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Open NEST Developer Video Conference Monday Feb 27 2023 11:30 CET (UTC+1)
by Dennis Terhorst 27 Feb '23

27 Feb '23

Dear NEST Users & Developers! I would like to invite you to our next fortnightly Open NEST Developer Video Conference, today Monday February 27, 11.30-12.30 CET (UTC+1). * Special topic for the in-depth today will be the introduction to "NEAT" a Neural Analysis Toolkit by @WillemWybo. * Additionally, @heplesser will shed more light on performance optimizations described in #2617: Integrating "deliver events first". Feel free to join the meeting also if it's just to bring your own quick questions for direct discussion in the in-depth section. 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/2023-02-27-Open-NEST-Developer-… Looking forward to seeing you! Cheers, 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

RunManager and STDP connections
by Xavier Otazu 27 Feb '23

27 Feb '23

Hello, In my model I am using STDP synapse connections. When running simulations with nest.Simulate(), everything seems to work fine. When using nest.Run() inside a "with RunManager():" execution is *MUCH* faster, but STDP connections are not updated. Is it a correct behaviour? Thanks a lot in advance, Xavier

3 5

how to record local field potential from the network
by 王梓瑞 21 Feb '23

21 Feb '23

Dear nest community, Is there anyone know how to record local field potential from the network since I only found spike/weight recorder in NEST. Thank you. Best, Zirui

3 2

Collect the calcium concentration of the neuron without structural plasticity
by Maryada Maryada 18 Feb '23

18 Feb '23

Dear NEST Users, I would like to "record" or read calcium concentration of the neurons (let's say aeif_cond_exp). For now Ca variable is 0 before and after I simulate, however the neuron spikes. Is there any neuron model that supports this, or do I need to edit the nestml of the desired model to achieve this. If so, a sample code snippet would be helpful. -- Thanks and Regards *Maryada*

2 2

Open NEST Developer Video Conference Monday Feb 13 2023 11:30 CET (UTC+1)
by Dennis Terhorst 13 Feb '23

13 Feb '23

Dear NEST Users & Developers! I would like to invite you to our next fortnightly Open NEST Developer Video Conference, today Monday February 13, 11.30-12.30 CET (UTC+1). Feel free to join the meeting also if it's just to bring your own quick questions for direct discussion in the in-depth section. 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/2023-02-13-Open-NEST-Developer-… Looking forward to seeing you! Cheers, 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

Fastest way to transfer dense connectivity data in a parallel simulation?
by Robin Gilbert De Schepper 01 Feb '23

01 Feb '23

Hi all! In the world of biophysical detail, it's commonplace that the connectome is generated with algorithms that specify connections as dense tabular data, with each row specifying a synaptic location on a cell pair (SONATA for example). A) In NEST I can't really find the opportunity to fit this data into any of the connection rules: I want to specify pairwise connections from the multiset A to multiset B. - Is this possible with `pairwise bernoulli`, or do the inputs have to be strict sets? - The probability step is superfluous, can it be skipped? B) Then there's the fact that NEST parallelizes transparently, but since this data was generated in parallel by tiling the biological volume, I have neatly fragmented data already available on each node in the distributed cluster. It would be such a waste to communicate all the data to each node, for NEST to communicate and distribute them back another way. The data is too big to allgather and fit into memory of any single node. Not only is this a lot of overhead to implement, but NEST will throw away all but `1 / Nnodes` of the data on each node again, leaving me with a reshuffled version of my starting data. Is there a way to bypass the transparency and to imperatively declare the cells and connections on each machine? -- Robin De Schepper, MSc (they/them) Department of Brain and Behavioral Sciences Unit of Neurophysiology University of Pavia, Italy Via Forlanini 6, 27100 Pavia - Italy Tel: (+39) 038298-7607 http://www-5.unipv.it/dangelo/ Interested in large scale network modelling? Discover our framework <https://bsb.readthedocs.io/en/latest/>: <https://github.com/dbbs-lab/bsb>

3 7

Re: Update: Ablating and executing a small subset of the Allen V1 model (layer23) using cpp intermediate objects where possible.
by Nicolai Haug 31 Jan '23

31 Jan '23

Hi Russell, Being able to easily build and simulate SONATA networks with NEST is hopefully imminent. We currently have a pull request under review which will add native NEST support for networks described by the SONATA format, see https://github.com/nest/nest-simulator/pull/2595. With our implementation, 64 GB of memory is more than sufficient for building and simulating the entire point neuron version of the Allen V1 model. Regarding a downscaled version of the V1 model, this cannot be achieved solely through the JSON configuration file for this particular model. This is due to all layers (V1 nodes) and associated edges being contained in single HDF5 files. In order to use a downscaled V1 model in the context of the upcoming NEST functionality, you would actually need to construct a new set of SONATA files that contain just the nodes and associated edges you are interested in. That is, you have to parse each nodes and edges .h5 and .csv file, extract the relevant entries, create new files and store the relevant entries in correctly named datasets and in the correct order. Unfortunately, I do not know of any examples that can guide you in this endeavour. You could try to reach out to the SONATA developers here https://github.com/AllenInstitute/sonata. They might have some ideas or even readily available examples. Hope this helps! Best regards, Nicolai

1 0

Need help Compiling NEST to use inside Julia
by Russell Jarvis 31 Jan '23

31 Jan '23

Dear Nest mailing list. I am trying to compile NEST to use inside Julia. Surprisingly or unsuprisingly Julia has great tools to support building external modules in cpp and c source code. I am using the tool BinaryBuilder.jl On a linux system with julia installed\, if I type: julia <ENTER> using Pkg Pkg.add("BinaryBuilder.jl") using BinaryBuilder BinaryBuilder.run_wizard() By following the wizard options, I can download the source code https://github.com/nest/nest-simulator.git and build the source tree in an alpine linux sand box. The building of the source tree in Alpine linux is related to how Julia does cross platform builds, an Alpine micro linux build is included with the Julia binary. From there I can optionally include the Binary file: Libtool_jll.jl Then the binary builder drops me into Alpine Linux environment, in order to test out (monkey patch a workable build script). When I navigate to: /workspace/srcdir/nest-simulator-3.3 I can run: sandbox:${WORKSPACE}/srcdir/nest-simulator-3.3 # cmake -DCMAKE_INSTALL_PREFIX=$prefix -DCMAKE_TOOLCHAIN_FILE=${CMAKE_TARGET_TOOLCHAIN} -DCMAKE_BUILD_TYPE=Release -Dwith-python=OFF -Dwith-warning=ON -Dwith-ltdl=ON and then run I get this output: Re-run cmake no build system arguments -- Could NOT find Doxygen (missing: DOXYGEN_EXECUTABLE) -- Host triple: x86_64-pc-linux -- Target triple: x86_64-pc-linux -- Could NOT find Readline (missing: READLINE_LIBRARY NCURSES_LIBRARY READLINE_INCLUDE_DIR) -- Could NOT find GSL (missing: GSL_INCLUDE_DIR GSL_LIBRARY GSL_CBLAS_LIBRARY) (found version "") -- Check the abort exitcode. -- Check the abort exitcode. -- Check the segmentation fault exitcode. -- Check the segmentation fault exitcode. -- Check whether the compiler ignores cmath makros. -- Check whether the compiler ignores cmath makros. OFF -- Check whether the compiler does NOT include <*.h> headers ISO conformant. -- Check whether the compiler does NOT include <*.h> headers ISO conformant. OFF -- Check whether the compiler respects symbolic signal names in signal.h. -- Check whether the compiler respects symbolic signal names in signal.h. OFF -- Check static template member declaration. -- Check static template member declaration. OFF -- Check for STL vector capacity base unity. -- Check for STL vector capacity base unity. ON -- Check for STL vector capacity doubling strategy. -- Check for STL vector capacity doubling strategy. ON -- Check whether the compiler fails with ICE. -- Check whether the compiler fails with ICE. OFF -- Check if ::nan is available from cmath. -- Check if ::nan is available from cmath. ON -- Check if ::isnan is available from cmath. -- Check if ::isnan is available from cmath. ON -- Check if Random123 generators work. PLEASE_FILL_OUT-NOTFOUND -- Check if Random123 generators work. OFF -- NEST version: 3.3 -------------------------------------------------------------------------------- NEST Configuration Summary -------------------------------------------------------------------------------- Build type : Release Target System : Linux Cross Compiling : TRUE C compiler : GNU 4.8.5 (/opt/bin/x86_64-linux-gnu-libgfortran3-cxx03/x86_64-linux-gnu-gcc) C compiler flags : -O2 -Wall -fopenmp -O3 -DNDEBUG C++ compiler : GNU 4.8.5 (/opt/bin/x86_64-linux-gnu-libgfortran3-cxx03/x86_64-linux-gnu-g++) C++ compiler flags : -O2 -std=c++11 -Wall -fopenmp -O3 -DNDEBUG Build dynamic : ON Built-in modules : models User modules : None Python bindings : No Use threading : Yes (OpenMP: -fopenmp) Use GSL : No Use Readline : No Use libltdl : Yes (LTDL 2.4.6) Includes : /opt/x86_64-linux-gnu/x86_64-linux-gnu/sys-root/usr/local/include Libraries : /opt/x86_64-linux-gnu/x86_64-linux-gnu/sys-root/usr/local/lib/libltdl.so Use doxygen : No Use MPI : No Detailed timers : No Use MUSIC : No Use libneurosim : No Use Boost : Yes (Boost 1.79.0) Includes : /workspace/destdir/include Libraries : Use SIONlib : No -------------------------------------------------------------------------------- The NEST executable will be installed to: /workspace/destdir/bin/ NEST dynamic libraries and user modules will be installed to: /workspace/destdir/lib/nest/ Documentation and examples will be installed to: /workspace/destdir/share/doc/nest/ To set necessary environment variables, add the following line to your ~/.bashrc : source /workspace/destdir/bin/nest_vars.sh -------------------------------------------------------------------------------- ATTENTION! You are about to compile NEST without the GNU Scientific Library or your GSL is too old (before v1.11). This means that conductance-based neuron models and some random number generators will not be available. -------------------------------------------------------------------------------- You can now build and install NEST with make make install make installcheck If you experience problems with the installation or the use of NEST, please see https://www.nest-simulator.org/frequently_asked_questions or go to https://www.nest-simulator.org/community to find out how to join the user mailing list. -- Configuring done -- Generating done -- Build files have been written to: /workspace/srcdir/nest-simulator-3.3 sandbox:${WORKSPACE}/srcdir/nest-simulator-3.3 # sandbox:${WORKSPACE}/srcdir/nest-simulator-3.3/make: but when I try to run make I hit this error: [ 26%] Building CXX object nestkernel/CMakeFiles/nestkernel.dir/recording_backend_ascii.cpp.o cd /workspace/srcdir/nest-simulator-3.3/nestkernel && /opt/bin/x86_64-linux-gnu-libgfortran3-cxx03/x86_64-linux-gnu-g++ --sysroot=/opt/x86_64-linux-gnu/x86_64-linux-gnu/sys-root/ -Dnestkernel_EXPORTS -I/workspace/srcdir/nest-simulator-3.3/thirdparty -I/workspace/srcdir/nest-simulator-3.3/libnestutil -I/workspace/srcdir/nest-simulator-3.3/sli -I/workspace/srcdir/nest-simulator-3.3/nestkernel -I/workspace/srcdir/nest-simulator-3.3/nestkernel/spatial -O2 -std=c++11 -Wall -fopenmp -O3 -DNDEBUG -fPIC -fopenmp -MD -MT nestkernel/CMakeFiles/nestkernel.dir/recording_backend_ascii.cpp.o -MF CMakeFiles/nestkernel.dir/recording_backend_ascii.cpp.o.d -o CMakeFiles/nestkernel.dir/recording_backend_ascii.cpp.o -c /workspace/srcdir/nest-simulator-3.3/nestkernel/recording_backend_ascii.cpp In file included from /opt/x86_64-linux-gnu/x86_64-linux-gnu/include/c++/4.8.5/bits/stl_algobase.h:64:0, from /opt/x86_64-linux-gnu/x86_64-linux-gnu/include/c++/4.8.5/bits/char_traits.h:39, from /opt/x86_64-linux-gnu/x86_64-linux-gnu/include/c++/4.8.5/ios:40, from /opt/x86_64-linux-gnu/x86_64-linux-gnu/include/c++/4.8.5/istream:38, from /opt/x86_64-linux-gnu/x86_64-linux-gnu/include/c++/4.8.5/sstream:38, from /workspace/srcdir/nest-simulator-3.3/thirdparty/compose.hpp:36, from /workspace/srcdir/nest-simulator-3.3/nestkernel/recording_backend_ascii.cpp:24: /opt/x86_64-linux-gnu/x86_64-linux-gnu/include/c++/4.8.5/bits/stl_pair.h: In instantiation of ‘constexpr std::pair<_T1, _T2>::pair(const _T1&, const _T2&) [with _T1 = long unsigned int; _T2 = nest::RecordingBackendASCII::DeviceData]’: /opt/x86_64-linux-gnu/x86_64-linux-gnu/include/c++/4.8.5/bits/stl_pair.h:281:72: required from ‘constexpr std::pair<typename std::__decay_and_strip<_Tp>::__type, typename std::__decay_and_strip<_T2>::__type> std::make_pair(_T1&&, _T2&&) [with _T1 = const long unsigned int&; _T2 = nest::RecordingBackendASCII::DeviceData; typename std::__decay_and_strip<_T2>::__type = nest::RecordingBackendASCII::DeviceData; typename std::__decay_and_strip<_Tp>::__type = long unsigned int]’ /workspace/srcdir/nest-simulator-3.3/nestkernel/recording_backend_ascii.cpp:69:108: required from here /opt/x86_64-linux-gnu/x86_64-linux-gnu/include/c++/4.8.5/bits/stl_pair.h:113:31: error: use of deleted function ‘nest::RecordingBackendASCII::DeviceData::DeviceData(const nest::RecordingBackendASCII::DeviceData&)’ : first(__a), second(__b) { } ^ In file included from /workspace/srcdir/nest-simulator-3.3/nestkernel/recording_backend_ascii.cpp:33:0: /workspace/srcdir/nest-simulator-3.3/nestkernel/recording_backend_ascii.h:195:10: note: ‘nest::RecordingBackendASCII::DeviceData::DeviceData(const nest::RecordingBackendASCII::DeviceData&)’ is implicitly deleted because the default definition would be ill-formed: struct DeviceData ^ /workspace/srcdir/nest-simulator-3.3/nestkernel/recording_backend_ascii.h:195:10: error: use of deleted function ‘std::basic_ofstream<char>::basic_ofstream(const std::basic_ofstream<char>&)’ In file included from /workspace/srcdir/nest-simulator-3.3/nestkernel/recording_device.h:27:0, from /workspace/srcdir/nest-simulator-3.3/nestkernel/recording_backend_ascii.cpp:27: /opt/x86_64-linux-gnu/x86_64-linux-gnu/include/c++/4.8.5/fstream:599:11: note: ‘std::basic_ofstream<char>::basic_ofstream(const std::basic_ofstream<char>&)’ is implicitly deleted because the default definition would be ill-formed: class basic_ofstream : public basic_ostream<_CharT,_Traits> ^ /opt/x86_64-linux-gnu/x86_64-linux-gnu/include/c++/4.8.5/fstream:599:11: error: use of deleted function ‘std::basic_ostream<char>::basic_ostream(const std::basic_ostream<char>&)’ In file included from /opt/x86_64-linux-gnu/x86_64-linux-gnu/include/c++/4.8.5/istream:39:0, from /opt/x86_64-linux-gnu/x86_64-linux-gnu/include/c++/4.8.5/sstream:38, from /workspace/srcdir/nest-simulator-3.3/thirdparty/compose.hpp:36, from /workspace/srcdir/nest-simulator-3.3/nestkernel/recording_backend_ascii.cpp:24: /opt/x86_64-linux-gnu/x86_64-linux-gnu/include/c++/4.8.5/ostream:58:11: note: ‘std::basic_ostream<char>::basic_ostream(const std::basic_ostream<char>&)’ is implicitly deleted because the default definition would be ill-formed: class basic_ostream : virtual public basic_ios<_CharT, _Traits> ^ /opt/x86_64-linux-gnu/x86_64-linux-gnu/include/c++/4.8.5/ostream:58:11: error: use of deleted function ‘std::basic_ios<char>::basic_ios(const std::basic_ios<char>&)’ In file included from /opt/x86_64-linux-gnu/x86_64-linux-gnu/include/c++/4.8.5/ios:44:0, from /opt/x86_64-linux-gnu/x86_64-linux-gnu/include/c++/4.8.5/istream:38, from /opt/x86_64-linux-gnu/x86_64-linux-gnu/include/c++/4.8.5/sstream:38, from /workspace/srcdir/nest-simulator-3.3/thirdparty/compose.hpp:36, from /workspace/srcdir/nest-simulator-3.3/nestkernel/recording_backend_ascii.cpp:24: /opt/x86_64-linux-gnu/x86_64-linux-gnu/include/c++/4.8.5/bits/basic_ios.h:66:11: note: ‘std::basic_ios<char>::basic_ios(const std::basic_ios<char>&)’ is implicitly deleted because the default definition would be ill-formed: class basic_ios : public ios_base ^ In file included from /opt/x86_64-linux-gnu/x86_64-linux-gnu/include/c++/4.8.5/ios:42:0, from /opt/x86_64-linux-gnu/x86_64-linux-gnu/include/c++/4.8.5/istream:38, from /opt/x86_64-linux-gnu/x86_64-linux-gnu/include/c++/4.8.5/sstream:38, from /workspace/srcdir/nest-simulator-3.3/thirdparty/compose.hpp:36, from /workspace/srcdir/nest-simulator-3.3/nestkernel/recording_backend_ascii.cpp:24: /opt/x86_64-linux-gnu/x86_64-linux-gnu/include/c++/4.8.5/bits/ios_base.h:786:5: error: ‘std::ios_base::ios_base(const std::ios_base&)’ is private ios_base(const ios_base&); ^ In file included from /opt/x86_64-linux-gnu/x86_64-linux-gnu/include/c++/4.8.5/ios:44:0, from /opt/x86_64-linux-gnu/x86_64-linux-gnu/include/c++/4.8.5/istream:38, from /opt/x86_64-linux-gnu/x86_64-linux-gnu/include/c++/4.8.5/sstream:38, from /workspace/srcdir/nest-simulator-3.3/thirdparty/compose.hpp:36, from /workspace/srcdir/nest-simulator-3.3/nestkernel/recording_backend_ascii.cpp:24: /opt/x86_64-linux-gnu/x86_64-linux-gnu/include/c++/4.8.5/bits/basic_ios.h:66:11: error: within this context class basic_ios : public ios_base ^ In file included from /workspace/srcdir/nest-simulator-3.3/nestkernel/recording_device.h:27:0, from /workspace/srcdir/nest-simulator-3.3/nestkernel/recording_backend_ascii.cpp:27: /opt/x86_64-linux-gnu/x86_64-linux-gnu/include/c++/4.8.5/fstream:599:11: error: use of deleted function ‘std::basic_ios<char>::basic_ios(const std::basic_ios<char>&)’ class basic_ofstream : public basic_ostream<_CharT,_Traits> ^ /opt/x86_64-linux-gnu/x86_64-linux-gnu/include/c++/4.8.5/fstream:599:11: error: use of deleted function ‘std::basic_filebuf<char>::basic_filebuf(const std::basic_filebuf<char>&)’ /opt/x86_64-linux-gnu/x86_64-linux-gnu/include/c++/4.8.5/fstream:72:11: note: ‘std::basic_filebuf<char>::basic_filebuf(const std::basic_filebuf<char>&)’ is implicitly deleted because the default definition would be ill-formed: class basic_filebuf : public basic_streambuf<_CharT, _Traits> ^ In file included from /opt/x86_64-linux-gnu/x86_64-linux-gnu/include/c++/4.8.5/ios:43:0, from /opt/x86_64-linux-gnu/x86_64-linux-gnu/include/c++/4.8.5/istream:38, from /opt/x86_64-linux-gnu/x86_64-linux-gnu/include/c++/4.8.5/sstream:38, from /workspace/srcdir/nest-simulator-3.3/thirdparty/compose.hpp:36, from /workspace/srcdir/nest-simulator-3.3/nestkernel/recording_backend_ascii.cpp:24: /opt/x86_64-linux-gnu/x86_64-linux-gnu/include/c++/4.8.5/streambuf:802:7: error: ‘std::basic_streambuf<_CharT, _Traits>::basic_streambuf(const std::basic_streambuf<_CharT, _Traits>&) [with _CharT = char; _Traits = std::char_traits<char>]’ is private basic_streambuf(const basic_streambuf& __sb) ^ In file included from /workspace/srcdir/nest-simulator-3.3/nestkernel/recording_device.h:27:0, from /workspace/srcdir/nest-simulator-3.3/nestkernel/recording_backend_ascii.cpp:27: /opt/x86_64-linux-gnu/x86_64-linux-gnu/include/c++/4.8.5/fstream:72:11: error: within this context class basic_filebuf : public basic_streambuf<_CharT, _Traits> ^ In file included from /opt/x86_64-linux-gnu/x86_64-linux-gnu/include/c++/4.8.5/bits/stl_algobase.h:64:0, from /opt/x86_64-linux-gnu/x86_64-linux-gnu/include/c++/4.8.5/bits/char_traits.h:39, from /opt/x86_64-linux-gnu/x86_64-linux-gnu/include/c++/4.8.5/ios:40, from /opt/x86_64-linux-gnu/x86_64-linux-gnu/include/c++/4.8.5/istream:38, from /opt/x86_64-linux-gnu/x86_64-linux-gnu/include/c++/4.8.5/sstream:38, from /workspace/srcdir/nest-simulator-3.3/thirdparty/compose.hpp:36, from /workspace/srcdir/nest-simulator-3.3/nestkernel/recording_backend_ascii.cpp:24: /opt/x86_64-linux-gnu/x86_64-linux-gnu/include/c++/4.8.5/bits/stl_pair.h: In instantiation of ‘constexpr std::pair<typename std::__decay_and_strip<_Tp>::__type, typename std::__decay_and_strip<_T2>::__type> std::make_pair(_T1&&, _T2&&) [with _T1 = const long unsigned int&; _T2 = nest::RecordingBackendASCII::DeviceData; typename std::__decay_and_strip<_T2>::__type = nest::RecordingBackendASCII::DeviceData; typename std::__decay_and_strip<_Tp>::__type = long unsigned int]’: /workspace/srcdir/nest-simulator-3.3/nestkernel/recording_backend_ascii.cpp:69:108: required from here /opt/x86_64-linux-gnu/x86_64-linux-gnu/include/c++/4.8.5/bits/stl_pair.h:281:72: error: use of deleted function ‘constexpr std::pair<_T1, _T2>::pair(std::pair<_T1, _T2>&&) [with _T1 = long unsigned int; _T2 = nest::RecordingBackendASCII::DeviceData]’ return __pair_type(std::forward<_T1>(__x), std::forward<_T2>(__y)); ^ /opt/x86_64-linux-gnu/x86_64-linux-gnu/include/c++/4.8.5/bits/stl_pair.h:128:17: note: ‘constexpr std::pair<_T1, _T2>::pair(std::pair<_T1, _T2>&&) [with _T1 = long unsigned int; _T2 = nest::RecordingBackendASCII::DeviceData]’ is implicitly deleted because the default definition would be ill-formed: constexpr pair(pair&&) = default; ^ /opt/x86_64-linux-gnu/x86_64-linux-gnu/include/c++/4.8.5/bits/stl_pair.h:128:17: error: use of deleted function ‘nest::RecordingBackendASCII::DeviceData::DeviceData(nest::RecordingBackendASCII::DeviceData&&)’ In file included from /workspace/srcdir/nest-simulator-3.3/nestkernel/recording_backend_ascii.cpp:33:0: /workspace/srcdir/nest-simulator-3.3/nestkernel/recording_backend_ascii.h:195:10: note: ‘nest::RecordingBackendASCII::DeviceData::DeviceData(nest::RecordingBackendASCII::DeviceData&&)’ is implicitly deleted because the default definition would be ill-formed: struct DeviceData ^ /workspace/srcdir/nest-simulator-3.3/nestkernel/recording_backend_ascii.h:195:10: error: use of deleted function ‘std::basic_ofstream<char>::basic_ofstream(const std::basic_ofstream<char>&)’ /workspace/srcdir/nest-simulator-3.3/nestkernel/recording_backend_ascii.cpp: In member function ‘virtual void nest::RecordingBackendASCII::enroll(const nest::RecordingDevice&, const DictionaryDatum&)’: /workspace/srcdir/nest-simulator-3.3/nestkernel/recording_backend_ascii.cpp:69:110: error: no matching function for call to ‘std::map<long unsigned int, nest::RecordingBackendASCII::DeviceData>::insert(std::pair<long unsigned int, nest::RecordingBackendASCII::DeviceData>)’ auto p = device_data_[ t ].insert( std::make_pair( node_id, DeviceData( modelname, vp_node_id_string ) ) ); ^ /workspace/srcdir/nest-simulator-3.3/nestkernel/recording_backend_ascii.cpp:69:110: note: candidates are: In file included from /opt/x86_64-linux-gnu/x86_64-linux-gnu/include/c++/4.8.5/map:61:0, from /workspace/srcdir/nest-simulator-3.3/thirdparty/compose.hpp:39, from /workspace/srcdir/nest-simulator-3.3/nestkernel/recording_backend_ascii.cpp:24: /opt/x86_64-linux-gnu/x86_64-linux-gnu/include/c++/4.8.5/bits/stl_map.h:594:7: note: std::pair<typename std::_Rb_tree<_Key, std::pair<const _Key, _Tp>, std::_Select1st<std::pair<const _Key, _Tp> >, _Compare, typename _Alloc::rebind<std::pair<const _Key, _Tp> >::other>::iterator, bool> std::map<_Key, _Tp, _Compare, _Alloc>::insert(const value_type&) [with _Key = long unsigned int; _Tp = nest::RecordingBackendASCII::DeviceData; _Compare = std::less<long unsigned int>; _Alloc = std::allocator<std::pair<const long unsigned int, nest::RecordingBackendASCII::DeviceData> >; typename std::_Rb_tree<_Key, std::pair<const _Key, _Tp>, std::_Select1st<std::pair<const _Key, _Tp> >, _Compare, typename _Alloc::rebind<std::pair<const _Key, _Tp> >::other>::iterator = std::_Rb_tree_iterator<std::pair<const long unsigned int, nest::RecordingBackendASCII::DeviceData> >; std::map<_Key, _Tp, _Compare, _Alloc>::value_type = std::pair<const long unsigned int, nest::RecordingBackendASCII::DeviceData>] insert(const value_type& __x) ^ /opt/x86_64-linux-gnu/x86_64-linux-gnu/include/c++/4.8.5/bits/stl_map.h:594:7: note: no known conversion for argument 1 from ‘std::pair<long unsigned int, nest::RecordingBackendASCII::DeviceData>’ to ‘const value_type& {aka const std::pair<const long unsigned int, nest::RecordingBackendASCII::DeviceData>&}’ /opt/x86_64-linux-gnu/x86_64-linux-gnu/include/c++/4.8.5/bits/stl_map.h:602:9: note: template<class _Pair, class> std::pair<typename std::_Rb_tree<_Key, std::pair<const _Key, _Tp>, std::_Select1st<std::pair<const _Key, _Tp> >, _Compare, typename _Alloc::rebind<std::pair<const _Key, _Tp> >::other>::iterator, bool> std::map<_Key, _Tp, _Compare, _Alloc>::insert(_Pair&&) [with _Pair = _Pair; <template-parameter-2-2> = <template-parameter-1-2>; _Key = long unsigned int; _Tp = nest::RecordingBackendASCII::DeviceData; _Compare = std::less<long unsigned int>; _Alloc = std::allocator<std::pair<const long unsigned int, nest::RecordingBackendASCII::DeviceData> >] insert(_Pair&& __x) ^ /opt/x86_64-linux-gnu/x86_64-linux-gnu/include/c++/4.8.5/bits/stl_map.h:602:9: note: template argument deduction/substitution failed: /opt/x86_64-linux-gnu/x86_64-linux-gnu/include/c++/4.8.5/bits/stl_map.h:598:32: error: no type named ‘type’ in ‘struct std::enable_if<false, void>’ template<typename _Pair, typename = typename ^ /opt/x86_64-linux-gnu/x86_64-linux-gnu/include/c++/4.8.5/bits/stl_map.h:615:7: note: void std::map<_Key, _Tp, _Compare, _Alloc>::insert(std::initializer_list<std::pair<const _Key, _Tp> >) [with _Key = long unsigned int; _Tp = nest::RecordingBackendASCII::DeviceData; _Compare = std::less<long unsigned int>; _Alloc = std::allocator<std::pair<const long unsigned int, nest::RecordingBackendASCII::DeviceData> >] insert(std::initializer_list<value_type> __list) ^ /opt/x86_64-linux-gnu/x86_64-linux-gnu/include/c++/4.8.5/bits/stl_map.h:615:7: note: no known conversion for argument 1 from ‘std::pair<long unsigned int, nest::RecordingBackendASCII::DeviceData>’ to ‘std::initializer_list<std::pair<const long unsigned int, nest::RecordingBackendASCII::DeviceData> >’ /opt/x86_64-linux-gnu/x86_64-linux-gnu/include/c++/4.8.5/bits/stl_map.h:644:7: note: std::map<_Key, _Tp, _Compare, _Alloc>::iterator std::map<_Key, _Tp, _Compare, _Alloc>::insert(std::map<_Key, _Tp, _Compare, _Alloc>::const_iterator, const value_type&) [with _Key = long unsigned int; _Tp = nest::RecordingBackendASCII::DeviceData; _Compare = std::less<long unsigned int>; _Alloc = std::allocator<std::pair<const long unsigned int, nest::RecordingBackendASCII::DeviceData> >; std::map<_Key, _Tp, _Compare, _Alloc>::iterator = std::_Rb_tree_iterator<std::pair<const long unsigned int, nest::RecordingBackendASCII::DeviceData> >; std::map<_Key, _Tp, _Compare, _Alloc>::const_iterator = std::_Rb_tree_const_iterator<std::pair<const long unsigned int, nest::RecordingBackendASCII::DeviceData> >; std::map<_Key, _Tp, _Compare, _Alloc>::value_type = std::pair<const long unsigned int, nest::RecordingBackendASCII::DeviceData>] insert(const_iterator __position, const value_type& __x) ^ /opt/x86_64-linux-gnu/x86_64-linux-gnu/include/c++/4.8.5/bits/stl_map.h:644:7: note: candidate expects 2 arguments, 1 provided /opt/x86_64-linux-gnu/x86_64-linux-gnu/include/c++/4.8.5/bits/stl_map.h:655:9: note: template<class _Pair, class> std::map<_Key, _Tp, _Compare, _Alloc>::iterator std::map<_Key, _Tp, _Compare, _Alloc>::insert(std::map<_Key, _Tp, _Compare, _Alloc>::const_iterator, _Pair&&) [with _Pair = _Pair; <template-parameter-2-2> = <template-parameter-1-2>; _Key = long unsigned int; _Tp = nest::RecordingBackendASCII::DeviceData; _Compare = std::less<long unsigned int>; _Alloc = std::allocator<std::pair<const long unsigned int, nest::RecordingBackendASCII::DeviceData> >] insert(const_iterator __position, _Pair&& __x) ^ /opt/x86_64-linux-gnu/x86_64-linux-gnu/include/c++/4.8.5/bits/stl_map.h:655:9: note: template argument deduction/substitution failed: /workspace/srcdir/nest-simulator-3.3/nestkernel/recording_backend_ascii.cpp:69:110: note: cannot convert ‘std::make_pair(_T1&&, _T2&&) [with _T1 = const long unsigned int&; _T2 = nest::RecordingBackendASCII::DeviceData; typename std::__decay_and_strip<_T2>::__type = nest::RecordingBackendASCII::DeviceData; typename std::__decay_and_strip<_Tp>::__type = long unsigned int]((* & nest::RecordingBackendASCII::DeviceData(std::basic_string<char>((*(const std::basic_string<char>*)(& modelname))), std::basic_string<char>((*(const std::basic_string<char>*)(& vp_node_id_string))))))’ (type ‘std::pair<long unsigned int, nest::RecordingBackendASCII::DeviceData>’) to type ‘std::map<long unsigned int, nest::RecordingBackendASCII::DeviceData>::const_iterator {aka std::_Rb_tree_const_iterator<std::pair<const long unsigned int, nest::RecordingBackendASCII::DeviceData> >}’ auto p = device_data_[ t ].insert( std::make_pair( node_id, DeviceData( modelname, vp_node_id_string ) ) ); ^ In file included from /opt/x86_64-linux-gnu/x86_64-linux-gnu/include/c++/4.8.5/map:61:0, from /workspace/srcdir/nest-simulator-3.3/thirdparty/compose.hpp:39, from /workspace/srcdir/nest-simulator-3.3/nestkernel/recording_backend_ascii.cpp:24: /opt/x86_64-linux-gnu/x86_64-linux-gnu/include/c++/4.8.5/bits/stl_map.h:670:9: note: template<class _InputIterator> void std::map<_Key, _Tp, _Compare, _Alloc>::insert(_InputIterator, _InputIterator) [with _InputIterator = _InputIterator; _Key = long unsigned int; _Tp = nest::RecordingBackendASCII::DeviceData; _Compare = std::less<long unsigned int>; _Alloc = std::allocator<std::pair<const long unsigned int, nest::RecordingBackendASCII::DeviceData> >] insert(_InputIterator __first, _InputIterator __last) ^ /opt/x86_64-linux-gnu/x86_64-linux-gnu/include/c++/4.8.5/bits/stl_map.h:670:9: note: template argument deduction/substitution failed: /workspace/srcdir/nest-simulator-3.3/nestkernel/recording_backend_ascii.cpp:69:110: note: candidate expects 2 arguments, 1 provided auto p = device_data_[ t ].insert( std::make_pair( node_id, DeviceData( modelname, vp_node_id_string ) ) ); ^ /workspace/srcdir/nest-simulator-3.3/nestkernel/recording_backend_ascii.cpp: In member function ‘void nest::RecordingBackendASCII::DeviceData::open_file()’: /workspace/srcdir/nest-simulator-3.3/nestkernel/recording_backend_ascii.cpp:266:9: error: use of deleted function ‘std::basic_ofstream<char>& std::basic_ofstream<char>::operator=(const std::basic_ofstream<char>&)’ file_ = std::ofstream( filename.c_str() ); ^ In file included from /workspace/srcdir/nest-simulator-3.3/nestkernel/recording_device.h:27:0, from /workspace/srcdir/nest-simulator-3.3/nestkernel/recording_backend_ascii.cpp:27: /opt/x86_64-linux-gnu/x86_64-linux-gnu/include/c++/4.8.5/fstream:599:11: note: ‘std::basic_ofstream<char>& std::basic_ofstream<char>::operator=(const std::basic_ofstream<char>&)’ is implicitly deleted because the default definition would be ill-formed: class basic_ofstream : public basic_ostream<_CharT,_Traits> ^ /opt/x86_64-linux-gnu/x86_64-linux-gnu/include/c++/4.8.5/fstream:599:11: error: use of deleted function ‘std::basic_ostream<char>& std::basic_ostream<char>::operator=(const std::basic_ostream<char>&)’ In file included from /opt/x86_64-linux-gnu/x86_64-linux-gnu/include/c++/4.8.5/istream:39:0, from /opt/x86_64-linux-gnu/x86_64-linux-gnu/include/c++/4.8.5/sstream:38, from /workspace/srcdir/nest-simulator-3.3/thirdparty/compose.hpp:36, from /workspace/srcdir/nest-simulator-3.3/nestkernel/recording_backend_ascii.cpp:24: /opt/x86_64-linux-gnu/x86_64-linux-gnu/include/c++/4.8.5/ostream:58:11: note: ‘std::basic_ostream<char>& std::basic_ostream<char>::operator=(const std::basic_ostream<char>&)’ is implicitly deleted because the default definition would be ill-formed: class basic_ostream : virtual public basic_ios<_CharT, _Traits> ^ /opt/x86_64-linux-gnu/x86_64-linux-gnu/include/c++/4.8.5/ostream:58:11: error: use of deleted function ‘std::basic_ios<char>& std::basic_ios<char>::operator=(const std::basic_ios<char>&)’ In file included from /opt/x86_64-linux-gnu/x86_64-linux-gnu/include/c++/4.8.5/ios:44:0, from /opt/x86_64-linux-gnu/x86_64-linux-gnu/include/c++/4.8.5/istream:38, from /opt/x86_64-linux-gnu/x86_64-linux-gnu/include/c++/4.8.5/sstream:38, from /workspace/srcdir/nest-simulator-3.3/thirdparty/compose.hpp:36, from /workspace/srcdir/nest-simulator-3.3/nestkernel/recording_backend_ascii.cpp:24: /opt/x86_64-linux-gnu/x86_64-linux-gnu/include/c++/4.8.5/bits/basic_ios.h:66:11: note: ‘std::basic_ios<char>& std::basic_ios<char>::operator=(const std::basic_ios<char>&)’ is implicitly deleted because the default definition would be ill-formed: class basic_ios : public ios_base ^ In file included from /opt/x86_64-linux-gnu/x86_64-linux-gnu/include/c++/4.8.5/ios:42:0, from /opt/x86_64-linux-gnu/x86_64-linux-gnu/include/c++/4.8.5/istream:38, from /opt/x86_64-linux-gnu/x86_64-linux-gnu/include/c++/4.8.5/sstream:38, from /workspace/srcdir/nest-simulator-3.3/thirdparty/compose.hpp:36, from /workspace/srcdir/nest-simulator-3.3/nestkernel/recording_backend_ascii.cpp:24: /opt/x86_64-linux-gnu/x86_64-linux-gnu/include/c++/4.8.5/bits/ios_base.h:789:5: error: ‘std::ios_base& std::ios_base::operator=(const std::ios_base&)’ is private operator=(const ios_base&); ^ In file included from /opt/x86_64-linux-gnu/x86_64-linux-gnu/include/c++/4.8.5/ios:44:0, from /opt/x86_64-linux-gnu/x86_64-linux-gnu/include/c++/4.8.5/istream:38, from /opt/x86_64-linux-gnu/x86_64-linux-gnu/include/c++/4.8.5/sstream:38, from /workspace/srcdir/nest-simulator-3.3/thirdparty/compose.hpp:36, from /workspace/srcdir/nest-simulator-3.3/nestkernel/recording_backend_ascii.cpp:24: /opt/x86_64-linux-gnu/x86_64-linux-gnu/include/c++/4.8.5/bits/basic_ios.h:66:11: error: within this context class basic_ios : public ios_base ^ In file included from /workspace/srcdir/nest-simulator-3.3/nestkernel/recording_device.h:27:0, from /workspace/srcdir/nest-simulator-3.3/nestkernel/recording_backend_ascii.cpp:27: /opt/x86_64-linux-gnu/x86_64-linux-gnu/include/c++/4.8.5/fstream:599:11: error: use of deleted function ‘std::basic_filebuf<char>& std::basic_filebuf<char>::operator=(const std::basic_filebuf<char>&)’ class basic_ofstream : public basic_ostream<_CharT,_Traits> ^ /opt/x86_64-linux-gnu/x86_64-linux-gnu/include/c++/4.8.5/fstream:72:11: note: ‘std::basic_filebuf<char>& std::basic_filebuf<char>::operator=(const std::basic_filebuf<char>&)’ is implicitly deleted because the default definition would be ill-formed: class basic_filebuf : public basic_streambuf<_CharT, _Traits> ^ In file included from /opt/x86_64-linux-gnu/x86_64-linux-gnu/include/c++/4.8.5/ios:43:0, from /opt/x86_64-linux-gnu/x86_64-linux-gnu/include/c++/4.8.5/istream:38, from /opt/x86_64-linux-gnu/x86_64-linux-gnu/include/c++/4.8.5/sstream:38, from /workspace/srcdir/nest-simulator-3.3/thirdparty/compose.hpp:36, from /workspace/srcdir/nest-simulator-3.3/nestkernel/recording_backend_ascii.cpp:24: /opt/x86_64-linux-gnu/x86_64-linux-gnu/include/c++/4.8.5/streambuf:810:7: error: ‘std::basic_streambuf<_CharT, _Traits>& std::basic_streambuf<_CharT, _Traits>::operator=(const std::basic_streambuf<_CharT, _Traits>&) [with _CharT = char; _Traits = std::char_traits<char>]’ is private operator=(const basic_streambuf&) { return *this; }; ^ In file included from /workspace/srcdir/nest-simulator-3.3/nestkernel/recording_device.h:27:0, from /workspace/srcdir/nest-simulator-3.3/nestkernel/recording_backend_ascii.cpp:27: /opt/x86_64-linux-gnu/x86_64-linux-gnu/include/c++/4.8.5/fstream:72:11: error: within this context class basic_filebuf : public basic_streambuf<_CharT, _Traits> ^ make[2]: *** [nestkernel/CMakeFiles/nestkernel.dir/build.make:818: nestkernel/CMakeFiles/nestkernel.dir/recording_backend_ascii.cpp.o] Error 1 make[2]: Leaving directory '/workspace/srcdir/nest-simulator-3.3' make[1]: *** [CMakeFiles/Makefile2:772: nestkernel/CMakeFiles/nestkernel.dir/all] Error 2 make[1]: Leaving directory '/workspace/srcdir/nest-simulator-3.3' make: *** [Makefile:146: all] Error 2 I wonder if the problem might be the GCC version? From this source it looks like 4.8.5 is the default GCC version https://github.com/JuliaPackaging/Yggdrasil/blob/master/RootFS.md#compiler-… GCC Binutils libgfortran SONAME libstdc++ SONAME string ABI 4.8.5 2.24 libgfortran.so.3 libstdc++.so.6.0.19 cxx03 5.2.0 2.25.1 libgfortran.so.3 libstdc++.so.6.0.21 cxx11 6.1.0* 2.26 libgfortran.so.3 libstdc++.so.6.0.22 cxx11 7.1.0 2.27 libgfortran.so.4 libstdc++.so.6.0.23 cxx11 8.1.0 2.31 libgfortran.so.5 libstdc++.so.6.0.25 cxx11 9.1.0 2.33.1 libgfortran.so.5 libstdc++.so.6.0.26 cxx11 10.2.0 2.34 libgfortran.so.5 libstdc++.so.6.0.28 cxx11 11.1.0 2.36 libgfortran.so.5 libstdc++.so.6.0.29 cxx11 Also I wonder if any one has any hints about what to try? I have noticed the Ubuntu Nest dependencies in the Dockerfile here: https://github.com/nest/nest-docker/blob/master/src/base/Dockerfile-build-b… Many of those dependencies have Alpine counter parts, but I'd rather not try to randomly install them. Russell.

3 5

Open NEST Developer Video Conference Monday Jan 30 2023 11:30 CET (UTC+1)
by Dennis Terhorst 30 Jan '23

30 Jan '23

Dear NEST Users & Developers! I would like to invite you to our next fortnightly Open NEST Developer Video Conference, today Monday January 30, 11.30-12.30 CET (UTC+1). Feel free to join the meeting also if it's just to bring your own quick questions for direct discussion in the in-depth section. 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/2023-01-30-Open-NEST-Developer-… Looking forward to seeing you! Cheers, 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

current recording for gap junction
by Hanjia Jiang 30 Jan '23

30 Jan '23

Dear all, I would like to ask if there is a way to measure the actual current that is transmitted through the gap junction in NEST. With the example file gap_junctions_two_neuron.py, I tried to use weight_recorder for the gap junction, but only got a constant value of 0.5 (which is the "weight" set in this file). It seems the "weight" here is only the conductance in nS, after I quickly read the reference Hahne et al., 2015 <https://www.frontiersin.org/articles/10.3389/fninf.2015.00022/full>. Is there a way in PyNEST to record the gap junction current? Thank you for answering! p.s. This is because I am developing astrocyte network models with NEST, which uses a "sic_connection" (slow inward current connection) that is adapted from gap_junction. I am trying to record its current in PyNEST if possible. Unfortunately because the other collaborators developed the sic_connection back then a while ago, I myself do not have an answer to this. I will try other indirect methods, if there is no way to do such a recording in PyNEST. If you have any relevant suggestions, please also kindly let me know. Thanks again. Happy new year, Han-Jia

2 1

Subsetting and executing a small subset of the Allen V1 model (layer23) using cpp intermediate objects where possible.
by Russell Jarvis 28 Jan '23

28 Jan '23

Hi there, I would like to subset and execute the subset of the Allen V1 model. I am also hoping to store intermediate simulation configuration files not as Python code, but if possible as cpp code. I am wondering if there is a way of storing the matrices in a cpp native way? Forinstance I have noticed the class https://github.com/nest/nest-simulator/blob/master/nestkernel/connection_ma… I think that this would class may have I acquired the config.json file from DropBox and all of the assoicated hdf5, and csv files from here: https://www.dropbox.com/sh/w5u31m3hq6u2x5m/AAB0B6OLRyLJwxCKjuWrG26pa/simula… I have found the nodes in the model pertaining to only layer 23 by wrangling data frames in Julia (see the code below). Calling the method `extract_subset` is slower than I would like. I suspect it would be faster to use the SL or /nest_kernel more directly, but I don't know what interventions I would need to do to get the PyNest instance to dump its intermediate objects in a cpp native way. I wonder if any one has any hints on how to do this? subset0 = get_layer_sub_net("i23Htr3a") subset1 = get_layer_sub_net("i23Pvalb") subset2 = get_layer_sub_net("i23Sst") subset3 = get_layer_sub_net("e23Cux2") For instance I would like to be able to use the nestkernel CLI to save using Pkg using Conda using PyCall ENV["PYTHON"] = $HOME/.julia/conda/3/lib/python3.10/ Pkg.build("PyCall") py""" def init_sim_to_call_from_julia():#slice_start,slice_end,nest=None,sim=None) import os, sys import math import numpy as np from bmtk.simulator import pointnet from bmtk.simulator.pointnet.pyfunction_cache import synaptic_weight from bmtk.simulator.pointnet.io_tools import io import nest import h5py try: nest.Install('glifmodule') except Exception as e: pass @synaptic_weight def DirectionRule_others(edges, src_nodes, trg_nodes): src_tuning = src_nodes['tuning_angle'].values tar_tuning = trg_nodes['tuning_angle'].values sigma = edges['weight_sigma'].values nsyn = edges['nsyns'].values syn_weight = edges['syn_weight'].values delta_tuning_180 = np.abs(np.abs(np.mod(np.abs(tar_tuning - src_tuning), 360.0) - 180.0) - 180.0) w_multiplier_180 = np.exp(-(delta_tuning_180 / sigma) ** 2) return syn_weight * w_multiplier_180 * nsyn @synaptic_weight def DirectionRule_EE(edges, src_nodes, trg_nodes): src_tuning = src_nodes['tuning_angle'].values tar_tuning = trg_nodes['tuning_angle'].values x_tar = trg_nodes['x'].values x_src = src_nodes['x'].values z_tar = trg_nodes['z'].values z_src = src_nodes['z'].values sigma = edges['weight_sigma'].values nsyn = edges['nsyns'].values syn_weight = edges['syn_weight'].values delta_tuning_180 = np.abs(np.abs(np.mod(np.abs(tar_tuning - src_tuning), 360.0) - 180.0) - 180.0) w_multiplier_180 = np.exp(-(delta_tuning_180 / sigma) ** 2) delta_x = (x_tar - x_src) * 0.07 delta_z = (z_tar - z_src) * 0.04 theta_pref = tar_tuning * (np.pi / 180.) xz = delta_x * np.cos(theta_pref) + delta_z * np.sin(theta_pref) sigma_phase = 1.0 phase_scale_ratio = np.exp(- (xz ** 2 / (2 * sigma_phase ** 2))) # To account for the 0.07 vs 0.04 dimensions. This ensures the horizontal neurons are scaled by 5.5/4 (from the # midpoint of 4 & 7). Also, ensures the vertical is scaled by 5.5/7. This was a basic linear estimate to get the # numbers (y = ax + b). theta_tar_scale = abs(abs(abs(180.0 - np.mod(np.abs(tar_tuning), 360.0)) - 90.0) - 90.0) phase_scale_ratio = phase_scale_ratio * (5.5 / 4.0 - 11.0 / 1680.0 * theta_tar_scale) return syn_weight * w_multiplier_180 * phase_scale_ratio * nsyn def main(config_file): configure = pointnet.Config.from_json(config_file) configure.build_env() graph = pointnet.PointNetwork.from_config(configure) sim = pointnet.PointSimulator.from_config(configure, graph) node_info = list(graph.get_node_populations()) dfv1 = node_info[0].nodes_df() pop_names = { k:v for k,v in zip(dfv1.index,dfv1["pop_name"].values) } dfv1e = dfv1[dfv1["ei"] == "e"].index dfv1i = dfv1[dfv1["ei"] == "i"].index dfv1e_pop = dfv1[dfv1["ei"] == "e"]["pop_name"].values dfv1i_pop = dfv1[dfv1["ei"] == "i"]["pop_name"].values lgn = node_info[1].nodes_df() lgne = lgn[lgn["ei"] == "e"].index return nest,sim,node_info,dfv1e,dfv1i,lgne,dfv1e_pop,dfv1i_pop,pop_names #,lgni nest,sim,node_info,dfv1e,dfv1i,lgne,dfv1e_pop,dfv1i_pop,pop_names = main('config.json') # ,lgni return (nest,sim,node_info,dfv1e,dfv1i,lgne,dfv1e_pop,dfv1i_pop,pop_names) """ (nest,sim,node_info,dfv1e,dfv1i,lgne,dfv1e_pop,dfv1i_pop,pop_names) = py"init_sim_to_call_from_julia"() function get_layer_sub_net(target) subset = Int64[] for (k,v) in pairs(pop_names) if v==target println(k,v) append!(subset,k) end end subset end subset0 = get_layer_sub_net("i23Htr3a") subset1 = get_layer_sub_net("i23Pvalb") subset2 = get_layer_sub_net("i23Sst") subset3 = get_layer_sub_net("e23Cux2") layer_23_ids = [] layer_23_ids = vcat(layer_23_ids,subset0) layer_23_ids = vcat(layer_23_ids,subset1) layer_23_ids = vcat(layer_23_ids,subset2) layer_23_ids = vcat(layer_23_ids,subset3) py"""def get_conns_from_py_nest(nest,sim,slice_start,nodes=None): conns = nest.GetConnections(nest.NodeCollection([slice_start])) nodes = nest.NodeCollection([slice_start]) node_ = nodes.get() dict_ = conns.get() return (dict_["source"],dict_["target"],dict_["weight"]) """ function extract_subset(nest,sim,subset) N = 230924+1#+17400#230901 exc_matrix = spzeros(N,N) @inbounds for srcv in ProgressBars.ProgressBar(subset) result = py"get_conns_from_py_nest"(nest,sim,srcv) @inbounds for (x,y,z) in zip(Vector{Int64}(result[1]),Vector{Int64}(result[2]),Vector{Float64}(result[3])) exc_matrix[y,x] = z end end exc_matrix end exc_matrix = extract_subset(nest,sim,layer_23_ids) Thanks for your help :) Russell.

1 1

NEST 3.3 installation error
by Petia Koprinkova 16 Jan '23

16 Jan '23

Dear NEST Developers, We are trying to install NEST 3.3 on a Linux machine in Windows 11 desktop computer and the following error report was obtained: -- Docs:https://docs.pytest.org/en/stable/how-to/capture-warnings.html - generated xml file: /nest-3.3.0-build/reports/07_pynesttests.xml - =========================== short testsummary info ============================ FAILED share/nest/testsuite/pytests/test_NodeCollection.py::TestNodeCollection::test_array_indexing FAILEDshare/nest/testsuite/pytests/test_NodeCollection.py::TestNodeCollection::test_array_indexing_bools FAILEDshare/nest/testsuite/pytests/test_NodeCollection.py::TestNodeCollection::test_slice_with_unsorted_raisesFAILEDshare/nest/testsuite/pytests/test_connect_arrays.py::TestConnectArrays::test_connect_array_list FAILEDshare/nest/testsuite/pytests/test_connect_arrays.py::TestConnectArrays::test_connect_arrays_additional_synspec_params FAILEDshare/nest/testsuite/pytests/test_connect_arrays.py::TestConnectArrays::test_connect_arrays_different_weights_delays FAILEDshare/nest/testsuite/pytests/test_connect_arrays.py::TestConnectArrays::test_connect_arrays_differnt_alpha FAILEDshare/nest/testsuite/pytests/test_connect_arrays.py::TestConnectArrays::test_connect_arrays_float_rtype FAILEDshare/nest/testsuite/pytests/test_connect_arrays.py::TestConnectArrays::test_connect_arrays_no_delays FAILED share/nest/testsuite/pytests/test_connect_arrays.py::TestConnectArrays::test_connect_arrays_no_weights FAILEDshare/nest/testsuite/pytests/test_connect_arrays.py::TestConnectArrays::test_connect_arrays_nonunique FAILEDshare/nest/testsuite/pytests/test_connect_arrays.py::TestConnectArrays::test_connect_arrays_nonunique_dict_conn_spec FAILEDshare/nest/testsuite/pytests/test_connect_arrays.py::TestConnectArrays::test_connect_arrays_receptor_type FAILEDshare/nest/testsuite/pytests/test_connect_arrays.py::TestConnectArrays::test_connect_arrays_rtype FAILEDshare/nest/testsuite/pytests/test_connect_arrays.py::TestConnectArrays::test_connect_arrays_threaded =========== 15 failed, 669 passed, 15skipped, 27 warnings in 43.13s =========== make[3]: *** [CMakeFiles/installcheck.dir/build.make:71:CMakeFiles/installcheck] Error 1 make[2]: *** [CMakeFiles/Makefile2:465:CMakeFiles/installcheck.dir/all] Error 2 make[1]: *** [CMakeFiles/Makefile2:472:CMakeFiles/installcheck.dir/rule] Error 2 make: *** [Makefile:179: installcheck]Error 2 Could you please help to resolve it?Best regards,Petia Koprinkova-Hristova

2 3

Open NEST Developer Video Conference Monday Jan 16 2023 11:30 CET (UTC+1)
by Dennis Terhorst 16 Jan '23

16 Jan '23

Dear NEST Users & Developers! I would like to invite you to our next fortnightly Open NEST Developer Video Conference, today Monday January 16, 11.30-12.30 CET (UTC+1). Feel free to join the meeting also if it's just to bring your own quick questions for direct discussion in the in-depth section. 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/2023-01-16-Open-NEST-Developer-… Looking forward to seeing you! Cheers, 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

Error installing extension module
by bstrohmer＠gmail.com 13 Jan '23

13 Jan '23

I would like to install a custom neuron model in NEST so I followed the instructions for the nest-extension-module. It is able to build the .so files but it errors during the final install of the project as seen in the below message. Install the project... -- Install configuration: "" -- Installing: /home/bs/git_repos/extension/nest-simulator/result/include/piftestmodule/pif_psc_alpha.h -- Installing: /home/bs/git_repos/extension/nest-simulator/result/lib/nest/piftestmodule.so -- Installing: /home/bs/git_repos/extension/nest-simulator/result/lib/nest/libpiftestmodule.so Traceback (most recent call last): File "<string>", line 1, in <module> File "/home/bs/git_repos/extension/nest-simulator/result/lib/python3.8/site-packages/nest/__init__.py", line 444 err = AttributeError(f"Cannot set attribute '{attr}' on module 'nest'") I am trying to install one of the example neurons provided first (pif_psc_alpha) so I do not expect that it is an issue within the source files. Thanks for any advice in correcting this issue!

4 6

stdp_dopamine_synapse model
by Behnam Ghazinouri 05 Jan '23

05 Jan '23

Hi all, Happy new year! I have a question about the "stdp_dopamine_synapse" model. In the documentation, they mentioned that they used it as a benchmark the model in [1], based on [2]. In [1], in the section "2.2 Benchmark Network Models", they have C_1 and C_2. They just mentioned these two parameters are constant coefficients. My question is: Does NEST implement these equations? If yes, how can I find the values of C_1 and C_2? (they are not listed under the nest.GetValues() and are not in the table of the documentation). If not, what is the exact model that the NEST implemented for "stdp_dopamine_synapse"? Best regards, Behnam [1] Potjans W, Morrison A, Diesmann M (2010). Enabling functional neural circuit simulations with distributed computing of neuromodulated plasticity. Frontiers in Computational Neuroscience, 4:141. DOI: https://doi.org/10.3389/fncom.2010.00141 <https://doi.org/10.3389/fncom.2010.00141> [2] Izhikevich EM (2007). Solving the distal reward problem through linkage of STDP and dopamine signaling. Cerebral Cortex, 17(10):2443-2452. DOI: https://doi.org/10.1093/cercor/bhl152 <https://doi.org/10.1093/cercor/bhl152>

2 1

Open NEST Developer Video Conference Monday Dec 19 2022 11:30 CET (UTC+1)
by Dennis Terhorst 19 Dec '22

19 Dec '22

Dear NEST Users & Developers! I would like to invite you to our next fortnightly Open NEST Developer Video Conference, today Monday December 19, 11.30-12.30 CET (UTC+1). Feel free to join the meeting also if it's just to bring your own questions for direct discussion in the in-depth section. 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/2022-12-19-Open-NEST-Developer-… As I will not be joining today, I delegated chairing the meeting. Looking forward to seeing you again next year! Merry Christmas and a happy new year! Cheers, 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

how to customize Ion channels and receptor types of "cm_default" neuron model through nestml
by 王梓瑞 08 Dec '22

08 Dec '22

Dear nest community, I wonder if any of you know how to customize Ion channels and receptor types of "cm_default" neuron model through nestml. I noticed some information on Extending NESTML- Running NESTML with custom templates, but I still found myself confused due to my poor understanding. Is there any way to acquire the .nestml file of the cm_default neuron model? Thank you. Best, Zirui

2 1

Open NEST Developer Video Conference Monday Dec 5 2022 11:30 CET (UTC+1)
by Dennis Terhorst 05 Dec '22

05 Dec '22

Dear NEST Users & Developers! I would like to invite you to our next fortnightly Open NEST Developer Video Conference, today Monday December 5, 11.30-12.30 CET (UTC+1). Feel free to join the meeting also if it's just to bring your own questions for direct discussion in the in-depth section. Special topic for the in-depth discussion for today are / Hackathon Results / 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/2022-12-05-Open-NEST-Developer-… Looking forward to seeing you again soon! Cheers, 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

docker questions
by 1538356357＠qq.com 05 Dec '22

05 Dec '22

I use Docker to create a nest environment. The version is v2.16.0 But when I execute the code as follows，vt_dummy = nest.Create("global_volume_transmitter", 1, {'deliver_interval': 10})， , I encounter an error, the error is pynestkernel.NESTError: UnknownModelName in GetDefaults_l: /global_volume_transmitter is not a known model name. Please check the modeldict for a list of available models . but after I use the nest2.16 source code to install, the same code executes successfully. I don't know why

2 3

About Polling Algorithm
by 1538356357＠qq.com 22 Nov '22

22 Nov '22

Dear NEST community： We all know that distributed computing is carried out in Nest, and neurons are distributed to each neuron through polling. However, considering the load balancing and sparsity of communication, this is a NP hard problem. Should we adopt some other methods, such as directed graph segmentation technology. Whether this will be considered in Nest, or whether graph segmentation is helpful in SNN simulation. If you can spare time to reply, thank you very much

2 1

Open NEST Developer Video Conference Monday Nov 21 2022 11:30 CET (UTC+1)
by Dennis Terhorst 21 Nov '22

21 Nov '22

Dear NEST Users & Developers! I would like to invite you to our next fortnightly Open NEST Developer Video Conference, today Monday November 21, 11.30-12.30 CET (UTC+1). Feel free to join the meeting also if it's just to bring your own questions for direct discussion in the in-depth section. Special topic for the in-depth discussion for today are mechanisms around /Tsodyks-style synapses/ 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/2022-11-21-Open-NEST-Developer-… Looking forward to seeing you again soon! Cheers, 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

errors when using command"d1_pop.set({"V_m":nest.random.uniform(-80.0, -55.0)})"
by 王梓瑞 15 Nov '22

15 Nov '22

Dear NEST community, Thank you so much for your previous suggestions on writing my own neuron model with NESTML. I constructed a multiple synapses version of simple integrate-and-fire ("iaf_cond_beta_multisynapse") neuron based on the existing "iaf_cond_beta" neuron model. And I did this by simply adding two synaptic channels (AMPA and NMDA) without changing the structure of the neuron model. But when I called this model on NEST to set the initial membrane potentials from a uniform distribution (from 280 to 255 mV), for example:"d1_pop.set({"V_m":nest.random.uniform(-80.0, -55.0)})", an error reporting NESTErrors.TypeMismatch: "TypeMismatch in SLI function SetStatus_id: Expected datatype: doubletype Provided datatype: parametertype" appeared. So I wonder is there any coding errors in my own neuron model, since it worked just fine when I set the initial membrane potentials to a number like -80, and how can I fix this error. Best, Zirui

2 1

Re: weight_recorder with large number of synapses
by Hans Ekkehard Plesser 14 Nov '22

14 Nov '22

Hello Alice, Setting repeated recording windows is currently not possible (but maybe create a feature request on Github). What you can do is the following n1 = nest.Create('iaf_psc_delta', params={'I_e': 1000.}) n2 = nest.Create('iaf_psc_delta') wr = nest.Create('weight_recorder', params={'origin': 0., 'start': 0, 'stop': 1000}) nest.CopyModel('stdp_synapse', 'stdp_synapse_rec', {'weight_recorder': wr}) nest.Connect(n1, n2, syn_spec={'synapse_model': 'stdp_synapse_rec', 'weight': 20}) nest.Connect(n2, sr) t_block = 5000 for k in range(10): wr.origin = k * t_block nest.Simulate(t_block) This will simulate in 5s blocks and record weights only during the first 1s of each block. The actual recording windows are given by (origin+start, origin+stop]. You need to do this with Simulate() calls since you need to change the origin parameter; therefore RunManager + run() does not work. You could also record to file if that is an option for your workflow, by setting wr.record_to = 'ascii'. If you want to combine that with a loop, you need to set wr.label to a different value for each loop iteration, otherwise data will be overwritten for each round through the loop. 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 From: Alice Geminiani <alice.geminiani(a)polimi.it> Reply to: NEST User Mailing List <users(a)nest-simulator.org> Date: Friday, 11 November 2022 at 18:47 To: "users(a)nest-simulator.org" <users(a)nest-simulator.org> Subject: [NEST Users] weight_recorder with large number of synapses Some people who received this message don't often get email from alice.geminiani(a)polimi.it. Learn why this is important<https://aka.ms/LearnAboutSenderIdentification> Dear NEST users, I am trying to record weights from a network with about 1.5 million synapses, for simulations of a 30-minute protocol, and using the weight_recorder causes memory errors. Is there a way to record only in specific time instants of the simulation (e.g. every 5 minutes)? Thanks a lot! Cheers, Alice ---------------------------- Alice Geminiani, PhD PostDoctoral Researcher NeuroEngineering And medical Robotics Laboratory - NEARLab Department of Electronics, Information and Bioengineering - DEIB Politecnico di Milano Neurocomputational laboratory Department of Brain and Behavioral Sciences University of Pavia

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weight_recorder with large number of synapses
by Alice Geminiani 11 Nov '22

11 Nov '22

Dear NEST users, I am trying to record weights from a network with about 1.5 million synapses, for simulations of a 30-minute protocol, and using the weight_recorder causes memory errors. Is there a way to record only in specific time instants of the simulation (e.g. every 5 minutes)? Thanks a lot! Cheers, Alice ---------------------------- Alice Geminiani, PhD PostDoctoral Researcher NeuroEngineering And medical Robotics Laboratory - NEARLab Department of Electronics, Information and Bioengineering - DEIB Politecnico di Milano Neurocomputational laboratory Department of Brain and Behavioral Sciences University of Pavia

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how to construct multiple synapse simple integrate-and-fire model
by 王梓瑞 07 Nov '22

07 Nov '22

Hi, I planned to use simple integrate-and-fire model (iaf_cond_beta) to construct the cortico-striatal network, but then it appeared some issues. Since striatum neurons have multiple synapses (AMPA and NMDA for example), ‘iaf_cond_beta’ seemed not to support multiple synapse input. I searched the whole Model directory and found multiple synapse neuron models like “aeif_cond_beta_multisynapse”, “aeif_cond_alpha_multisynapse” and “aeif_psc_alpha_multisynaps”. So I wondered if there’s a multiple synapse version of simple integrate-and-fire model (iaf_cond_beta), or can I construct a multiple synapse simple integrate-and-fire model through nestml. Thank you Best, Zirui

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Open NEST Developer Video Conference Monday Nov 7 2022 11:30 CET (UTC+1)
by Dennis Terhorst 07 Nov '22

07 Nov '22

Dear NEST Users & Developers! I would like to invite you to our next fortnightly Open NEST Developer Video Conference, today Monday November 7, 11.30-12.30 CET (UTC+1). (note the changed timezone!) Feel free to join the meeting also if it's just to bring your own questions for direct discussion in the in-depth section. Special topic for the in-depth discussion for today is /Eligibility Propagation/ 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/2022-11-07-Open-NEST-Developer-… Looking forward to seeing you again soon! Cheers, 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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Tips for getting a scaled-down version of the Allen Brain V1 model to work using NEST/Sonata/BMTK?
by Russell Jarvis 27 Oct '22

27 Oct '22

I am just wondering if anyone in the Nest community has any tips for running the Allen Brain V1 model? A lot of the code and Sonata/HDF5 files are hosted on DropBox. model_nest_2.20 - Dropbox <https://www.dropbox.com/sh/w5u31m3hq6u2x5m/AAA1ZQrM-4pgfK5dlRtWYdJNa/GLIF%2…> I have been busy trying to get the model to work with PyGeNN and even Julia. It occurred to me that I should probably start with what has been known to work, ie Nest. Thanks for any advice. Russell. -- Russell Jarvis (he/him) PhD Personal Website <https://russelljjarvis.github.io/home/> *I respectfully acknowledge the Traditional Owners of the land on which we work and learn, and pay respect to the First Nations Peoples and their elders, past, present and future.* *phone: *614 <623-404-9322>44576301 *email:* russelljarvis(a)protonmail.com

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Dendritic Arbors at Scale
by Ryan O'Loughlin 26 Oct '22

26 Oct '22

Hello NEST community, I am at the outset of a large project and I would like to start off with the right simulator. Perhaps someone here can advise on the viability of NEST for my particular needs. I will be modeling neuromorphic hardware with some unique design constraints, such as: - A complex dendritic arbor - Dendrite potentials may be coupled with their neighbors - Several dendrites may feed into other dendrites (a several-layer-deep dendritic tree) - The arbor eventually feeds into the soma which has typical LIF behavior, with a membrane potential determined by the sum of all directly connected dendrites - The solution for the leaky-integrator term of dendrites must be drawn from a precalculated lookup table The question here is how best to facilitate these dendritic nuances within NEST? Any counsel on whether it makes sense to pursue modeling such a system in NEST would be highly appreciated. We would like to eventually scale to the maximum number of neurons our hardware/clusters and your simulator can facilitate. Thank you, Ryan

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Problems with Github CI on macOS / Temporary solution
by Hans Ekkehard Plesser 25 Oct '22

25 Oct '22

Dear NEST Developers, For the last few days, all CI builds on macOS have failed. This is most likely due to Homebrew now providing libomp 15.0 instead of 14.0, see issue #2515 (https://github.com/nest/nest-simulator/issues/2515). I have temporarily disabled OpenMP-dependent tests for the macOS builds (#2516). Please pull current master into all open PRs so that most of the macOS tests can run. Please note that considerable recent improvements in the code base (systematic use of nullptr #2496, of "and" and "or" instead of && and || #2498, removal of "void" arguments, systematic use of "override" and removal of "virtual" where not needed #2493; removal of unused imports #2490 as well as #2479) may lead to some merge conflicts. Please resolve them in the spirit of the new style and consult the listed PRs if in doubt about what is the new style. 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

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Open NEST Developer Video Conference Monday Oct 24 2022 11:30 CEST (UTC+2)
by Dennis Terhorst 24 Oct '22

24 Oct '22

Dear NEST Users & Developers! I would like to invite you to our next fortnightly Open NEST Developer Video Conference, today Monday October 24, 11.30-12.30 CEST (UTC+2). Feel free to join the meeting also if it's just to bring your own questions for direct discussion in the in-depth section. Special topic for the in-depth discussion for today are /Compressed Spikes/ 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/2022-10-24-Open-NEST-Developer-… Looking forward to seeing you again soon! Cheers, 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 Oct 10 2022 11:30 CEST (UTC+2)
by Dennis Terhorst 10 Oct '22

10 Oct '22

Dear NEST Users & Developers! I would like to invite you to our next fortnightly Open NEST Developer Video Conference, today Monday October 10, 11.30-12.30 CEST (UTC+2). Feel free to join the meeting also if it's just to bring your own questions for direct discussion in the in-depth section. Special topic for the in-depth discussion for today is the /NEST implementation of eligibility propagation/. 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/2022-10-10-Open-NEST-Developer-… Looking forward to seeing you again soon! Cheers, 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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Assertion error during connection when using CopyModel and own neuron model
by Barna Zajzon 07 Oct '22

07 Oct '22

Dear all, I'm encountering the following error python: /home/zbarni/software/packages/nest/znest/nestkernel/model_manager.h:296: nest::Model* nest::ModelManager::get_node_model(nest::index) const: Assertion `m < node_models_.size()' failed. when using the following code: nest.SetKernelStatus({'total_num_virtual_procs':16, 'local_num_threads':16}) nest.Install('my_neuron_module') for iin range(16): nest.CopyModel('MyNeuron', f'MyNeuron_{i}') neurons = nest.Create('MyNeuron_0', 2) nest.Connect(neurons, neurons) The script uses a neuron model that I wrote in C++ and is loaded without errors. The error is thrown upon nest.Connect(), and goes away if I create the neurons using `MyNeuron` and not `MyNeuron_x` (copied) or if the #vp and #threads is 1. I've used the model with NEST 2.20.0 without problems, but I'd like to port the code to the latest version. Maybe I'm just missing something new functionality/API related to CopyModel and multiprocessing - have there been any critical changes in the model requirements? Any help would be greatly appreciated. Barni

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NEST, CMake, Xcode, Eclipse & Co: the magic -G
by Hans Ekkehard Plesser 07 Oct '22

07 Oct '22

Dear NEST Developers, I would like to share some insights I gained over the last few days concerning NEST and IDEs. As you might know, we have some instructions for how to use NEST with IDEs (https://nest-simulator-sg.readthedocs.io/en/latest/developer_space/workflow…), but these instructions are at best complicated and at worst awfully outdated. I now discover the magic -G flag for CMake (https://cmake.org/cmake/help/latest/manual/cmake-generators.7.html), where CMake does all the heavy configuration lifting for you. Proceed as follows: - Create a build directory - Prepare your normal cmake invocation and add - for XCode: -GXcode - for Eclipse: -G"Eclipse CDT4 - Unix Makefiles" - Then open the build directory in XCode or Eclipse For other build systems, run cmake –help and see if your system is listed. Unfortunately, VSCode seems unsupported at the moment. In Xcode, you can then choose the "install" target and run it to build NEST and afterwards the "nest" target to run nest—and it will stop in the debugger if you just set a breakpoint or something goes wrong. There are still a few problems, and if any of you have more experience than me with setting up Xcode or Eclipse problems, we can maybe work it out together: 1. In Eclipse, the project will only include files in the build directory, not the source code. How to fix that? 2. Xcode * Files are ordered a bit strangely (subfolders for headers and non-headers) and "libnestutil" is shown as "nestutil" in the folder list * The "installcheck" target does not work because Xcode runs everything in the conda "base" environment—how to either force a "conda activate nest" before each run or explicitly set PYTHONPATH? * I have not yet found out how to run PyNEST from Xcode, which would also depend on conda activate/Pythonpath setting Once we have a little more experience, I will prepare a PR to update the IDE instructions. 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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using mpi4py with nest | parallel write to a file
by Aadhar Sharma 28 Sep '22

28 Sep '22

Hi there! I am using the structural plasticity module to simulate large-scale networks on HPC. The way I run these simulations with MPI creates a large number of small data files (.npy) which I organize into a HDF5 file in a post hoc manner. This has hitherto not been a problem, however, I recently increased the size of my simulations and the number of files that I create exceeds my HPCinode quota. So, I have to come up with a way of handling all these files or the way I export them. Ideally, I would like to concurrently write to a file (like zarr) with multiple processes. However, parallel zarr writes are only optimal when the chunk size are uniform. For me, they are not uniform---so, I abandoned the idea of using zarr. Currently, I am trying to use mpi4py to gather the data I want and save it through a mother MPI process. I ran some test simulations and all was fine (see attached script). However, when I use structural plasticity with mpi4py I get an error that: "nest.lib.hl_api_exceptions.DimensionMismatch: ('DimensionMismatch in SetStatus_id: Expected dimension size: 1\nProvided dimension size: 20', 'DimensionMismatch', <SLILiteral: SetStatus_id>, ': Expected dimension size: 1\nProvided dimension size: 20". I believe that mpi4py somehow interferes with nest's internal mpi mechanism. Perhaps it signals nest kernel to use 1 process rather than the mentioned 20. If I remove the mpi4py import call, all works fine. So, I cannot run the simulation using this mpi4py hack. Do you notice something wrong with my approach? I'm just beginning to use mpi4py, so I may be missing something here. Alternatively, could you recommend a way to reduce the number of exported files. For example, through zarr or other file formats which support parallel writes. I'd appreciate any suggestions. Thanks! pyNEST version: 2.20.2 python version: Python 3.7.10 mpiexec/mpirun version: MPI Library for Linux* OS, Version 2021.3 Best, Ady

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[Precise Spikes]small bug in ./pynest/examples/hpc_benchmark.py (nest-3.3)
by Tianxiang Lyu 26 Sep '22

26 Sep '22

Hi, all! I try to replace "iaf_psc_alpha" with "iaf_psc_alpha_ps" and "poisson_generator" with "poisson_generator_ps" for using precise spikes neuron template in the simulation However, there are somethings wrong with the logs related to SLI with which I hadn't been familiar: (If the randomizing of membrane potentials is removed, hpc_benchmark.py could run as usual) Traceback (most recent call last): File "./hpc_benchmark.py", line 456, in <module> run_simulation() File "./hpc_benchmark.py", line 362, in run_simulation sr = build_network(logger) File "./hpc_benchmark.py", line 227, in build_network nest.GetLocalNodeCollection(E_neurons).V_m = random_vm File "/GPUFS/sysu_hpcedu_302/lvtx/tools/nest-simulator/3.3-intel-2021/lib64/python3.8/site-packages/nest/lib/hl_api_types.py", line 543, in __setattr__ self.set({attr: value}) File "/GPUFS/sysu_hpcedu_302/lvtx/tools/nest-simulator/3.3-intel-2021/lib64/python3.8/site-packages/nest/lib/hl_api_types.py", line 477, in set sli_func('SetStatus', self._datum, params) File "/GPUFS/sysu_hpcedu_302/lvtx/tools/nest-simulator/3.3-intel-2021/lib64/python3.8/site-packages/nest/ll_api.py", line 165, in sli_func sli_run(slifun) # SLI support code to execute s on args File "/GPUFS/sysu_hpcedu_302/lvtx/tools/nest-simulator/3.3-intel-2021/lib64/python3.8/site-packages/nest/ll_api.py", line 115, in catching_sli_run raise exceptionCls(commandname, message) nest.lib.hl_api_exceptions.TypeMismatch: TypeMismatch in SLI function SetStatus_id: Expected datatype: doubletype Provided datatype: parametertype How could I fix that? Or another way to implement randomizing of membrane potentials? Tianxiang Lyu Department of Mechanic Sun Yet-Sen University No. 66, Gongchang Road, Guangming District, Shenzhen, 518107, P. R. China

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Open NEST Developer Video Conference Monday Sep 26 2022 11:30 CEST (UTC+2)
by Dennis Terhorst 26 Sep '22

26 Sep '22

Dear NEST Users & Developers! I would like to invite you to our next fortnightly Open NEST Developer Video Conference, today Monday September 26, 11.30-12.30 CEST (UTC+2). Feel free to join the meeting also if it's just to bring your own questions for direct discussion in the in-depth section. 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/2022-09-26-Open-NEST-Developer-… Looking forward to seeing you again soon! Cheers, 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 save and reload an already trained network created with Nest Simulator?
by salvatore.taffara＠phd.unict.it 21 Sep '22

21 Sep '22

Hi, can anyone answer to my question in subject? I am using Nest 3.3. Thanks in advance, Salvo

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which neuron model supports shunting inhibition
by Aadhar Sharma 14 Sep '22

14 Sep '22

Hi all! I want to use investigate the effects of shunting inhibition in one of my experiments. I tried iaf_cond_alpha, but couldn't reproduce the shunting effect. Could someone please suggest which neuron model to use? There should be a way to also change the V_th, V_rest, C_m, tau_m or g_L for this model. I am working with NEST 2.20.2 Best, Ady

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Open NEST Developer Video Conference Monday Aug 15 2022 11:30 CEST (UTC+2)
by Dennis Terhorst 12 Sep '22

12 Sep '22

Dear NEST Users & Developers! I would like to invite you to our next fortnightly Open NEST Developer Video Conference, today Monday August 15, 11.30-12.30 CEST (UTC+2). Feel free to join the meeting also if it's just to bring your own questions for direct discussion in the in-depth section. 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/2022-08-15-Open-NEST-Developer-… Looking forward to seeing you again soon! Cheers, 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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Upcoming conference in Computational Neuroscience - Neuromatch 2022
by Alberto Antonietti 30 Aug '22

30 Aug '22

Dear NEST users and developers, I am glad to invite you to the upcoming fifth edition of the Neuromatch Conference (NMC), which will take place online on September 27-28! The scope of NMC 2022 includes computational neuroscience and machine learning work that has a biological link. We are excited to have a slate of excellent speakers and panelists lined up including: - Keynotes from Larry Abbott, Rosa Chan, Ida Momennejad and Mac Shine - Panel on spiking computation: Priya Panda, Katie Schuman, and Peter Suma - Panel on the future of scientific publishing: Tim Behrens, Simine Vazire, and Abeni Wickham - Bridging-the-gap with computational psychiatry: Xiaosi Gu and Quentin Huys Registration costs are set at 15 USD to cover technical costs, and if this is a difficulty, the fee can be waived without questions. **Important dates** September 5, 2022: Abstract submission deadline September 7, 2022: Abstract acceptance and live talk selection news September 22, 2022: Video submission deadline for flashtalks September 27 - 28, 2022: NMC 2022 Each of the two conference days will have two sessions, each of which is 4 hours long. Here are the hours for each of the sessions, as they would occur across five time zones from around the world: Read more at http://conference.neuromatch.io I hope to see many of you there! Best, Alberto

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Spike->Synapse->Update
by lvtx＠mail2.sysu.edu.cn 25 Aug '22

25 Aug '22

I wrote a simple python code(without nest) for a E-I random balanced network with poisson noise stimulus. Then I try to build it on nest. However, the response firing rates are changed.(not a computing error) Is there anything wrong? neurons -> spike synapse -> wait delay post_neurons -> add weight from connected synapses to corresponding input channel neurons -> update ODE each step I figured out that without connections but with poisson noise input, the firing rates of my python code is the same as the code on nest. (Seems that the ODE calculations are the same in my python code and nest) However, the firing rates show differ greatly when I add the connections on both.

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Open NEST Developer Video Conference Monday Aug 15 2022 11:30 CEST (UTC+2)
by Hans Ekkehard Plesser 15 Aug '22

15 Aug '22

Dear NEST Users & Developers! I would like to invite you to our next fortnightly Open NEST Developer Video Conference, today Monday August 15, 11.30-12.30 CEST (UTC+2). Feel free to join the meeting also if it's just to bring your own questions for direct discussion in the in-depth section. 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/2022-08-15-Open-NEST-Developer-… Looking forward to seeing you again soon! Best regards, 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<mailto: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, 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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Compiling nest-simulator from source
by Daniel Naoumenko 11 Aug '22

11 Aug '22

Hi, I've been trying to compile the latest version on github (c1cebdc) without success. The system is a HPC running RHEL7. Pre-installed software includes gsl-2.7, cmake 3.17.5 and openMPI-1.10.3-gnu, although I have tried variations with similar results. I've created a fresh conda environment with packages necessary for nest and nestml: conda create --name pythonfornestml -c conda-forge boost readline ipython pyqt wxpython cython pip install mpi4py cmake -DCMAKE_INSTALL_PREFIX:PATH=/headnode1/dnao/nest-installs/nest3-23.07.2022 \ -Dwith-mpi=ON \ /headnode1/dnao/gitnest/nest-simulator make make fails at 47%. I have uploaded the make output here: https://drive.google.com/file/d/1FXVsidFLXYvnHk4Tob2zDi4wQJJNW-yw/view?usp=… As well as the output of cmake to show the build configuration: https://drive.google.com/file/d/1HWH_KqILEyQYujzd4B1ma4ZrzUXbG231/view?usp=… Thank you in advance for any assistance.

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Fwd: Building nest 3.3
by Mikael Lindahl 05 Aug '22

05 Aug '22

Hi, I am trying to build NEST on debian 11 with cmake 3.16.9 and conda python=3.9. I have attached my installation script asswell as the full logs for make and install steps. ( I run the script with using source to conda activate will play nice) During "make install" I get the following message error -- Set runtime path of "/home/mikael/git/bgmodel/nest/dist/install/nest-simulator-3.3/lib/python3.9/site-packages/nest/pynestkernel.so" to "$ORIGIN/../lib/nest:$ORIGIN/../../lib/nest:$ORIGIN/../../../nest:/home/mikael/opt/anaconda3/envs/nest-3.3/lib" running install_egg_info /home/mikael/opt/anaconda3/envs/nest-3.3/lib/python3.9/site-packages/setuptools/command/install.py:34: SetuptoolsDeprecationWarning: setup.py install is deprecated. Use build and pip and other standards-based tools. warnings.warn( running egg_info creating nest_simulator.egg-info writing nest_simulator.egg-info/PKG-INFO writing dependency_links to nest_simulator.egg-info/dependency_links.txt writing requirements to nest_simulator.egg-info/requires.txt writing top-level names to nest_simulator.egg-info/top_level.txt writing manifest file 'nest_simulator.egg-info/SOURCES.txt' reading manifest file 'nest_simulator.egg-info/SOURCES.txt' writing manifest file 'nest_simulator.egg-info/SOURCES.txt' Copying nest_simulator.egg-info to /home/mikael/git/bgmodel/nest/dist/install/nest-simulator-3.3/lib/python3.9/site-packages/nest_simulator-3.3-py3.9.egg-info Traceback (most recent call last): File "<string>", line 1, in <module> File "/home/mikael/opt/anaconda3/envs/nest-3.3/lib/python3.9/site-packages/pkg_resources/__init__.py", line 477, in get_distribution dist = get_provider(dist) File "/home/mikael/opt/anaconda3/envs/nest-3.3/lib/python3.9/site-packages/pkg_resources/__init__.py", line 353, in get_provider return working_set.find(moduleOrReq) or require(str(moduleOrReq))[0] File "/home/mikael/opt/anaconda3/envs/nest-3.3/lib/python3.9/site-packages/pkg_resources/__init__.py", line 897, in require needed = self.resolve(parse_requirements(requirements)) File "/home/mikael/opt/anaconda3/envs/nest-3.3/lib/python3.9/site-packages/pkg_resources/__init__.py", line 783, in resolve raise DistributionNotFound(req, requirers) pkg_resources.DistributionNotFound: The 'nest-simulator' distribution was not found and is required by the application And for make installcheck i get this error Scanning dependencies of target installcheck Executing NEST's testsuite... make[3]: *** [CMakeFiles/installcheck.dir/build.make:61: CMakeFiles/installcheck] Error 1 make[2]: *** [CMakeFiles/Makefile2:524: CMakeFiles/installcheck.dir/all] Error 2 make[1]: *** [CMakeFiles/Makefile2:531: CMakeFiles/installcheck.dir/rule] Error 2 make: *** [Makefile:178: installcheck] Error 2 It took 160 seconds Anyone who knows how to solve this? /Mikael -- Mikael Lindahl Phd Phone: +46735119429 Email: m <lindahlm(a)csc.kth.se>ickelindahl(a)gmail.com

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Open NEST Developer Video Conference Monday Aug 1 2022 11:30 CEST (UTC+2)
by Dennis Terhorst 01 Aug '22

01 Aug '22

Dear NEST Users & Developers! I would like to invite you to our next fortnightly Open NEST Developer Video Conference, today Monday August 1, 11.30-12.30 CEST (UTC+2). Feel free to join the meeting also if it's just to bring your own questions for direct discussion in the in-depth section. 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/2022-08-01-Open-NEST-Developer-… Looking forward to seeing you again soon! Cheers, 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 use the update block in NESTML?
by lea.driessens＠ensea.fr 31 Jul '22

31 Jul '22

Hello, We are trying to plot an exponential synaptic trace in a custom made synapse model made with NESTML, and to do that we are trying to use the print function within the model. But when we try to print something or to change the value of a variable (initialized in the state block) inside the update block, nothing happens. We started with a simple string "Hello", and nothing was printed. We then tried to add 1 to a variable initialized to 0 and its value didn't change. If the print command is written in the onReceive block, it works without problems; as for the variable, its value can be changed in the onReceive block, but if we print its value in the onReceive block and change the value in the update block, we see that the value is not updated from 0. Since we would like to get the value of the synaptic trace to plot its change during simulation, we would need to get the value of the trace not just when a spike is received (there would be no point) but more often. Do you know what we could do? (And why the update block is not working properly?) Best regards, Léa D.

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Open NEST Developer Video Conference Monday July 18 2022 11:30 CEST (UTC+2)
by Dennis Terhorst 18 Jul '22

18 Jul '22

Dear NEST Users & Developers! I would like to invite you to our next fortnightly Open NEST Developer Video Conference, today Monday July 18, 11.30-12.30 CEST (UTC+2). Feel free to join the meeting also if it's just to bring your own questions for direct discussion in the in-depth section. 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/2022-07-18-Open-NEST-Developer-… Looking forward to seeing you again soon! Cheers, 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

Access weight_recorder data during simulation
by francescojamal.sheiban＠polimi.it 15 Jul '22

15 Jul '22

Dear all, I was wondering if it is possible to access the events collected by a weight_recorder during a simulation: I am able to collect and plot the recorded data once the simulation is over, but I found no information about accessing the device in real-time. Specifically, I would like to know if there is a way to pass the data as input to a custom NESTML synapse model dynamically during a simulation. Best regards, Francesco Sheiban

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Decreased simulation speed using nest v2.20.1 compared to v2.2.2
by Hartmut Schmidt 13 Jul '22

13 Jul '22

Hi, I recently upgraded from nest v2.2.2 to v2.20.1 and experienced a decrease in simulation speed. I tested it using the /brunel_alpha_nest.py/ example script that is available in both versions. For better comparison I set the option /to_file/ in the new version to /False/. Simulating the network for 10s using v2.2.2 I get: 100 %: network time: 9999.0 ms, realtime factor: 0.0672 Simulation finished. Brunel network simulation (Python) Number of neurons : 12500 Number of synapses: 15637600 Exitatory : 12512500 Inhibitory : 3125000 Excitatory rate : 28.84 Hz Inhibitory rate : 28.78 Hz Building time : 5.56 s Simulation time : 149.01 s Using v2.20.1: 100 %: network time: 9999.0 ms, realtime factor: 0.0601 Simulation finished. Brunel network simulation (Python) Number of neurons : 12500 Number of synapses: 15637600 Exitatory : 12512500 Inhibitory : 3125000 Excitatory rate : 28.84 Hz Inhibitory rate : 28.78 Hz Building time : 2.39 s Simulation time : 168.58 s Adding /'total_num_virtual_procs': 48/and running it for 100s on a 48 core node using v2.2.2 I get: Simulation time : 98.49 s Using v2.20.1: Simulation time : 120.08 s Both versions are build with OpenMp support and without mpi. Is this expected or do you have any idea where this behavior comes from? Thank you in advance! Best, Hartmut

1 0

Get MPI time
by 512491013＠qq.com 06 Jul '22

06 Jul '22

Dear all, I used 10 PyNQ nodes to run SNN using mpirun, which is faster than a single node. but I want to know how long each node takes to start MPI and wait for MPI_all_gether to end. Where do I need to print the time in the source code?Or what tools can I use to test MPI communication times?（my nest version is 2.14） Best regards Cong

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