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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

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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

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