- NEST Users - NEST Initiative Mail

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

1 0

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

2 1

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

2 1

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

1 0

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

1 0

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

2 1

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

3 2

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

1 1

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.

2 1

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 ****************************************************************

1 0

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

3 3

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

2 2

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

1 0

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.

1 0

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.

1 0

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,

5 5

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 ------------------------------------------------------------------------------------------------ ------------------------------------------------------------------------------------------------

2 2

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

2 3

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

4 5

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 ****************************************************************

2 1

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

2 1

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

2025

2024

2023

2022

2021

2020

2019

NEST Users