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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*

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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

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

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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

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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

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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

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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

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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

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