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Generating and building code in NESTML
by Shavika Rastogi 25 Nov '24

25 Nov '24

Hello everyone, I am Shavika Rastogi, a PhD student at the International Centre for Neuromorphic Systems, Western Sydney University, Australia. I currently use NEST and NESTML to write and test any arbitrary neuron model. Before writing my own neuron model, I wanted to test neuron models already existing in NESTML. I am using NEST and NESTML using docker. I am running the Izhikevich tutorial available in the documentation ( https://nestml.readthedocs.io/en/latest/tutorials/izhikevich/nestml_izhikev…). As per this tutorial, we can generate and build code using the following statement : "module_name,neuron_model_name=NESTCodeGeneratorUtils.generate_code_for("izhikevich_solution.nestml")" When I am using this function, I get the following error : "AttributeError: 'NESTCodeGeneratorUtils' object has no attribute 'generate_code_for'" Does anyone know whether the generate_code_for() function exists in the NESTCodeGeneratorUtils package? If not, what could be the alternative function we can use for generating and building neuron models ? Thanks in advance. With Warm Regards Shavika Rastogi, Research Scholar (Dual Award PhD) International Centre for Neuromorphic Systems The MARCS Institute of Brain, Behaviour and Development Western Sydney University Sydney, Australia & Biocomputation Research Group University of Hertfordshire, UK

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Re: NESTML Dopa Synapse - Error during parsing
by Jona Scholz 15 Nov '24

15 Nov '24

Hello everyone, quick update on my problem: I was using the latest .nestml models from the main branch with NESTML version 8.0.0-rc3. There is a slight difference between these and apparently that caused it. It works now and I hope everyone has a great weekend. Kind regards, Jona

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NESTML Dopa Synapse - Error during parsing
by Jona Scholz 13 Nov '24

13 Nov '24

Dear NESTML enthusiasts, I'm trying to do the NESTML dopamine-modulated STDP synapse tutorial ( https://nestml.readthedocs.io/en/latest/tutorials/stdp_dopa_synapse/stdp_do…) and get an error during the first code generation (see bottom of the message). This is the line where it fails: NESTCodeGeneratorUtils.generate_code_for("../../../models/neurons/iaf_psc_delta_neuron.nestml", nestml_stdp_dopa_model, ...) I am running the tutorial notebook as is, except for a change in the neuron model path. I changed it like this: NESTCodeGeneratorUtils.generate_code_for("iaf_psc_delta_neuron.nestml", nestml_stdp_dopa_model, ...) With this model https://github.com/nest/nestml/blob/master/models/neurons/iaf_psc_delta_neu… in the same folder as the notebook. I am using NESTML version 8.0.0rc3 and Nest 3.8. If I only generate code for the neuron model everything is fine. module_name, neuron_model_name = NESTCodeGeneratorUtils.generate_code_for( "iaf_psc_delta_neuron.nestml") [100%] Built target nestml_24dea23d173448c9b2a52d4f6a232dbd_module_module Install the project... Additionally, in the SFA tutorial I am able to change the neuron model and run it without any problems ( https://nestml.readthedocs.io/en/latest/tutorials/spike_frequency_adaptatio… ). With all of that said, here is the error: [1,GLOBAL, INFO]: List of files that will be processed: [2,GLOBAL, INFO]: /home/jona/rstdp-gym/iaf_psc_delta_neuron.nestml [3,GLOBAL, INFO]: /home/jona/rstdp-gym/neuromodulated_stdp_synapse.nestml [4,GLOBAL, INFO]: Target platform code will be generated in directory: '/home/jona/rstdp-gym/target' [5,GLOBAL, INFO]: Target platform code will be installed in directory: '/tmp/nestml_target_8uqeeze7' -- N E S T -- Copyright (C) 2004 The NEST Initiative Version: 3.8.0 Built: Aug 27 2024 04:33:09 This program is provided AS IS and comes with NO WARRANTY. See the file LICENSE for details. Problems or suggestions? Visit https://www.nest-simulator.org Type 'nest.help()' to find out more about NEST. [6,GLOBAL, INFO]: The NEST Simulator version was automatically detected as: v3.8.0 [7,GLOBAL, INFO]: Given template root path is not an absolute path. Creating the absolute path with default templates directory '/home/jona/mambaforge/envs/neuro/lib/python3.11/site-packages/pynestml/codegeneration/resources_nest/point_neuron' [8,GLOBAL, INFO]: Given template root path is not an absolute path. Creating the absolute path with default templates directory '/home/jona/mambaforge/envs/neuro/lib/python3.11/site-packages/pynestml/codegeneration/resources_nest/point_neuron' [9,GLOBAL, INFO]: Given template root path is not an absolute path. Creating the absolute path with default templates directory '/home/jona/mambaforge/envs/neuro/lib/python3.11/site-packages/pynestml/codegeneration/resources_nest/point_neuron' [10,GLOBAL, INFO]: The NEST Simulator installation path was automatically detected as: /home/jona/mambaforge/envs/neuro [11,GLOBAL, INFO]: Start processing '/home/jona/rstdp-gym/iaf_psc_delta_neuron.nestml'! [13,GLOBAL, INFO]: Start processing '/home/jona/rstdp-gym/neuromodulated_stdp_synapse.nestml'! [14,GLOBAL, ERROR]: Error occurred during parsing: abort [15,iaf_psc_delta_neuron_nestml, WARNING, [43:0;85:0]]: Model 'iaf_psc_delta_neuron_nestml' contains errors. No code generated! line 37:13 mismatched input '(' expecting NEWLINE line 39:4 extraneous input 'onReceive' expecting {<EOF>, NEWLINE, 'model'} line 40:8 extraneous input ' ' expecting {<EOF>, NEWLINE, 'model'} line 40:4 extraneous input ' ' expecting {<EOF>, NEWLINE, 'model'} line 43:8 extraneous input ' ' expecting {<EOF>, NEWLINE, 'model'} line 46:8 extraneous input 'c' expecting {<EOF>, NEWLINE, 'model'} line 46:4 extraneous input ' ' expecting {<EOF>, NEWLINE, 'model'} line 49:8 extraneous input ' ' expecting {<EOF>, NEWLINE, 'model'} line 52:8 extraneous input 'c' expecting {<EOF>, NEWLINE, 'model'} line 55:8 extraneous input 'emit_spike' expecting {<EOF>, NEWLINE, 'model'} line 55:4 extraneous input ' ' expecting {<EOF>, NEWLINE, 'model'} line 59:8 extraneous input ' ' expecting {<EOF>, NEWLINE, 'model'} line 63:8 extraneous input 'w' expecting {<EOF>, NEWLINE, 'model'} line 64:8 extraneous input 'w' expecting {<EOF>, NEWLINE, 'model'} line 65:8 extraneous input 'c' expecting {<EOF>, NEWLINE, 'model'} line 66:8 extraneous input 'n' expecting {<EOF>, NEWLINE, 'model'} line 66:0 extraneous input '\n' expecting {<EOF>, NEWLINE, 'model'} Any help is appreciated. Kind regards, Jona

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Open NEST Developer Video Conference Monday November 4, at 11:30 CET (UTC+0100)
by Dennis Terhorst 04 Nov '24

04 Nov '24

Dear NEST Users & Developers! I would like to invite you to our next fortnightly Open NEST Developer Video Conference today *Monday November 4, at 11:30 CET (UTC+0100).* As usual, in the Project team round, a contact person of each team will give a short statement summarizing ongoing and planned work in the team and highlight 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. 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. 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/2024-11-04-Open-NEST-Developer-… <https://github.com/nest/nest-simulator/wiki/2024-11-04-Open-NEST-Developer-…> Looking forward to seeing you soon! Cheers, Dennis Terhorst Log-in information We use a virtual conference room provided by DFN <https://www.dfn.de/en/> (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 <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 <http://vcc.zih.tu-dresden.de/index.php?linkid=1.1.3.4> -- Dipl.-Phys. Dennis Terhorst Coordinator Software Development Institute for Advanced Simulation (IAS-6) Computational and Systems Neuroscience & JARA-Institute Brain Structure-Function Relationships (INM-10) Institute of Neuroscience and Medicine Jülich Research Center, Member of the Helmholz Association 52425 Jülich, Germany http://www.csn.fz-juelich.de/ Phone +49 2461 61-85062 ---------------------------------------------------------------------- Forschungszentrum Jülich GmbH 52425 Jülich Sitz der Gesellschaft: Jülich Eingetragen im Handelsregister des Amtsgerichts Düren Nr. HR B 3498 Vorsitzender des Aufsichtsrats: MinDir Stefan Müller Geschäftsführung: Prof. Dr. Astrid Lambrecht (Vorsitzende), Karsten Beneke (stellv. Vorsitzender), Prof. Dr. Ir. Pieter Jansens ----------------------------------------------------------------------

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Simulation execution time for extended runs
by Peter Mason 01 Nov '24

01 Nov '24

The simulation of C.elegans now is implemented in a multi processing environment. The simulation of each individual object and various observation tools such as visualisation, matplotlib spike data plotting and configuration of the simulation parameters have their own process. An issue has arisen with only one object being simulated in that the execution 'time' for the constant 'simulation step time', increases with subsequent call to pynn.nest.Simulate(self.simulation_step). I presume nest continues the simulation from the previous iteration state. A crude plot suggests that the time increase is linear. Eventually the simulation stalls. I have a recorder connected to each of the 302 nodes and multiple recorders connected to some of the nodes. These use multiprocessor queues and a manged list to transfer data and as far as I can tell they do not overflow. I have disabled the recorders by not connecting them to the neurons and the phenomenon persists. It looks as if the issue is in the nest simulation. I have increased the process priority to -1. It does not help. Also does anyone know of the work of Ramin Hasani at Wien. He seems to have done the same thing and is now using 19 neurons to steer a car. How can I get a copy of the report of work done by him and his students? Peter Mason

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NEST & NESTML do things right :)
by Hans Ekkehard Plesser 24 Oct '24

24 Oct '24

Dear NEST Users, I have just published a paper in Frontiers in Neuroinformatics Plesser HE (2024) Commentary: Accelerating spiking neural network simulations with PymoNNto and PymoNNtorch. Front. Neuroinform. 18:1446620. doi: 10.3389/fninf.2024.1446620 confirming that NEST/NESTML provide correct simulations. I just wanted to let you know about this result because a paper earlier this year had included a figure showing that NEST got different results than several other simulators. It turned out that exact integration is exact as the name says, while forward Euler is not. Best, Hans Ekkehard -- Prof. Dr. Hans Ekkehard Plesser Research Committee Chair, Faculty of Science and Technology Head, Department of Data Science 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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Application-Oriented Hackathons
by Kunkel, Susanne 21 Oct '24

21 Oct '24

Dear NEST Users, We would like to inquire your interest in Application-Oriented Hackathons, and are thus reaching out to you with this survey: https://ictsurvey.helmholtz-muenchen.de/index.php?r=survey/index&sid=234889… which will be active till 25 October, 2024. For now, we plan to organize two such hackathons: 1. in Aachen, Germany in the week 9-13 December, 2024 2. in Aas, Norway in the week 23-27 June, 2025 These in-person events would allow you to bring your ideas for new NEST features and get started implementing them with the help of experienced NEST developers. Please note that your participation would be at your own expense. We look forward to your feedback! Best wishes, Susanne Kunkel on behalf of NEST Initiative ------------------------------------------------------------------------------------------------ ------------------------------------------------------------------------------------------------ Forschungszentrum Jülich GmbH 52425 Jülich Sitz der Gesellschaft: Jülich Eingetragen im Handelsregister des Amtsgerichts Düren Nr. HR B 3498 Vorsitzender des Aufsichtsrats: MinDir Stefan Müller Geschäftsführung: Prof. Dr. Astrid Lambrecht (Vorsitzende), Karsten Beneke (stellv. Vorsitzender), Prof. Dr. Ir. Pieter Jansens ------------------------------------------------------------------------------------------------ ------------------------------------------------------------------------------------------------

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Open NEST Developer Video Conference Monday October 21, at 11:30 CEST (UTC+0200)
by Dennis Terhorst 21 Oct '24

21 Oct '24

Dear NEST Users & Developers! I would like to invite you to our next fortnightly Open NEST Developer Video Conference today *Monday October 21, at 11:30 CEST (UTC+0200).* As usual, in the Project team round, a contact person of each team will give a short statement summarizing ongoing and planned work in the team and highlight 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. 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. 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/2024-10-21-Open-NEST-Developer-… <https://github.com/nest/nest-simulator/wiki/2024-10-21-Open-NEST-Developer-…> Looking forward to seeing you soon! Cheers, Dennis Terhorst Log-in information We use a virtual conference room provided by DFN <https://www.dfn.de/en/> (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 <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 <http://vcc.zih.tu-dresden.de/index.php?linkid=1.1.3.4> -- Dipl.-Phys. Dennis Terhorst Coordinator Software Development Institute for Advanced Simulation (IAS-6) Computational and Systems Neuroscience & JARA-Institute Brain Structure-Function Relationships (INM-10) Institute of Neuroscience and Medicine Jülich Research Center, Member of the Helmholz Association 52425 Jülich, Germany http://www.csn.fz-juelich.de/ Phone +49 2461 61-85062 ---------------------------------------------------------------------- Forschungszentrum Jülich GmbH 52425 Jülich Sitz der Gesellschaft: Jülich Eingetragen im Handelsregister des Amtsgerichts Düren Nr. HR B 3498 Vorsitzender des Aufsichtsrats: MinDir Stefan Müller Geschäftsführung: Prof. Dr. Astrid Lambrecht (Vorsitzende), Karsten Beneke (stellv. Vorsitzender), Prof. Dr. Ir. Pieter Jansens ----------------------------------------------------------------------

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MPI-based error on v3.8
by Ady Sharma 20 Oct '24

20 Oct '24

Hi all! What I'm doing: I've used v2.20.2 on HPC (bwForCluster NEMO) for my large-scale simulations involving structural plasticity. Now I'm trying to move to v3.8. How am I doing this? I built NESTv3.8 on my HPC workspace following the cmake instructions mentioned at: https://nest-simulator.readthedocs.io/en/v3.8/installation/cmake_options.ht… Here's an overview of my build and installation commands: ``` source /<some_path>/NESTv3.8/bin/activate # activate a fresh python venv (v3.9.7) [optional] module load mpi/openmpi/4.0-gnu-9.2 # cmake version 3.30.4 cmake --debug-find \ -DMPI_C_COMPILER=$(which mpicc) \ -DMPI_CXX_COMPILER=$(which mpicxx) \ -DMPI_HOME=$(which mpirun) \ -Dwith-mpi=ON \ -Dwith-openmp=ON \ -DCYTHON_EXECUTABLE=/<some_path>/intel/oneapi/2022.1/intelpython/latest/bin/cython \ -DCMAKE_INSTALL_PREFIX:PATH=/<some_path>/nest-simulator-3.8-build \ /<path_to_extracted_tar>/nest-simulator-3.8/ # if I don't specify the Cython path, cmake picks an outdated (uncompatible) cython version. I did not try the -Dcythonize-pynest=OFF option because I don't know how to build PyNEST from a pre-cythonized pynestkernel.pyx. make make install make installcheck ``` Once this finishes, I do the usual `source`-ing of `nest_vars.sh`. I also add the NEST path to my python venv's `site-packages`. This has always worked for all NEST versions I ever installed. `installcheck` finishes with 1 error. See below: ``` THE NEST TESTSUITE DISCOVERED PROBLEMS The following tests failed | regressiontests.issue-1703.py 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 ``` THE WARNING: Ignoring this, if I proceed with pyNEST in the venv by `import nest`, I get the following warning: ``` -------------------------------------------------------------------------- WARNING: There is at least non-excluded one OpenFabrics device found, but there are no active ports detected (or Open MPI was unable to use them). This is most certainly not what you wanted. Check your cables, subnet manager configuration, etc. The openib BTL will be ignored for this job. Local host: n4669 -------------------------------------------------------------------------- n4669.nemo.privat.74030PSM2 no hfi units are active (err=23) -------------------------------------------------------------------------- Open MPI failed an OFI Libfabric library call (fi_endpoint). This is highly unusual; your job may behave unpredictably (and/or abort) after this. Local host: n4669 Location: mtl_ofi_component.c:627 Error: Invalid argument (22) -------------------------------------------------------------------------- -- N E S T -- Copyright (C) 2004 The NEST Initiative Version: 3.8.0 Built: Oct 10 2024 16:21:41 This program is provided AS IS and comes with NO WARRANTY. See the file LICENSE for details. Problems or suggestions? Visit https://www.nest-simulator.org Type 'nest.help()' to find out more about NEST. ``` THE CRASH: If I ignore this warning and proceed to submit a job, the execution eventually crashes with exit code: 134. If you'd like to see the crash dump, check this MD file on GitLab.: https://gitlab.rz.uni-freiburg.de/as2013/mpi-hpc-nestv3.8.git Any idea what's going wrong here? If I follow the same build and installation steps on my local machine (other than specifying the Cython path in cmake; because no need). Neither do I get any warnings nor does any simulation crash. I'm guessing this has to do with the build and installation on the cluster. I'd appreciate any input. Thanks! Best, Ady

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aeif_cond_beta_multisynapse in NESTML
by tanguy.damart＠protonmail.com 11 Oct '24

11 Oct '24

Hello everyone, Is there a NESTML version of the NEST model aeif_cond_beta_multisynapse ? (https://nest-simulator.readthedocs.io/en/stable/models/aeif_cond_beta_multi…) If not, is there any difficulties that I might face implementing it in NESTML that I need to be aware of ? (Like how to handle multiple types of synapses). Best, Tanguy

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