- NEST Users - NEST Initiative Mail

Random seed in NEST 3.0
by Maryada Maryada 26 Nov '21

26 Nov '21

Dear NEST users, As I understood from the documentation unless you set the seed using nest.rng_seed, nest.random.normal (for instance) should return the same value nest.ResetKernel() nest.rng_seed = 21#69696 v_m = nest.random.normal(mean=-51., std=10.) v_m.GetValue() In this code, I always receive the same v_m value for both cases, if the seed is set as 21 or 69696. The only time it changes is if I remove ResetKernel() call, which then is expected to return different values irrespective of rng_seed. With this code below, I also got the same results irrespective of rng_seed value nest.ResetKernel() nest.rng_seed = 3333#69696 for _ in range(10): v_m = nest.random.normal(mean=-51., std=10.) print(v_m.GetValue()) So, maybe rng_seed doesn't reflect on nest.random.normal distribution. However, then how can I make sure it draws a different set of values? -- Thanks and Regards *Maryada*

5 8

Izhikevich Simulation
by Allen Rabayda 22 Nov '21

22 Nov '21

Dear Nest Users, Has anyone used any NEST Synapse Models to create Gamma Rhythms during a simulation with the NEST Izhikevich Neuron model? My simulation, which uses the Stdp-Synapse model (additive type) does not appear to be converging into gamma rhythms (w/bi-model wt distribution) using super-threshold poisson point process (ref: Polychronization Computation With Spikes (Izhikevich, 2006), - DOI: 10.1162/089976606775093882 <https://doi.org/10.1162/089976606775093882>) - - - - Thanks for any suggestions, Best Regards, --Allen

2 2

Open NEST Developer Video Conference Monday 22 November 2021 11:30 CET (UTC+1)
by Dennis Terhorst 22 Nov '21

22 Nov '21

Dear NEST Users & Developers! I would like to invite you to our next fortnightly Open NEST Developer Video Conference, today Monday 22 November, 11.30-12.30 CET (UTC+1). Feel free to join the meeting also 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/2021-11-22-Open-NEST-Developer-… Looking forward to seeing you soon! best, Dennis Terhorst ------------------ Log-in information ------------------ We use a virtual conference room provided by DFN (Deutsches Forschungsnetz). You can use the web client to connect. We however encourage everyone to use a headset for better audio quality or even a proper video conferencing system (see below) or software when available. Web client * Visit https://conf.dfn.de/webapp/conference/97938800 * Enter your name and allow your browser to use camera and microphone * The conference does not need a PIN to join, just click join and you're in. In case you see a dfnconf logo and the phrase "Auf den Meetingveranstalter warten", just be patient, the meeting host needs to join first (a voice will tell you). VC system/software How to log in with a video conferencing system, depends on you VC system or software. - Using the H.323 protocol (eg Polycom): vc.dfn.net##97938800 or 194.95.240.2##97938800 - Using the SIP protocol:97938800@vc.dfn.de - By telephone: +49-30-200-97938800 For those who do not have a video conference system or suitable software, Polycom provides a pretty good free app for iOS and Android, so you can join from your tablet (Polycom RealPresence Mobile, available from AppStore/PlayStore). Note that firewalls may interfere with videoconferencing in various and sometimes confusing ways. For more technical information on logging in from various VC systems, please see http://vcc.zih.tu-dresden.de/index.php?linkid=1.1.3.4

1 0

Call for Papers: Reproducibility in Neuroscience
by Alberto Antonietti 19 Nov '21

19 Nov '21

2 2

Installation procedure of NEST on M1 mac
by Julien Ballbé 18 Nov '21

18 Nov '21

Dear Madam, Dear Sir As a starting doctoral student in the field of computational neurosciences, I am particularly interested in using NEST in my research works. However, I am a bit confused about the procedure to install NEST on a M1 macbook pro, therefore, I prefer to ask you before doing anything. From what I understood from your website here are the steps that, I suppose, I should do to install NEST properly: - as I use a M1MAX Mac (MacOS 12.0) , I can't just install nest, I have to build it. To do so: - Download Miniforge for arm64 (from which I will be able to use Conda right?) - Install Python 3.9.4 for arm Mac macOS 64-bit universal2 installer <https://www.python.org/ftp/python/3.9.8/python-3.9.8-macos11.pkg> - Download the nest source code directly from github ( https://github.com/nest/nest-simulator) - Create a conda environment using the following command conda env create -f extras/conda-nest-simulator-dev.yml - Activate this environment ( conda activate...) - Create a build directory outside the NEST source and go into it - Install cmake package using conda ( conda install -c anaconda cmake) - Configure NEST by running: cmake -DCMAKE_INSTALL_PREFIX:PATH=<nest_install_dir> <nest_source_dir> - Once done I can run make. make install. make installcheck Here are my questions: - Is this installation procedure correct? - Once installed, how can I launch NEST from a python interpreter such as Spyder? Or is it only possible to launch it within a terminal window? - I am quite new to managing packages, so correct me if I am wrong, but have I to install everything using exclusively Conda ? - What is the purpose of creating a new environment to build NEST -Is there anything I missed or misunderstood? I realize how many questions I ask you, and I am very grateful for every advice you could give me. If it is more convenient for you, we can have a phone call when you want. -- *Julien BALLBÉ Y SABATÉ* *Étudiant en thèse - PhD student* *Neurophysiology of Visual Computation* Centre Giovanni Borelli - CNRS UMR 9010 Université de Paris 45 rue des Saint-Pères, 75006 Paris, France Tel: +33 6 79 03 40 35

4 12

[NEST 3.1] autapses/multapses switch for structural plasticity
by Aadhar Sharma 17 Nov '21

17 Nov '21

3 2

NESTML's versioning policy
by Robin Gilbert De Schepper 16 Nov '21

16 Nov '21

Hi all, I was wondering what NESTML's versioning scheme looks like, and what versions of NEST each NESTML version supports! e.g. can I generate code for multiple NEST versions with 1 NESTML version? Best regards, -- Robin De Schepper, MSc Department of Brain and Behavioral Sciences Unit of Neurophysiology University of Pavia, Italy Via Forlanini 6, 27100 Pavia - Italy Tel: (+39) 038298-7607 http://www-5.unipv.it/dangelo/ Interested in network modelling? Discover our framework <https://github.com/dbbs-lab/bsb>: <https://github.com/dbbs-lab/bsb>

3 2

New Izhikevich neuron model; nest_names and synapse dynamics
by Nina Doorn 15 Nov '21

15 Nov '21

Good afternoon, I have adapted the current nest izhikevich neuron model in C++ to obtain a more general izhikevich neuron where more parameters can be set (for example voltage shifts and the membrane capacitance), and the b-parameter can change over time according to some condition, such that also thalamic neurons can be simulated. The new extension module works very well (with much thanks to all earlier help regarding installing extension modules). So hopefully people can eventually, with this model, obtain all the kinds of neurons that Izhikevich describes. As soon as everything is cleaned up and finished, I will upload the code to github. However, before I do that, I have two questions: 1. For the new parameters I added to the existing izhikevich model, I could only use parameter names that are in nest::names. However, for generality and to make it easy to use, I thought it would be better to use the same symbols that Izhikevich uses to describe his model. That way, people can easily replicate all the different types of neurons that Izhikevich describes. He uses these parameters: [image: image.png] Is it possible to include these parameters in the neuron model? Or is it better to just replace them with other parameter names that are already in the nest_names file? 2. The current izhikevich neuron model doesn't model realistic synapses. The membrane potential just jumps on each spike arrival. I would like to include different post-synaptic dynamics with different and preferably multiple timescales (like the beta_multisynapse). Someone mentioned before that a lot of the synaptic dynamics can be defined outside the neuron. So can I use beta synapses with the izhikevich neuron as it is now? Or should I somehow include these dynamics in the C++ file of my new module? I hope the questions are clear. Please let me know if I should provide any additional information. Thanks in advance and have a very nice weekend! Kind regards, Nina

2 1

Installing an extension module in tvb-nest docker
by Nina Doorn 11 Nov '21

11 Nov '21

Dear experts, To develop a spiking neuronal network model of the thalamus, I want to adapt the Izhikevich neuron model to account for the behavior of thalamocortical neurons. Before I do this, I wanted to test if it was possible to install an extension module in my setup. Therefore I followed these steps: https://nest-extension-module.readthedocs.io/en/latest/extension_modules.ht… to install this example nest-extension-module: https://github.com/nest/nest-extension-module . I am working with the tvb-multiscale docker container ( https://github.com/the-virtual-brain/tvb-multiscale/tree/master/tvb_multisc…) in VScode on windows. I've been working with this succesfully and easily managed to make thalamus models with the available aeIF neuron model of NEST. I'm using a python 3.7.3 interpreter and NEST 3. I've succesfully "made" the module with: > docker@84fabd16af99:~/mmb$ cmake > -Dwith-nest=/home/docker/env/neurosci/nest_build/bin/nest-config > ../nest-extension-module-master It gives me the message: > You can now build and install 'mymodule' using > make > make install > The library file libmymodule.so will be installed to > /home/docker/env/neurosci/nest_build/lib/nest/ > Help files will be installed to > /home/docker/env/neurosci/nest_build/share/doc/nest > The module can be loaded into NEST using > nest.Install('mymodule') (in PyNEST) > (mymodule) Install (in SLI > -- Configuring done > -- Generating done > -- Build files have been written to: /home/docker/mmb However, when I try to "make". I get a bunch of errors that I have added at the end of this email. My colleague tried to install exactly the same module in exactly the same way on his linux machine and it worked perfectly. But somehow for me, I get these weird errors that I haven't been able to resolve so far. Does anyone have an idea what the problem might be? It would be greatly appreciated. If you need any additional information please let me know. Thank you in advance and have a nice day! Kind regards, Nina Doorn Error message: docker@84fabd16af99:~/mmb$ make Scanning dependencies of target mymodule_module [ 10%] Building CXX object src/CMakeFiles/mymodule_module.dir/mymodule.cpp.o In file included from /home/docker/nest-extension-module-master/src/mymodule.cpp:30: /home/docker/nest-extension-module-master/src/pif_psc_alpha.h:92:1: error: expected class-name before ‘{’ token { ^ /home/docker/nest-extension-module-master/src/pif_psc_alpha.h:115:21: error: type ‘nest::Node’ is not a base type for type ‘mynest::pif_psc_alpha’ using nest::Node::handle; ^~~~~~ /home/docker/nest-extension-module-master/src/pif_psc_alpha.h:116:21: error: type ‘nest::Node’ is not a base type for type ‘mynest::pif_psc_alpha’ using nest::Node::handles_test_event; ^~~~~~~~~~~~~~~~~~ /home/docker/nest-extension-module-master/src/pif_psc_alpha.h:121:14: error: ‘nest::port mynest::pif_psc_alpha::send_test_event(nest::Node&, nest::port, nest::synindex, bool)’ marked ‘override’, but does not override nest::port send_test_event( nest::Node&, nest::port, nest::synindex, bool ) override; ^~~~~~~~~~~~~~~ /home/docker/nest-extension-module-master/src/pif_psc_alpha.h:129:8: error: ‘void mynest::pif_psc_alpha::handle(nest::SpikeEvent&)’ marked ‘override’, but does not override void handle( nest::SpikeEvent& ) override; //! accept spikes ^~~~~~ /home/docker/nest-extension-module-master/src/pif_psc_alpha.h:130:8: error: ‘void mynest::pif_psc_alpha::handle(nest::CurrentEvent&)’ marked ‘override’, but does not override void handle( nest::CurrentEvent& ) override; //! accept input current ^~~~~~ /home/docker/nest-extension-module-master/src/pif_psc_alpha.h:131:8: error: ‘void mynest::pif_psc_alpha::handle(nest::DataLoggingRequest&)’ marked ‘override’, but does not override void handle( nest::DataLoggingRequest& ) override; //! allow recording with multimeter ^~~~~~ /home/docker/nest-extension-module-master/src/pif_psc_alpha.h:133:14: error: ‘nest::port mynest::pif_psc_alpha::handles_test_event(nest::SpikeEvent&, nest::port)’ marked ‘override’, but does not override nest::port handles_test_event( nest::SpikeEvent&, nest::port ) override; ^~~~~~~~~~~~~~~~~~ /home/docker/nest-extension-module-master/src/pif_psc_alpha.h:134:14: error: ‘nest::port mynest::pif_psc_alpha::handles_test_event(nest::CurrentEvent&, nest::port)’ marked ‘override’, but does not override nest::port handles_test_event( nest::CurrentEvent&, nest::port ) override; ^~~~~~~~~~~~~~~~~~ /home/docker/nest-extension-module-master/src/pif_psc_alpha.h:135:14: error: ‘nest::port mynest::pif_psc_alpha::handles_test_event(nest::DataLoggingRequest&, nest::port)’ marked ‘override’, but does not override nest::port handles_test_event( nest::DataLoggingRequest&, nest::port ) override; ^~~~~~~~~~~~~~~~~~ /home/docker/nest-extension-module-master/src/pif_psc_alpha.h:138:8: error: ‘void mynest::pif_psc_alpha::get_status(DictionaryDatum&) const’ marked ‘override’, but does not override void get_status( DictionaryDatum& ) const override; ^~~~~~~~~~ /home/docker/nest-extension-module-master/src/pif_psc_alpha.h:139:8: error: ‘void mynest::pif_psc_alpha::set_status(const DictionaryDatum&)’ marked ‘override’, but does not override void set_status( const DictionaryDatum& ) override; ^~~~~~~~~~ /home/docker/nest-extension-module-master/src/pif_psc_alpha.h:143:8: error: ‘void mynest::pif_psc_alpha::init_buffers_()’ marked ‘override’, but does not override void init_buffers_() override; ^~~~~~~~~~~~~ /home/docker/nest-extension-module-master/src/pif_psc_alpha.h:146:8: error: ‘void mynest::pif_psc_alpha::calibrate()’ marked ‘override’, but does not override void calibrate() override; ^~~~~~~~~ /home/docker/nest-extension-module-master/src/pif_psc_alpha.h:149:8: error: ‘void mynest::pif_psc_alpha::update(const nest::Time&, long int, long int)’ marked ‘override’, but does not override void update( nest::Time const&, const long, const long ) override; ^~~~~~ /home/docker/nest-extension-module-master/src/pif_psc_alpha.h: In member function ‘nest::port mynest::pif_psc_alpha::send_test_event(nest::Node&, nest::port, nest::synindex, bool)’: /home/docker/nest-extension-module-master/src/pif_psc_alpha.h:324:23: error: no matching function for call to ‘nest::SpikeEvent::set_sender(mynest::pif_psc_alpha&)’ e.set_sender( *this ); ^ In file included from /home/docker/env/neurosci/nest_build/include/nest/connector_model.h:34, from /home/docker/env/neurosci/nest_build/include/nest/common_synapse_properties.h:27, from /home/docker/env/neurosci/nest_build/include/nest/connection.h:27, from /home/docker/nest-extension-module-master/src/drop_odd_spike_connection.h:27, from /home/docker/nest-extension-module-master/src/mymodule.cpp:29: /home/docker/env/neurosci/nest_build/include/nest/event.h:1288:1: note: candidate: ‘void nest::Event::set_sender(nest::Node&)’ Event::set_sender( Node& s ) ^~~~~ /home/docker/env/neurosci/nest_build/include/nest/event.h:1288:1: note: no known conversion for argument 1 from ‘mynest::pif_psc_alpha’ to ‘nest::Node&’ In file included from /home/docker/nest-extension-module-master/src/mymodule.cpp:30: /home/docker/nest-extension-module-master/src/pif_psc_alpha.h: In member function ‘nest::port mynest::pif_psc_alpha::handles_test_event(nest::SpikeEvent&, nest::port)’: /home/docker/nest-extension-module-master/src/pif_psc_alpha.h:337:53: error: ‘get_name’ was not declared in this scope throw nest::UnknownReceptorType( receptor_type, get_name() ); ^~~~~~~~ /home/docker/nest-extension-module-master/src/pif_psc_alpha.h:337:53: note: suggested alternative: ‘get_V_m_’ throw nest::UnknownReceptorType( receptor_type, get_name() ); ^~~~~~~~ get_V_m_ /home/docker/nest-extension-module-master/src/pif_psc_alpha.h: In member function ‘nest::port mynest::pif_psc_alpha::handles_test_event(nest::CurrentEvent&, nest::port)’: /home/docker/nest-extension-module-master/src/pif_psc_alpha.h:351:53: error: ‘get_name’ was not declared in this scope throw nest::UnknownReceptorType( receptor_type, get_name() ); ^~~~~~~~ /home/docker/nest-extension-module-master/src/pif_psc_alpha.h:351:53: note: suggested alternative: ‘get_V_m_’ throw nest::UnknownReceptorType( receptor_type, get_name() ); ^~~~~~~~ get_V_m_ /home/docker/nest-extension-module-master/src/pif_psc_alpha.h: In member function ‘nest::port mynest::pif_psc_alpha::handles_test_event(nest::DataLoggingRequest&, nest::port)’: /home/docker/nest-extension-module-master/src/pif_psc_alpha.h:366:53: error: ‘get_name’ was not declared in this scope throw nest::UnknownReceptorType( receptor_type, get_name() ); ^~~~~~~~ /home/docker/nest-extension-module-master/src/pif_psc_alpha.h:366:53: note: suggested alternative: ‘get_V_m_’ throw nest::UnknownReceptorType( receptor_type, get_name() ); ^~~~~~~~ get_V_m_ /home/docker/nest-extension-module-master/src/pif_psc_alpha.h: In member function ‘void mynest::pif_psc_alpha::get_status(DictionaryDatum&) const’: /home/docker/nest-extension-module-master/src/pif_psc_alpha.h:380:3: error: ‘ArchivingNode’ has not been declared ArchivingNode::get_status( d ); ^~~~~~~~~~~~~ /home/docker/nest-extension-module-master/src/pif_psc_alpha.h: In member function ‘void mynest::pif_psc_alpha::set_status(const DictionaryDatum&)’: /home/docker/nest-extension-module-master/src/pif_psc_alpha.h:397:3: error: ‘ArchivingNode’ has not been declared ArchivingNode::set_status( d ); ^~~~~~~~~~~~~ In file included from /home/docker/env/neurosci/nest_build/include/nest/connection_manager_impl.h:33, from /home/docker/nest-extension-module-master/src/mymodule.cpp:38: /home/docker/env/neurosci/nest_build/include/nest/conn_builder_factory.h: In instantiation of ‘nest::ConnBuilder* nest::ConnBuilderFactory<ConnBuilderType>::create(nest::NodeCollectionPTR, nest::NodeCollectionPTR, const DictionaryDatum&, const DictionaryDatum&) const [with ConnBuilderType = mynest::StepPatternBuilder; nest::NodeCollectionPTR = std::shared_ptr<nest::NodeCollection>; DictionaryDatum = lockPTRDatum<Dictionary, (& SLIInterpreter::Dictionarytype)>]’: /home/docker/env/neurosci/nest_build/include/nest/conn_builder_factory.h:67:3: required from here /home/docker/env/neurosci/nest_build/include/nest/conn_builder_factory.h:72:12: error: no matching function for call to ‘mynest::StepPatternBuilder::StepPatternBuilder(nest::NodeCollectionPTR&, nest::NodeCollectionPTR&, const DictionaryDatum&, const DictionaryDatum&)’ return new ConnBuilderType( sources, targets, conn_spec, syn_spec ); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /home/docker/nest-extension-module-master/src/mymodule.cpp:31: /home/docker/nest-extension-module-master/src/step_pattern_builder.h:35:3: note: candidate: ‘mynest::StepPatternBuilder::StepPatternBuilder(nest::NodeCollectionPTR, nest::NodeCollectionPTR, const DictionaryDatum&, const std::vector<lockPTRDatum<Dictionary, (& SLIInterpreter::Dictionarytype)> >&)’ StepPatternBuilder( const nest::NodeCollectionPTR sources, ^~~~~~~~~~~~~~~~~~ /home/docker/nest-extension-module-master/src/step_pattern_builder.h:35:3: note: no known conversion for argument 4 from ‘const DictionaryDatum’ {aka ‘const lockPTRDatum<Dictionary, (& SLIInterpreter::Dictionarytype)>’} to ‘const std::vector<lockPTRDatum<Dictionary, (& SLIInterpreter::Dictionarytype)> >&’ /home/docker/nest-extension-module-master/src/step_pattern_builder.h:32:7: note: candidate: ‘mynest::StepPatternBuilder::StepPatternBuilder(const mynest::StepPatternBuilder&)’ class StepPatternBuilder : public nest::ConnBuilder ^~~~~~~~~~~~~~~~~~ /home/docker/nest-extension-module-master/src/step_pattern_builder.h:32:7: note: candidate expects 1 argument, 4 provided /home/docker/nest-extension-module-master/src/step_pattern_builder.h:32:7: note: candidate: ‘mynest::StepPatternBuilder::StepPatternBuilder(mynest::StepPatternBuilder&&)’ /home/docker/nest-extension-module-master/src/step_pattern_builder.h:32:7: note: candidate expects 1 argument, 4 provided In file included from /home/docker/env/neurosci/nest_build/include/nest/model_manager.h:31, from /home/docker/env/neurosci/nest_build/include/nest/kernel_manager.h:31, from /home/docker/env/neurosci/nest_build/include/nest/connector_base_impl.h:26, from /home/docker/env/neurosci/nest_build/include/nest/connection.h:29, from /home/docker/nest-extension-module-master/src/drop_odd_spike_connection.h:27, from /home/docker/nest-extension-module-master/src/mymodule.cpp:29: /home/docker/env/neurosci/nest_build/include/nest/genericmodel.h: In instantiation of ‘bool nest::GenericModel<ElementT>::has_proxies() [with ElementT = mynest::pif_psc_alpha]’: /home/docker/env/neurosci/nest_build/include/nest/genericmodel.h:174:1: required from here /home/docker/env/neurosci/nest_build/include/nest/genericmodel.h:176:17: error: ‘class mynest::pif_psc_alpha’ has no member named ‘has_proxies’ return proto_.has_proxies(); ~~~~~~~^~~~~~~~~~~ /home/docker/env/neurosci/nest_build/include/nest/genericmodel.h: In instantiation of ‘bool nest::GenericModel<ElementT>::one_node_per_process() [with ElementT = mynest::pif_psc_alpha]’: /home/docker/env/neurosci/nest_build/include/nest/genericmodel.h:181:1: required from here /home/docker/env/neurosci/nest_build/include/nest/genericmodel.h:183:17: error: ‘class mynest::pif_psc_alpha’ has no member named ‘one_node_per_process’ return proto_.one_node_per_process(); ~~~~~~~^~~~~~~~~~~~~~~~~~~~ /home/docker/env/neurosci/nest_build/include/nest/genericmodel.h: In instantiation of ‘bool nest::GenericModel<ElementT>::is_off_grid() [with ElementT = mynest::pif_psc_alpha]’: /home/docker/env/neurosci/nest_build/include/nest/genericmodel.h:188:1: required from here /home/docker/env/neurosci/nest_build/include/nest/genericmodel.h:190:17: error: ‘class mynest::pif_psc_alpha’ has no member named ‘is_off_grid’ return proto_.is_off_grid(); ~~~~~~~^~~~~~~~~~~ /home/docker/env/neurosci/nest_build/include/nest/genericmodel.h: In instantiation of ‘void nest::GenericModel<ElementT>::calibrate_time(const nest::TimeConverter&) [with ElementT = mynest::pif_psc_alpha]’: /home/docker/env/neurosci/nest_build/include/nest/genericmodel.h:195:1: required from here /home/docker/env/neurosci/nest_build/include/nest/genericmodel.h:197:10: error: ‘class mynest::pif_psc_alpha’ has no member named ‘calibrate_time’; did you mean ‘calibrate’? proto_.calibrate_time( tc ); ~~~~~~~^~~~~~~~~~~~~~ calibrate /home/docker/env/neurosci/nest_build/include/nest/genericmodel.h: In instantiation of ‘void nest::GenericModel<ElementT>::sends_secondary_event(nest::GapJunctionEvent&) [with ElementT = mynest::pif_psc_alpha]’: /home/docker/env/neurosci/nest_build/include/nest/genericmodel.h:209:1: required from here /home/docker/env/neurosci/nest_build/include/nest/genericmodel.h:211:17: error: ‘class mynest::pif_psc_alpha’ has no member named ‘sends_secondary_event’; did you mean ‘send_test_event’? return proto_.sends_secondary_event( ge ); ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ send_test_event /home/docker/env/neurosci/nest_build/include/nest/genericmodel.h:211:43: error: return-statement with a value, in function returning ‘void’ [-fpermissive] return proto_.sends_secondary_event( ge ); ^ /home/docker/env/neurosci/nest_build/include/nest/genericmodel.h: In instantiation of ‘void nest::GenericModel<ElementT>::sends_secondary_event(nest::InstantaneousRateConnectionEvent&) [with ElementT = mynest::pif_psc_alpha]’: /home/docker/env/neurosci/nest_build/include/nest/genericmodel.h:216:1: required from here /home/docker/env/neurosci/nest_build/include/nest/genericmodel.h:218:17: error: ‘class mynest::pif_psc_alpha’ has no member named ‘sends_secondary_event’; did you mean ‘send_test_event’? return proto_.sends_secondary_event( re ); ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ send_test_event /home/docker/env/neurosci/nest_build/include/nest/genericmodel.h:218:43: error: return-statement with a value, in function returning ‘void’ [-fpermissive] return proto_.sends_secondary_event( re ); ^ /home/docker/env/neurosci/nest_build/include/nest/genericmodel.h: In instantiation of ‘void nest::GenericModel<ElementT>::sends_secondary_event(nest::DiffusionConnectionEvent&) [with ElementT = mynest::pif_psc_alpha]’: /home/docker/env/neurosci/nest_build/include/nest/genericmodel.h:223:1: required from here /home/docker/env/neurosci/nest_build/include/nest/genericmodel.h:225:17: error: ‘class mynest::pif_psc_alpha’ has no member named ‘sends_secondary_event’; did you mean ‘send_test_event’? return proto_.sends_secondary_event( de ); ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ send_test_event /home/docker/env/neurosci/nest_build/include/nest/genericmodel.h:225:43: error: return-statement with a value, in function returning ‘void’ [-fpermissive] return proto_.sends_secondary_event( de ); ^ /home/docker/env/neurosci/nest_build/include/nest/genericmodel.h: In instantiation of ‘void nest::GenericModel<ElementT>::sends_secondary_event(nest::DelayedRateConnectionEvent&) [with ElementT = mynest::pif_psc_alpha]’: /home/docker/env/neurosci/nest_build/include/nest/genericmodel.h:230:1: required from here /home/docker/env/neurosci/nest_build/include/nest/genericmodel.h:232:17: error: ‘class mynest::pif_psc_alpha’ has no member named ‘sends_secondary_event’; did you mean ‘send_test_event’? return proto_.sends_secondary_event( re ); ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ send_test_event /home/docker/env/neurosci/nest_build/include/nest/genericmodel.h:232:43: error: return-statement with a value, in function returning ‘void’ [-fpermissive] return proto_.sends_secondary_event( re ); ^ /home/docker/env/neurosci/nest_build/include/nest/genericmodel.h: In instantiation of ‘nest::SignalType nest::GenericModel<ElementT>::sends_signal() const [with ElementT = mynest::pif_psc_alpha]’: /home/docker/env/neurosci/nest_build/include/nest/genericmodel.h:237:1: required from here /home/docker/env/neurosci/nest_build/include/nest/genericmodel.h:239:17: error: ‘const class mynest::pif_psc_alpha’ has no member named ‘sends_signal’ return proto_.sends_signal(); ~~~~~~~^~~~~~~~~~~~ /home/docker/env/neurosci/nest_build/include/nest/genericmodel.h: In instantiation of ‘const nest::Node& nest::GenericModel<ElementT>::get_prototype() const [with ElementT = mynest::pif_psc_alpha]’: /home/docker/env/neurosci/nest_build/include/nest/genericmodel.h:267:1: required from here /home/docker/env/neurosci/nest_build/include/nest/genericmodel.h:269:10: error: invalid initialization of reference of type ‘const nest::Node&’ from expression of type ‘const mynest::pif_psc_alpha’ return proto_; ^~~~~~ /home/docker/env/neurosci/nest_build/include/nest/genericmodel.h: In instantiation of ‘void nest::GenericModel<ElementT>::set_model_id(int) [with ElementT = mynest::pif_psc_alpha]’: /home/docker/env/neurosci/nest_build/include/nest/genericmodel.h:274:1: required from here /home/docker/env/neurosci/nest_build/include/nest/genericmodel.h:276:10: error: ‘class mynest::pif_psc_alpha’ has no member named ‘set_model_id’ proto_.set_model_id( i ); ~~~~~~~^~~~~~~~~~~~ /home/docker/env/neurosci/nest_build/include/nest/genericmodel.h: In instantiation of ‘int nest::GenericModel<ElementT>::get_model_id() [with ElementT = mynest::pif_psc_alpha]’: /home/docker/env/neurosci/nest_build/include/nest/genericmodel.h:281:1: required from here /home/docker/env/neurosci/nest_build/include/nest/genericmodel.h:283:17: error: ‘class mynest::pif_psc_alpha’ has no member named ‘get_model_id’ return proto_.get_model_id(); ~~~~~~~^~~~~~~~~~~~ /home/docker/env/neurosci/nest_build/include/nest/genericmodel.h: In instantiation of ‘DictionaryDatum nest::GenericModel<ElementT>::get_status_() [with ElementT = mynest::pif_psc_alpha; DictionaryDatum = lockPTRDatum<Dictionary, (& SLIInterpreter::Dictionarytype)>]’: /home/docker/env/neurosci/nest_build/include/nest/genericmodel.h:251:1: required from here /home/docker/env/neurosci/nest_build/include/nest/genericmodel.h:253:30: error: ‘class mynest::pif_psc_alpha’ has no member named ‘get_status_base’; did you mean ‘get_status’? DictionaryDatum d = proto_.get_status_base(); ~~~~~~~^~~~~~~~~~~~~~~ get_status /home/docker/env/neurosci/nest_build/include/nest/genericmodel.h: In instantiation of ‘nest::Node* nest::GenericModel<ElementT>::allocate_(void*) [with ElementT = mynest::pif_psc_alpha]’: /home/docker/env/neurosci/nest_build/include/nest/genericmodel.h:159:1: required from here /home/docker/env/neurosci/nest_build/include/nest/genericmodel.h:161:9: error: cannot convert ‘mynest::pif_psc_alpha*’ to ‘nest::Node*’ in initialization Node* n = new ( adr ) ElementT( proto_ ); ^ make[2]: *** [src/CMakeFiles/mymodule_module.dir/build.make:63: src/CMakeFiles/mymodule_module.dir/mymodule.cpp.o] Error 1 make[1]: *** [CMakeFiles/Makefile2:125: src/CMakeFiles/mymodule_module.dir/all] Error 2 make: *** [Makefile:152: all] Error 2

5 18

Using NEST in Spyder/anaconda
by Julien Ballbé 10 Nov '21

10 Nov '21

Dear Sir, Dear Madam, I am currently trying to install NEST in order to be able to use it within an IDE, like Spyder. For the moment I am only able to do the following: open Terminal python3 import nest This works when I use it in the terminal of the computer, but when I open Spyder and execute the following: import nest neuron=nest.Create("iaf_psc_alpha") neuron.get() I get the following error message in the IPython console: runfile('/Users/julienballbe/NEST/untitled0.py', wdir='/Users/julienballbe/NEST') Traceback (most recent call last): File "/Users/julienballbe/NEST/untitled0.py", line 11, in <module> neuron=nest.Create("iaf_psc_alpha") AttributeError: module 'nest' has no attribute 'Create' I am using a Macbook pro M1Max, MacOS 12.0, Spyder 5.1.5, Python 3.9.7. I followed the instruction for building nest on your website ( https://nest-simulator.readthedocs.io/en/latest/installation/mac_install.ht…) and used your recommendation for M1 macs ( https://nest-simulator.readthedocs.io/en/latest/installation/conda_tips.html ). I build Nest following your instruction, the only error I got was when I ran : (nest-simulator-dev) julienballbe@pclnrs241 NEST % make installcheck NEST Testsuite Results ---------------------------------------------------------------------- Phase Tests Skipped Failures Errors Time ---------------------------------------------------------------------- 01 basetests 6 0 0 0 2.0 02 selftests 8 0 0 0 1.0 03 unittests 179 0 0 0 47.0 04 regressiontests 94 2 0 0 55.0 07 pynesttests 93 0 0 93 2.0 07 pynesttests nc 0 0 0 0 0.0 08 cpptests 30 0 0 0 0.0 ---------------------------------------------------------------------- Total 410 2 0 93 107.0 ---------------------------------------------------------------------- THE NEST TESTSUITE DISCOVERED PROBLEMS The following tests failed | .share.nest.testsuite.pytests.test_NodeCollection | .share.nest.testsuite.pytests.test_aeif_lsodar | .share.nest.testsuite.pytests.test_changing_tic_base | .share.nest.testsuite.pytests.test_clopath_synapse | .share.nest.testsuite.pytests.test_connect_all_to_all | .share.nest.testsuite.pytests.test_connect_array_fixed_indegree | .share.nest.testsuite.pytests.test_connect_array_fixed_outdegree | .share.nest.testsuite.pytests.test_connect_arrays | .share.nest.testsuite.pytests.test_connect_conngen | .share.nest.testsuite.pytests.test_connect_fixed_indegree | .share.nest.testsuite.pytests.test_connect_fixed_outdegree | .share.nest.testsuite.pytests.test_connect_fixed_total_number | .share.nest.testsuite.pytests.test_connect_one_to_one | .share.nest.testsuite.pytests.test_connect_pairwise_bernoulli | .share.nest.testsuite.pytests.test_connect_symmetric_pairwise_bernoulli | .share.nest.testsuite.pytests.test_create | .share.nest.testsuite.pytests.test_current_recording_generators | .share.nest.testsuite.pytests.test_erfc_neuron | .share.nest.testsuite.pytests.test_errors | .share.nest.testsuite.pytests.test_events | .share.nest.testsuite.pytests.test_facetshw_stdp | .share.nest.testsuite.pytests.test_get_set | .share.nest.testsuite.pytests.test_getconnections | .share.nest.testsuite.pytests.test_getnodes | .share.nest.testsuite.pytests.test_glif_cond | .share.nest.testsuite.pytests.test_glif_psc | .share.nest.testsuite.pytests.test_helper_functions | .share.nest.testsuite.pytests.test_jonke_synapse | .share.nest.testsuite.pytests.test_json | .share.nest.testsuite.pytests.test_labeled_synapses | .share.nest.testsuite.pytests.test_mc_neuron | .share.nest.testsuite.pytests.test_multiple_synapses | .share.nest.testsuite.pytests.test_nodeParametrization | .share.nest.testsuite.pytests.test_onetooneconnect | .share.nest.testsuite.pytests.test_parameter | .share.nest.testsuite.pytests.test_parrot_neuron | .share.nest.testsuite.pytests.test_parrot_neuron_ps | .share.nest.testsuite.pytests.test_poisson_generator_rate_change | .share.nest.testsuite.pytests.test_pp_psc_delta | .share.nest.testsuite.pytests.test_pp_psc_delta_stdp | .share.nest.testsuite.pytests.test_quantal_stp_synapse | .share.nest.testsuite.pytests.test_random123 | .share.nest.testsuite.pytests.test_random_parameter | .share.nest.testsuite.pytests.test_rate_copy_model | .share.nest.testsuite.pytests.test_rate_instantaneous_and_delayed | .share.nest.testsuite.pytests.test_rate_neuron | .share.nest.testsuite.pytests.test_rate_neuron_communication | .share.nest.testsuite.pytests.test_recording_backend_ascii | .share.nest.testsuite.pytests.test_recording_backend_memory | .share.nest.testsuite.pytests.test_recording_backends | .share.nest.testsuite.pytests.test_refractory | .share.nest.testsuite.pytests.test_regression_issue-1034 | .share.nest.testsuite.pytests.test_regression_issue-1409 | .share.nest.testsuite.pytests.test_regression_issue-2069 | .share.nest.testsuite.pytests.test_regression_issue-2125 | .share.nest.testsuite.pytests.test_siegert_neuron | .share.nest.testsuite.pytests.test_split_simulation | .share.nest.testsuite.pytests.test_stack | .share.nest.testsuite.pytests.test_status | .share.nest.testsuite.pytests.test_stdp_multiplicity | .share.nest.testsuite.pytests.test_stdp_nn_synapses | .share.nest.testsuite.pytests.test_stdp_synapse | .share.nest.testsuite.pytests.test_stdp_triplet_synapse | .share.nest.testsuite.pytests.test_step_rate_generator | .share.nest.testsuite.pytests.test_synapsecollection | .share.nest.testsuite.pytests.test_threads | .share.nest.testsuite.pytests.test_tsodyks2_synapse | .share.nest.testsuite.pytests.test_urbanczik_synapse | .share.nest.testsuite.pytests.test_visualization | .share.nest.testsuite.pytests.test_vogels_sprekeler_synapse | .share.nest.testsuite.pytests.test_weight_recorder | .share.nest.testsuite.pytests.test_weights_as_lists | .share.nest.testsuite.pytests.test_sp.test_conn_builder | .share.nest.testsuite.pytests.test_sp.test_disconnect | .share.nest.testsuite.pytests.test_sp.test_disconnect_multiple | .share.nest.testsuite.pytests.test_sp.test_enable_multithread | .share.nest.testsuite.pytests.test_sp.test_growth_curves | .share.nest.testsuite.pytests.test_sp.test_sp_manager | .share.nest.testsuite.pytests.test_sp.test_synaptic_elements | .share.nest.testsuite.pytests.test_sp.test_update_synaptic_elements | .share.nest.testsuite.pytests.test_spatial.test_SynapseCollection_distance | .share.nest.testsuite.pytests.test_spatial.test_basics | .share.nest.testsuite.pytests.test_spatial.test_connect_layers | .share.nest.testsuite.pytests.test_spatial.test_connect_sliced | .share.nest.testsuite.pytests.test_spatial.test_connection_with_elliptical_mask | .share.nest.testsuite.pytests.test_spatial.test_create_spatial | .share.nest.testsuite.pytests.test_spatial.test_dumping | .share.nest.testsuite.pytests.test_spatial.test_layerNodeCollection | .share.nest.testsuite.pytests.test_spatial.test_layer_GetStatus_SetStatus | .share.nest.testsuite.pytests.test_spatial.test_plotting | .share.nest.testsuite.pytests.test_spatial.test_rotated_rect_mask | .share.nest.testsuite.pytests.test_spatial.test_selection_function_and_elliptical_mask | .share.nest.testsuite.pytests.test_spatial.test_spatial_distributions Please report test failures by creating an issue at https://github.com/nest/nest_simulator/issues ---------------------------------------------------------------------- make[3]: *** [CMakeFiles/installcheck] Error 1 make[2]: *** [CMakeFiles/installcheck.dir/all] Error 2 make[1]: *** [CMakeFiles/installcheck.dir/rule] Error 2 make: *** [installcheck] Error 2 Can you please help me with this? I stay at your disposal for any further information. Thank you for your help, Best feelings, Julien Ballbé -- *Julien BALLBÉ Y SABATÉ* *Étudiant en thèse - PhD student* *Neurophysiology of Visual Computation* Centre Giovanni Borelli - CNRS UMR 9010 Université de Paris 45 rue des Saint-Pères, 75006 Paris, France Tel: +33 6 79 03 40 35

2 1

2025

2024

2023

2022

2021

2020

2019

NEST Users