projects". These projects aim to help developers to work on special or cross-cutting topics and are expected to be "finished" at some point. The open VC will cover them similar to the long-term projects if required. We hope these changes improve the overview over the work ongoing in all the many areas for users and developers, facilitate detailed discussions between relevant and interested people and make the work on the simulator more transparent. Best, Dennis

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Open NEST Developer Video Conference Monday 13 April 2020 SKIPPED (Easter Monday)
by Dennis Terhorst 13 Apr '20

13 Apr '20

Dear NEST Users & Developers! I would like to wish you all a happy Easter time and I hope you are all well despite the current circumstances. Since it is Easter Monday in some parts of the world, we will skip this meeting. I am looking forward to seeing you again in our next Open NEST Developer Video Conference on April 27th. Stay safe, best, Dennis Terhorst

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Custom input for neurons
by Nicolas Martorell 06 Apr '20

06 Apr '20

Dear all, I'm new at NEST, and I've been trying to recreate a neural system from my work. This involves an IAF neuron which receives two different stimuli (they would be represented by inputs to the neuron - increases in post-synaptic potential). Since these are stimuli I control in my experiments, I need to be able to control their dynamics as the simulation progresses (for example, one of the stimuli has an exponentially larger effect as time progresses). Therefore, it's important for me to be able to control the dynamic of these inputs. However, I have not been able to find a way to do this. One idea I've had is to set the amplitude of a noise-generator to change according to a function of my choosing (going back to the previous example, it would be an exponential function). But this would require for this parameter to be changed mid-simulation, or to be assigned to a function and interpreted by NEST. Is any of this possible? Or alternatively, do you know of another way of accomplishing this? Thank you! Nicolas

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Open NEST Developer Video Conference Monday 30 March 2020 11:30 CEST (UTC+2)
by Dennis Terhorst 30 Mar '20

30 Mar '20

Dear NEST Users & Developers! I would like to invite you to our next bi-weekly Open NEST Developer Video Conference, today Monday 30 March, 11.30-12.30 CEST (UTC+2). Given the current circumstances today's meeting will be again via video conference only, so please do not meet in person! Stay safe! We discuss development status of relevant pull-requests/issues for the upcoming releases. Agenda Welcome Review of NEST User Mailing List Projects & Branches Review of open Github Pull Request Review of open Github Issues The agenda for this meeting is also available online, see https://github.com/nest/nest-simulator/wiki/2020-03-30-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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Memory issues arising in small neural networks
by sternj＠college.harvard.edu 27 Mar '20

27 Mar '20

Hello all, Hope everyone is staying safe and well in these difficult times. I am an undergrad who is just getting started with this library, so I want to apologize in advance for the basic question. I am having issues I believe are memory-related when I call GetConnections on rather small networks. Here is my script: import nest # memory testing nest.ResetKernel() n = 5 # number of neurons epop1 = nest.Create("iaf_psc_alpha",n) epop2 = nest.Create("iaf_psc_alpha",n) nest.Connect(epop1,epop2,{'rule': 'all_to_all'}) # we can now query the synapses using GetConnections conns = nest.GetConnections(epop1,target = epop2) nest.GetStatus(conns,["target","weight"]) This runs fine for n < 5, but I get the following error with n >=5: Assertion failed: (source_lid < MAX_LID), function set_source_lid, file /usr/local/miniconda/conda-bld/nest-simulator_1583214474797/work/nestkernel/target_data.h, line 264. Abort trap: 6 I have run some of the example scripts like brunel_alpha_numpy with a few thousand neurons and they work just fine. Am I making an improper call to GetConnections here? And if so, what is a better way to dynamically check connectivity? Alternatively, might there be something wrong with my Nest environment? And if so, what should I look at to troubleshoot this? Thank you so much for your help. Best wishes, Josh

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Error message when installing with cmake
by benedikt.s.vogler＠tum.de 22 Mar '20

22 Mar '20

Hello everyone! I tried installing nest using cmake version 3.14 on ubuntu. This is the command I tried from the nest-simulator directory: cmake -DCMAKE_INSTALL_PREFIX:PATH=/home/bsvogler/Dokumente/nest /home/bsvogler/Dokumente/nest-simulator/nest I get the following two error messages and cannot find any information on how to resolve this issue ========= CMake Error at CMakeLists.txt:97 (install): install TARGETS given no RUNTIME DESTINATION for executable target "nest". CMake Error at CMakeLists.txt:106 (FILTER_HEADERS): Unknown CMake command "FILTER_HEADERS". CMake Warning (dev) in CMakeLists.txt: No cmake_minimum_required command is present. A line of code such as cmake_minimum_required(VERSION 3.13) should be added at the top of the file. The version specified may be lower if you wish to support older CMake versions for this project. For more information run "cmake --help-policy CMP0000". This warning is for project developers. Use -Wno-dev to suppress it. -- Configuring incomplete, errors occurred! See also "/home/bsvogler/Dokumente/nest-simulator/nestinstall/CMakeFiles/CMakeOutput.log". ======= I tried the master branch and the nest3 branch. I need a working nest 3 simulator. I managed to compile just yesterday but in the meantime, I reinstalled the operating system. Please help me out. Kind regards, Benedikt S. Vogler

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Using music_cont_in_proxy as current source
by Mohammadreza Mohagheghi Nejad 16 Mar '20

16 Mar '20

Dear all, I would like to receive a continuous stream of data via ‘music_cont_in_proxy’ and use it as input current to a neuron. I used ‘iaf_cond_alpha_mc’ as model neuron because I could specify the input that should target the neuron via the receptor_type that accepts current {‘receptor_type’: 7} (’soma_curr’: 7) and connected the ‘music_cont_in_proxy’ via this receptor to the neuron. Currently, for testing purposes, I used ‘constsource’ music binary continuous data stream, which is also used in NEST guides (https://bit.ly/2xBNfpO). As I imagined, it didn’t work maybe because the output type of the music port doesn’t match the input type of the receptor type (’the following error’). Does anyone know how I can overcome this problem (that I can use ‘music_cont_in_proxy’ as current source)? Thank you very much in advance. ########ERROR######## Traceback (most recent call last): File "./conttest.py", line 39, in <module> nest.Connect(mcip, mc, 'one_to_one', {'receptor_type': 7}) File "/local/work/Projects/closed-loop-learning/NEST/lib/python3.7/site-packages/nest/ll_api.py", line 246, in stack_checker_func return f(*args, **kwargs) File "/local/work/Projects/closed-loop-learning/NEST/lib/python3.7/site-packages/nest/lib/hl_api_connections.py", line 362, in Connect sr('Connect') File "/local/work/Projects/closed-loop-learning/NEST/lib/python3.7/site-packages/nest/ll_api.py", line 132, in catching_sli_run raise exceptionCls(commandname, message) nest.ll_api.UnexpectedEvent: ('UnexpectedEvent in Connect_g_g_D_D: Node cannot handle received event.', 'UnexpectedEvent', <SLILiteral: Connect_g_g_D_D>, ': Node cannot handle received event.’) ########ERROR######## Best wishes, Mohammad -- Mohammadreza Mohagheghi Nejad Postdoctoral researcher in computational neuroscience, Institute of Neural Computation, Ruhr University Bochum, Germany https://www.ini.rub.de/the_institute/people/mohammadreza-mohagheghi_nejad/

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MUSIC - music_cont_in/out_proxy - Guide
by Mohammadreza Mohagheghi Nejad 16 Mar '20

16 Mar '20

Dear all, I am trying to use music ports for my simulations, which requires continuous transmission of data to NEST. I would like to test them in a toy example before integrating them in my project to make sure I am using them as I should. So, under section "Receiving continuous data" in "Guides\Using NEST with MUSIC" ( https://nest-simulator.readthedocs.io/en/stable/guides/using_nest_with_musi…), I found a guide for this functionality of NEST, however, the binary "constsource" is not available. Does anybody have any idea where I can find it? Thank you very much in advance for your help, Best wishes, Mohammad -- Mohammadreza Mohagheghi Nejad Postdoctoral researcher in computational neuroscience, Institute of Neural Computation, Ruhr University Bochum, Germany https://www.ini.rub.de/the_institute/people/mohammadreza-mohagheghi_nejad/

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Open NEST Developer Video Conference Monday 16 March 2020 11:30 CET (UTC+1)
by Dennis Terhorst 16 Mar '20

16 Mar '20

Dear NEST Users & Developers! I would like to invite you to our next bi-weekly Open NEST Developer Video Conference, today Monday 16 March, 11.30-12.30 CET (UTC+1). Given the current circumstances today's meeting will be *via VIDEO CONFERENCE**ONLY*, so please do not meet in person! We will focus on the organization of our now even more decentralized work and discuss development status of relevant pull-requests/issues for the upcoming releases. Agenda Welcome Review of NEST User Mailing List Review of open Github Pull Request Review of open Github Issues The agenda for this meeting is also available online, see https://github.com/nest/nest-simulator/wiki/2020-03-16-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

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Please merge master if you have open pull requests / Issue #1449
by Hans Ekkehard Plesser 12 Mar '20

12 Mar '20

Dear NEST Developers! If you currently have an open pull request against the NEST master branch on Github, please merge the most recent updates from master into your branch. A bug described in #1449 and fixed by #1458 lead to non-deterministic test suite failures. Once you have merged master into your branch, please push again to Github to re-run the tests on Travis. Best, Hans Ekkehard -- Prof. Dr. Hans Ekkehard Plesser Head, Data Science Section 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 Home http://arken.nmbu.no/~plesser

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A question about NESTML: parameters inherited from Archiving Node aren't exposed to Get/SetStatus
by Alexey Serenko 06 Mar '20

06 Mar '20

Dear community, Sorry if this is off-topic for this list, but I am facing a problem with NESTML. After compiling any of the example neuron models present in the repository, the model seems not to have parameters inherited from ArchivingNode (such as, for instance, an STDP parameter tau_minus) available for GetStatus() or SetStatus(). Oddly enough, the model probably does possess these parameters, because can be connected to/from TDP synapses, but just does not expose them to Get/SetStatus. Could you please advise what I should do to examine the problem? I am using NEST version 2.20 and NESTML version 3.0.post0.dev5 (pip-installed). Faithfully yours, Alex Serenko, graduate student at Kurchatov Institute, Moscow, Russia

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nest3: How to create composite of SynapseCollections
by benedikt.s.vogler＠tum.de 03 Mar '20

03 Mar '20

Hello everyone! I am transitioning my Code from nest 2 to nest 3. In nest 2 I used a list of connections and could use this list with nest.Get/SetStatus(). With nest 3 I now have a list of SynapseCollections instances, where each synapse collection contains only one connection. For node collections, there seems to be an operator to create a composite (https://nest-simulator.readthedocs.io/en/latest/guides/from_nest2_to_nest3.…). For SynapseCollections, however, I was unable to use the plus operator and could not find similar documentation as in the transition guide. My current workaround is to loop over each instance the list and call Set() on each instance/synapse. What is the recommended way to create a SynapseCollections from many? Is there somewhere more documentation covering nest 3 than the two pages covering the changes form nest 2 to 3? Kind regards, Benedikt S. Vogler

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Open NEST Developer Video Conference Monday 2 March 2020 11:30 CET (UTC+1)
by Dennis Terhorst 02 Mar '20

02 Mar '20

Dear NEST Users & Developers! I would like to invite you to our next bi-weekly Open NEST Developer Video Conference, today Monday 2 March, 11.30-12.30 CET (UTC+1). In today's meeting we will focus on the development status of some critical pull-requests/issues. Agenda Welcome Review of NEST User Mailing List Critical issues Issue #1394, PR #1442 Issue #1409, PR #1409 Issue #1449 Random numbers in NEST3 see Issue #1440 Review of open Github Pull Request Review of open Github Issues If you feel uncomfortable to join meetings in larger groups, consider to dial in via video from your desk (details how to log in are given below, as usual). The agenda for this meeting is also available online, see https://github.com/nest/nest-simulator/wiki/2020-03-02-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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Install nest-simulator-2.20.0 failed in Ubuntu 14.04
by 1033471810＠qq.com 01 Mar '20

01 Mar '20

Hello everyone, I followed the instructions to install nest-simulator-2.20.0 in my Ubuntu. When I do the things follow: ------------------------------------------------------------------------------- cmake -DCMAKE_INSTALL_PREFIX:PATH=/usr/bin/nest /home/visapy_and_dependencies/nest-simulator-2.20.0 make make install -------------------------------------------------------------------------------- Unfortunately, during "make" it reports some Error, see following: [ 49%] Building CXX object nestkernel/CMakeFiles/nestkernel.dir/connection_manage.cpp.o /home/visapy_and_dependencies/nest-simulator-2.20.0/nestkernel/connection_managercpp:419:1: error: prototype for ‘void nest::ConnectionManager::connect(nest::inde, nest::Node*, nest::thread, nest::synindex, const DictionaryDatum&, double, doube)’ does not match any in class ‘nest::ConnectionManager’ nest::ConnectionManager::connect( const index sgid, ^~~~ In file included from /home/visapy_and_dependencies/nest-simulator-2.20.0/nestkerel/connection_manager.cpp:23:0: /home/visapy_and_dependencies/nest-simulator-2.20.0/nestkernel/connection_managerh:135:8: error: candidates are: bool nest::ConnectionManager::connect(nest::inde nest::index, const DictionaryDatum&, nest::synindex) bool connect( const index sgid, const index target, const DictionaryDatum& parms, const synindex syn_id ); ^~~~~~~ /home/visapy_and_dependencies/nest-simulator-2.20.0/nestkernel/connection_managerh:117:8: error: void nest::ConnectionManager::connect(nest::index nest::Node*, nest::thread, nest::synindex, const DictionaryDatum&, double_t, doule_t) void connect( const index sgid, ^~~~~~~ /home/visapy_and_dependencies/nest-simulator-2.20.0/nestkernel/connection_managercpp:352:1: error: void nest::ConnectionManager::connect(const nes::GIDCollection&, const nest::GIDCollection&, const DictionaryDatum&, const DictinaryDatum&) nest::ConnectionManager::connect( const GIDCollection& sources, ^~~~ make[2]: *** [nestkernel/CMakeFiles/nestkernel.dir/connection_manager.cpp.o] Erro 1 make[1]: *** [nestkernel/CMakeFiles/nestkernel.dir/all] Error 2 make: *** [all] Error 2 I have no idea about this, I'd appreciate it if you could help me. and my cmake version 3.10.1, gcc version 7.4.0

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warning: 'GetConnections' are now invalid
by Lea Steffen 28 Feb '20

28 Feb '20

Hi everybody, I switched from Nest 2.16 to 2.20 and now I get this warning message: ConnectionManager [Warning]: New connections created, connection descriptors previously obtained using 'GetConnections' are now invalid This happens at several parts in my code while building synapses with 'sim.Projection(...)'. I use a 'FromListConnector' and 'STDPMechanism' as synapse_type. I neversaw this warning in the previous Nest version, is it something to be concerned about? I am not quite sure what it is trying to tell me. Thanks in advance, Lea ......................................................... M. Sc. Lea Steffen Wissenschaftlicher Mitarbeiter | Research Scientist Intelligent Systems and Production Engineering (ISPE) Interactive Diagnosis and Service Systems (IDS) FZI Forschungszentrum Informatik Haid-und-Neu-Str. 10–14 76131 Karlsruhe, Germany Tel.: +49 721 9654-218 steffen(a)fzi.de www.fzi.de/mitarbeiter/steffen ......................................................... FZI Forschungszentrum Informatik am Karlsruher Institut für Technologie Stiftung des bürgerlichen Rechts Stiftung Az: 14-0563.1 Regierungspräsidium Karlsruhe Vorstand: Prof. Dr. Andreas Oberweis, Jan Wiesenberger, Prof. Dr.-Ing. J. Marius Zöllner Vorsitzender des Kuratoriums: Ministerialdirigent Günther Leßnerkraus .........................................................

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How to stimulate neurons in a network with different amplitudes
by Daphne Cornelisse 22 Feb '20

22 Feb '20

Dear nest community, I have a network of 'iaf_cond_alpha' neurons and want to use the 'dc_generator' to apply two different current amplitudes to the network. (see code below) - A subset of the neurons should receive a sub-threshold amplitude so that they won't spike. - A subset of the neurons should receive a suprathreshold amplitude, making them spike. I created a random number of indices of neurons that should receive a suprathreshold current, the rest of the neurons should receive the subthreshold current. However, there doesn't seem any way to set the current amplitude to a subset of neurons. I have looked at all the examples using the dc_generator but couldn't find anything about it. How can this be done? Is it possible? If it's not possible could you point me to the source code so I could potentially write a something for it? Thank you. Kind regards, Daphne *=== code ===* np.random.seed(0) # for reproducibility # amplitudes Asub = 300.6 Asupra = 367.4 # list of all neurons neuron_idx_lst = np.arange(0,N_total) # create random array, these are the neurons that should be stimulated with supra Amplitude supra_indices = np.random.randint(1, N_total, size=int(N_total/neuron_groups-1)) # the rest should receive sub threshold current sub_indices = np.setdiff1d(neuron_idx_lst,supra_indices) # here is where it goes wrong nest.SetStatus(dc_gen[supra_indices], params={'amplitude':Asupra, 'start':stim_start, 'stop':stim_end}) nest.SetStatus(dc_gen[sub_indices], params={'amplitude':Asub, 'start':stim_start, 'stop':stim_end}) >>> TypeError: tuple indices must be integers or slices, not tuple

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Re: Multi-compartmental models
by Benedikt Rank 20 Feb '20

20 Feb '20

Dear Charl, thank you for the specific pointers. This sounds very promising! Best, Benedikt

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Re: Multi-compartmental models
by Benedikt Rank 20 Feb '20

20 Feb '20

Dear Charl, thank you for the specific pointers. This sounds very promising! Best, Benedikt ⁣

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NEST3 is now the Master Branch
by Hans Ekkehard Plesser 20 Feb '20

20 Feb '20

Dear NEST Developers and Users! After more than two years of intense work, NEST 3 is sufficiently close to completion that we merged the nest-3 branch into the NEST master branch in Github yesterday, closing a large number of issues in the process. What does this mean for you? If you are a NEST User, you can continue to use an existing NEST release for now, ideally NEST 2.20.0, the most recent release. If you are a NEST User and feel just a little adventurous, or are a developer, we encourage you to get the newest version of NEST from Github and adapt you model scripts to NEST3. You will find informations about what changed here: https://nest-simulator.readthedocs.io/en/nest-3/guides/from_nest2_to_nest3.… https://nest-simulator.readthedocs.io/en/nest-3/ref_material/nest2_vs_3.html We very much look forward to hear about your experiences with NEST 3 (the good and the not so good ones), so that we can fix any remaining problems before releasing NEST 3.0. Please file bug reports as Github issues. Best, Hans Ekkehard ps: For our colleagues with the HBP and Partnering Projects: We have a session on NEST 3 at the HBP Summit, Wednesday 15.30 in MC3.4. We also have a poster. -- Prof. Dr. Hans Ekkehard Plesser Head, Data Science Section 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 Home http://arken.nmbu.no/~plesser

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Multi-compartmental models
by benediktr＠hotmail.de 19 Feb '20

19 Feb '20

Dear nest developer, Is there a pre-implemented nest model allowing multiplicative aggregation of compartments/dendritic branches. I am looking for a model that will allow multiplicative aggregation of two dendritic branches at the soma. I very much appreciate any support provided. Best regards, Benedikt

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nest::BadProperty error that behaves like a OOM error
by angpap＠kth.se 17 Feb '20

17 Feb '20

Hello, I am fairly new to NEST and I have been struggling with the following issue. Github repo: https://github.com/angpapadi/wm-net My simulation code consists of 3 python files: - sim.py, the main simulation script, where the model is built and the simulation program is specified - helpers.py a collection of helper functions - parameters.py a script where all parameters are specified. In order to be able to run the code successfully, I have to set certain parameters to unrealistic values. If I try to move any of these parameters towards a more realistic regime, NEST crashes (see end of post for full error message). Most relevant is the fact that setting these parameters to more reasonable values, increases by a lot the amount of spikes that NEST has to keep track of. Examples of such parameters that currently have wrong values: > the DOWNSCALE_FACTOR, that essentially controls the neural network's size. Right now my network size is downscaled 95% of what I would want it to be. There are 2 hypercolumns with 4 minicolumns each. Each minicolumn consists of 4 neurons. > E_rev is a list of the reversal potential for each synaptic port. My neuron model has 3 synaptic ports for AMPA, NMDA and GABA, in that order. The Erev for GABA is correctly set but for AMPA and NMDA I cannot get it to work for values bigger than -25, when the correct reversal potential for both is 0. I cannot find the issue with my code, if there is any. When the simulation is very limited (the aforementioned parameters are set to unrealistic values), the code runs flawlessly and produces the expected plots and spike rasters. Also, if I allocate more resources by running on multiple mpi processes, I can be slightly closer to the correct parameter ranges before the nest::badproperty error occurs. To reproduce the error: 1. You can optionally first run the code as is to verify that it works (by running the sim.py script) 2. Then try setting one of the parameters mentioned above to a more plausible value. You can do so by going to the parameters.py file and either reducing the DOWNSCALE_FACTOR parameter (line 7) or increasing the first two entries of the E_rev list (line 203) that correspond to the AMPA and NMDA reversal potentials, or doing both if you 're feeling adventurous! The error is the following: terminate called after throwing an instance of 'nest::BadProperty' what(): BadProperty [59eb791543aa:00113] *** Process received signal *** [59eb791543aa:00113] Signal: Aborted (6) [59eb791543aa:00113] Signal code: (-6) [59eb791543aa:00113] [ 0] /lib/x86_64-linux-gnu/libc.so.6(+0x3ef20)[0x7f2c117b7f20] [59eb791543aa:00113] [ 1] /lib/x86_64-linux-gnu/libc.so.6(gsignal+0xc7)[0x7f2c117b7e97] [59eb791543aa:00113] [ 2] /lib/x86_64-linux-gnu/libc.so.6(abort+0x141)[0x7f2c117b9801] [59eb791543aa:00113] [ 3] /usr/lib/x86_64-linux-gnu/libstdc++.so.6(+0x8c957)[0x7f2c0a55a957] [59eb791543aa:00113] [ 4] /usr/lib/x86_64-linux-gnu/libstdc++.so.6(+0x92ab6)[0x7f2c0a560ab6] [59eb791543aa:00113] [ 5] /usr/lib/x86_64-linux-gnu/libstdc++.so.6(+0x91b19)[0x7f2c0a55fb19] [59eb791543aa:00113] [ 6] /usr/lib/x86_64-linux-gnu/libstdc++.so.6(__gxx_personality_v0+0x2a8)[0x7f2c0a560488] [59eb791543aa:00113] [ 7] /lib/x86_64-linux-gnu/libgcc_s.so.1(+0x10613)[0x7f2c0d6f1613] [59eb791543aa:00113] [ 8] /lib/x86_64-linux-gnu/libgcc_s.so.1(_Unwind_Resume+0x125)[0x7f2c0d6f1e95] [59eb791543aa:00113] [ 9] /opt/nest/lib/python3.6/site-packages/nest/../../../libnestkernel.so(_ZN4nest20EventDeliveryManager18gather_spike_data_INS_9SpikeDataEEEviRSt6vectorIT_SaIS4_EES7_+0x10ed)[0x7f2c0af0684d] [59eb791543aa:00113] [10] /opt/nest/lib/python3.6/site-packages/nest/../../../libnestkernel.so(+0xf4894)[0x7f2c0aee4894] [59eb791543aa:00113] [11] /usr/lib/x86_64-linux-gnu/libgomp.so.1(GOMP_parallel+0x3f)[0x7f2c08d79ecf] [59eb791543aa:00113] [12] /opt/nest/lib/python3.6/site-packages/nest/../../../libnestkernel.so(_ZN4nest17SimulationManager7update_Ev+0x151)[0x7f2c0aee0f61] [59eb791543aa:00113] [13] /opt/nest/lib/python3.6/site-packages/nest/../../../libnestkernel.so(_ZN4nest17SimulationManager12call_update_Ev+0x5a5)[0x7f2c0aee1915] [59eb791543aa:00113] [14] /opt/nest/lib/python3.6/site-packages/nest/../../../libnestkernel.so(_ZN4nest17SimulationManager3runERKNS_4TimeE+0x1d3)[0x7f2c0aee6713] [59eb791543aa:00113] [15] /opt/nest/lib/python3.6/site-packages/nest/../../../libnestkernel.so(_ZN4nest17SimulationManager8simulateERKNS_4TimeE+0x1c)[0x7f2c0aee699c] [59eb791543aa:00113] [16] /opt/nest/lib/python3.6/site-packages/nest/../../../libnestkernel.so(_ZN4nest8simulateERKd+0xc2)[0x7f2c0aecb972] [59eb791543aa:00113] [17] /opt/nest/lib/python3.6/site-packages/nest/../../../libnestkernel.so(_ZNK4nest10NestModule16SimulateFunction7executeEP14SLIInterpreter+0x43)[0x7f2c0ae97a53] [59eb791543aa:00113] [18] /opt/nest/lib/python3.6/site-packages/nest/../../../libsli.so(_ZN13FunctionDatum7executeEP14SLIInterpreter+0x43)[0x7f2c0a8e9063] [59eb791543aa:00113] [19] /opt/nest/lib/python3.6/site-packages/nest/../../../libsli.so(_ZN14SLIInterpreter8execute_Em+0x222)[0x7f2c0a8e6d42] [59eb791543aa:00113] [20] /opt/nest/lib/python3.6/site-packages/nest/../../../libsli.so(_ZN14SLIInterpreter7executeERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEE+0x15e)[0x7f2c0a8e72be] [59eb791543aa:00113] [21] /opt/nest/lib/python3.6/site-packages/nest/pynestkernel.so(+0x29ac8)[0x7f2c0c5caac8] [59eb791543aa:00113] [22] python[0x50a94c] [59eb791543aa:00113] [23] python(_PyEval_EvalFrameDefault+0x449)[0x50c5b9] [59eb791543aa:00113] [24] python[0x509d48] [59eb791543aa:00113] [25] python[0x50aa7d] [59eb791543aa:00113] [26] python(_PyEval_EvalFrameDefault+0x449)[0x50c5b9] [59eb791543aa:00113] [27] python[0x508245] [59eb791543aa:00113] [28] python[0x589471] [59eb791543aa:00113] [29] python(PyObject_Call+0x3e)[0x5a067e] [59eb791543aa:00113] *** End of error message *** Let me know if you need any additional information and I thank you for your time Angeliki

4 6

Open NEST Developer Video Conference Monday 17 February 2020 11:30 CET (UTC+1)
by Dennis Terhorst 17 Feb '20

17 Feb '20

Dear NEST Users & Developers! I would like to invite you to our next bi-weekly Open NEST Developer Video Conference, today Monday 17 February, 11.30-12.30 CET (UTC+1). For details how to log in see below. As usual the agenda for this meeting is also available online, see https://github.com/nest/nest-simulator/wiki/2020-02-17-Open-NEST-Developer-… Agenda * Welcome * Review of NEST User Mailing List * Review of open Github Pull Request * Review of open Github Issues 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

Neuron Model for a Generalized LIF Neuron (No alpha or exponential shaped psc)
by shanka19＠purdue.edu 14 Feb '20

14 Feb '20

Hello NEST Users, I wanted to create a neural network with generalized LIF Neurons. I do not want any exponential or alpha shaped PSCs. Since I cannot draw to describe its shape, I am posting a link from google images to help understand what I mean by a generalized LIF. https://www.google.com/url?sa=i&url=https%3A%2F%2Fwww.researchgate.net%2Ffi… Thanks in advance!

4 5

Realtime access to spikes in simulation
by Benjamin Staude 04 Feb '20

04 Feb '20

Hi NEST-Team, To use the NEST-Simluator in an interactive installation, I would need to 1) have access to the spike in the network in realtime, and 2) send signals (spikes) to neurons in the simulation in realtime. For 1), I could imagine writing the spike-times to a file and then reading that file while the simulation is running. However, I currently don’t see an option for 2). Then I heard that you are actually working on module that would enable realtime I/O-access. Is that the case? And, if so, is there a timeline? Best, Benjamin -- -- -- Dr. Benjamin Staude | Paul-Lincke-Ufer 7 | 10999 Berlin | benjamin.staude(a)gmail.com

3 4

Stop Printing Simulation Details on Terminal (NEST)
by shanka19＠purdue.edu 04 Feb '20

04 Feb '20

Hi, I wanted to know how to stop printing the simulation details on my terminal window. For instance I can see the number of open mpi process, simulation time being printed every time I run a model. I do not want to see the details on my terminal screen, is there a way to do it?

2 1

Using GPU's to run NEST simulaton
by Daphne Cornelisse 04 Feb '20

04 Feb '20

Hi NEST-team, I would like to run a simulation of > 1000 neurons, and to make my computing time faster I am looking into how to use parallel computing with NEST. I have seen this <https://www.nest-simulator.org/parallel-computing/> page but I can't seem to find anything about using the cloud (e.g. google cloud, colab etc.) and the use of GPU's. I am quite new to this so it could be I missed something. - Is it possible to use a GPU for the nest simulations? - Are the some resources I could learn from? Thank you! Best, Daphne

4 4

NEST 2.20.0 released / Issue 1394 / NEST 3 to become Master Branch soon
by Hans Ekkehard Plesser 31 Jan '20

31 Jan '20

Dear NEST Users! We are very excited about the release of NEST 2.20.0 earlier today, including 454 commits in 82 pull requests by 25 developers since NEST 2.18.0. NEST 2.20.0 brings a wide range of improvements, including * generalized leaky integrate-and-fire neuron models developed by the Allen Institute (Teeter et al, 2018) * STDP synapses with nearest-neighbor spike paring schemes * improved documentation on Read The Docs<https://nest-simulator.readthedocs.io/en/latest/>. Please see below for a complete list of changes. NEST 2.20.0 is available for download from https://github.com/nest/nest-simulator/releases/tag/v2.20.0 To cite NEST 2.20.0, please refer to the Zenodo entry at https://doi.org/10.5281/zenodo.3605514 WARNING: NEST 2.20.0 is affected by issue #1394<https://github.com/nest/nest-simulator/issues/1394>, which may lead to incorrect results under certain circumstances when simulating very large networks across many MPI processes and threads. Simulations using only MPI parallelism, but no threads, work correctly according to our tests. The same holds for simulations using only thread-parallelism. The issue also affects NEST 2.18.0 and 2.16.0, but not 2.14.0. According to our analysis, in affected simulations, a very small number of connections is not created correctly. This happens under random cirucmstances, so that in one series of tests, out of ten identical simulations, five simulations produced correct results, while the remaining five simulations produced different results. For details, please follow the issue on GitHub. We are currently working hard to identify the cause of this issue and hope to be able to provide a fix soon. The next big step forward in NEST development will be the merge of the nest-3 development branch into the master branch on GitHub. NEST 3 will bring major improvements to the user interface and considerable changes under the hood. Please see https://nest-simulator.readthedocs.io/en/nest-3/guides/from_nest2_to_nest3.… https://nest-simulator.readthedocs.io/en/nest-3/ref_material/nest2_vs_3.html for more information on changes to come and modifications required to existing scripts. Best regards, Hans Ekkehard Plesser President, The NEST Initiative ------------------------------------------------ NEST 2.20.0<https://doi.org/10.5281/zenodo.3605514> is the result of 454 commits in 82 pull requests by 25 developers since NEST 2.18.0<https://doi.org/10.5281/zenodo.2605422> which was released on June 7, 2019. This release wraps up the 2.x series of NEST and contains many improvements and bug fixes. Highlights are the addition of the generalized leaky integrate-and-fire neuron models by the Allen Institute<https://portal.brain-map.org/explore/models/glif-single-neuron>, STDP synapses with nearest-neighbor spike pairing schemes and improved documentation, available on Read The Docs<https://nest-simulator.readthedocs.io/en/latest/>. Following is a list of all merged pull requests: Enhancements Models * Add STDP synapses with nearest-neighbor spike pairing schemes<https://github.com/nest/nest-simulator/pull/865> * Add generalized leaky integrate-and-fire (GLIF) neuron models by Allen Institute<https://github.com/nest/nest-simulator/pull/1126> * Add iaf_psc_alpha_ps neuron model<https://github.com/nest/nest-simulator/pull/1169> Installation * Add conda-forge installation documentation for Linux and MacOSX<https://github.com/nest/nest-simulator/pull/1204> * Add Fugaku platform CMake file<https://github.com/nest/nest-simulator/pull/1231> * Clean the build process for the NEST Debian packages<https://github.com/nest/nest-simulator/pull/1316> * Hike minimum required CMake to 3.12 and add support for OpenMP with Apple Clang<https://github.com/nest/nest-simulator/pull/1386> * More informative compiler information in CMake summary<https://github.com/nest/nest-simulator/pull/1403> Documentation * Added initial membrane potential options to microcircuit example<https://github.com/nest/nest-simulator/pull/1206> * Add initial membrane potential options to microcircuit example<https://github.com/nest/nest-simulator/pull/1260> * Add new options for installation and improve instructions for NEST<https://github.com/nest/nest-simulator/pull/1262> * Updated/extended macOS install instructions<https://github.com/nest/nest-simulator/pull/1297> * Update DOI and release buttons in README; add Zenodo reference to NEST 2.18.0<https://github.com/nest/nest-simulator/pull/1314> * Add link on website to new PyNEST templates and update citations<https://github.com/nest/nest-simulator/pull/1351> * Provide guidelines to writing to mailing list in documentation<https://github.com/nest/nest-simulator/pull/1368> Kernel * Introduce time-driven spiking connections<https://github.com/nest/nest-simulator/pull/1160> * Add support for sending secondary events to and from devices<https://github.com/nest/nest-simulator/pull/1244> * Add warning about invalid connection descriptors when new connections are created<https://github.com/nest/nest-simulator/pull/1250> * Use an unsigned data type for thread in spike data<https://github.com/nest/nest-simulator/pull/1308> Infrastructure * Fast static check in Travis CI<https://github.com/nest/nest-simulator/pull/1267> PyNEST * New templates for pynest examples and api<https://github.com/nest/nest-simulator/pull/1139> * Add getattr/setattr to GIDCollection<https://github.com/nest/nest-simulator/pull/1249> * Allow specifying arrays of values in the synapse specification when connecting with fixed_total_number<https://github.com/nest/nest-simulator/pull/1266> * Use shape as argument instead of columns/rows/depth and update topology examples to NEST3<https://github.com/nest/nest-simulator/pull/1287> Bug fixes Models * Fix uninitialized variable in iaf_psc_exp<https://github.com/nest/nest-simulator/pull/1225> * Fix handling of rate change in poisson_generator_ps<https://github.com/nest/nest-simulator/pull/1280> Documentation * Remove spurious brackets from code example in tutorial<https://github.com/nest/nest-simulator/pull/1270> * Fix MUSIC example<https://github.com/nest/nest-simulator/pull/1312> Kernel * Fix multiple definition of rho build complain observed on AArch64 with FCC<https://github.com/nest/nest-simulator/pull/1233> * Fix GetConnections to correctly get connections where the target is a global receiving device<https://github.com/nest/nest-simulator/pull/1251> * Fix logical error in elseif-statements in connect functions<https://github.com/nest/nest-simulator/pull/1254> * Check variables of GSL binomial random generator where they are set<https://github.com/nest/nest-simulator/pull/1299> * Ensure number of connections for fixed total number is properly set<https://github.com/nest/nest-simulator/pull/1367> * Fix MyModule by incorporating modelsmodule refactoring from #1069<https://github.com/nest/nest-simulator/pull/1383> * Avoid segfault when using a weight recorder with a probabilistic synapse<https://github.com/nest/nest-simulator/pull/1402> Infrastructure * Fix cppcheck in Travis CI testsuite<https://github.com/nest/nest-simulator/pull/1306> Maintenance Models * Fix namespaces in Hodgkin-Huxley neuron models<https://github.com/nest/nest-simulator/pull/1256> * Make multimeter and voltmeter class names lower case<https://github.com/nest/nest-simulator/pull/1345> Installation * Fix nest_vars in case of undefined PYTHONPATH<https://github.com/nest/nest-simulator/pull/1218> * Cleanup for the K computer specific CMake file for v2.18<https://github.com/nest/nest-simulator/pull/1228> * Fix up dependencies in Ubuntu install instructions<https://github.com/nest/nest-simulator/pull/1230> * Files needed to build Debian packages (.deb)<https://github.com/nest/nest-simulator/pull/1255> * Fix extraction of version number if sources are inside another Git repository<https://github.com/nest/nest-simulator/pull/1362> * Let uninstall of NEST Debian package also delete script in profile.d<https://github.com/nest/nest-simulator/pull/1363> Interpreter * Remove handling of external POSIX signals sent to NEST<https://github.com/nest/nest-simulator/pull/1385> Documentation * Convert topology user manual to ReStructuredText<https://github.com/nest/nest-simulator/pull/1214> * Update links to model directory in docs<https://github.com/nest/nest-simulator/pull/1227> * Documentation update pertaining to maximum line length<https://github.com/nest/nest-simulator/pull/1234> * Fix PyNEST installation instructions<https://github.com/nest/nest-simulator/pull/1240> * Update download page for 2.18 and conda-forge<https://github.com/nest/nest-simulator/pull/1247> * Correct typo in random number documentation<https://github.com/nest/nest-simulator/pull/1268> * Fix PyNEST API generation for documentation using mock<https://github.com/nest/nest-simulator/pull/1274> * Add updated NEST examples to Read The Docs <https://github.com/nest/nest-simulator/pull/1277> * Replace iaf_neuron by iaf_psc_alpha in MUSIC tutorial<https://github.com/nest/nest-simulator/pull/1330> * Autogenerate PyNEST examples from source with sphinx_gallery<https://github.com/nest/nest-simulator/pull/1336> * Update syntax formatting for terms in documentation<https://github.com/nest/nest-simulator/pull/1343> * Fix broken CSS style<https://github.com/nest/nest-simulator/pull/1344> * Update mailing list email address<https://github.com/nest/nest-simulator/pull/1346> * Small typographical updates to user documentation<https://github.com/nest/nest-simulator/pull/1397> Kernel * Refactor registration of models in modelsmodule<https://github.com/nest/nest-simulator/pull/1069> * Increase maximum line length in source code formatting style from 80 to 120<https://github.com/nest/nest-simulator/pull/1177> * Unify coeffarray_as_d and coeffarray_as_uint via union<https://github.com/nest/nest-simulator/pull/1243> * Add missing include of sys/time.h<https://github.com/nest/nest-simulator/pull/1273> * Fix threading issue when connecting<https://github.com/nest/nest-simulator/pull/1276> * Remove spurious thread_local_connectors update<https://github.com/nest/nest-simulator/pull/1333> * Fix rounding issue when setting small resolution<https://github.com/nest/nest-simulator/pull/1356> * Improve information given by error messages typically triggered by Connect<https://github.com/nest/nest-simulator/pull/1399> Infrastructure * Add tests for libnestutil/streamers.h<https://github.com/nest/nest-simulator/pull/1219> * Make version information consistent<https://github.com/nest/nest-simulator/pull/1223> * Update FindLibNeurosim to take Python version into account<https://github.com/nest/nest-simulator/pull/1235> * Remove the remaining markdown config in docs<https://github.com/nest/nest-simulator/pull/1263> * Skip deployment in Travis CI testsuite when not running a build<https://github.com/nest/nest-simulator/pull/1300> * Deploy build artifacts only when the build flag is set in the reply section<https://github.com/nest/nest-simulator/pull/1302> * Change the deployment branch to master<https://github.com/nest/nest-simulator/pull/1304> * Fix cppcheck usage in Travis CI testsuite<https://github.com/nest/nest-simulator/pull/1307> * Switch to GCC8 as default in continuous integration tests on Travis<https://github.com/nest/nest-simulator/pull/1310> * Fix formatting in test_stdp_nn_synapses.py<https://github.com/nest/nest-simulator/pull/1311> * Add security guidelines<https://github.com/nest/nest-simulator/pull/1329> * Moving to Python3.x on OsX<https://github.com/nest/nest-simulator/pull/1335> * Replace Python version by newest available on Travis<https://github.com/nest/nest-simulator/pull/1342> PyNEST * Fix warnings when Cythonizing pynestkernel.pyx<https://github.com/nest/nest-simulator/pull/1322> * Allow installation with Python 3.8<https://github.com/nest/nest-simulator/pull/1340> -- Prof. Dr. Hans Ekkehard Plesser Head, Data Science Section 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 Home http://arken.nmbu.no/~plesser

1 0

Issue with NEST 2.18.0/python 3.6
by Angeliki Papadimitriou 20 Jan '20

20 Jan '20

Hello, I have an issue regarding random generation in nest version 2.18 with Python3.6. I attach a small python script that replicates my issue (less than 50 lines). In short, I am trying to create two Poisson generators and connect them to the same neuron. I noticed that if I reverse the order by which these Poisson generators are created (using the nest.Create()) function, then I get a different membrane potential response over time. In the code, noise_exc is created before noise_inh. If that order is reversed, the plot is different. My hunch is that this has to do with how nest generates random numbers. So I tried to force the creation of Poisson generators by providing a seed (lines 15 and 18). However this behavior persists. Do you have any insights as to why this happens? At the end of the script (lines 32-43) I provide a trivial case of the desired behavior I am trying to replicate. Thank you for your time Angeliki -- [image: Kth Logo] Angeliki Papadimitriou Research EngineerKTH Royal Institute of Technology *School of Electrical Engineering and Computer Science (EECS)**Division of Computational Science and Technology (CST)* Computational Brain Science Unit Room 4438, Floor 4, Lindstedtsvägen 5 11428 Stockholm, Sweden angpap(a)kth.se <namn(a)kth.se>

2 2

Open NEST Developer Video Conference Monday 20 January 2020 11:30 CET (UTC+1)
by Hans Ekkehard Plesser 19 Jan '20

19 Jan '20

Dear NEST Users & Developers! I would like to invite you to this years first Open NEST Developer Video Conference, tomorrow Monday 20 January, 11.30-12.30 CET (UTC+1). As usual the agenda for this meeting is also available online, see https://github.com/nest/nest-simulator/wiki/2020-01-20-Open-NEST-Developer-… For details how to log in see below. Agenda * Welcome * Preparing NEST 2.20 release * Preparing merge of nest-3 branch to master * Review of NEST User Mailing List * Review of open Github Pull Request * Review of open Github Issues Looking forward to seeing you soon! Hans Ekkehard Plesser ------------------ 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 _______________________________________________ NEST Users mailing list -- users(a)nest-simulator.org To unsubscribe send an email to users-leave(a)nest-simulator.org

1 0

Segmentation Fault loading custom nest module
by Benedikt Feldotto 17 Jan '20

17 Jan '20

Dear all, I tried to install a custom module into Nest first using the MyModule example as described here https://nest.github.io/nest-simulator/extension_modules The installation works fine without errors, however when I try to load the model into pynest with import nest import('mymodule') I get a "Segmentation fault (core dumped)". The last traceback of debbugging with python pdb is the following: -> engine.run('{%s} runprotected' % decode(cmd)) (Pdb) s --Call-- > /home/user/.local/lib/python2.7/site-packages/nest/__init__.py(107)decode() -> def decode(s): (Pdb) s > /home/user/.local/lib/python2.7/site-packages/nest/__init__.py(108)decode() -> return s.decode('utf-8') (Pdb) s --Call-- > /usr/lib/python2.7/encodings/utf_8.py(15)decode() -> def decode(input, errors='strict'): (Pdb) s > /usr/lib/python2.7/encodings/utf_8.py(16)decode() -> return codecs.utf_8_decode(input, errors, True) (Pdb) s --Return-- > /usr/lib/python2.7/encodings/utf_8.py(16)decode()->(u'(cereb... Install', 26) -> return codecs.utf_8_decode(input, errors, True) (Pdb) s --Return-- > /home/user/.local/lib/python2.7/site-packages/nest/__init__.py(108)decode()->u'(mymod... Install' -> return s.decode('utf-8') (Pdb) s Segmentation fault (core dumped) I already added the model path to my LD_LIBRARY_PATH variable so that the module can be found, but now it cannot be loaded. It looks like a decoding issue, but I don't know what went wrong during the installation. Do you have any idea what could be the issue? I am using python 2.7 and NEST 2.3.1 Thanks! Benedikt Feldotto -- 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 3

NEST Creating a simple network
by shanka19＠purdue.edu 16 Jan '20

16 Jan '20

Hello everyone, Happy New Year! I want to create a simple neural network consisting of a single neuron connected by multiple inputs (spike generators). I am aware that I can create single spike generators and then connect them but it becomes infeasible as the size of input grows. Is there a way to create a network of maybe 100 spike generators connected to a single LIF Neuron without explicitly creating 100 of them? Once the connections are made is there a way that the network is updated when the weights are updated. I want the network to get updated as I update the weights. Now, I update the weights and reset the network to create it again with new weights. Any help would be appreciated. Thanks in advance!

4 3

nest user in nest-docker entrypoint file
by bignamini＠cscs.ch 14 Jan '20

14 Jan '20

Hi all, I have a question about nest user creation/usage in nest docker entrypoint file: I am working with Sarus and Singularity and due to some permission limits I can't create a new user inside a container. I have tried to modify the entrypoint.sh file as follows https://github.com/ChristopherBignamini/nest-docker/blob/no_nest_user_creat… in order to skip the creation of the nest user. I am not a nest expert but everything seems to work, at least if I try to run a couple of examples like one_neuron.py and twoneurons.py. My question is: what is the reason behind the creation and usage of the nest user? Thank you in advance. Cheers Christopher

2 1

Error when compiling MyModule, the example extension module
by eben.cowley42＠gmail.com 10 Jan '20

10 Jan '20

Hi, I'm on Ubuntu 18.10 and I've successfully installed nest to `/usr`. I'm interested in writing my own synapse models and found these instructions for getting started: https://nest.github.io/nest-simulator/extension_modules The configuration step, `cmake -Dwith-nest=/usr/bin/nest-config ../MyModule` works fine. However, when I ran `make` I received the following compiler error: ``` ~/Projects/NEST/MyModule/mymodule.cpp: In member function ‘virtual void mynest::MyModule::init(SLIInterpreter*)’: ~/Projects/NEST/MyModule/mymodule.cpp:128:24: error: no matching function for call to ‘nest::ModelManager::register_connection_model<mynest::DropOddSpikeConnection<nest::TargetIdentifierPtrRport> >(const char [17])’ "drop_odd_synapse" ); ^ In file included from /usr/include/nest/kernel_manager.h:31, from /usr/include/nest/connector_base_impl.h:26, from /usr/include/nest/connection.h:29, from /home/ebanflo/Projects/NEST/MyModule/drop_odd_spike_connection.h:27, from /home/ebanflo/Projects/NEST/MyModule/mymodule.cpp:29: /usr/include/nest/model_manager.h:197:8: note: candidate: ‘template<template<class targetidentifierT> class ConnectionT> void nest::ModelManager::register_connection_model(const string&, nest::RegisterConnectionModelFlags)’ void register_connection_model( const std::string& name, ^~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/nest/model_manager.h:197:8: note: template argument deduction/substitution failed: make[2]: *** [CMakeFiles/mymodule_module.dir/build.make:63: CMakeFiles/mymodule_module.dir/mymodule.cpp.o] Error 1 make[1]: *** [CMakeFiles/Makefile2:73: CMakeFiles/mymodule_module.dir/all] Error 2 make: *** [Makefile:152: all] Error 2 ``` I am not sure how to deal with this, and any help would be appreciated. Thank you!

1 0

Issue review VC Friday 10 Jan 10-13
by Hans Ekkehard Plesser 09 Jan '20

09 Jan '20

Dear all! We are going to have a NEST issue review VC tomorrow morning (Friday 10 Jan 10-13 CET) in the usual VC room for developer VCs (https://github.com/nest/nest-simulator/wiki/Connection-Details). The main aim is to review open issues in preparation of the NEST 3 merge and (eventually) release. Excuse the short notice, still booting up for 2020. Best, Hans Ekkehard -- Prof. Dr. Hans Ekkehard Plesser Head, Data Science Section 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 Home http://arken.nmbu.no/~plesser

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Open NEST Developer Video Conference Monday 6 January 2020 11:30 CET (UTC+1)
by Dennis Terhorst 05 Jan '20

05 Jan '20

Dear NEST Users & Developers! Happy new year 2020! I would like to invite you to this years first Open NEST Developer Video Conference, tomorrow Monday 6 January, 11.30-12.30 CET (UTC+1). As usual the agenda for this meeting is also available online, see https://github.com/nest/nest-simulator/wiki/2020-01-06-Open-NEST-Developer-… For details how to log in see below. Agenda * Welcome * Review of NEST User Mailing List * Review of open Github Pull Request * Review of open Github Issues 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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NO open NEST Developer Video Conference on 23 December 2019
by Dennis Terhorst 23 Dec '19

23 Dec '19

Dear NEST Developers! Best of seasons greetings to everyone! Since many people will not be available today we will skip the video conference. Our next regular meeting will be on January 6th. Merry Christmas to everyone! Enjoy the last days of 2019 and have a nice new-years! Looking forward to seeing all of you again in 2020! best, Dennis Terhorst https://github.com/nest/nest-simulator/wiki/Open-NEST-Developer-Video-Confe…

1 0

NEST Conference 2020 — Save the Date: 29/30 June 2020 at Ås, Norway
by Hans Ekkehard Plesser 17 Dec '19

17 Dec '19

Dear NEST Users, We are happy to announce that the NEST Conference 2020 will again be held on NMBU's beautiful campus in Ås, Norway on 29 / 30 June 2020 followed by a NEST Hackathon until 3 July. More information will follow in a few weeks. Save the date & see you in the summer! Hans Ekkehard -- Prof. Dr. Hans Ekkehard Plesser Head, Data Science Section 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 Home http://arken.nmbu.no/~plesser

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Hackathon on CEREBELLUM MODELLING
by Dennis Terhorst 17 Dec '19

17 Dec '19

Dear simulation enthusiasts, The group in Pavia is preparing an event around CEREBELLUM MODELLING, in which you can see NEST and other simulators put to use on larger scale. It will be a nice occasion to meet with many other users, exchange experience and learn about model construction. Egidio, Claudia, Simona and team are organising this as a hackathon: Hackathon on CEREBELLUM MODELLING 13-15 January 2020, in Pavia. If you are interested in joining, please drop Simona Tritto an email:simona.tritto@unipv.it<mailto:simona.tritto@unipv.it> You can find the program attached. best, Dennis -- 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

1 1

Reset Network with to_file
by Maryada Maryada 08 Dec '19

08 Dec '19

Hi all, I am currently using nest.ResetNetwork() with to_file option and when I reset the network, seemingly it also deletes everything recorded so far by connected probes (spike detector, for instance). Any suggestions on how to avoid the deletion of previously written data on files. -- Thanks and Regards *Maryada*

2 2

NEST 3 merge outlook
by Itaru Kitayama 06 Dec '19

06 Dec '19

Can somebody comment on this plan? I’m using the nest-3 branch heavily on FUGAKU and am wondering when it’ll be merged in the master.

2 2

Multiplicity value + presynaptic spike history
by Benedikt Feldotto 27 Nov '19

27 Nov '19

Dear all, I have two questions that arise when implementing my adapted C++ synapse model. 1) Postsynaptic spikes have a "multiplicity" variable. Am I correct that if I receive a single spike object with a multiplicity value of 3, I actually receive 3 spikes? Since I do only get one time, what are the exact spike times of the other spikes? 2) For the postsynaptic spikes I can easily access the spike history and search for spikes in a certain time range, as for example done in the STDP synapse. Is it possible to also access the overall spike history of presynaptic spikes? So far I only found that in the std_dopamine synapse as an example the last spike time is stored manually. Thank you very much ! Best Regards, Benedikt Feldotto -- 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 1

NO Open NEST Developer Video Conference Monday 25 November 2019
by Dennis Terhorst 23 Nov '19

23 Nov '19

Dear NEST Developers! On Monday there will be no Open NEST Developer Video Conference, since many of the NEST users and developers are traveling at that time to join the HBP CodeJam#10 and adjoined events. As usual, if you would have something you want to add to the agenda, please don't hesitate to contact me anyway. I will then add it in the the following meeting. Looking forward to seeing you soon! best, Dennis Terhorst https://github.com/nest/nest-simulator/wiki/Open-NEST-Developer-Video-Confe…

1 0

About the spike_detector records
by zhe.sun.vk＠riken.jp 18 Nov '19

18 Nov '19

Dear all, Recently I always have an error when I tried to keep the spike_detector information into files. ********************** Nov 18 19:22:09 RecordingDevice::calibrate() [Error]: I/O error while opening file '0-94476-15.gdf'. This may be caused by too many open files in networks with many recording devices and threads. ********************** And I also found most of the gdf files are empty. Do you have any idea to solve this issue? And do you know how to avoid to keeping empty gdf files. Best wishes Sun

2 1

Open NEST Developer Video Conference Monday 11 November 2019 11:30 CET (UTC+1)
by Dennis Terhorst 10 Nov '19

10 Nov '19

Dear NEST Developers! I would like to invite you to our next bi-weekly Open NEST Developer Video Conference tomorrow Monday 11 November, 11.30-12.30 CET (UTC+1). See below for information about how to log into the meeting. The agenda for this meeting is also available online, see https://github.com/nest/nest-simulator/wiki/2019-11-11-Open-NEST-Developer-… Agenda * Welcome * Review of NEST User Mailing List3 * Review of open Github Pull Request * Review of open Github Issues 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

Re: Issues with make under OSX
by Hans Ekkehard Plesser 08 Nov '19

08 Nov '19

Hi Benjamin, It is curious that MPI is not found on your system. Could you double check that you have installed open-mpi via Homebrew? What does which mpicxx return on your system? Best, Hans Ekkehard On 26 Oct 2019, at 17:04, Benjamin Staude <benjamin.staude(a)gmail.com<mailto:benjamin.staude@gmail.com>> wrote: Hi Hans-Ekkehard, Thanks for the support, that solved one issue. But now, I get the same for OPEN_MPI: -- Could NOT find MPI_C (missing: MPI_C_WORKS) -- Could NOT find MPI_CXX (missing: MPI_CXX_WORKS) -- Could NOT find MPI (missing: MPI_C_FOUND MPI_CXX_FOUND) (I need open_mpi because I need the MUSIC interface). This is my cmake-call: cmake \ -DCMAKE_C_COMPILER=gcc-9 \ -DCMAKE_CXX_COMPILER=g++-9 \ -Dwith-music=ON \ -Dwith-mpi=ON \ -Dwith-openmp=ON \ -DCMAKE_INSTALL_PREFIX=/Users/staude/.pyenv/versions/3.7.2/ \ /Users/staude/Projekte/RainerDunkel/SensoryNetwork/Skripte/snn/NEST/nest-simulator-2.18.0 And the output: -- The CXX compiler identification is GNU 9.2.0 -- The C compiler identification is GNU 9.2.0 -- Checking whether CXX compiler has -isysroot -- Checking whether CXX compiler has -isysroot - yes -- Checking whether CXX compiler supports OSX deployment target flag -- Checking whether CXX compiler supports OSX deployment target flag - yes -- Check for working CXX compiler: /usr/local/bin/g++-9 -- Check for working CXX compiler: /usr/local/bin/g++-9 -- works -- Detecting CXX compiler ABI info -- Detecting CXX compiler ABI info - done -- Detecting CXX compile features -- Detecting CXX compile features - done -- Checking whether C compiler has -isysroot -- Checking whether C compiler has -isysroot - yes -- Checking whether C compiler supports OSX deployment target flag -- Checking whether C compiler supports OSX deployment target flag - yes -- Check for working C compiler: /usr/local/bin/gcc-9 -- Check for working C compiler: /usr/local/bin/gcc-9 -- works -- Detecting C compiler ABI info -- Detecting C compiler ABI info - done -- Detecting C compile features -- Detecting C compile features - done -- Could NOT find Doxygen (missing: DOXYGEN_EXECUTABLE) -- Looking for include file inttypes.h -- Looking for include file inttypes.h - found -- Looking for include file mach-o/dyld.h -- Looking for include file mach-o/dyld.h - found -- Looking for include file mach/mach.h -- Looking for include file mach/mach.h - found -- Looking for include file memory.h -- Looking for include file memory.h - found -- Looking for include file stdint.h -- Looking for include file stdint.h - found -- Looking for include file sys/types.h -- Looking for include file sys/types.h - found -- Looking for C++ include istream -- Looking for C++ include istream - not found -- Looking for C++ include ostream -- Looking for C++ include ostream - not found -- Looking for C++ include sstream -- Looking for C++ include sstream - not found -- Looking for stddef.h -- Looking for stddef.h - found -- Check size of long long -- Check size of long long - done -- Check size of u_int16_t -- Check size of u_int16_t - done -- Check size of uint16_t -- Check size of uint16_t - done -- Check size of u_int64_t -- Check size of u_int64_t - done -- Check size of uint64_t -- Check size of uint64_t - done -- Looking for NAN -- Looking for NAN - found -- Looking for isnan -- Looking for isnan - found -- Looking for M_E -- Looking for M_E - found -- Looking for M_PI -- Looking for M_PI - found -- Looking for expm1 -- Looking for expm1 - found -- Host triple: x86_64-apple-darwin -- Target triple: x86_64-apple-darwin -- Found LTDL: /usr/local/lib/libltdl.dylib (found version "2.4.6") -- Found Readline: /usr/lib/libreadline.dylib (found version "4.2") -- Found PkgConfig: /usr/local/bin/pkg-config (found version "0.29.2") -- Found GSL: /usr/local/Cellar/gsl/2.6/include (found version "2.6") -- Found PythonInterp: /Users/staude/.pyenv/shims/python (found version "3.7.2") -- Found PythonLibs: /Users/staude/.pyenv/versions/3.7.2/lib/libpython3.7m.a (found suitable exact version "3.7.2") -- Found Cython: /Users/staude/.pyenv/shims/cython (found version "0.29.13") -- Found OpenMP_C: -fopenmp -- Found OpenMP_CXX: -fopenmp -- Found OpenMP: TRUE -- Could NOT find MPI_C (missing: MPI_C_WORKS) -- Could NOT find MPI_CXX (missing: MPI_CXX_WORKS) -- Could NOT find MPI (missing: MPI_C_FOUND MPI_CXX_FOUND) CMake Error at cmake/ProcessOptions.cmake:528 (message): MUSIC requires -Dwith-mpi=ON. Call Stack (most recent call first): CMakeLists.txt:167 (nest_process_with_music) And the cmake-version: cmake --version cmake version 3.15.3 On 26. Oct 2019, at 14:11, Hans Ekkehard Plesser <hans.ekkehard.plesser(a)nmbu.no<mailto:hans.ekkehard.plesser@nmbu.no>> wrote: Hi Benjamin, The CMake output shows that you are using the AppleClang compiler, which does not support OpenMP. If you want to use that compiler, you need to turn off OpenMP with -Dwith-openmp=OFF. If you want NEST with OpenMP on the Mac, I would recommend using the GCC compiler installed via Homebrew, see https://nest-simulator.readthedocs.io/en/latest/installation/mac_install.ht… for instructions. Best, Hans Ekkehard On 25 Oct 2019, at 18:12, Benjamin Staude <benjamin.staude(a)gmail.com> wrote: Hi there, I am trying to install nest under OSX Mojave and run into the following cmake-error (see below for a full trace): -- Could NOT find OpenMP_C (missing: OpenMP_C_FLAGS OpenMP_C_LIB_NAMES) -- Could NOT find OpenMP_CXX (missing: OpenMP_CXX_FLAGS OpenMP_CXX_LIB_NAMES) -- Could NOT find OpenMP (missing: OpenMP_C_FOUND OpenMP_CXX_FOUND) I already tried various tricks (http://stechschulte.net/2016/03/20/openmp-osx-cmake.html, https://stackoverflow.com/questions/48825416/missing-openmp-c-flags-openmp-…), but had no success. Does anybody have experience? Thanks in advance, Benjamin ######################################################### -- The CXX compiler identification is AppleClang 9.0.0.9000038 -- The C compiler identification is AppleClang 9.0.0.9000038 -- Check for working CXX compiler: /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/c++ -- Check for working CXX compiler: /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/c++ -- works -- Detecting CXX compiler ABI info -- Detecting CXX compiler ABI info - done -- Detecting CXX compile features -- Detecting CXX compile features - done -- Check for working C compiler: /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/cc -- Check for working C compiler: /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/cc -- works -- Detecting C compiler ABI info -- Detecting C compiler ABI info - done -- Detecting C compile features -- Detecting C compile features - done -- Could NOT find Doxygen (missing: DOXYGEN_EXECUTABLE) -- Looking for include file inttypes.h -- Looking for include file inttypes.h - found -- Looking for include file mach-o/dyld.h -- Looking for include file mach-o/dyld.h - found -- Looking for include file mach/mach.h -- Looking for include file mach/mach.h - found -- Looking for include file memory.h -- Looking for include file memory.h - found -- Looking for include file stdint.h -- Looking for include file stdint.h - found -- Looking for include file sys/types.h -- Looking for include file sys/types.h - found -- Looking for C++ include istream -- Looking for C++ include istream - found -- Looking for C++ include ostream -- Looking for C++ include ostream - found -- Looking for C++ include sstream -- Looking for C++ include sstream - found -- Looking for stddef.h -- Looking for stddef.h - found -- Check size of long long -- Check size of long long - done -- Check size of u_int16_t -- Check size of u_int16_t - done -- Check size of uint16_t -- Check size of uint16_t - done -- Check size of u_int64_t -- Check size of u_int64_t - done -- Check size of uint64_t -- Check size of uint64_t - done -- Looking for NAN -- Looking for NAN - found -- Looking for isnan -- Looking for isnan - found -- Looking for M_E -- Looking for M_E - found -- Looking for M_PI -- Looking for M_PI - found -- Looking for expm1 -- Looking for expm1 - found -- Host triple: x86_64-apple-darwin -- Target triple: x86_64-apple-darwin -- Found LTDL: /usr/local/lib/libltdl.dylib (found version "2.4.6") -- Found Readline: /usr/lib/libreadline.dylib (found version "4.2") -- Found PkgConfig: /usr/local/bin/pkg-config (found version "0.29.2") -- Found GSL: /usr/local/Cellar/gsl/2.6/include (found version "2.6") -- Found PythonInterp: /Users/staude/.pyenv/shims/python (found version "3.7.2") -- Found PythonLibs: /Users/staude/.pyenv/versions/3.7.2/lib/libpython3.7m.a (found suitable exact version "3.7.2") -- Found Cython: /Users/staude/.pyenv/shims/cython (found version "0.29.13") -- Could NOT find OpenMP_C (missing: OpenMP_C_FLAGS OpenMP_C_LIB_NAMES) -- Could NOT find OpenMP_CXX (missing: OpenMP_CXX_FLAGS OpenMP_CXX_LIB_NAMES) -- Could NOT find OpenMP (missing: OpenMP_C_FOUND OpenMP_CXX_FOUND) CMake Error at cmake/ProcessOptions.cmake:452 (message): CMake can not find OpenMP. Call Stack (most recent call first): CMakeLists.txt:164 (nest_process_with_openmp) _______________________________________________ NEST Users mailing list -- users(a)nest-simulator.org To unsubscribe send an email to users-leave(a)nest-simulator.org -- Prof. Dr. Hans Ekkehard Plesser Head, Data Science Section 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 Home http://arken.nmbu.no/~plesser -- -- -- Dr. Benjamin Staude | Paul-Lincke-Ufer 7 | 10999 Berlin | benjamin.staude(a)gmail.com<mailto:benjamin.staude@gmail.com> -- Prof. Dr. Hans Ekkehard Plesser Head, Data Science Section 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 Home http://arken.nmbu.no/~plesser

3 10

VoIP Engineers jobs
by fieldengineer77＠gmail.com 06 Nov '19

06 Nov '19

Available in the Field Engineer marketplace are experts with Voice over Internet Protocol (VoIP) skills, which is a mix of voice, video, and knowledge on one network. VoIP allows people to make telephone calls over broadband Internet connections rather than analog landlines. A VoIP engineer designs, tests, installs and maintains both local VoIP systems in business and large networks that cover entire regions. VoIP Engineers use their experience with computer science, digital audio hardware, and VoIP software to install cutting-edge technologies. They also work with information technology (IT) professionals and system administrators to explain the functionality of VoIP. Many industries employ VoIP engineers to complete telecommunications work on a full-time or contract basis. More info: https://www.fieldengineer.com/skills/voip-engineer

1 0

Educational qualifications and other certifications for Apple Certified Technical Coordinators
by kaitlyn.kristy9494＠gmail.com 06 Nov '19

06 Nov '19

A High school diploma or equivalent along with an Apple Certified Technical Coordinator certification is necessary. An A + certification from CompTIA gives candidates an edge over other aspirants. They should be conversant with various network configurations and hardware devices. Salaries for Apple Certified Technical Coordinators Payscale.com reveals that the average salary of an Apple Certified Technical Coordinator is $65,000 per year in the United States. If they freelance, they will earn $26 per hour. Read More: https://www.fieldengineer.com/skills/apple-certified-technical-coordinator

1 0

PC Technician
by ashaikfe＠gmail.com 06 Nov '19

06 Nov '19

A PC technician often referred to as a computer technician or PC repair technician is responsible for identifying, troubleshooting and resolving computer issues. They are experienced and knowledgeable professionals with hands-on experience with different tools of repair and maintaining computer hardware, software and network/Internet issues. Read More: https://www.fieldengineer.com/skills/what-is-a-pc-technician

1 0

Newbie questions
by Roman Kalivoda 04 Nov '19

04 Nov '19

Hello Nest users, I recently started to work on my bachelor thesis and the first step is to find existing simulators of neural networks and analyze them. Regarding that, I have some questions about the Nest to which I cannot find answers. Is there some graphical interface for Nest? I have found a GitHub project called nest-desktop (https://github.com/babsey/nest-desktop), but I could not find it being mentioned anywhere in the nest simulator documentation. Does anyone have some experience with this? Is it reliable? What is it capable of? If there is not any official Nest GUI, how do you typically work on new simulations? Do you just write plain python scripts for PyNest interface? The last request is directed more to the developers, but maybe someone can lead me in the right way. My thesis lead would like to see some schema of the Nest architecture or some overview of how the simulator is designed. Thank you very much, Roman Kalivoda

2 1

Re: parrot neurons PORT 1
by Charl Linssen 01 Nov '19

01 Nov '19

Dear Nikolas, Could the following example in NEST Simulator be what you're looking for? https://github.com/nest/nest-simulator/blob/f28b138f469354264f65c3b5c9d05e5… """Check STDP protocol between two parrot_neurons connected by a stdp_synapse. Exact pre- and post-synaptic spike times are set by spike_generators connected to each parrot neuron. Additional spikes sent through the stdp_synapse are explicitly ignored in the postsynaptic parrot_neuron by setting the stdp_synapse to connect to port 1. """ With kind regards, Charl On Wed, Oct 30, 2019, at 11:58, Nikolaos Chrysanthidis wrote: > Hi Charl, > I want to test the weight change of a single synapse providing stimulation at 2 parrot neurons, so for that reason, > If I excite two pre-,post- parrot neurons (parrot_A,B) using port 0, then the parrot_A will excite the parrot_B as well, so the parrot_B will end up having more spikes than expected. > I think this can be overcome by using port1 of parrot_B in order to ignore the extra excitation from parrot_A. > Please, I'd be grateful if you could provide a way to avoid extra excitation from parrot_A onto parrot_B. > > Kind regards, > Nikolas > > *From:* Charl Linssen <nest-users(a)turingbirds.com> > *Sent:* 28 October 2019 12:11 > *To:* users(a)nest-simulator.org > *Subject:* [NEST Users] Re: parrot neurons PORT 1 > > Dear Nikolaos, > > I'm a little confused as to why you wish to use port 1 for this. A synapse is not aware of incoming or outgoing ports, so if you want to test a particular synapse model, you can connect it between port 0 of a presynaptic parrot neuron, and port 0 of a postsynaptic parrot neuron. Could you otherwise please clarify your use case a bit? > > With kind regards, > Charl > > > On Thu, Oct 17, 2019, at 17:00, Nikolaos Chrysanthidis wrote: >> Hi NEST users, >> >> I have a pre- and post-synaptic spike train and I want to impose these spike trains onto a plastic synapse to see the weight development. >> >> To this end, I thought of having 2 "parrot_neuron_ps" as pre- and post-synaptic neurons connected with the plastic synapse which uses AMPA receptor. >> By doing this, NEST yields the following error: "NESTError: UnknownReceptorType in Connect_g_g_D_D: Receptor type 1 is not available in parrot_neuron_ps." which in my case Receptor type 1 is the AMPA receptor. >> >> At the nest documentation about "parrot_neuron_ps" I found out that I can have the plastic synapse onto port 1 of the postsynaptic parrot neuron >> which I hope it will solve the error with the receptor. >> >> From nest documentation -> "Only spikes arriving on connections to port 0 will be repeated. Connections onto port 1 will be accepted, but spikes incoming >> through port 1 will be ignored. This allows setting exact pre- and post-synaptic spike times for STDP protocols by connecting >> >> two parrot neurons spiking at desired times by, e.g., a stdp_synapse onto port 1 on the post-synaptic parrot neuron." >> >> My query is, how to connect the 2 neurons using port 1 of the post synaptic neuron ? >> If this approach with parrot neurons doesn't seem the right choice, what is the most commonly used approach ? >> >> Thank you very much, >> Kind regards, >> Nikolas >> >> >> >> >> _______________________________________________ >> NEST Users mailing list -- users(a)nest-simulator.org >> To unsubscribe send an email to users-leave(a)nest-simulator.org >> >

1 0

Random balanced network with conductance based synapses
by Adam Haber 31 Oct '19

31 Oct '19

Hi, I'm trying to port to NEST this "conductance-based" network from Brian: https://brian2.readthedocs.io/en/stable/examples/frompapers.Stimberg_et_al_… I'm unable to reproduce their results (qualitatively - I'm not expecting identical results since I assume RNGs, solvers and other implementation details differ in many ways). Is there any publicly available example of a random balanced network with conductance based synapses? From what I've seen, all the brunel-style example networks are current based (as in the original paper). Thanks in advance, Adam

2 1

parrot neurons PORT 1
by Nikolaos Chrysanthidis 28 Oct '19

28 Oct '19

Hi NEST users, I have a pre- and post-synaptic spike train and I want to impose these spike trains onto a plastic synapse to see the weight development. To this end, I thought of having 2 "parrot_neuron_ps" as pre- and post-synaptic neurons connected with the plastic synapse which uses AMPA receptor. By doing this, NEST yields the following error: "NESTError: UnknownReceptorType in Connect_g_g_D_D: Receptor type 1 is not available in parrot_neuron_ps." which in my case Receptor type 1 is the AMPA receptor. At the nest documentation about "parrot_neuron_ps" I found out that I can have the plastic synapse onto port 1 of the postsynaptic parrot neuron which I hope it will solve the error with the receptor. From nest documentation -> "Only spikes arriving on connections to port 0 will be repeated. Connections onto port 1 will be accepted, but spikes incoming through port 1 will be ignored. This allows setting exact pre- and post-synaptic spike times for STDP protocols by connecting two parrot neurons spiking at desired times by, e.g., a stdp_synapse onto port 1 on the post-synaptic parrot neuron." My query is, how to connect the 2 neurons using port 1 of the post synaptic neuron ? If this approach with parrot neurons doesn't seem the right choice, what is the most commonly used approach ? Thank you very much, Kind regards, Nikolas

2 1

Open NEST Developer Video Conference Monday 28 October 2019 11.30 CET (UTC+1)
by Dennis Terhorst 28 Oct '19

28 Oct '19

Dear NEST Developers! I would like to invite you to our next bi-weekly Open NEST Developer Video Conference today (please excuse the late invitation) Monday 28 October, 11.30-12.30 CET (UTC+1). See below for information about how to log into the meeting. The agenda for this meeting is also available online, see https://github.com/nest/nest-simulator/wiki/2019-10-14-Open-NEST-Developer-… Agenda 1. Welcome 2. Planning of HBP High-Level Support Event in Heidelberg <https://www.humanbrainproject.eu/en/education/participatecollaborate/infras…> next month 3. Review of NEST User Mailing List <https://www.nest-simulator.org/mailinglist/hyperkitty/list/users@nest-simul…> 4. Review of open Github Pull Request <https://github.com/nest/nest-simulator/pulls> 5. Review of open Github Issues <https://github.com/nest/nest-simulator/issues> 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

ok
by 岳训 26 Oct '19

26 Oct '19

1 0

Issues with make under OSX
by Benjamin Staude 25 Oct '19

25 Oct '19

Hi there, I am trying to install nest under OSX Mojave and run into the following cmake-error (see below for a full trace): -- Could NOT find OpenMP_C (missing: OpenMP_C_FLAGS OpenMP_C_LIB_NAMES) -- Could NOT find OpenMP_CXX (missing: OpenMP_CXX_FLAGS OpenMP_CXX_LIB_NAMES) -- Could NOT find OpenMP (missing: OpenMP_C_FOUND OpenMP_CXX_FOUND) I already tried various tricks (http://stechschulte.net/2016/03/20/openmp-osx-cmake.html, https://stackoverflow.com/questions/48825416/missing-openmp-c-flags-openmp-…), but had no success. Does anybody have experience? Thanks in advance, Benjamin ######################################################### -- The CXX compiler identification is AppleClang 9.0.0.9000038 -- The C compiler identification is AppleClang 9.0.0.9000038 -- Check for working CXX compiler: /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/c++ -- Check for working CXX compiler: /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/c++ -- works -- Detecting CXX compiler ABI info -- Detecting CXX compiler ABI info - done -- Detecting CXX compile features -- Detecting CXX compile features - done -- Check for working C compiler: /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/cc -- Check for working C compiler: /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/cc -- works -- Detecting C compiler ABI info -- Detecting C compiler ABI info - done -- Detecting C compile features -- Detecting C compile features - done -- Could NOT find Doxygen (missing: DOXYGEN_EXECUTABLE) -- Looking for include file inttypes.h -- Looking for include file inttypes.h - found -- Looking for include file mach-o/dyld.h -- Looking for include file mach-o/dyld.h - found -- Looking for include file mach/mach.h -- Looking for include file mach/mach.h - found -- Looking for include file memory.h -- Looking for include file memory.h - found -- Looking for include file stdint.h -- Looking for include file stdint.h - found -- Looking for include file sys/types.h -- Looking for include file sys/types.h - found -- Looking for C++ include istream -- Looking for C++ include istream - found -- Looking for C++ include ostream -- Looking for C++ include ostream - found -- Looking for C++ include sstream -- Looking for C++ include sstream - found -- Looking for stddef.h -- Looking for stddef.h - found -- Check size of long long -- Check size of long long - done -- Check size of u_int16_t -- Check size of u_int16_t - done -- Check size of uint16_t -- Check size of uint16_t - done -- Check size of u_int64_t -- Check size of u_int64_t - done -- Check size of uint64_t -- Check size of uint64_t - done -- Looking for NAN -- Looking for NAN - found -- Looking for isnan -- Looking for isnan - found -- Looking for M_E -- Looking for M_E - found -- Looking for M_PI -- Looking for M_PI - found -- Looking for expm1 -- Looking for expm1 - found -- Host triple: x86_64-apple-darwin -- Target triple: x86_64-apple-darwin -- Found LTDL: /usr/local/lib/libltdl.dylib (found version "2.4.6") -- Found Readline: /usr/lib/libreadline.dylib (found version "4.2") -- Found PkgConfig: /usr/local/bin/pkg-config (found version "0.29.2") -- Found GSL: /usr/local/Cellar/gsl/2.6/include (found version "2.6") -- Found PythonInterp: /Users/staude/.pyenv/shims/python (found version "3.7.2") -- Found PythonLibs: /Users/staude/.pyenv/versions/3.7.2/lib/libpython3.7m.a (found suitable exact version "3.7.2") -- Found Cython: /Users/staude/.pyenv/shims/cython (found version "0.29.13") -- Could NOT find OpenMP_C (missing: OpenMP_C_FLAGS OpenMP_C_LIB_NAMES) -- Could NOT find OpenMP_CXX (missing: OpenMP_CXX_FLAGS OpenMP_CXX_LIB_NAMES) -- Could NOT find OpenMP (missing: OpenMP_C_FOUND OpenMP_CXX_FOUND) CMake Error at cmake/ProcessOptions.cmake:452 (message): CMake can not find OpenMP. Call Stack (most recent call first): CMakeLists.txt:164 (nest_process_with_openmp)

1 0

C/C++ interface
by Xavier Otazu 24 Oct '19

24 Oct '19

Hello, I would like to make a suggestion for future development. Now there is a Python interface, but some of us have been working with C/C++ for many years (and we have a lot of data processing software developed in this language). Please, could you include a C/C++ interface for NEST? Thanks a lot in advance! Xavier

4 5

RGN
by Maryada Maryada 22 Oct '19

22 Oct '19

Hi all, I have a question regarding random number generator. I am intend to randomly choose neuron population but keep this same across multiple processes. (see attached) mpirun -np 4 python network_population.py However, seemingly I am missing something. Also, in case I try to use different population count I am getting error while connecting nodes with input or probes. (see mpi_example) -- Thanks and Regards *Maryada*

1 0

precise firing events
by Nikolaos Chrysanthidis 22 Oct '19

22 Oct '19

Dear NEST users, I would like to ask you if there is any way to have an AdEx neuron model firing at specific times (ms) in NEST. Kind regards,

2 4

HBP event in Heidelberg
by Dennis Terhorst 17 Oct '19

17 Oct '19

Dear NEST colleagues, We like to inform you all about an event of the Human Brain Project, that will take place in Heidelberg on November 25-28. It will be comprised of introductory sessions on different types of infrastructure that is being built for the neuroscience community. Among these will be several NEST related sessions which may be of interest to you (see attached file). This is a combined event with a CodeJam and infrastructure trainings, which will take place in close space-time proximity: * 25 Nov: [Public event] EBRAINS - New enabling infrastructure for neuroscience * 26 Nov: How to increase the FAIRness of your research - an HBP training course about data sharing * *26-28 Nov: 2nd HPAC Platform Training * * *26-28 Nov: CodeJam#10 * The 2nd HPAC Platform Training will introduce the tools and services of the High-Performance Analysis and Computing Platform and Fenix, including an interactive session on how to apply for those resources. There will also be several sessions about the simulators with different resolutions being (co)developed in the HBP (Arbor, NEST and TVB). More info and registration can be found here: https://www.humanbrainproject.eu/en/education/participatecollaborate/infras… The registration is already open but requires an account to register. If you would like join the event please send an email to Maren Frings <m.frings(a)fz-juelich.de> so we can create a guest account for you. Then you can*register e.g. for the HPAC Training*. The events will have joint breaks and it will be possible to switch to another event for the one or the other session. You need to register only for the event you are most interested in. It would be great to see you there! :-) Best regards, Dennis & Maren

1 0

MUSIC in nest-docker
by Benjamin Staude 17 Oct '19

17 Oct '19

Hi there, I tried to run the basic example from https://nest-simulator.readthedocs.io/en/latest/guides/using_nest_with_musi… <https://nest-simulator.readthedocs.io/en/latest/guides/using_nest_with_musi…> in the docker environment of NEST (https://github.com/nest/nest-docker <https://github.com/nest/nest-docker>) on my OSX host. To be precise, I create the files minimalmusicsetup.music, minimalmusicsetup_sendnest.py and minimalmusicsetup_receivenest.py in the root directory (~/nest-docker) of the host system, and then called mpirun -np 2 music minimalmusicsetup.music from within docker. The output was: MUSIC: Unable to determine process rank. MUSIC: Did you launch music using mpirun? MUSIC: If so, check the comments about porting in README. ------------------------------------------------------- Primary job terminated normally, but 1 process returned a non-zero exit code.. Per user-direction, the job has been aborted. ------------------------------------------------------- MUSIC: Unable to determine process rank. MUSIC: Did you launch music using mpirun? MUSIC: If so, check the comments about porting in README. -------------------------------------------------------------------------- mpirun detected that one or more processes exited with non-zero status, thus causing the job to be terminated. The first process to do so was: Process name: [[46746,1],0] Exit code: 1 Can anyone help? Thanks in advance, Benjamin -- -- -- Dr. Benjamin Staude | Paul-Lincke-Ufer 7 | 10999 Berlin | benjamin.staude(a)gmail.com

2 4

+me for HBP members
by Dennis Terhorst 15 Oct '19

15 Oct '19

Dear HBP-NEST users! // This mail only regards people involved in the Human Brain Project (HBP). // For making your usage of NEST more visible to the HBP internal reporting, we would be happy to see you in the list of the so called /component users/. For this you just need to go to the NEST component page https://plus.humanbrainproject.org/components/209/ and do *three clicks*: 1. click the green [edit] button 2. click [+me] at "Component User Group", and finally 3. click [Save] at the bottom of the page. This ensures the continued support of many developers and helps to show the multitude of research using NEST simulations, and is highly appreciated. If you use or intend to use any number of the following specific NEST features, please feel free to also add yourself there, to show your appreciation to the respective developers: * optimizations for simulations on high-performance computing platforms https://plus.humanbrainproject.org/components/1666/ and https://plus.humanbrainproject.org/components/1667/ * models with continuous dynamics / gap-junctions https://plus.humanbrainproject.org/components/510/ * models with 3rd factor plasticity https://plus.humanbrainproject.org/components/2696/ * the NEST modeling language (NESTML) https://plus.humanbrainproject.org/components/2679/ * connection generation in very large networks https://plus.humanbrainproject.org/components/2678/ There are many other related components that you may also want to add yourself, like simulator-simulator interactions (e.g. 2693), visualization (e.g. 2697), and many more. Please contact me if you feel like you can't find something that you would like to "+me". best, Dennis -- 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

1 0

Open NEST Developer Video Conference Monday 14 October 2019 11.30 CEST (UTC+2)
by Dennis Terhorst 14 Oct '19

14 Oct '19

Dear NEST Developers! I would like to invite you to our next bi-weekly Open NEST Developer Video Conference today (please excuse the late invitation) Monday 14 October, 11.30-12.30 CEST (UTC+2). See below for information about how to log into the meeting. The agenda for this meeting is also available online, see https://github.com/nest/nest-simulator/wiki/2019-10-14-Open-NEST-Developer-… Agenda • Welcome • Python 2 support in NEST3? • Review of NEST User Mailing List • Review of open Github Pull Request • Review of open Github Issues 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

IF COND EXP Model
by vergani.aa＠gmail.com 17 Sep '19

17 Sep '19

Dear experts, do you have any suggestions where could I find the explicit model for the IF COND EXP neuron? I mean the mathematical formulation of the model. Thanks Alberto

3 2

Poisson - crash when changing the rate and delay of rate change
by nest-simulator.org＠weinzierl.it 16 Sep '19

16 Sep '19

I use NEST (Version 2.16.0) by using PyNN. While using I came across the problem that NEST throws an error, when the rate of a SpikeSourcePoisson (in PyNN) is updated from any positive value to 0 and to any positive value again. In other words, once the rate is set to zero, it cannot be changed anymore. It seems like this issue is independant of the temporal location. The exception thrown is the following: > python2.7: /pathToNestSimulator/nest-simulator-2.16.0/nestkernel/event_delivery_manager.h:564: nest::delay nest::EventDeliveryManager::get_slice_modulo(nest::delay): Assertion `static_cast< std::vector< delay >::size_type >( d ) < slice_moduli_.size()' failed. Further, any rate change of a specific neuron is not applied before the next spike at the previous rate. This is problematic when dealing with low rates as spikes occur only rarely. For instance, with a rate of 1 it is not unlikely that there is not a spike for a few seconds. As a result, a rate change can and will be applied extremely delayed. I initially reported this at PyNN, but it seems to be a NEST issue: https://github.com/NeuralEnsemble/PyNN/issues/650 What would you advise?

3 2

Open NEST Developer Video Conference Monday 16 September 2019 11.30 CEST (UTC+2)
by Dennis Terhorst 15 Sep '19

15 Sep '19

Dear NEST Developers! I would like to invite you to our next bi-weekly Open NEST Developer Video Conference tomorrow Monday 16 September, 11.30-12.30 CEST (UTC+2). See below for information about how to log into the meeting. The agenda for this meeting is also available online, see https://github.com/nest/nest-simulator/wiki/2019-09-16-Open-NEST-Developer-… Agenda • Welcome • Review of NEST User Mailing List • Review of open Github Pull Request • Review of open Github Issues 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

installation issue PyNest: outdated libgsl.so.23 dependency on recent linux release
by samuel.bottani＠parisdescartes.fr 07 Sep '19

07 Sep '19

Hi, nestsimulator-2.18.0 fails PyNEST installation as requesting libgsl.so.23 while libgsl.so.25 is available (see brelow --1-- log of installcheck for PyNEST tests) cmake reports no errors with GSL (see bleow --2-- log extract of cmake output ) configuration: linux manjaro latest system update 2019-09-05 Sorry for my ignorance : is there a way to force linking with most recent gsl library ? Or is it necessary to install also the old library version somehow? If then how ? Thank you in advance for any help Samuel Bottani --1-- Phase 7: Running PyNEST tests. ------------------------------ Using nosetests. Failure: ImportError (libgsl.so.23: cannot open shared object file: No such file or directory) ... ERROR Failure: ImportError (libgsl.so.23: cannot open shared object file: No such file or directory) ... ERROR ERROR: Failure: ImportError (libgsl.so.23: cannot open shared object file: No such file or directory) File "/usr/lib/python3.7/site-packages/nose/failure.py", line 39, in runTest ImportError: libgsl.so.23: cannot open shared object file: No such file or directory ERROR: Failure: ImportError (libgsl.so.23: cannot open shared object file: No such file or directory) File "/usr/lib/python3.7/site-packages/nose/failure.py", line 39, in runTest ImportError: libgsl.so.23: cannot open shared object file: No such file or directory FAILED (errors=2) PyNEST tests: 2 Passed: 0 Skipped: 0 Failed: 2 --2-- Concerning GLS log : Use GSL : Yes (GSL 2.6) Includes : /usr/include Libraries : /usr/lib/libgsl.so;/usr/lib/libgslcblas.so

2 2

get/set status conductance based synapses
by Mikkel Elle Lepperød 04 Sep '19

04 Sep '19

Hi! Is it possible to get and set the status of a neuron with conductance based synapses (iaf_cond_alpha)? I only see V_m after getting the status of the nodes, but I need to get/set the synapse states as well (g_ex, g_in). Best -- Mikkel Elle Lepperød <http://cinpla.org/people/> Centre for Integrative Neuroplasticity (CINPLA <http://cinpla.org>) University of Oslo (UiO <http://uio.no>) Kristine Bonnevies hus, room 2513

1 0

problem loading pynn nest installed from live media
by Julian Martin Leslie Budd 04 Sep '19

04 Sep '19

Hi After installing NEST ubuntu 18.04 live media (lubuntu-18.04_nest-2.18.0.ova downloaded a few days ago), I get the following error message but a m able to import nest in python3 ok: nest@nestvm:~$ python3 Python 3.6.8 (default, Jan 14 2019, 11:02:34) [GCC 8.0.1 20180414 (experimental) [trunk revision 259383]] on linux Type "help", "copyright", "credits" or "license" for more information. >>> import pyNN.nest as sim [INFO] [2019.8.21 14:31:47 /home/nest/work/nest-simulator-2.18.0/nestkernel/rng_manager.cpp:217 @ Network::create_rngs_] : Creating default RNGs [INFO] [2019.8.21 14:31:47 /home/nest/work/nest-simulator-2.18.0/nestkernel/rng_manager.cpp:260 @ Network::create_grng_] : Creating new default global RNG -- N E S T -- Copyright (C) 2004 The NEST Initiative Version: nest-2.18.0 Built: Jul 2 2019 15:09:55 This program is provided AS IS and comes with NO WARRANTY. See the file LICENSE for details. Problems or suggestions? Visit https://www.nest-simulator.org Type 'nest.help()' to find out more about NEST. Traceback (most recent call last): File "<stdin>", line 1, in <module> File "/usr/local/lib/python3.6/dist-packages/pyNN/nest/__init__.py", line 18, in <module> from . import simulator File "/usr/local/lib/python3.6/dist-packages/pyNN/nest/simulator.py", line 257, in <module> state = _State() # a Singleton, so only a single instance ever exists File "/usr/local/lib/python3.6/dist-packages/pyNN/nest/simulator.py", line 59, in __init__ self.verbosity = "warning" File "/usr/local/lib/python3.6/dist-packages/pyNN/nest/simulator.py", line 120, in _set_verbosity nest.sli_run("M_%s setverbosity" % verbosity.upper()) AttributeError: module 'nest' has no attribute 'sli_run' >>> Any suggestions? Thanks.

2 1

installation issue: make installcheck fail pynest tests
by Julian Martin Leslie Budd 03 Sep '19

03 Sep '19

Hi Please could someone suggest the most likely reason why current NEST (v2.16.0) appears to install ok (tutorials tested work) but fails during make installcheck for pynest tests: $ make installcheck ... Phase 7: Running PyNEST tests. ------------------------------ Using nosetests. [cajal:07463] Failing at address: 0x44000099 [cajal:07463] *** End of error message *** Segmentation fault (core dumped) PyNEST tests: Passed: 0 Skipped: 0 Failed: 0 /home/julianb/Documents/NEST/share/nest/extras/do_tests.sh: 790: /home/julianb/Documents/NEST/share/nest/extras/do_tests.sh: arithmetic expression: expecting primary: " 363 + " CMakeFiles/installcheck.dir/build.make:57: recipe for target 'CMakeFiles/installcheck' failed make[3]: *** [CMakeFiles/installcheck] Error 2 CMakeFiles/Makefile2:99: recipe for target 'CMakeFiles/installcheck.dir/all' failed make[2]: *** [CMakeFiles/installcheck.dir/all] Error 2 CMakeFiles/Makefile2:106: recipe for target 'CMakeFiles/installcheck.dir/rule' failed make[1]: *** [CMakeFiles/installcheck.dir/rule] Error 2 Makefile:208: recipe for target 'installcheck' failed make: *** [installcheck] Error 2 $ Current setup: ubuntu 16.04, python 2.7.12, and nose 1.3.7. Thanks.

2 1

weigth recorder does not record recorded eligibility trace and neuromodulator concentration.
by anduls＠web.de 02 Sep '19

02 Sep '19

2 1

Open NEST Developer Video Conference Monday 2 September 2019 11.30 CEST (UTC+2)
by Dennis Terhorst 02 Sep '19

02 Sep '19

Dear NEST Developers! I would like to invite you to our next bi-weekly Open NEST Developer Video Conference today Monday 2 September, 11.30-12.30 CEST (UTC+2). See below for information about how to log into the meeting. The agenda for this meeting is also available online https://github.com/nest/nest-simulator/wiki/2019-09-02-Open-NEST-Developer-… • Welcome • Review of NEST User Mailing List • Review of open Github Pull Request • Review of open Github Issues See you soon! 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 _______________________________________________ NEST Users mailing list -- users(a)nest-simulator.org To unsubscribe send an email to users-leave(a)nest-simulator.org

1 0

stdp_dopamine_synapse weight_recorder eligibility trace and neuromodulator concentration.
by anduls＠web.de 23 Aug '19

23 Aug '19

2 1

cannot "import nest" in virtual box installation?
by r.doursat＠mmu.ac.uk 19 Aug '19

19 Aug '19

Hello, I followed the NEST LIVE MEDIA Installation instructions, and the NEST 2.18.0 VirtualBox lubuntu 18.04_1 seems to be running fine. But then in a terminal window in the home directory, and whether running from inside ipython or python, after I type "import nest" at the prompt, I get an error message: "ImportError: dynamic module does not define init function (initpynestkernel)" (line 74 of ll_api.py). There is also another error message just before it: "Import kernel in __init__ after initializing low-level APIs" (line 28 of __init__.py) How can this be fixed? Thanks! -Rene

2 2

Save all weights, set new weights and update to the simulation.
by zhe.sun.vk＠riken.jp 19 Aug '19

19 Aug '19

Hi everyone, I am SUN, working in RIKEN, Japan. I am working on one issue. I am useing the GetConnections to get the weights and keep it in the text. connections = nest.GetConnections(source, target) When I want to update the weight with the new information. I am using this: conn=nest.GetConnections(gid,gid) nest.SetStatus(conn, newweight) But it is not working, do you have any ideas? Best wishes, Sun

3 4

Open NEST Developer Video Conference Monday 19 August 2019 11.30 CEST (UTC+2)
by Hans Ekkehard Plesser 19 Aug '19

19 Aug '19

Dear NEST Developers! I would like to invite you to our next bi-weekly Open NEST Developer Video Conference tomorrow Monday 19 August, 11.30-12.30 CEST (UTC+2). See below for information about how to log into the meeting. The agenda for this meeting is also available online https://github.com/nest/nest-simulator/wiki/2019-08-19-Open-NEST-Developer-… • Welcome • Review of NEST User Mailing List • Review of open Github Pull Request • Review of open Github Issues See you soon! Hans Ekkehard Plesser ------------------ 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 -- Prof. Dr. Hans Ekkehard Plesser Head, Data Science Section 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 Home http://arken.nmbu.no/~plesser _______________________________________________ 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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NEST 2.18.0 (and 2.16.0) now available in NeuroFedora
by Ankur Sinha 13 Aug '19

13 Aug '19

Hello, On behalf of the NeuroFedora team, I'm happy to report that NEST 2.18.0 and 2.16.0 are both available for use on Fedora. Information on using NEST on NeuroFedora is documented here: https://docs.fedoraproject.org/en-US/neurofedora/nest/ Here are a few quick FAQs for your convenience: Q. How do I use NEST on NeuroFedora? A. It only takes two steps to install NEST using `dnf` (the default package manager): - Download and run (optionally install) a "live" Fedora Workstation image from https://getfedora.org - Install NEST 2.18.0: Run `sudo dnf install python3-nest` in a terminal. Q. How do I use version 2.16.0? A. 2.16.0 is provided as a "module". To install the 2.16.0 version: - Download and run (optionally install) a "live" Fedora Workstation image from https://getfedora.org - Install NEST 2.16.0: Run `sudo dnf module install nest:2.16.0` in a terminal. Please note that only one version of NEST can be installed at once. Q. Does NEST in NeuroFedora include MPI support? A. Yes---variants built with both MPICH and OpenMPI are available to use. Q. Does NEST in NeuroFedora include libneurosim/MUSIC/CSA support? A. Not all of them yet. - libneurosim: Yes - MUSIC: No (under review: https://pagure.io/neuro-sig/NeuroFedora/issue/28) - CSA: No (WIP: https://pagure.io/neuro-sig/NeuroFedora/issue/33) Q. Where do I get help? A. The NeuroFedora team maintains multiple communication channels for support and general discussion: https://docs.fedoraproject.org/en-US/neurofedora/communicating/ Q. What other tools does NeuroFedora provide? A. The complete list includes neuron, auryn, PyLEMS, NineML and lots more: https://src.fedoraproject.org/group/neuro-sig Fedora also includes more software that is not specific to computational neuroscience---such as productivity and development tools, a variety of desktop environments, server and container focussed editions, and other science related software: - https://getfedora.org/ - https://labs.fedoraproject.org/ - https://spins.fedoraproject.org/ Q. How can I help? A. The NeuroFedora team is made up of volunteers that believe in Free Software and Open Science. Information on how you can join us and help is summarised here: https://docs.fedoraproject.org/en-US/neurofedora/contributing/ -- Thanks, Regards, Ankur Sinha (He / Him / His) | https://ankursinha.in PhD candidate in computational neuroscience at UH Biocomputation | http://biocomputation.herts.ac.uk/ Free/Open source community volunteer at the Fedora project | https://fedoraproject.org/wiki/User:Ankursinha Time zone: Europe/London

1 0

Error running tutorial notebook
by Filip Vercruysse 05 Aug '19

05 Aug '19

(CNS2019_NEST) Filips-MacBook-Pro:CNS2019_NEST_Tutorial filip$ jupyter-notebook [I 11:01:50.427 NotebookApp] The port 8888 is already in use, trying another port. [I 11:01:50.439 NotebookApp] Serving notebooks from local directory: /Users/filip/Desktop/Research/Conferences/CNS Barcelona/NEST tutorial/CNS2019_NEST_Tutorial [I 11:01:50.439 NotebookApp] The Jupyter Notebook is running at: [I 11:01:50.439 NotebookApp] http://localhost:8889/?token=f4b50440467ee8d87607f84e947be0022dbd7aa394a0b4… [I 11:01:50.439 NotebookApp] Use Control-C to stop this server and shut down all kernels (twice to skip confirmation). [C 11:01:50.445 NotebookApp] To access the notebook, open this file in a browser: file:///Users/filip/Library/Jupyter/runtime/nbserver-31158-open.html Or copy and paste one of these URLs: http://localhost:8889/?token=f4b50440467ee8d87607f84e947be0022dbd7aa394a0b4… [I 11:01:57.768 NotebookApp] Kernel started: 103ab68f-95af-4961-8f9d-3756f2192fd2 [I 11:01:58.401 NotebookApp] Adapting to protocol v5.1 for kernel 103ab68f-95af-4961-8f9d-3756f2192fd2 [INFO] [2019.7.13 11:2:4 /usr/local/miniconda/conda-bld/nest-simulator_1562094389587/work/nestkernel/rng_manager.cpp:217 @ Network::create_rngs_] : Creating default RNGs [INFO] [2019.7.13 11:2:4 /usr/local/miniconda/conda-bld/nest-simulator_1562094389587/work/nestkernel/rng_manager.cpp:260 @ Network::create_grng_] : Creating new default global RNG Assertion failed: (out != NULL), function execute, file /usr/local/miniconda/conda-bld/nest-simulator_1562094389587/work/sli/sli_io.cc, line 422. [Filips-MacBook-Pro:31166] *** Process received signal *** [Filips-MacBook-Pro:31166] Signal: Abort trap: 6 (6) [Filips-MacBook-Pro:31166] Signal code: (0) [Filips-MacBook-Pro:31166] [ 0] 0 libsystem_platform.dylib 0x00007fff791bfb3d _sigtramp + 29 [Filips-MacBook-Pro:31166] [ 1] 0 ??? 0x0000000000000001 0x0 + 1 [Filips-MacBook-Pro:31166] [ 2] 0 libsystem_c.dylib 0x00007fff7907e1c9 abort + 127 [Filips-MacBook-Pro:31166] [ 3] 0 libsystem_c.dylib 0x00007fff79046868 basename_r + 0 [Filips-MacBook-Pro:31166] [ 4] 0 libsli.dylib 0x0000000110a01077 _ZNK18StrSStreamFunction7executeEP14SLIInterpreter + 759 [Filips-MacBook-Pro:31166] [ 5] 0 libsli.dylib 0x00000001109edb2e _ZN13FunctionDatum7executeEP14SLIInterpreter + 446 [Filips-MacBook-Pro:31166] [ 6] 0 libsli.dylib 0x00000001109ebe42 _ZN14SLIInterpreter8execute_Em + 466 [Filips-MacBook-Pro:31166] [ 7] 0 libsli.dylib 0x00000001109ebc58 _ZN14SLIInterpreter7startupEv + 40 [Filips-MacBook-Pro:31166] [ 8] 0 libnest.dylib 0x0000000110031ffa _Z11neststartupPiPPPcR14SLIInterpreterNSt3__112basic_stringIcNS5_11char_traitsIcEENS5_9allocatorIcEEEE + 3306 [Filips-MacBook-Pro:31166] [ 9] 0 pynestkernel.so 0x000000010ffd5cb8 _ZL42__pyx_pw_12pynestkernel_10NESTEngine_5initP7_objectS0_S0_ + 3464 [Filips-MacBook-Pro:31166] [10] 0 python 0x00000001025a948a _PyCFunction_FastCallDict + 362 [Filips-MacBook-Pro:31166] [11] 0 python 0x000000010268042f call_function + 143 [Filips-MacBook-Pro:31166] [12] 0 python 0x000000010267dfc2 _PyEval_EvalFrameDefault + 46802 [Filips-MacBook-Pro:31166] [13] 0 python 0x00000001026807ec fast_function + 188 [Filips-MacBook-Pro:31166] [14] 0 python 0x000000010268048c call_function + 236 [Filips-MacBook-Pro:31166] [15] 0 python 0x000000010267dfc2 _PyEval_EvalFrameDefault + 46802 [Filips-MacBook-Pro:31166] [16] 0 python 0x0000000102671729 _PyEval_EvalCodeWithName + 425 [Filips-MacBook-Pro:31166] [17] 0 python 0x000000010266bf99 builtin_exec + 345 [Filips-MacBook-Pro:31166] [18] 0 python 0x00000001025a8dd2 PyCFunction_Call + 66 [Filips-MacBook-Pro:31166] [19] 0 python 0x000000010267e2b2 _PyEval_EvalFrameDefault + 47554 [Filips-MacBook-Pro:31166] [20] 0 python 0x0000000102671729 _PyEval_EvalCodeWithName + 425 [Filips-MacBook-Pro:31166] [21] 0 python 0x000000010268089a fast_function + 362 [Filips-MacBook-Pro:31166] [22] 0 python 0x000000010268048c call_function + 236 [Filips-MacBook-Pro:31166] [23] 0 python 0x000000010267dfc2 _PyEval_EvalFrameDefault + 46802 [Filips-MacBook-Pro:31166] [24] 0 python 0x00000001026807ec fast_function + 188 [Filips-MacBook-Pro:31166] [25] 0 python 0x000000010268048c call_function + 236 [Filips-MacBook-Pro:31166] [26] 0 python 0x000000010267dfc2 _PyEval_EvalFrameDefault + 46802 [Filips-MacBook-Pro:31166] [27] 0 python 0x00000001026807ec fast_function + 188 [Filips-MacBook-Pro:31166] [28] 0 python 0x000000010268048c call_function + 236 [Filips-MacBook-Pro:31166] [29] 0 python 0x000000010267dfc2 _PyEval_EvalFrameDefault + 46802 [Filips-MacBook-Pro:31166] *** End of error message *** [I 11:02:06.763 NotebookApp] KernelRestarter: restarting kernel (1/5), keep random ports WARNING:root:kernel 103ab68f-95af-4961-8f9d-3756f2192fd2 restarted [I 11:03:57.801 NotebookApp] Saving file at /part1_NEST/0_hello_world.ipynb

2 2

Open NEST Developer Video Conference Monday 5 August 2019 11.30 CEST (UTC+2)
by Hans Ekkehard Plesser 05 Aug '19

05 Aug '19

Dear NEST Developers! I would like to invite you to our next bi-weekly Open NEST Developer Video Conference tomorrow Monday 5 August, 11.30-12.30 CEST (UTC+2). See below for information about how to log into the meeting. The agenda for this meeting is also available online https://github.com/nest/nest-simulator/wiki/2019-08-05-Open-NEST-Developer-… • Welcome • Review of NEST User Mailing List • Review of open Github Pull Request • Review of open Github Issues See you soon! Hans Ekkehard Plesser ------------------ 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 -- Prof. Dr. Hans Ekkehard Plesser Head, Data Science Section 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 Home http://arken.nmbu.no/~plesser

1 0

[stdp_dopamine] Different concentrations for different number of threads
by Guilherme Miotto 22 Jul '19

22 Jul '19

Hi everyone, I'm getting strangely different results if I use stdp_dopamine_synapse with more than 1 local thread. For instance, the mini-code bellow creates a connection with an initial non-zero DA concentration and at t=1000 ms a spike arrives at the volume transmitter. If I run it with one thread I get an initial decay on the DA concentration and then a bump at t=1000 ms. Which is the expected behavior. But if I run the same thing with 2 threads, then I get just the decay. As if the spike hasn't arrived at the volume transmitter. Is this the expected behavior or is it maybe a bug? Best, Gui [image: Screenshot from 2019-06-25 18-32-58.png] [image: 1thread.png] [image: 2threads.png]

2 2

Open NEST Developer Video Conference Monday 22 June 2019 11.30 CEST (UTC+2)
by Dennis Terhorst 21 Jul '19

21 Jul '19

Dear NEST Developers! I would like to invite you to our next bi-weekly Open NEST Developer Video Conference tomorrow Monday 22 June, 11.30-12.30 CEST (UTC+2). See below for information about how to log into the meeting. The agenda for this meeting is also available online https://github.com/nest/nest-simulator/wiki/2019-07-22-Open-NEST-Developer-… 1. Welcome 2. Review of NEST User Mailing List <https://www.nest-simulator.org/mailinglist/hyperkitty/list/users@nest-simul…> 3. Review of open Github Pull Request <https://github.com/nest/nest-simulator/pulls> 4. Review of open Github Issues <https://github.com/nest/nest-simulator/issues> See 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 -- 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

1 0

Record weights of synapses
by deluca.1665541＠studenti.uniroma1.it 15 Jul '19

15 Jul '19

Hello everyone! I need to take track of the weight of a set of synapses through time. I know that there already is a device to do that implemented in nest. According to its documentation, the 'weight recorder' should be created and, then, specified in a synapse model through the command: wr = nest.Create('weight_recorder') nest.CopyModel('stdp_synapse', 'model_name', {'weight_recorder': wr}) nest.Connect(..., syn_spec = 'model_name') The problem is that my synapses have weights distributed by a uniform distribution defined as: 'weight': {"distribution": "uniform", "low": w_min, "high": w_max} but whenever I try to set this in CopyModel I get the following error: terminate called without an active exception [q035:13577] *** Process received signal *** [q035:13577] Signal: Aborted (6) [q035:13577] Signal code: (-6) [q035:13577] [ 0] /lib64/libpthread.so.0(+0xf370)[0x2b4ae83d4370] [q035:13577] [ 1] /lib64/libc.so.6(gsignal+0x37)[0x2b4ae8d1f1d7] [q035:13577] [ 2] /lib64/libc.so.6(abort+0x148)[0x2b4ae8d208c8] [q035:13577] [ 3] /lib64/libstdc++.so.6(_ZN9__gnu_cxx27__verbose_terminate_handlerEv+0x165)[0x2b4b3cb049d5] [q035:13577] [ 4] /lib64/libstdc++.so.6(+0x5e946)[0x2b4b3cb02946] [q035:13577] [ 5] /lib64/libstdc++.so.6(+0x5e973)[0x2b4b3cb02973] [q035:13577] [ 6] /opt/NEST-nesters/lib64/python2.7/site-packages/nest/../../../libnestkernel.so(+0x85edc)[0x2b4b3b2eeedc] [q035:13577] [ 7] /lib64/libgomp.so.1(GOMP_parallel+0x3f)[0x2b4b3cdbb08f] [q035:13577] [ 8] /opt/NEST-nesters/lib64/python2.7/site-packages/nest/../../../libnestkernel.so(_ZN4nest12ModelManager21set_synapse_defaults_EmRK12lockPTRDatumI10DictionaryXadL_ZN14SLIInterpreter14DictionarytypeEEEE+0x65)[0x2b4b3b2eaae5] [q035:13577] [ 9] /opt/NEST-nesters/lib64/python2.7/site-packages/nest/../../../libnestkernel.so(_ZN4nest12ModelManager10copy_modelE4NameS1_12lockPTRDatumI10DictionaryXadL_ZN14SLIInterpreter14DictionarytypeEEEE+0x2bd)[0x2b4b3b2ecfdd] [q035:13577] [10] /opt/NEST-nesters/lib64/python2.7/site-packages/nest/../../../libnestkernel.so(_ZNK4nest10NestModule23CopyModel_l_l_DFunction7executeEP14SLIInterpreter+0x112)[0x2b4b3b2f93f2] [q035:13577] [11] /opt/NEST-nesters/lib64/python2.7/site-packages/nest/../../../libsli.so(_ZN13FunctionDatum7executeEP14SLIInterpreter+0x123)[0x2b4b3bf70473] [q035:13577] [12] /opt/NEST-nesters/lib64/python2.7/site-packages/nest/../../../libsli.so(_ZN14SLIInterpreter8execute_Em+0x312)[0x2b4b3bf6d382] [q035:13577] [13] /opt/NEST-nesters/lib64/python2.7/site-packages/nest/../../../libsli.so(_ZN14SLIInterpreter7executeERKSs+0x128)[0x2b4b3bf6d8a8] [q035:13577] [14] /opt/NEST-nesters/lib64/python2.7/site-packages/nest/pynestkernel.so(+0x23cf5)[0x2b4b3a160cf5] [q035:13577] [15] /lib64/libpython2.7.so.1.0(PyEval_EvalFrameEx+0x6d62)[0x2b4ae80dea62] [q035:13577] [16] /lib64/libpython2.7.so.1.0(PyEval_EvalFrameEx+0x67bd)[0x2b4ae80de4bd] [q035:13577] [17] /lib64/libpython2.7.so.1.0(PyEval_EvalCodeEx+0x7ed)[0x2b4ae80e0e3d] [q035:13577] [18] /lib64/libpython2.7.so.1.0(+0x7088d)[0x2b4ae806a88d] [q035:13577] [19] /lib64/libpython2.7.so.1.0(PyObject_Call+0x43)[0x2b4ae80458e3] [q035:13577] [20] /lib64/libpython2.7.so.1.0(PyEval_EvalFrameEx+0x17fd)[0x2b4ae80d94fd] [q035:13577] [21] /lib64/libpython2.7.so.1.0(PyEval_EvalCodeEx+0x7ed)[0x2b4ae80e0e3d] [q035:13577] [22] /lib64/libpython2.7.so.1.0(PyEval_EvalFrameEx+0x663c)[0x2b4ae80de33c] [q035:13577] [23] /lib64/libpython2.7.so.1.0(PyEval_EvalCodeEx+0x7ed)[0x2b4ae80e0e3d] [q035:13577] [24] /lib64/libpython2.7.so.1.0(PyEval_EvalCode+0x32)[0x2b4ae80e0f42] [q035:13577] [25] /lib64/libpython2.7.so.1.0(+0x10037f)[0x2b4ae80fa37f] [q035:13577] [26] /lib64/libpython2.7.so.1.0(PyRun_InteractiveOneFlags+0x150)[0x2b4ae80fc430] [q035:13577] [27] /lib64/libpython2.7.so.1.0(PyRun_InteractiveLoopFlags+0x5e)[0x2b4ae80fc61e] [q035:13577] [28] /lib64/libpython2.7.so.1.0(PyRun_AnyFileExFlags+0x3e)[0x2b4ae80fccae] [q035:13577] [29] /lib64/libpython2.7.so.1.0(Py_Main+0xc9f)[0x2b4ae810d91f] [q035:13577] *** End of error message *** Annullato (core dumped) Can somebody help me? Thank you! Chiara

3 3

Recording from synapses
by Guilherme Miotto 08 Jul '19

08 Jul '19

Hi everyone, Is there a generic way of recording from connections? I know that for weights we can use a weight_recorder, but what about other parameters? For instance, right now I would like to record the dopamine concentration (aka "n") from stdp_dopamine_synapse connections. Is this possible? Best, -- Gui Miotto

2 1

Open NEST Developer Video Conference Monday 8 June 2019 11.30 CEST (UTC+2)
by Dennis Terhorst 08 Jul '19

08 Jul '19

Dear NEST Developers! I would like to invite you to our next bi-weekly Open NEST Developer Video Conference today Monday 8 June, 11.30-12.30 CEST (UTC+2). See below for information about how to log into the meeting. The agenda for this meeting is also available online https://github.com/nest/nest-simulator/wiki/2019-07-08-Open-NEST-Developer-… 1. Welcome * /release celebration/ for *nest-2.18.0 <https://github.com/nest/nest-simulator/releases/tag/v2.18.0>* 2. Review of NEST User Mailing List <https://www.nest-simulator.org/mailinglist/hyperkitty/list/users@nest-simul…> 3. Discussion about #1195 CMAKE_INSTALL_PREFIX /usr/local <https://github.com/nest/nest-simulator/issues/1195> 4. Review of open Github Pull Request <https://github.com/nest/nest-simulator/pulls> 5. Review of open Github Issues <https://github.com/nest/nest-simulator/issues> See 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 * Enter your name and allow your browser to use camera and microphone * Click green video-call button to open the call panel * In the "Search to call" box at the top right enter *97938800* and connect * 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 -- 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

2 1

NEST 2.18.0 released
by Hans Ekkehard Plesser 04 Jul '19

04 Jul '19

Dear NEST Users! It is a great pleasure to announce the release of NEST 2.18.0, which provides a number of new neuron and plasticity models and additional functionality. It improves memory allocation and performance during network construction. It includes a number of bug fixes and is the first release that can be installed via aptitude and in a Conda environment directly from conda-forge. For details, please see the change log at https://github.com/nest/nest-simulator/releases. NEST 2.18.0 is the result of 116 pull-requests (1128 commits) by 31 developers since NEST 2.16.0 which was released on 2018-08-21. Enjoy! Hans Ekkehard Plesser President, The NEST Initiative -- Prof. Dr. Hans Ekkehard Plesser Head, Data Science Section 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 Home http://arken.nmbu.no/~plesser

1 0

Create new neuron module
by tschoepe＠techfak.uni-bielefeld.de 02 Jul '19

02 Jul '19

Dear All, I am relatively new to nest and want to implement a new neuron model. I've worked a lot with SpiNNaker previously. I am a research assistant and PhD student at the Technical Faculty in Bielefeld, Germany. Currently, I am trying to implement a new neuron model into nest. Because I want to use this model later on in the neurorbotics platform (NRP) I directly installed the NRP and I am using the nest version installed together with the NRP. I followed the instructions at: https://nest.github.io/nest-simulator/extension_modules I am able to install mymodule and to run the neuron model pif_psc_alpha coming with it. Now I tried to extend mymodule with a new neuron model. To achieve that I copied the iaf_psc_exp model's cpp and h file, renamed them to iaf_psc_exp_semd and changed them according to pif_psc_alpha. I was able to include the model into the nest library and run a short example script. Unfortunately, the iaf_psc_exp_semd model doesn't react to any stimulation with spikes. The membrane potential always stays at E_L. When I use the same python script but with the iad_psc_exp model I see a clear change in the membrane potential. Could someone check the files I've created for the new iaf_psc_exp_semd model to see what is wrong/missing? Thanks a lot and best regards, Thorben Schoepe First file: /* * iaf_psc_exp_semd.h * * This file is part of NEST. * * Copyright (C) 2004 The NEST Initiative * * NEST is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by * the Free Software Foundation, either version 2 of the License, or * (at your option) any later version. * * NEST is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * GNU General Public License for more details. * * You should have received a copy of the GNU General Public License * along with NEST. If not, see <http://www.gnu.org/licenses/>. * */ #ifndef IAF_PSC_EXP_SEMD_H #define IAF_PSC_EXP_SEMD_H // Includes from nestkernel: #include "archiving_node.h" #include "connection.h" #include "event.h" #include "nest_types.h" #include "recordables_map.h" #include "ring_buffer.h" #include "universal_data_logger.h" // Includes from sli: #include "dictdatum.h" namespace mynest { /* BeginDocumentation Name: iaf_psc_exp - Leaky integrate-and-fire neuron model with exponential PSCs. Description: iaf_psc_expp is an implementation of a leaky integrate-and-fire model with exponential shaped postsynaptic currents (PSCs) according to [1]. Thus, postsynaptic currents have an infinitely short rise time. The threshold crossing is followed by an absolute refractory period (t_ref) during which the membrane potential is clamped to the resting potential and spiking is prohibited. The linear subthresold dynamics is integrated by the Exact Integration scheme [2]. The neuron dynamics is solved on the time grid given by the computation step size. Incoming as well as emitted spikes are forced to that grid. An additional state variable and the corresponding differential equation represents a piecewise constant external current. The general framework for the consistent formulation of systems with neuron like dynamics interacting by point events is described in [2]. A flow chart can be found in [3]. Remarks: The present implementation uses individual variables for the components of the state vector and the non-zero matrix elements of the propagator. Because the propagator is a lower triangular matrix no full matrix multiplication needs to be carried out and the computation can be done "in place" i.e. no temporary state vector object is required. The template support of recent C++ compilers enables a more succinct formulation without loss of runtime performance already at minimal optimization levels. A future version of iaf_psc_exp will probably address the problem of efficient usage of appropriate vector and matrix objects. Parameters: The following parameters can be set in the status dictionary. E_L double - Resting membrane potential in mV. C_m double - Capacity of the membrane in pF tau_m double - Membrane time constant in ms. tau_syn_ex double - Time constant of postsynaptic excitatory currents in ms tau_syn_in double - Time constant of postsynaptic inhibitory currents in ms t_ref double - Duration of refractory period (V_m = V_reset) in ms. V_m double - Membrane potential in mV V_th double - Spike threshold in mV. V_reset double - Reset membrane potential after a spike in mV. I_e double - Constant input current in pA. t_spike double - Point in time of last spike in ms. Remarks: If tau_m is very close to tau_syn_ex or tau_syn_in, the model will numerically behave as if tau_m is equal to tau_syn_ex or tau_syn_in, respectively, to avoid numerical instabilities. For details, please see IAF_Neruons_Singularity.ipynb in the NEST source code (docs/model_details). iaf_psc_exp can handle current input in two ways: Current input through receptor_type 0 are handled as stepwise constant current input as in other iaf models, i.e., this current directly enters the membrane potential equation. Current input through receptor_type 1, in contrast, is filtered through an exponential kernel with the time constant of the excitatory synapse, tau_syn_ex. For an example application, see [4]. References: [1] Misha Tsodyks, Asher Uziel, and Henry Markram (2000) Synchrony Generation in Recurrent Networks with Frequency-Dependent Synapses, The Journal of Neuroscience, 2000, Vol. 20 RC50 p. 1-5 [2] Rotter S & Diesmann M (1999) Exact simulation of time-invariant linear systems with applications to neuronal modeling. Biologial Cybernetics 81:381-402. [3] Diesmann M, Gewaltig M-O, Rotter S, & Aertsen A (2001) State space analysis of synchronous spiking in cortical neural networks. Neurocomputing 38-40:565-571. [4] Schuecker J, Diesmann M, Helias M (2015) Modulated escape from a metastable state driven by colored noise. Physical Review E 92:052119 Sends: SpikeEvent Receives: SpikeEvent, CurrentEvent, DataLoggingRequest SeeAlso: iaf_psc_exp_ps FirstVersion: March 2006 Author: Moritz Helias */ /** * Leaky integrate-and-fire neuron with exponential PSCs. */ class iaf_psc_exp_semd : public nest::Archiving_Node { public: iaf_psc_exp_semd(); iaf_psc_exp_semd( const iaf_psc_exp_semd& ); /** * Import sets of overloaded virtual functions. * @see Technical Issues / Virtual Functions: Overriding, Overloading, and * Hiding */ using nest::Node::handle; using nest::Node::handles_test_event; nest::port send_test_event( Node&, nest::port, nest::synindex, bool ); void handle( nest::SpikeEvent& ); void handle( nest::CurrentEvent& ); void handle( nest::DataLoggingRequest& ); nest::port handles_test_event( nest::SpikeEvent&, nest::port ); nest::port handles_test_event( nest::CurrentEvent&, nest::port ); nest::port handles_test_event( nest::DataLoggingRequest&, nest::port ); void get_status( DictionaryDatum& ) const; void set_status( const DictionaryDatum& ); private: void init_state_( const Node& proto ); void init_buffers_(); void calibrate(); void update(nest::Time const&, const long, const long ); // The next two classes need to be friends to access the State_ class/member friend class nest::RecordablesMap< iaf_psc_exp_semd >; friend class nest::UniversalDataLogger< iaf_psc_exp_semd >; // ---------------------------------------------------------------- /** * Independent parameters of the model. */ struct Parameters_ { /** Membrane time constant in ms. */ double Tau_; /** Membrane capacitance in pF. */ double C_; /** Refractory period in ms. */ double t_ref_; /** Resting potential in mV. */ double E_L_; /** External current in pA */ double I_e_; /** Threshold, RELATIVE TO RESTING POTENTAIL(!). I.e. the real threshold is (E_L_+Theta_). */ double Theta_; /** reset value of the membrane potential */ double V_reset_; /** Time constant of excitatory synaptic current in ms. */ double tau_ex_; /** Time constant of inhibitory synaptic current in ms. */ double tau_in_; Parameters_(); //!< Sets default parameter values void get( DictionaryDatum& ) const; //!< Store current values in dictionary /** Set values from dictionary. * @returns Change in reversal potential E_L, to be passed to State_::set() */ double set( const DictionaryDatum& ); }; // ---------------------------------------------------------------- /** * State variables of the model. */ struct State_ { // state variables //! synaptic stepwise constant input current, variable 0 double i_0_; double i_1_; //!< presynaptic stepwise constant input current double i_syn_ex_; //!< postsynaptic current for exc. inputs, variable 1 double i_syn_in_; //!< postsynaptic current for inh. inputs, variable 1 double V_m_; //!< membrane potential, variable 2 //! absolute refractory counter (no membrane potential propagation) int r_ref_; State_(); //!< Default initialization void get( DictionaryDatum&, const Parameters_& ) const; /** Set values from dictionary. * @param dictionary to take data from * @param current parameters * @param Change in reversal potential E_L specified by this dict */ void set( const DictionaryDatum&, const Parameters_&, const double ); }; // ---------------------------------------------------------------- /** * Buffers of the model. */ struct Buffers_ { Buffers_( iaf_psc_exp_semd& ); Buffers_( const Buffers_&, iaf_psc_exp_semd& ); /** buffers and sums up incoming spikes/currents */ nest::RingBuffer spikes_ex_; nest::RingBuffer spikes_in_; std::vector< nest::RingBuffer > currents_; //! Logger for all analog data nest::UniversalDataLogger< iaf_psc_exp_semd > logger_; }; // ---------------------------------------------------------------- /** * Internal variables of the model. */ struct Variables_ { /** Amplitude of the synaptic current. This value is chosen such that a post-synaptic potential with weight one has an amplitude of 1 mV. @note mog - I assume this, not checked. */ // double PSCInitialValue_; // time evolution operator double P20_; double P11ex_; double P11in_; double P21ex_; double P21in_; double P22_; double weighted_spikes_ex_; double weighted_spikes_in_; int RefractoryCounts_; }; // Access functions for UniversalDataLogger ------------------------------- //! Read out the real membrane potential inline double get_V_m_() const { return S_.V_m_ + P_.E_L_; } inline double get_weighted_spikes_ex_() const { return V_.weighted_spikes_ex_; } inline double get_weighted_spikes_in_() const { return V_.weighted_spikes_in_; } inline double get_I_syn_ex_() const { return S_.i_syn_ex_; } inline double get_I_syn_in_() const { return S_.i_syn_in_; } // ---------------------------------------------------------------- /** * @defgroup iaf_psc_exp_data * Instances of private data structures for the different types * of data pertaining to the model. * @note The order of definitions is important for speed. * @{ */ Parameters_ P_; State_ S_; Variables_ V_; Buffers_ B_; /** @} */ //! Mapping of recordables names to access functions static nest::RecordablesMap< iaf_psc_exp_semd > recordablesMap_; }; inline nest::port mynest::iaf_psc_exp_semd::send_test_event( Node& target, nest::port receptor_type, nest::synindex, bool ) { nest::SpikeEvent e; e.set_sender( *this ); return target.handles_test_event( e, receptor_type ); } inline nest::port mynest::iaf_psc_exp_semd::handles_test_event( nest::SpikeEvent&, nest::port receptor_type ) { if ( receptor_type != 0 ) throw nest::UnknownReceptorType( receptor_type, get_name() ); return 0; } inline nest::port mynest::iaf_psc_exp_semd::handles_test_event( nest::CurrentEvent&, nest::port receptor_type ) { if ( receptor_type == 0 ) return 0; else if ( receptor_type == 1 ) return 1; else throw nest::UnknownReceptorType( receptor_type, get_name() ); } inline nest::port mynest::iaf_psc_exp_semd::handles_test_event( nest::DataLoggingRequest& dlr, nest::port receptor_type ) { if ( receptor_type != 0 ) throw nest::UnknownReceptorType( receptor_type, get_name() ); return B_.logger_.connect_logging_device( dlr, recordablesMap_ ); } inline void iaf_psc_exp_semd::get_status( DictionaryDatum& d ) const { P_.get( d ); S_.get( d, P_ ); Archiving_Node::get_status( d ); ( *d )[ nest::names::recordables ] = recordablesMap_.get_list(); } inline void iaf_psc_exp_semd::set_status( const DictionaryDatum& d ) { Parameters_ ptmp = P_; // temporary copy in case of errors const double delta_EL = ptmp.set( d ); // throws if BadProperty State_ stmp = S_; // temporary copy in case of errors stmp.set( d, ptmp, delta_EL ); // throws if BadProperty // We now know that (ptmp, stmp) are consistent. We do not // write them back to (P_, S_) before we are also sure that // the properties to be set in the parent class are internally // consistent. Archiving_Node::set_status( d ); // if we get here, temporaries contain consistent set of properties P_ = ptmp; S_ = stmp; } } // namespace #endif // IAF_PSC_EXP_SEMD_H Second file: /* * iaf_psc_exp_semd.cpp * * This file is part of NEST. * * Copyright (C) 2004 The NEST Initiative * * NEST is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by * the Free Software Foundation, either version 2 of the License, or * (at your option) any later version. * * NEST is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * GNU General Public License for more details. * * You should have received a copy of the GNU General Public License * along with NEST. If not, see <http://www.gnu.org/licenses/>. * */ #include "iaf_psc_exp_semd.h" // C++ includes: #include <limits> // Includes from libnestutil: #include "numerics.h" #include "propagator_stability.h" // Includes from nestkernel: #include "event_delivery_manager_impl.h" #include "exceptions.h" #include "kernel_manager.h" #include "universal_data_logger_impl.h" // Includes from sli: #include "dict.h" #include "dictutils.h" #include "doubledatum.h" #include "integerdatum.h" #include "lockptrdatum.h" using namespace nest; /* ---------------------------------------------------------------- * Recordables map * ---------------------------------------------------------------- */ nest::RecordablesMap< mynest::iaf_psc_exp_semd > mynest::iaf_psc_exp_semd::recordablesMap_; namespace nest { // Override the create() method with one call to RecordablesMap::insert_() // for each quantity to be recorded. template <> void RecordablesMap< mynest::iaf_psc_exp_semd >::create() { // use standard names whereever you can for consistency! insert_( names::V_m, &mynest::iaf_psc_exp_semd::get_V_m_ ); insert_( names::weighted_spikes_ex, &mynest::iaf_psc_exp_semd::get_weighted_spikes_ex_ ); insert_( names::weighted_spikes_in, &mynest::iaf_psc_exp_semd::get_weighted_spikes_in_ ); insert_( names::I_syn_ex, &mynest::iaf_psc_exp_semd::get_I_syn_ex_ ); insert_( names::I_syn_in, &mynest::iaf_psc_exp_semd::get_I_syn_in_ ); } } /* ---------------------------------------------------------------- * Default constructors defining default parameters and state * ---------------------------------------------------------------- */ mynest::iaf_psc_exp_semd::Parameters_::Parameters_() : Tau_( 10.0 ) // in ms , C_( 250.0 ) // in pF , t_ref_( 2.0 ) // in ms , E_L_( -70.0 ) // in mV , I_e_( 0.0 ) // in pA , Theta_( -55.0 - E_L_ ) // relative E_L_ , V_reset_( -70.0 - E_L_ ) // in mV , tau_ex_( 2.0 ) // in ms , tau_in_( 2.0 ) // in ms { } mynest::iaf_psc_exp_semd::State_::State_() : i_0_( 0.0 ) , i_syn_ex_( 0.0 ) , i_syn_in_( 0.0 ) , V_m_( 0.0 ) , r_ref_( 0 ) { } /* ---------------------------------------------------------------- * Parameter and state extractions and manipulation functions * ---------------------------------------------------------------- */ void mynest::iaf_psc_exp_semd::Parameters_::get( DictionaryDatum& d ) const { def< double >( d, names::E_L, E_L_ ); // resting potential def< double >( d, names::I_e, I_e_ ); def< double >( d, names::V_th, Theta_ + E_L_ ); // threshold value def< double >( d, names::V_reset, V_reset_ + E_L_ ); def< double >( d, names::C_m, C_ ); def< double >( d, names::tau_m, Tau_ ); def< double >( d, names::tau_syn_ex, tau_ex_ ); def< double >( d, names::tau_syn_in, tau_in_ ); def< double >( d, names::t_ref, t_ref_ ); } double mynest::iaf_psc_exp_semd::Parameters_::set( const DictionaryDatum& d ) { // if E_L_ is changed, we need to adjust all variables defined relative to // E_L_ const double ELold = E_L_; updateValue< double >( d, names::E_L, E_L_ ); const double delta_EL = E_L_ - ELold; if ( updateValue< double >( d, names::V_reset, V_reset_ ) ) V_reset_ -= E_L_; else V_reset_ -= delta_EL; if ( updateValue< double >( d, names::V_th, Theta_ ) ) Theta_ -= E_L_; else Theta_ -= delta_EL; updateValue< double >( d, names::I_e, I_e_ ); updateValue< double >( d, names::C_m, C_ ); updateValue< double >( d, names::tau_m, Tau_ ); updateValue< double >( d, names::tau_syn_ex, tau_ex_ ); updateValue< double >( d, names::tau_syn_in, tau_in_ ); updateValue< double >( d, names::t_ref, t_ref_ ); if ( V_reset_ >= Theta_ ) throw nest::BadProperty( "Reset potential must be smaller than threshold." ); if ( C_ <= 0 ) throw nest::BadProperty( "Capacitance must be strictly positive." ); if ( Tau_ <= 0 || tau_ex_ <= 0 || tau_in_ <= 0 ) throw nest::BadProperty( "Membrane and synapse time constants must be strictly positive." ); if ( t_ref_ < 0 ) throw nest::BadProperty( "Refractory time must not be negative." ); return delta_EL; } void mynest::iaf_psc_exp_semd::State_::get( DictionaryDatum& d, const Parameters_& p ) const { def< double >( d, names::V_m, V_m_ + p.E_L_ ); // Membrane potential } void mynest::iaf_psc_exp_semd::State_::set( const DictionaryDatum& d, const Parameters_& p, double delta_EL ) { if ( updateValue< double >( d, names::V_m, V_m_ ) ) V_m_ -= p.E_L_; else V_m_ -= delta_EL; } mynest::iaf_psc_exp_semd::Buffers_::Buffers_( iaf_psc_exp_semd& n ) : logger_( n ) { } mynest::iaf_psc_exp_semd::Buffers_::Buffers_( const Buffers_&, iaf_psc_exp_semd& n ) : logger_( n ) { } /* ---------------------------------------------------------------- * Default and copy constructor for node * ---------------------------------------------------------------- */ mynest::iaf_psc_exp_semd::iaf_psc_exp_semd() : Archiving_Node() , P_() , S_() , B_( *this ) { recordablesMap_.create(); } mynest::iaf_psc_exp_semd::iaf_psc_exp_semd( const iaf_psc_exp_semd& n ) : Archiving_Node( n ) , P_( n.P_ ) , S_( n.S_ ) , B_( n.B_, *this ) { } /* ---------------------------------------------------------------- * Node initialization functions * ---------------------------------------------------------------- */ void mynest::iaf_psc_exp_semd::init_state_( const Node& proto ) { const iaf_psc_exp_semd& pr = downcast< iaf_psc_exp_semd >( proto ); S_ = pr.S_; } void mynest::iaf_psc_exp_semd::init_buffers_() { B_.spikes_ex_.clear(); // includes resize B_.spikes_in_.clear(); // includes resize B_.currents_.clear(); // includes resize B_.logger_.reset(); Archiving_Node::clear_history(); } void mynest::iaf_psc_exp_semd::calibrate() { B_.currents_.resize( 2 ); // ensures initialization in case mm connected after Simulate B_.logger_.init(); const double h = Time::get_resolution().get_ms(); // numbering of state vaiables: i_0 = 0, i_syn_ = 1, V_m_ = 2 // commented out propagators: forward Euler // needed to exactly reproduce Tsodyks network // these P are independent V_.P11ex_ = std::exp( -h / P_.tau_ex_ ); // P11ex_ = 1.0-h/tau_ex_; V_.P11in_ = std::exp( -h / P_.tau_in_ ); // P11in_ = 1.0-h/tau_in_; V_.P22_ = std::exp( -h / P_.Tau_ ); // P22_ = 1.0-h/Tau_; // these are determined according to a numeric stability criterion V_.P21ex_ = propagator_32( P_.tau_ex_, P_.Tau_, P_.C_, h ); V_.P21in_ = propagator_32( P_.tau_in_, P_.Tau_, P_.C_, h ); // P21ex_ = h/C_; // P21in_ = h/C_; V_.P20_ = P_.Tau_ / P_.C_ * ( 1.0 - V_.P22_ ); // P20_ = h/C_; // TauR specifies the length of the absolute refractory period as // a double in ms. The grid based iaf_psc_exp can only handle refractory // periods that are integer multiples of the computation step size (h). // To ensure consistency with the overall simulation scheme such conversion // should be carried out via objects of class nest::Time. The conversion // requires 2 steps: // 1. A time object r is constructed defining representation of // TauR in tics. This representation is then converted to computation // time steps again by a strategy defined by class nest::Time. // 2. The refractory time in units of steps is read out get_steps(), a // member function of class nest::Time. // // Choosing a TauR that is not an integer multiple of the computation time // step h will leed to accurate (up to the resolution h) and self-consistent // results. However, a neuron model capable of operating with real valued // spike time may exhibit a different effective refractory time. V_.RefractoryCounts_ = Time( Time::ms( P_.t_ref_ ) ).get_steps(); // since t_ref_ >= 0, this can only fail in error assert( V_.RefractoryCounts_ >= 0 ); } void mynest::iaf_psc_exp_semd::update( const Time& origin, const long from, const long to ) { assert( to >= 0 && ( delay ) from < kernel().connection_manager.get_min_delay() ); assert( from < to ); // evolve from timestep 'from' to timestep 'to' with steps of h each for ( long lag = from; lag < to; ++lag ) { if ( S_.r_ref_ == 0 ) // neuron not refractory, so evolve V S_.V_m_ = S_.V_m_ * V_.P22_ + S_.i_syn_ex_ * V_.P21ex_ // membrane potential equals membrane potential times exponetial decay plus postsynpatic excitatory/inhibitory currents time numerical stability factor plus new input current times exponential decay + S_.i_syn_in_ * V_.P21in_ + ( P_.I_e_ + S_.i_0_ ) * V_.P20_; // S_.V_m : membrane potential else // V_.P22 : membrane potential decay { // S_.i_syn_ex / S_.i_syn_in : excitatory / inhibitory postsynaptic current } // V_.P21in / V_.P21ex : numeric stability criterion parameter // P_.I_e : static input current { // S_.i_0_ : presynaptic input current this timestep } // S_.i_1_ : presynaptic input current next timestep { } --S_.r_ref_; // neuron is absolute refractory // exponential decaying PSCs S_.i_syn_ex_ *= V_.P11ex_; S_.i_syn_in_ *= V_.P11in_; // add evolution of presynaptic input current S_.i_syn_ex_ += ( 1. - V_.P11ex_ ) * S_.i_1_; // the spikes arriving at T+1 have an immediate effect on the state of the // neuron V_.weighted_spikes_ex_ = B_.spikes_ex_.get_value( lag ); V_.weighted_spikes_in_ = B_.spikes_in_.get_value( lag ); S_.i_syn_ex_ += V_.weighted_spikes_ex_; S_.i_syn_in_ += V_.weighted_spikes_in_; if ( S_.V_m_ >= P_.Theta_ ) // threshold crossing { S_.r_ref_ = V_.RefractoryCounts_; S_.V_m_ = P_.V_reset_; set_spiketime( Time::step( origin.get_steps() + lag + 1 ) ); SpikeEvent se; kernel().event_delivery_manager.send( *this, se, lag ); } // set new input current S_.i_0_ = B_.currents_[ 0 ].get_value( lag ); S_.i_1_ = B_.currents_[ 1 ].get_value( lag ); // log state data B_.logger_.record_data( origin.get_steps() + lag ); } } void mynest::iaf_psc_exp_semd::handle( SpikeEvent& e ) { assert( e.get_delay() > 0 ); if ( e.get_weight() >= 0.0 ) B_.spikes_ex_.add_value( e.get_rel_delivery_steps( kernel().simulation_manager.get_slice_origin() ), e.get_weight() * e.get_multiplicity() ); else B_.spikes_in_.add_value( e.get_rel_delivery_steps( kernel().simulation_manager.get_slice_origin() ), e.get_weight() * e.get_multiplicity() ); } void mynest::iaf_psc_exp_semd::handle( CurrentEvent& e ) { assert( e.get_delay() > 0 ); const double c = e.get_current(); const double w = e.get_weight(); // add weighted current; HEP 2002-10-04 if ( 0 == e.get_rport() ) { B_.currents_[ 0 ].add_value( e.get_rel_delivery_steps( kernel().simulation_manager.get_slice_origin() ), w * c ); } if ( 1 == e.get_rport() ) { B_.currents_[ 1 ].add_value( e.get_rel_delivery_steps( kernel().simulation_manager.get_slice_origin() ), w * c ); } } void mynest::iaf_psc_exp_semd::handle( DataLoggingRequest& e ) { B_.logger_.handle( e ); }

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Installation of Nest Simulator with csa
by yannicknodem＠gmail.com 27 Jun '19

27 Jun '19

Hi, I try to install csa package with libneurosim to use with nest simulator. The installation of libneurosim with python support take place without any issues. When I try to install csa with these commands: ./autogen.sh ./configure ./configure --prefix=$HOME/opt/csa --with-libneurosim=$HOME/opt/libneurosim make The installation fails at the make step with these output errors: _/home/yannick/Downloads/csa-master/libpycsa/pycsa.cpp:189: undefined reference to PyGILState_Ensure' /home/yannick/Downloads/csa-master/libpycsa/pycsa.cpp:190: undefined reference to PyList_New' /home/yannick/Downloads/csa-master/libpycsa/pycsa.cpp:197: undefined reference to PyObject_CallFunctionObjArgs' /home/yannick/Downloads/csa-master/libpycsa/pycsa.cpp:198: undefined reference to PyList_SetItem' /home/yannick/Downloads/csa-master/libpycsa/pycsa.cpp:202: undefined reference to PyLong_FromLong' /home/yannick/Downloads/csa-master/libpycsa/pycsa.cpp:202: undefined reference to PyObject_CallFunctionObjArgs' /home/yannick/Downloads/csa-master/libpycsa/pycsa.cpp:209: undefined reference to PyGILState_Release' .libs/libpycsa_la-pycsa.o: In function error(std::_cxx11::basic_string<char, std::char_traits, std::allocator >)': /home/yannick/Downloads/csa-master/libpycsa/pycsa.cpp:53: undefined reference to PyGILState_Release' .libs/libpycsa_la-pycsa.o: In function PyCSA::PyCSAGenerator::setMask(std::vector<ConnectionGenerator::Mask, std::allocatorConnectionGenerator::Mask >&, int)': /home/yannick/Downloads/csa-master/libpycsa/pycsa.cpp:214: undefined reference to `PyGILState_Release' collect2: error: ld returned 1 exit status Makefile:444: recipe for target 'libpycsa.la' failed make[2]: *** [libpycsa.la] Error 1 make[2]: Leaving directory '/home/yannick/Downloads/csa-master/libpycsa' Makefile:420: recipe for target 'all-recursive' failed make[1]: *** [all-recursive] Error 1 make[1]: Leaving directory '/home/yannick/Downloads/csa-master' Makefile:350: recipe for target 'all' failed make: *** [all] Error 2 I work on ubuntu 18.04 with python 3.7.3 Thank you

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Open NEST Developer *real* Conference Monday 24-25 June 2019
by Dennis Terhorst 21 Jun '19

21 Jun '19

Dear NEST Developers! Our next meeting will be the _real_ Open NEST User and Developer Conference (non-video!) in Ås, Norway. This will of course replace the usual video meeting. Looking forward to seeing you all there! best, Dennis Terhorst -- Dipl.-Phys. Dennis Terhorst Coordinator Software Development Institute of Neuroscience and Medicine (INM-6) Computational and Systems Neuroscience & Theoretical Neuroscience, Institute for Advanced Simulation (IAS-6) Jülich Research Centre, Member of the Helmholz Association and JARA 52425 Jülich, Germany Building 15.22 Room 4004 Phone +49 2461 61-85062 Fax +49 2461 61- 9460 d.terhorst(a)fz-juelich.de

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Options for plotting simulated data
by TOM BUGNON 21 Jun '19

21 Jun '19

Hi all, I was wondering if the community had any suggestions of toolboxes to plot the output of simulations (ideally in python) and make publication-quality figures. I am mostly thinking of eg spike rasterplots or heatmaps (time x variable) with large datasets. Ideally in such a way that those can be aligned with other figures easily (spike histograms, LFP, you name it) This is a very general problem that I suppose a lot of us have been confronted with, and I actually haven't found so far a good solution: -matplotlib (python) is robust and can handle large datasets but looks bad and is a nightmare to deal with when trying to make figures with multiple subplots of specific sizes etc - altair (python) looked promising and versatile but is actually struggling with large datasets - The existing projects for (analysis and) visualization of neural data that I have checked (elephant spykes etc) are either quite specific/limited or not very active. Additionally they are focused on real ePhys data: either multiunit spike data or single neuron continuous data, while simulations provide both. Happy to get any suggestions and share some code ! Thanks, Tom

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AdEx gap junctions
by domenico.guarino＠cnrs.fr 19 Jun '19

19 Jun '19

Hello, from the NEST docs(https://www.nest-simulator.org/simulations-with-gap-junctions/), I see that only the cell model 'hh_psc_alpha_gap' can use gap junctions. Is it true? If true, are there any plans (or hacks) to have it also for the AdEx model? Thanks!

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Nest installation
by gerlach.mi＠gmx.de 13 Jun '19

13 Jun '19

Hello, I am using Anaconda on a Mac OS X platform. I installed nest using homebrew by following the instructions on this page: https://nest-simulator.readthedocs.io/en/latest/installation/mac_install.ht… After finishing the installation, IPython first could not find the nest module, so I manually copied the nest folder that was created in /Users/name/opt/nest/lib/python3.7/site-packages/nest into /anaconda/lib/python3.7/site-packages/nest Now IPython can import the nest module, but returns an error message when I try to run a basic nest example: "module 'nest' has no attribute 'Create' ". I am sorry for failing at a very basic level here, but I tried for quite some time and could not get it running despite trying different instructions. I would greatly appreciate it if anyone could help me or give me a hint into the right direction, thanks in advance!

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Where are the archive questions?
by Abolfazl Ziaeemehr 12 Jun '19

12 Jun '19

I remember before the new mailing list I had access to the archived questions and some times by digging into them I could find some answers to simple questions. Now I can not find them. Thank you let me know if there are still available. One more silly question. Do we have access to synaptic current in iaf psc alpha model. We can simply plot the post synaptic potential for two couple neuron (in tutorial <https://nest-simulator.readthedocs.io/en/latest/tutorials/pynest_tutorial/p…>), how about the I_syn? Excuse me if seems easy, and thanks for guide.

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parallel computing on a shared cluster
by Jimmy Mulder 03 Jun '19

03 Jun '19

Hi everyone, For my masters thesis I'm using (py)NEST for the first time. I have some questions about parallel computing. first a short intro to give you the context: My research group has access to 4 clusters; 2 with a focus on RAM/CPU on 2 with focus on GPU. These are shared systems; resources are dynamically allocated depending on the number of users doing calculations. The way these clusters are set up allows me to simply set "local_num_threads" to a value of 10, and if no one else is using it the cluster manager will say I get 1000% CPU power, and the speed will increase about 8-fold as expected. (in case you find that number confusing: the manager rates 1 core as 100%, so 56 cores translates to 5600% CPU power) However, problems start to occur when others are using the cluster as well. I might get 500% CPU power one moment, and just 300% the next. At this point it is actually FASTER to only request 1 thread and get the full 100% power. I'm guessing this is due to the architecture; something with nodes A and B waiting on node C which has been temporarily allocated to my colleague? *So, the questions:* 1. Does NEST prefer CPU or GPU? Is it RAM intensive? I couldn't find this on your website, or anywhere really. Are there ballpark numbers for the memory required for 10^9 connections? 2. Am I abusing the "local_num_threads" mechanic by applying it to a cluster like this? Why is 1 thread sometimes faster than 10 threads? 3. Would switching to MPI help? 4. If so: the documentation says I need to run $NEST_SOURCE_DIR/configure -- with-mpi, but there is no "configure" folder or command to be found anywhere, and this line fails. What and where is this "configure"? Any help would be greatly appreciated. Thank you for your time. Kind regards, Jimmy Mulder

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Open NEST Developer Video Conference Monday 3 June 2019 11.30 CET (UTC+2)
by Dennis Terhorst 02 Jun '19

02 Jun '19

Dear NEST Developers! I would like to invite you to our next bi-weekly Open NEST Developer Video Conference tomorrow Monday 3 June, 11.30-12.30 CET (UTC+2). This is the substitute for the postponed meeting from last week and the missing meeting next week (pentecost). See below for information about how to log into the meeting. The agenda for this meeting is also available online https://github.com/nest/nest-simulator/wiki/2019-06-03-Open-NEST-Developer-… 1. Welcome 2. New features in NEST3 / current developments 3. Review of NEST User Mailing List <https://www.nest-simulator.org/mailinglist/postorius/lists/users.nest-simul…> 4. Review of open Github Pull Request <https://github.com/nest/nest-simulator/pulls> 5. Review of open Github Issues <https://github.com/nest/nest-simulator/issues> See 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 * Enter your name and allow your browser to use camera and microphone * Click green video-call button to open the call panel * In the "Search to call" box at the top right enter *97938800* and connect * 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 -- Dipl.-Phys. Dennis Terhorst Coordinator Software Development Institute of Neuroscience and Medicine (INM-6) Computational and Systems Neuroscience & Theoretical Neuroscience, Institute for Advanced Simulation (IAS-6) Jülich Research Centre, Member of the Helmholz Association and JARA 52425 Jülich, Germany Building 15.22 Room 4004 Phone +49 2461 61-85062 Fax +49 2461 61- 9460 d.terhorst(a)fz-juelich.de

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Open NEST Developer Video Conference Monday 27 May 2019 -- POSTPONED
by Dennis Terhorst 27 May '19

27 May '19

Dear NEST Developers! our next bi-weekly Open NEST Developer Video Conference would be today. However, due to many participants not being available and the next meeting falling on Pentecost Monday we decided to do one meeting on the out-of-phase Monday June 3rd. Monday 3 June, 11.30-12.30 CET (UTC+2). (note: out-of-phase) An invitation to that meeting will be sent separately. best, Dennis Terhorst -- Dipl.-Phys. Dennis Terhorst Coordinator Software Development Institute of Neuroscience and Medicine (INM-6) Computational and Systems Neuroscience & Theoretical Neuroscience, Institute for Advanced Simulation (IAS-6) Jülich Research Centre, Member of the Helmholz Association and JARA 52425 Jülich, Germany Building 15.22 Room 4004 Phone +49 2461 61-85062 Fax +49 2461 61- 9460 d.terhorst(a)fz-juelich.de

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Passing options to recording backends via Python
by Simon Oehrl 23 May '19

23 May '19

Hello everyone, I am currently working on a custom recording backend based on the nestio branch of this fork: https://github.com/jougs/nest-simulator/. I want the user to be able to customize the behavior of my backend from their python code. I can see that the RecordingBackend class has the virtual functions set_status() and get_status() that would enable such a thing and I see that other recording backends implement them accordingly. However, I haven't found an example yet how to get access to the recording backend to call these functions. Can anyone give me hint on how to do that? Kind regards Simon

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Fwd: Re: Nest Neuron Modelling - Tonic Neuron Input and Synaptic Weight Normalization
by Abigail Morrison 20 May '19

20 May '19

Dear Benedikt > 1) Are there any implementations for tonic neuron input, that means an > additional Neuron input channel that mulitplies with all synaptic inputs? We don't have an implementation that does this, but I don't see any reason why you can't make your own. The most effective way to do this is using NESTML, then you don't have to worry about C++ or numerics. A brief description of NESTML with links to publications and Github is here: https://www.fz-juelich.de/ias/jsc/EN/Expertise/SimLab/slns/research/nestml/… we are happy to support you in using this. > > 2) Can synaptic weights be normalized, in particular keeping the sum of > all inputs of a single neuron equal to 1? This is tricky. We did implement something close to this for a paper: https://www.frontiersin.org/articles/10.3389/fncom.2010.00160/full but we did not merge the infrastructure changes with master, because we felt it wasn't general enough. Making a general version would be a large, complicated job. As a workaround, you could consider running your simulation in small time segments, and after each segment you can read-out, sum and normalise the incoming weights for each neuron 'manually' from your simulation script. For a small network this will work fine, but it won't scale. All the best, Abigail -- Prof. Dr. Abigail Morrison IAS-6 / INM-6 / SimLab Neuroscience Jülich Research Center & Institute of Cognitive Neuroscience Ruhr-University Bochum http://www.fz-juelich.de/inm/inm-6 http://www.fz-juelich.de/ias/jsc/slns http://www.ikn.psy.ruhr-uni-bochum.de Office: +49 2461 61-9805 Fax # : +49 2461 61-9460 ------------------------------------------------------------------------------------------------ ------------------------------------------------------------------------------------------------ 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. Sebastian M. Schmidt ------------------------------------------------------------------------------------------------ ------------------------------------------------------------------------------------------------

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PhD scholarship within Data Science and Computational Neuroscience at the Norwegian University of Life Sciences (NMBU)
by Kristin Tøndel 15 May '19

15 May '19

The Faculty of Science and Technology at the Norwegian University of Life Sciences (NMBU) has a vacant 3-year PhD-position related to Data Science and Computational Neuroscience: https://www.jobbnorge.no/en/available-jobs/job/168816/phd-scholarship-withi… Please share with your network. Best regards, Kristin Tøndel

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