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NEST Conference 2025 - Extension of abstract submission deadline
by Dennis Terhorst 14 Apr '25

14 Apr '25

Dear all, We are inviting contributions to the conference, including talks, "posters" and workshops on specific topics. We are looking forward to your contributions! Due to unrelated organizational circumstances we decided to *extend the abstract submission deadline* for the NEST Conference 2025 *to 30 April*. The NEST Conference provides an opportunity for the NEST Community to meet, exchange success stories, swap advice, learn about current developments in and around NEST spiking network simulation and its application. Take the opportunity to advance your skills in using NEST at our hands-on workshops! This year's conference will again take place as a *virtual conference* on Tuesday/Wednesday *17/**18 June 2025*. We are delighted to welcome * Marja-Leena Linne, Tampere University, Finland * Daniela Gandolfi, Università degli Studi di Modena e Reggio Emilia, Italy * Barna Zajzon, Forschungszentrum Jülich, Germany * Bernhard Vogginger, TU Dresden, Germany as keynote speakers at the conference. For more information on how to submit your contribution, register and participate, please visit the conference website *https://nest-simulator.org/conference* <https://nest-simulator.org/conference> *Important dates* *25 April*2025 - Deadline for NEST Initiative membership applications eligible for fee reduction *30 April*2025 - Extended deadline for submission of contributions *09 May*2025 - Notification of acceptance *11 June*2025 - Registration deadline *17 June*2025 - NEST Conference 2025 starts We are looking forward to seeing you all in June! on behalf of Hans Ekkehard Plesser and the conference organizing committee best Dennis Terhorst

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install issue: MUSIC working from SLI but not pyNEST
by Paolo Marzolo 14 Apr '25

14 Apr '25

Hey all! First time poster here on the mailing list, so don't hesitate to correct me or ask for more information. I'm building a container to package a simulation, but I've ran into an unusual issue that I can't seem to fix: MUSIC proxy nodes are found and created correctly from NEST SLI, but raise `nest.lib.hl_api_exceptions.NESTErrors.UnknownModelName` when created from pyNEST. Here's some more info about my setup. - Both MUSIC and NEST are built from source (`git clone --depth 1 --branch v3.7 https://github.com/nest/nest-simulator/`) - I've tried both `-Dwith-music=ON` and `-Dwith-music=$MUSIC_INSTALL_DIR` to no avail. I'll keep the latter. - other flags are `-Dwith-mpi=ON -Dwith-openmp=ON -Dwith-ltdl=ON` - here are the relevant sections of the cmake output (full output at the end) ``` #18 11.02 Python bindings : Yes (Python 3.10.17: /sim/venv/bin/python3) #18 11.02 Includes : /usr/local/include/python3.10 #18 11.02 Libraries : #18 11.02 Cython : Yes (Cython 3.0.12: /sim/venv/bin/cython) #18 11.02 MPI4Py : Yes (/sim/venv/lib/python3.10/site-packages/mpi4py/include) ... #18 11.02 Use MUSIC : Yes (MUSIC 1.2.1) #18 11.02 Includes : /sim/install/music/include #18 11.02 Libraries : /sim/install/music/lib/libmusic.so ``` - the presence of MUSIC version in `cmake` output makes me hopeful that it's found correctly - image based on Debian 12 (`FROM python:3.10-slim-bookworm AS runner`) - first thing i do is create a venv and set it as first in path (`ENV PATH="$VIRTUAL_ENV/bin:$PATH"`) - when i attempt to run the [MUSIC with pyNEST example](https://nest-simulator.readthedocs.io/en/stable/tutorials/music_tutorial/music_tutorial_2.html) i get `nest.lib.hl_api_exceptions.NESTErrors.UnknownModelName: UnknownModelName in SLI function Create_l_i: /music_event_in_proxy is not a known model name.`, while running the [MUSIC in SLI example](https://nest-simulator.readthedocs.io/en/stable/tutorials/music_tutorial/music_tutorial_sli.html) works correctly - i read the [official Dockerfile](https://github.com/nest/nest-docker/blob/master/src/3.8/Dockerf… but I couldn't spot any steps I might be missing, the [cmake options](https://nest-simulator.readthedocs.io/en/stable/installation/cmake_options.html#cmake-options), the [install_music.sh script](https://github.com/nest/nest-simulator/blob/master/build_support/in…, the [docker entrypoint](https://github.com/nest/nest-docker/blob/master/src/3.8/entrypo… and the $NEST_INSTALL_DIR/bin/nest_vars.sh scripts, but I didn't find anything other than what I already had. - I'm guessing this is user error on my part, hence the mailing list instead of github issues. If necessary I can share a smaller version of the dockerfile... not sure what else to try. On one hand, I'd think of a compilation issue, but the cmake output and the fact that SLI works correctly makes me doubt so. On the other, I might be missing an env var, but from what I could gather in pyNEST `nest.node_models` is asked to the kernel, which correctly creates the node when called from the SLI... Is there any esoteric configuration I might've missed? I'll take any and all suggestions! Thanks a lot, Paolo full cmake output: ``` #18 11.02 -------------------------------------------------------------------------------- #18 11.02 NEST Configuration Summary #18 11.02 -------------------------------------------------------------------------------- #18 11.02 #18 11.02 Target System : Linux #18 11.02 Cross Compiling : FALSE #18 11.02 C compiler : GNU 12.2.0 (/usr/bin/cc) #18 11.02 C compiler flags : -Wall -fopenmp -O2 -fdiagnostics-color=auto #18 11.02 C++ compiler : GNU 12.2.0 (/usr/bin/c++) #18 11.02 C++ compiler flags : -std=c++17 -Wall -fopenmp -O2 -fdiagnostics-color=auto #18 11.02 Build dynamic : ON #18 11.02 #18 11.02 Built-in modelset : full #18 11.02 #18 11.02 Python bindings : Yes (Python 3.10.17: /sim/venv/bin/python3) #18 11.02 Includes : /usr/local/include/python3.10 #18 11.02 Libraries : #18 11.02 Cython : Yes (Cython 3.0.12: /sim/venv/bin/cython) #18 11.02 MPI4Py : Yes (/sim/venv/lib/python3.10/site-packages/mpi4py/include) #18 11.02 #18 11.02 Documentation : No #18 11.02 #18 11.02 Use threading : Yes (OpenMP: -fopenmp) #18 11.02 Libraries : /usr/lib/gcc/x86_64-linux-gnu/12/libgomp.so;/usr/lib/x86_64-linux-gnu/libpthread.a #18 11.02 #18 11.02 Use GSL : Yes (GSL 2.7.1) #18 11.02 Includes : /usr/include #18 11.02 Libraries : /usr/lib/x86_64-linux-gnu/libgsl.so;/usr/lib/x86_64-linux-gnu/libgslcblas.so #18 11.02 #18 11.02 Use Readline : Yes (GNU Readline 8.2) #18 11.02 Includes : /usr/include #18 11.02 Libraries : /usr/lib/x86_64-linux-gnu/libreadline.so;/usr/lib/x86_64-linux-gnu/libncurses.so #18 11.02 #18 11.02 Use libltdl : Yes (LTDL 2.4.7) #18 11.02 Includes : /usr/include #18 11.02 Libraries : /usr/lib/x86_64-linux-gnu/libltdl.so #18 11.02 #18 11.02 Use MPI : Yes (MPI: /usr/bin/mpicxx) #18 11.02 Includes : /usr/lib/x86_64-linux-gnu/openmpi/include;/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi #18 11.02 Libraries : /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi_cxx.so;/usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so #18 11.02 Launcher : /usr/bin/mpiexec -n <np> <prog> <args> #18 11.02 #18 11.02 Detailed timers : No #18 11.02 #18 11.02 Use MUSIC : Yes (MUSIC 1.2.1) #18 11.02 Includes : /sim/install/music/include #18 11.02 Libraries : /sim/install/music/lib/libmusic.so #18 11.02 #18 11.02 Use libneurosim : No #18 11.02 #18 11.02 Use Boost : Yes (Boost 1.74.0) #18 11.02 Includes : /usr/include #18 11.02 Libraries : #18 11.02 #18 11.02 Use SIONlib : No #18 11.02 #18 11.02 Use HDF5 : No #18 11.02 #18 11.02 For details on setting specific flags for your MPI launcher command, see the #18 11.02 CMake documentation at https://cmake.org/cmake/help/latest/module/FindMPI.html #18 11.02 #18 11.02 -------------------------------------------------------------------------------- #18 11.02 #18 11.02 The NEST executable will be installed to: #18 11.02 /sim/install/nest/bin/ #18 11.02 #18 11.02 NEST dynamic libraries and user modules will be installed to: #18 11.02 /sim/install/nest/lib/nest/ #18 11.02 #18 11.02 PyNEST will be installed to: #18 11.02 /sim/install/nest/lib/python3.10/site-packages #18 11.02 #18 11.02 To set necessary environment variables, add the following line #18 11.02 to your ~/.bashrc : #18 11.02 source /sim/install/nest/bin/nest_vars.sh #18 11.02 #18 11.02 -------------------------------------------------------------------------------- #18 11.02 #18 11.02 You can now build and install NEST with #18 11.02 make #18 11.02 make install #18 11.02 make installcheck #18 11.02 #18 11.02 If you experience problems with the installation or the use of NEST, #18 11.02 please see https://www.nest-simulator.org/frequently_asked_questions #18 11.02 or go to https://www.nest-simulator.org/community to find out how to #18 11.02 join the user mailing list. #18 11.02 ```

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Open NEST Developer Video Conference Monday April 7, at 11:30 CEST (UTC+0200)
by Dennis Terhorst 07 Apr '25

07 Apr '25

Dear NEST Users & Developers! I would like to invite you to our next fortnightly Open NEST Developer Video Conference today *Monday April 7, 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/2025-04-07-Open-NEST-Developer-… <https://github.com/nest/nest-simulator/wiki/2025-04-07-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/ --------------------------------------------------------------------------------------------- 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), Dr. Stephanie Bauer (stellvertretende Vorsitzende), Prof. Dr. Ir. Pieter Jansens, Prof. Dr. Laurens Kuipers ---------------------------------------------------------------------------------------------

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using NEST in C++ examples
by johnpapad24＠gmail.com 02 Apr '25

02 Apr '25

Dear NEST team, I would like to intergrate nest in my c++ project however I couldn't find any examples on how to use nest in the C++ programing language. Can you give me some simple examples like conecting 3 neurons? Thanks in advance.

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using NEST in C++ examples
by johnpapad24＠gmail.com 01 Apr '25

01 Apr '25

Dear NEST team, I would like to intergrate nest in my c++ project however I couldn't find any examples on how to use nest in the C++ programing language. Can you give me some simple examples like conecting 3 neurons? Thanks in advance.

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What exactly should one do to customize one's own extension module?
by Alex Serenko 28 Mar '25

28 Mar '25

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Documentation
by Peter Mason 25 Mar '25

25 Mar '25

To Jessica Mitchell. using::: https://nest-jessica-mitchell.readthedocs.io/en/stable/documentation_workfl… Should this read 'bottom right of the screen' ? Also the 'Stable' page raises an Error Peter [image: image.png]

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Disconnecting a recurrently connected population fails
by Willem Wybo 24 Mar '25

24 Mar '25

Dear Nest users, I’ve been trying to disconnect a population of neurons that is recurrently connected to itself. This works for a simple connection rule, like conn_spec=‘all_to_all’, but it fails for a more complex rule, like, conn_spec={'rule': 'pairwise_bernoulli', 'p': 1.0, 'allow_autapses': False}. When connecting two different populations to each other, disconnecting works with this rule. However, when connecting to the same population, the output of nest.GetConnections states that there are no connections, and calling nest.Disconnect() results in an error: nest.lib.hl_api_exceptions.NESTErrors.The connection does not exist: The connection does not exist in SLI function Disconnect_g_g_D_D: Deletion of connection is not possible. I’ve added a minimal example reproducing the issue in the attachment, Nest version is 3.8.0-post0.dev0. Btw, I’ve gotten this issue in a network model that was developed for Nest 3.5, so it seemed to work in that version. Best regards, Willem ---------------------- Dr. Willem Wybo, group leader Peter Grünberg Institute 15 - Neuromorphic Software Ecosystems Forschungszentrum Jülich www.fz-juelich.de/pgi/PGI-15 ——————————— ------------------------------------------------------------------------------------------------ ------------------------------------------------------------------------------------------------ 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), Dr. Stephanie Bauer (stellv. Vorsitzende), Prof. Dr. Ir. Pieter Jansens, Prof. Dr. Laurens Kuipers ------------------------------------------------------------------------------------------------ ------------------------------------------------------------------------------------------------

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Open NEST Developer Video Conference Monday March 24, at 11:30 CET (UTC+0100)
by Dennis Terhorst 24 Mar '25

24 Mar '25

Dear NEST Users & Developers! I would like to invite you to our next fortnightly Open NEST Developer Video Conference today *Monday March 24, 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/2025-03-24-Open-NEST-Developer-… <https://github.com/nest/nest-simulator/wiki/2025-03-24-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/ --------------------------------------------------------------------------------------------- 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), Dr. Stephanie Bauer (stellvertretende Vorsitzende), Prof. Dr. Ir. Pieter Jansens, Prof. Dr. Laurens Kuipers ---------------------------------------------------------------------------------------------

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NESTML - Error when generating code in an EasyBuild installation
by Pablo Alejandro 20 Mar '25

20 Mar '25

Hi everyone, I am currently working with nest/nestml that was installed with EasyBuild <https://docs.easybuild.io/> (i.e. a tool to manage software in HPC systems). Nest was installed with OpenMPI support (see nest_easybuild.eb attached) and it seems to be working fine. Nestml is failing when I try the stdp tutorial <https://nestml.readthedocs.io/en/latest/tutorials/stdp_windows/stdp_windows…> (see error log slurm-782.out and test.py script attached). I also attached the installation steps for nestml (nestml_easybuild.eb) and the slurm script (run_job_simple.sh) to this email. Could someone please assist me with further debugging this? This looks like an installation problem, but I get no errors if I'm using no synapse models. Thanks -- Pablo Alejandro

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