- NEST Users - NEST Initiative Mail

nestml generate_target spinnaker failed
by Chris Huyck 16 Apr '25

16 Apr '25

I'm trying to generate a nestml model for spinnaker. I run the generate target and nest, and it works fine. If I change to spinnaker, it crashes with a CoCosManager not found. The spinnaker runs correctly, and I get correct behaviour on my board. I just can't generate target. Has anyone generated spinnaker models recently? -Chris

2 1

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

1 0

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 ```

1 0

Fwd: Usage of the nest-server-mpi
by Viktor Vorobev 10 Apr '25

10 Apr '25

Hello, dear nest team! I am trying to launch the experiment, using nest-server-mpi and NRP on the HPC. We also use a module generated by nestml. But I faced the issue, which I so far cannot solve myself... Probably you could help me. We have a working experiment for the nest-server v3.7, which also works with v3.8. I tried to launch nest-simulator in the container on the HPC, but I faced some mpi incompatibility issues, could not solve it fast and gave up for now. Then I installed nest-simulator 3.7 from source on the HPC. The simulation with nest-server also worked. After patching nest-server-mpi (serialization issue) I could launch it on the HPC and communicate with the API, but the experiment didn't work, and I switched to the local nest-simulator container for the test. Locally, in the original nest/nest-simulator:3.7 and 3.8 containers, the nest-server-mpi is not starting. After the fixing the issue (with docopt and serialization) the nest-server-mpi is launching in nest/nest-simulator:dev container. But here is the problem, with this version the experiment is crashing even with nest-server, as well as with nest-server-mpi. And I cannot figure out the reason from the logs and git history... I tried patching versions 3.7 and 3.8, then I can start nest-server-mpi, can use API, but the experiment itself doesn't work. So, the summary: The experiment works with nest-server 3.7 and 3.8, but doesn't work with the patched nest-server-mpi The experiment doesn't work with the nest-server with :dev container What happens in the latest container with the nest-server: nrp-nest-simulator | > nrp-nest-simulator | Apr 03 16:11:15 SimulationManager::set_status [Info]: > nrp-nest-simulator | Temporal resolution changed from 0.1 to 0.1 ms. > nrp-nest-simulator | > nrp-nest-simulator | Apr 03 16:11:15 Install [Info]: > nrp-nest-simulator | loaded module controller_module And that's it, on the other side I get [json.exception.out_of_range.403] key 'data' not found The nest script, which is executed at this moment is nest.ResetKernel() > nest.SetKernelStatus({"resolution": res}) > nest.Install("controller_module") > for i in range(njt): > planner_p = nest.Create("tracking_neuron_nestml", n=N, params={"kp": > plan_params["kp"], "base_rate": plan_params["base_rate"], "pos": True, > "traj": trj, "simulation_steps": len(trj)}) > planner_n = nest.Create("tracking_neuron_nestml", n=N, params={"kp": > plan_params["kp"], "base_rate": plan_params["base_rate"], "pos": False, > "traj": trj, "simulation_steps": len(trj)}) The same piece of code works in nest-server v3.7 and v3.8 What happens in the patched nest-server-mpi v 3.8 or 3.7, here it at least throws an exception nrp-nest-simulator | ======================================== > nrp-nest-simulator | > nrp-nest-simulator | ==> MASTER 0/1743700791.3478301 (route_api_call): > call=GetStatus, args=[[303]], kwargs={} > nrp-nest-simulator | ==> MASTER 0/1743700791.3478405 (GetStatus): sending > call bcast > nrp-nest-simulator | ==> MASTER 0/1743700791.3478618 (GetStatus): sending > data bcast, data=([[303]], {}) > nrp-nest-simulator | ==> MASTER 0/1743700791.3480251 (GetStatus): local > call, args=[NodeCollection(metadata=None, model=spike_recorder, size=1, > first=303)], kwargs={} > nrp-nest-simulator | ==> MASTER 0/1743700791.3480933 (GetStatus): waiting > for response gather > nrp-nest-simulator | ==> MASTER 0/1743700791.3484681 (GetStatus): > received response gather, data=[({'element_type': 'recorder', 'events': > {'senders': array([204]), 'times': array([13.5])}, 'frozen': False, > 'global_id': 303, 'label': 'Brain stem pos', 'local': True, 'model': > 'spike_recorder', 'model_id': 96, 'n_events': 1, 'node_uses_wfr': False, > 'origin': 0.0, 'record_to': 'memory', 'start': 0.0, 'stop': > 1.7976931348623157e+308, 'thread': 0, 'thread_local_id': 152, > 'time_in_steps': False, 'vp': 0},), [{'element_type': 'recorder', 'events': > {'senders': [], 'times': []}, 'frozen': False, 'global_id': 303, 'label': > 'Brain stem pos', 'local': True, 'model': 'spike_recorder', 'model_id': 96, > 'n_events': 0, 'node_uses_wfr': False, 'origin': 0.0, 'record_to': > 'memory', 'start': 0.0, 'stop': 1.7976931348623157e+308, 'thread': 0, > 'thread_local_id': 152, 'time_in_steps': False, 'vp': 1}]] > nrp-nest-simulator | [2025-04-03 19:19:51,348] ERROR in app: Exception on > /api/GetStatus [POST] > nrp-nest-simulator | Traceback (most recent call last): > nrp-nest-simulator | File > "/usr/lib/python3/dist-packages/flask/app.py", line 2070, in wsgi_app > nrp-nest-simulator | response = self.full_dispatch_request() > nrp-nest-simulator | File > "/usr/lib/python3/dist-packages/flask/app.py", line 1515, in > full_dispatch_request > nrp-nest-simulator | rv = self.handle_user_exception(e) > nrp-nest-simulator | File > "/usr/lib/python3/dist-packages/flask_cors/extension.py", line 165, in > wrapped_function > nrp-nest-simulator | return > cors_after_request(app.make_response(f(*args, **kwargs))) > nrp-nest-simulator | File > "/usr/lib/python3/dist-packages/flask/app.py", line 1513, in > full_dispatch_request > nrp-nest-simulator | rv = self.dispatch_request() > nrp-nest-simulator | File > "/usr/lib/python3/dist-packages/flask/app.py", line 1499, in > dispatch_request > nrp-nest-simulator | return > self.ensure_sync(self.view_functions[rule.endpoint])(**req.view_args) > nrp-nest-simulator | File > "/opt/nest/lib/python3.10/site-packages/nest/server/hl_api_server.py", line > 317, in route_api_call > nrp-nest-simulator | return jsonify(response) > nrp-nest-simulator | File > "/usr/lib/python3/dist-packages/flask/json/__init__.py", line 348, in > jsonify > nrp-nest-simulator | f"{dumps(data, indent=indent, > separators=separators)}\n", > nrp-nest-simulator | File > "/usr/lib/python3/dist-packages/flask/json/__init__.py", line 129, in dumps > nrp-nest-simulator | rv = _json.dumps(obj, **kwargs) > nrp-nest-simulator | File "/usr/lib/python3.10/json/__init__.py", line > 238, in dumps > nrp-nest-simulator | **kw).encode(obj) > nrp-nest-simulator | File "/usr/lib/python3.10/json/encoder.py", line > 199, in encode > nrp-nest-simulator | chunks = self.iterencode(o, _one_shot=True) > nrp-nest-simulator | File "/usr/lib/python3.10/json/encoder.py", line > 257, in iterencode > nrp-nest-simulator | return _iterencode(o, 0) > nrp-nest-simulator | File > "/usr/lib/python3/dist-packages/flask/json/__init__.py", line 56, in default > nrp-nest-simulator | return super().default(o) > nrp-nest-simulator | File "/usr/lib/python3.10/json/encoder.py", line > 179, in default > nrp-nest-simulator | raise TypeError(f'Object of type > {o.__class__.__name__} ' > nrp-nest-simulator | TypeError: Object of type int64 is not JSON > serializable > nrp-nest-simulator | [2025-04-03 19:19:51,349] INFO in _internal: > 172.18.0.3 - - [03/Apr/2025 19:19:51] "POST /api/GetStatus HTTP/1.1" 500 - Do you have any clues where I should dig? I would appreciate any help. Best wishes, Viktor

1 0

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 ---------------------------------------------------------------------------------------------

1 0

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.

2 1

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.

1 0

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

28 Mar '25

2 1

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]

2 1

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 ------------------------------------------------------------------------------------------------ ------------------------------------------------------------------------------------------------

1 1

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 ---------------------------------------------------------------------------------------------

1 0

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

2 9

Test message, please ignore
by Hans Ekkehard Plesser 19 Mar '25

19 Mar '25

-- 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

1 0

NEST Conference 2025 – registration and call for contributions are open
by Hans Ekkehard Plesser 16 Mar '25

16 Mar '25

Dear colleagues, The NEST Initiative is excited to invite everyone interested in Neural Simulation Technology and the NEST Simulator to the NEST Conference 2025. 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! We explicitly encourage young scientists to participate in the conference! 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 * as keynote speakers at the conference. Registration and submission of contributions are now open! We are inviting contributions to the conference, including talks, "posters" and workshops on specific topics. Please register and submit your contribution(s) via the conference website https://nest-simulator.org/conference Important dates 15 April 2025 - Deadline for submission of contributions 25 April 2025 - Deadline for NEST Initiative membership applications eligible for fee reduction 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! Hans Ekkehard Plesser and the conference organizing committee -- 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

1 0

First LTP interaction in STDP and synaptic time delay in STDP
by iiro.ahokainen＠tuni.fi 10 Mar '25

10 Mar '25

I'm a bit confused with NEST's STDP models. I'm not sure if the issues that I have found are design choices or unintended bugs. To debug stdp models, I added print statements in the stdp_synapse.h file: double minus_dt; while ( start != finish ) { minus_dt = t_lastspike_ - ( start->t_ + dendritic_delay ); std::cout<<"minus_dt: "<<minus_dt<<std::endl; std::cout<<"postspike time: "<<start->t_<<std::endl; ++start; // get_history() should make sure that // start->t_ > t_lastspike - dendritic_delay, i.e. minus_dt < 0 assert( minus_dt < -1.0 * kernel().connection_manager.get_stdp_eps() ); weight_ = facilitate_( weight_, Kplus_ * std::exp( minus_dt / tau_plus_ ) ); } I created two parrot neurons and fed spike times to the first neuron. I set the syn_delay to 0.3 ms. I found two issues: 1. If the spike train consists of only one spike, no STDP updates are performed. I would expect one positive update since the postsynaptic spike arrives 0.3 ms after the presynaptic spike. 2. minus_dt=-0.6 instead of -0.3. The spike separation is 0.3 ms, however for the STDP calculation, one uses 0.6 ms which confuses me. Indeed, simulating with presynaptic spike train [10., 20.] leads to weight change 1.0->35.5443 (lamba=1, mu_plus=mu_minus=0, otherwise defaults). Analytically, the same can be achieved by calculating (1/100 + np.exp(-0.6/20) - np.exp(-9.4/20))*100 = np.float64(35.54432652658074) This confirms that indeed minus_dt=-0.6 ms and that the first LTP STDP interaction is neglected. Are these known issues or new findings? I tested with NEST 3.3 and 3.8 and both had the same issues. I do not understand the point of having dendritic_delay in minus_dt = t_lastspike_ - ( start->t_ + dendritic_delay ), as it is already included in the start->t_ (?).

3 3

Open NEST Developer Video Conference Monday March 10, at 11:30 CET (UTC+0100)
by Dennis Terhorst 10 Mar '25

10 Mar '25

Dear NEST Users & Developers! I would like to invite you to our next fortnightly Open NEST Developer Video Conference today *Monday March 10, 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/2025-03-10-Open-NEST-Developer-… <https://github.com/nest/nest-simulator/wiki/2025-03-10-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 ---------------------------------------------------------------------------------------------

1 0

Exponential Euler Support in NESTML
by justin.r.davis＠essie.ufl.edu 05 Mar '25

05 Mar '25

I've got a version of the HH model (via a NESTML file) which seems to be requiring an exponential Euler solver (ie the one commonly used for e^x dependent biologic systems) to most efficiently solve the equations*. From my reading of the NESTML code generator tools source, only rk45 and forward-Euler are supported. The difference between Euler and Exponential Euler doesn't seem that significant, so I wanted to see if I could get the exponential version implemented....however, what's become unclear to me is whether or not this is a limitation of NEST, NESTML or the underlying solvers and how I'd go about getting a different solver implemented. Are there any guides around on how one would implement a new solver and/or information which would help me figure this out. thx. jrd *=forward Euler does work for some (might work with even smaller timestep) cases, but it requires a time step of 0.01ms. I'm comparing with a Brian2 version of the model running with a 0.1ms time step with it's natively supported exponential Euler solver which is what is making me look into other solvers for my NESTML-based code.

5 5

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

24 Feb '25

Dear NEST Users & Developers! I would like to invite you to our next fortnightly Open NEST Developer Video Conference today *Monday February 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/2025-02-24-Open-NEST-Developer-… <https://github.com/nest/nest-simulator/wiki/2025-02-24-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/ 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 ----------------------------------------------------------------------

1 0

export NEST_MLMODULES=nestmlmodule breaks nest
by Chris Huyck 14 Feb '25

14 Feb '25

I've been using nestml with pynn and nest for some time. I think I built a new model (combining a synapse and a neuron) and it broke nest. So, I can start an environment that has nest, and run nest (sli), pynest and pynn files with nest. However, if I export NEST_MLMODULES=nestmlmodule it breaks nest (sli). That is, I invoke nest, and it says it can't find nestmlmodule. However, if I start a new shell, and do not export NEST_MLMODULES I can run python, import nest, then nest.Install("./nestmlmodule") # in the right directory neuron = nest.Create("iaf_cond_beta_neuron") If I then export NEST_MLMODULES=nestmlmodule I can't import nest from python. Somewhere in the middle of all this, I reran nestml to create just the iaf_cond_beta_neuron, so that's the library I'm using. I'm pretty sure that library works fine. Any idea how to fix it? -Chris From: Chris Huyck <C.Huyck(a)mdx.ac.uk> Sent: 31 January 2025 12:10 To: NEST User Mailing List <users(a)nest-simulator.org> Subject: [NEST Users] Re: nestml synapses in pyNN I'm trying to use my own short term potentiation model with an existing model. The model is the IF_cond_exp model from PyNN. I tried your nestml integrate and fire models from Git.../nestml/master/models/neurons, and none seem to be the IF_cond_exp model. The closest I could find was the iaf_cond_beta_neuron. Am I missing something. Is the IF_cond_exp model done somewhere in nestml? (I'm relatively vested in that IF_cond_exp model. I need the nestml neuron model before I can properly use the nestml synapse model.) -Chris From: Charl Linssen <nest-users(a)turingbirds.com<mailto:nest-users@turingbirds.com>> Sent: 23 July 2024 11:25 To: users(a)nest-simulator.org<mailto:users@nest-simulator.org> Subject: [NEST Users] Re: nestml synapses in pyNN You don't often get email from nest-users(a)turingbirds.com<mailto:nest-users@turingbirds.com>. Learn why this is important<https://aka.ms/LearnAboutSenderIdentification> Hi Chris, Thank you for writing in! It would be great to have a better compatibility and better documentation for using NESTML models in pyNN, but as of now this is not yet in place, please let us know if you have any tips or experience to share. On SpiNNaker, only neuron models are supported for now, we have an open position for a student project to implement synaptic plasticity as well! With kind regards, Charl On Mon, Jul 22, 2024, at 16:32, Chris Huyck wrote: I've taken your noisy_synapse model and got that to run in pyNest. When I try it in PyNN it fails (can't find weight if you set w, weight not an argument if you use weight). I understand that you don't support pyNN. Do you support SpiNNaker (as it's a target)? If so, how do you access the model on SpiNNaker? (I only access SpiNNaker through PyNN). -Chris _______________________________________________ NEST Users mailing list -- users(a)nest-simulator.org<mailto:users@nest-simulator.org> To unsubscribe send an email to users-leave(a)nest-simulator.org<mailto:users-leave@nest-simulator.org>

2 9

nestml synapses in pyNN
by Chris Huyck 14 Feb '25

14 Feb '25

I've taken your noisy_synapse model and got that to run in pyNest. When I try it in PyNN it fails (can't find weight if you set w, weight not an argument if you use weight). I understand that you don't support pyNN. Do you support SpiNNaker (as it's a target)? If so, how do you access the model on SpiNNaker? (I only access SpiNNaker through PyNN). -Chris

2 8

nestml doesn't work on synapse models
by Chris Huyck 12 Feb '25

12 Feb '25

I've got a new conda environment. I compile nest (3.7) from a tarball and it runs. I pip install pyNN I pip install nestml (which now gives me nestml8.0.0. Is there some way to tell the version without just uninstalling it?) The neuron models work. The synapse models fail to nestml I tried my models, but went to the noisy_synapse and static_synapse models (from git) Both fail in nest_code_generator.py line 267 (variables_special_cases = ...) Any thoughts about how to get synapses to work in nestml? -Chris

2 5

wrong results eprop examples
by Xavier Otazu Porter 11 Feb '25

11 Feb '25

Hello, I have downloaded several of the eprop python examples, and none of them generate the correct results. For example, the handwritten example, generates a rather random result (the red points data) that do not fit with the expected results. The sinus generation, also generates wrong results. If you want, I can send a small image (not did it now to avoid image spamming). I am using NEST 3.8 with python 3.9 in a linux Rocks enviornment, and python 3.11 in a FreeBSD environment. Thanks a lot in advance. Xavier Computer Vision Center<http://www.cvc.uab.cat> CONFIDENTIALITY WARNING<http://www.cvc.uab.es/?page_id=7475>

3 2

`tsodyks_synapse` and `tsodyks2_synapse` models have different behavior for short term depression
by Pavel Haman 10 Feb '25

10 Feb '25

Hello, I have followed the example script comparing `tsodyks_synapse` and `tsodyks2_synapse` models, which can be found here: https://nest-simulator.readthedocs.io/en/stable/auto_examples/evaluate_tsod… Using the parameter set for depression instead of facilitation I found that `tsodyks2_synapse` model leads to weird peaks of synaptic currents (at least I would not expect that for short term depression) - during the second stimulation the weight rescaling seems to be shifted by one spike compared to tsodyks_synapse (as if parameter "u" would be updated after rescaling the weight instead of before). Does anybody know why is there this difference between the two synapse models? Thank you. All the best, PH

3 12

Building a nest simulation for mnist dataset
by Aditya Srivastava 10 Feb '25

10 Feb '25

I have built a nest simulation for a binary dataset where we have two classes normal and anomalous . So i tried to built a model iun such a way so that the model learns to produce no spike in case of a normal data but when it sees a anomalous data it is producing the spikes. So this model was working fine. Now I am trying to move forward with it and try it on image dataset where I am using simple MNIST data and I have just taken image for one digit and trying to build a same kind of architecture where it should produce almost no spike when it sees a digit one and oin case of other digits it should produce spikes but I am facing issues in it . The model is not able to produce enough spikes and when I am creating more exc connections then spikes are not reducing with each epochs so can you please suggest me a better approach or some suggestion for my current approach. # loading dataset from sklearn.datasets import fetch_openml import numpy as np def preprocess_mnist_digit(digit=1): """ Load and preprocess the MNIST dataset to only include images of a specific digit. Normalize pixel values by dividing by 4 and flatten images. Args: digit (int): The digit to filter (e.g., 1 for digit '1'). num_samples (int): Number of samples to retain. Returns: flattened_images (array): Flattened MNIST images of the specified digit. labels (array): Corresponding labels. """ # Load MNIST data mnist = fetch_openml('mnist_784', version=1) data, labels = mnist['data'], mnist['target'].astype(int) # Convert labels to integers # Filter images that correspond to the specified digit digit_indices = np.where(labels == digit)[0] # Get indices where label is equal to the specified digit # Extract the corresponding images and labels filtered_images = data.iloc[digit_indices].to_numpy(dtype=float) / 4.0 # Normalize filtered_labels = labels[digit_indices] return filtered_images, filtered_labels # Load only images of the digit '1' images, labels = preprocess_mnist_digit(digit=1) # building simulation nest.ResetKernel() # Simulation parameters dt = 0.01 # Simulation time step in ms nest.SetKernelStatus({"resolution": dt}) N = 784 # Number of neurons images=images[:10] gmax = 3 neuron_params = { "tau_m": 140.0, # Membrane time constant in ms "E_L": -70.6, # Resting potential (in mV) "V_th": -40.4, # Threshold potential (in mV) "V_reset": -70.6, # Reset potential (in mV) "V_m":0.0, } nest.CopyModel("stdp_synapse", "stdp_synapse_exc", {"weight":gmax,"alpha":1,"Wmax":gmax, "tau_plus": 20.0,"lambda": -0.0005, "mu_minus": 0, "mu_plus": 0}) nest.CopyModel("stdp_synapse", "stdp_synapse_inh", {"weight":-gmax/(N-1),"alpha":1,"Wmax":-gmax, "tau_plus": 20.0,"lambda": 0.005, "mu_minus": 0, "mu_plus": 0}) G_spike_gen = nest.Create("poisson_generator",N) G_input = nest.Create("parrot_neuron", N) input_spike_recorder = nest.Create("spike_recorder",N) nest.Connect(G_input, input_spike_recorder,"one_to_one") G_hidden = nest.Create("iaf_psc_delta", N,params=neuron_params) G_output = nest.Create("iaf_psc_delta", 1,params=neuron_params) hidden_spike_recorder = nest.Create("spike_recorder",N) nest.Connect(G_hidden, hidden_spike_recorder,"one_to_one") S_in = nest.Connect(G_spike_gen, G_input, "one_to_one") # Connect input to hidden layer with excitatory STDP synapses S_exc = nest.Connect(G_input, G_hidden,"one_to_one",syn_spec = "stdp_synapse_exc") # Retrieve the neuron IDs for G_input and G_hidden input_ids = G_input.tolist() hidden_ids = G_hidden.tolist() # Get the existing excitatory connections and extract their source-target ID pairs exc_connections = nest.GetConnections(G_input, G_hidden) exc_connection_pairs = set(zip(exc_connections.get("source"), exc_connections.get("target"))) for i in input_ids: for h in hidden_ids: if (i, h) not in exc_connection_pairs: nc1 = nest.NodeCollection([i]) nc2 = nest.NodeCollection([h]) nest.Connect(nc1, nc2, syn_spec= "stdp_synapse_inh") S_out = nest.Connect(G_hidden, G_output,"all_to_all",syn_spec = {"weight": 40.4/N}) # training function def train_net(images, spike_tol=0): output_spike_recorder = nest.Create("spike_recorder") output_membrane_recorder = nest.Create("voltmeter", 1) nest.Connect(G_output, output_spike_recorder) # Record output layer spikes nest.Connect(output_membrane_recorder, G_output, "one_to_one") while True: for image in images: for i in range(784): G_spike_gen[i].rate=image[i] nest.Simulate(500) for i in range(784): spikes = nest.GetStatus(hidden_spike_recorder[i], "events")[0] # if length of spikes is not zero then print the number of spikes and the times of spikes also print the index of the input_spike_recorder if len(spikes["times"]) != 0: print("Number of spikes in hidden_spike_recorder",i,":", len(spikes["times"])) print("Times of spikes in hidden_spike_recorder",i,":", spikes["times"]) print("\n") output_spikes_num = len(output_spike_recorder.get()["events"]["times"]) print("# of output spikes: " + str(output_spikes_num)) # del recorder_for_epoch if output_spikes_num <= spike_tol: print("Training finished") break return output_membrane_recorder, output_spike_recorder v, spk = train_net(images, spike_tol = 2) ___________________________________________

2 1

Open NEST Developer Video Conference Monday February 10, at 11:30 CET (UTC+0100)
by Dennis Terhorst 10 Feb '25

10 Feb '25

Dear NEST Users & Developers! I would like to invite you to our next fortnightly Open NEST Developer Video Conference today *Monday February 10, 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/2025-02-10-Open-NEST-Developer-… <https://github.com/nest/nest-simulator/wiki/2025-02-10-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 ----------------------------------------------------------------------

1 0

Invitation to EBRAINS events in Heidelberg from 12-13 March
by Dennis Terhorst 10 Feb '25

10 Feb '25

Hi everyone, I would like to forward the invitation to the EBRAINS events in Heidelberg next month. Many experts of tools will be there including quite a number of NEST users and developers. You have the opportunity to join tutorials, learn about more interesting tools and directly exchange experience with others. Have a look! --- Dear NEST Community, We are delighted to invite you to join us in Heidelberg, Germanyat theEINC <https://einc.eu/>, from 12-13 March 2025, for a series of EBRAINS events. On*Wednesday,**12 March*, we will host an*EBRAINS Tutorials and Users Day*. It is aimed at both newcomers and experienced users of EBRAINS tools. Newcomers will have the chance to explore the wide range of Open Science Tools and Services available on the research infrastructure, while seasoned EBRAINS users can dive deeper with advanced tutorials and discuss with developers. You can find out more about the Tutorials and Users Day here:https://www.ebrains.eu/news-and-events/accelerate-your-neuroscience-research-with-ebrains-tutorials-and-users-day-in-heidelberg <https://www.ebrains.eu/news-and-events/accelerate-your-neuroscience-researc…> On*Thursday, 13 March*, we will host an*EBRAINS Developers Day*. It will feature introductions for developers on how to integrate tools and services into the EBRAINS software distribution or to integrate services via EBRAINS (workflows). You can find out more about the Developers Day here:https://www.ebrains.eu/news-and-events/developers-day-2025 <https://www.ebrains.eu/news-and-events/developers-day-2025> If you have any questions, please don't hesitate to contactcommunications(a)ebrains.eu <mailto:communications@ebrains.eu>. We hope to see you in Heidelberg! Kind regards, EBRAINSAISBL --- -- 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 ----------------------------------------------------------------------

1 0

Test
by Jochen Martin Eppler 10 Feb '25

10 Feb '25

1 1

Building a nest simulation for mnist dataset
by Aditya Srivastava 28 Jan '25

28 Jan '25

I have built a nest simulation for a binary dataset where we have two classes normal and anomalous . So i tried to built a model iun such a way so that the model learns to produce no spike in case of a normal data but when it sees a anomalous data it is producing the spikes. So this model was working fine. Now I am trying to move forward with it and try it on image dataset where I am using simple MNIST data and I have just taken image for one digit and trying to build a same kind of architecture where it should produce almost no spike when it sees a digit one and oin case of other digits it should produce spikes but I am facing issues in it . The model is not able to produce enough spikes and when I am creating more exc connections then spikes are not reducing with each epochs so can you please suggest me a better approach or some suggestion for my current approach. # loading dataset from sklearn.datasets import fetch_openml import numpy as np def preprocess_mnist_digit(digit=1): """ Load and preprocess the MNIST dataset to only include images of a specific digit. Normalize pixel values by dividing by 4 and flatten images. Args: digit (int): The digit to filter (e.g., 1 for digit '1'). num_samples (int): Number of samples to retain. Returns: flattened_images (array): Flattened MNIST images of the specified digit. labels (array): Corresponding labels. """ # Load MNIST data mnist = fetch_openml('mnist_784', version=1) data, labels = mnist['data'], mnist['target'].astype(int) # Convert labels to integers # Filter images that correspond to the specified digit digit_indices = np.where(labels == digit)[0] # Get indices where label is equal to the specified digit # Extract the corresponding images and labels filtered_images = data.iloc[digit_indices].to_numpy(dtype=float) / 4.0 # Normalize filtered_labels = labels[digit_indices] return filtered_images, filtered_labels # Load only images of the digit '1' images, labels = preprocess_mnist_digit(digit=1) # building simulation nest.ResetKernel() # Simulation parameters dt = 0.01 # Simulation time step in ms nest.SetKernelStatus({"resolution": dt}) N = 784 # Number of neurons images=images[:10] gmax = 3 neuron_params = { "tau_m": 140.0, # Membrane time constant in ms "E_L": -70.6, # Resting potential (in mV) "V_th": -40.4, # Threshold potential (in mV) "V_reset": -70.6, # Reset potential (in mV) "V_m":0.0, } nest.CopyModel("stdp_synapse", "stdp_synapse_exc", {"weight":gmax,"alpha":1,"Wmax":gmax, "tau_plus": 20.0,"lambda": -0.0005, "mu_minus": 0, "mu_plus": 0}) nest.CopyModel("stdp_synapse", "stdp_synapse_inh", {"weight":-gmax/(N-1),"alpha":1,"Wmax":-gmax, "tau_plus": 20.0,"lambda": 0.005, "mu_minus": 0, "mu_plus": 0}) G_spike_gen = nest.Create("poisson_generator",N) G_input = nest.Create("parrot_neuron", N) input_spike_recorder = nest.Create("spike_recorder",N) nest.Connect(G_input, input_spike_recorder,"one_to_one") G_hidden = nest.Create("iaf_psc_delta", N,params=neuron_params) G_output = nest.Create("iaf_psc_delta", 1,params=neuron_params) hidden_spike_recorder = nest.Create("spike_recorder",N) nest.Connect(G_hidden, hidden_spike_recorder,"one_to_one") S_in = nest.Connect(G_spike_gen, G_input, "one_to_one") # Connect input to hidden layer with excitatory STDP synapses S_exc = nest.Connect(G_input, G_hidden,"one_to_one",syn_spec = "stdp_synapse_exc") # Retrieve the neuron IDs for G_input and G_hidden input_ids = G_input.tolist() hidden_ids = G_hidden.tolist() # Get the existing excitatory connections and extract their source-target ID pairs exc_connections = nest.GetConnections(G_input, G_hidden) exc_connection_pairs = set(zip(exc_connections.get("source"), exc_connections.get("target"))) for i in input_ids: for h in hidden_ids: if (i, h) not in exc_connection_pairs: nc1 = nest.NodeCollection([i]) nc2 = nest.NodeCollection([h]) nest.Connect(nc1, nc2, syn_spec= "stdp_synapse_inh") S_out = nest.Connect(G_hidden, G_output,"all_to_all",syn_spec = {"weight": 40.4/N}) # training function def train_net(images, spike_tol=0): output_spike_recorder = nest.Create("spike_recorder") output_membrane_recorder = nest.Create("voltmeter", 1) nest.Connect(G_output, output_spike_recorder) # Record output layer spikes nest.Connect(output_membrane_recorder, G_output, "one_to_one") while True: for image in images: for i in range(784): G_spike_gen[i].rate=image[i] nest.Simulate(500) for i in range(784): spikes = nest.GetStatus(hidden_spike_recorder[i], "events")[0] # if length of spikes is not zero then print the number of spikes and the times of spikes also print the index of the input_spike_recorder if len(spikes["times"]) != 0: print("Number of spikes in hidden_spike_recorder",i,":", len(spikes["times"])) print("Times of spikes in hidden_spike_recorder",i,":", spikes["times"]) print("\n") output_spikes_num = len(output_spike_recorder.get()["events"]["times"]) print("# of output spikes: " + str(output_spikes_num)) # del recorder_for_epoch if output_spikes_num <= spike_tol: print("Training finished") break return output_membrane_recorder, output_spike_recorder v, spk = train_net(images, spike_tol = 2)

1 0

Open NEST Developer Video Conference Monday January 27, at 11:30 CET (UTC+0100)
by Dennis Terhorst 27 Jan '25

27 Jan '25

Dear NEST Users & Developers! I would like to invite you to our next fortnightly Open NEST Developer Video Conference today *Monday January 27, 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 o Welcome NEAT * 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/2025-01-27-Open-NEST-Developer-… <https://github.com/nest/nest-simulator/wiki/2025-01-27-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 ----------------------------------------------------------------------

1 0

Error during NESTML make
by Beck Strohmer 16 Jan '25

16 Jan '25

Hi, I am trying to create a dopamine modulated synapse using NESTML. You can find the nestml file and the file for creating the neuron attached. I am using NEST version 3.8.0 and running within a conda environment (v. 24.1.2). I get a make error in the end so the files are created except for the .so file that I need for loading the model. I attached the terminal error for further details. Has anyone else had this issue? How were you able to resolve it? Thanks for any advice! Best, Beck

2 6

Save the date: NEST Conference 2025 will take place 17–18 June (online)
by Hans Ekkehard Plesser 16 Jan '25

16 Jan '25

Dear Colleagues, The NEST Initiative is excited to invite everyone interested in neural simulation technology, simulation-based neuroscience and NEST Software to the NEST Conference 2025. Save the date for the virtual conference, taking place online on 17–18 June 2025! The annual 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. We particularly encourage young scientists to participate in the conference! Registration and abstract submission will open soon. For more information on the event please visit the conference website https://nest-simulator.org/conference We are looking forward to seeing you in June! Hans Ekkehard Plesser on behalf of the conference organizing committee -- 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

1 0

Using nest server to run nestml models
by Pablo Alejandro 16 Jan '25

16 Jan '25

Hi Everyone, Apologies for sending the message below again. I think my last post was done incorrectly and no one got notifications. ----------------------------------------- Does nest server currently support nestml models? I couldn't find examples in the documentation (even though `nestml-server` binary exists in nest3.8 docker image). Ideally, I would like to run it with MPI too. I can run a simple example (`python test.py`) with `nest-server` running from a docker container, but the same code fails if I use `nestml-server`: ``` docker run -it --rm -e LOCAL_USER_ID=`id -u $USER` -p 52425:52425 nest/nest-simulator:3.8 nest-server start ``` works, but ``` docker run -it --rm -e LOCAL_USER_ID=`id -u $USER` -p 52426:52426 nest/nest-simulator:3.8 nestml-server start ``` fails with ``` Traceback (most recent call last): File "/usr/local/lib/python3.10/dist-packages/urllib3/connection.py", line 199, in _new_conn sock = connection.create_connection( File "/usr/local/lib/python3.10/dist-packages/urllib3/util/connection.py", line 85, in create_connection raise err File "/usr/local/lib/python3.10/dist-packages/urllib3/util/connection.py", line 73, in create_connection sock.connect(sa) ConnectionRefusedError: [Errno 111] Connection refused The above exception was the direct cause of the following exception: Traceback (most recent call last): File "/usr/local/lib/python3.10/dist-packages/urllib3/connectionpool.py", line 789, in urlopen response = self._make_request( File "/usr/local/lib/python3.10/dist-packages/urllib3/connectionpool.py", line 495, in _make_request conn.request( File "/usr/local/lib/python3.10/dist-packages/urllib3/connection.py", line 441, in request self.endheaders() File "/usr/lib/python3.10/http/client.py", line 1278, in endheaders self._send_output(message_body, encode_chunked=encode_chunked) File "/usr/lib/python3.10/http/client.py", line 1038, in _send_output self.send(msg) File "/usr/lib/python3.10/http/client.py", line 976, in send self.connect() File "/usr/local/lib/python3.10/dist-packages/urllib3/connection.py", line 279, in connect self.sock = self._new_conn() File "/usr/local/lib/python3.10/dist-packages/urllib3/connection.py", line 214, in _new_conn raise NewConnectionError( urllib3.exceptions.NewConnectionError: <urllib3.connection.HTTPConnection object at 0x7fb8b63ea440>: Failed to establish a new connection: [Errno 111] Connection refused The above exception was the direct cause of the following exception: Traceback (most recent call last): File "/usr/lib/python3/dist-packages/requests/adapters.py", line 439, in send resp = conn.urlopen( File "/usr/local/lib/python3.10/dist-packages/urllib3/connectionpool.py", line 843, in urlopen retries = retries.increment( File "/usr/local/lib/python3.10/dist-packages/urllib3/util/retry.py", line 519, in increment raise MaxRetryError(_pool, url, reason) from reason # type: ignore[arg-type] urllib3.exceptions.MaxRetryError: HTTPConnectionPool(host='localhost', port=52425): Max retries exceeded with url: /exec (Caused by NewConnectionError('<urllib3.connection.HTTPConnection object at 0x7fb8b63ea440>: Failed to establish a new connection: [Errno 111] Connection refused')) During handling of the above exception, another exception occurred: Traceback (most recent call last): File "/home/pablo/git/nest-client/test_server.py", line 4, in <module> response = nsc.from_file('examples/NESTClient_script.py', return_vars='n_events') File "/home/pablo/git/nest-client/nest_client/nest_client.py", line 68, in from_file return self.exec_script(script, return_vars) File "/home/pablo/git/nest-client/nest_client/nest_client.py", line 56, in exec_script response = requests.post(self.url + 'exec', json=params, headers=self.headers) File "/usr/lib/python3/dist-packages/requests/api.py", line 119, in post return request('post', url, data=data, json=json, **kwargs) File "/usr/lib/python3/dist-packages/requests/api.py", line 61, in request return session.request(method=method, url=url, **kwargs) File "/usr/lib/python3/dist-packages/requests/sessions.py", line 544, in request resp = self.send(prep, **send_kwargs) File "/usr/lib/python3/dist-packages/requests/sessions.py", line 657, in send r = adapter.send(request, **kwargs) File "/usr/lib/python3/dist-packages/requests/adapters.py", line 516, in send raise ConnectionError(e, request=request) requests.exceptions.ConnectionError: HTTPConnectionPool(host='localhost', port=52425): Max retries exceeded with url: /exec (Caused by NewConnectionError('<urllib3.connection.HTTPConnection object at 0x7fb8b63ea440>: Failed to establish a new connection: [Errno 111] Connection refused')) ``` The simple python code used is shown below. ``` from nest_client import NESTClient nsc = NESTClient() response = nsc.from_file('examples/NESTClient_script.py', return_vars='n_events') n_events = response['data'] print('Number of events:', n_events) ``` No nestml models are being tested for now because I don't know which functions should be used to generate code with `nest-client` e.g. ``` from pynestml.codegeneration.nest_code_generator_utils import NESTCodeGeneratorUtils module_name, neuron_model_name, synapse_model_name = \ NESTCodeGeneratorUtils.generate_code_for( "neuron.nestml", "synapse.nestml", post_ports=["post_spikes"], codegen_opts=codegen_opts ) ``` should be rewritten to use `from nest_client import NESTClient`. Thanks in advance, Pablo Alejandro

2 3

Segmentation faults with Structural Plasticity in NEST v3.6 onwards
by Ady Sharma 15 Jan '25

15 Jan '25

Hello, TL;DR: using structural plasticity with mpi-based simulation leads to spontaneous crashes in NESTv3.6 onward. A minimal script reproducing the crash is provided This is a followup to my previous mailing list post (https://www.nest-simulator.org/mailinglist/hyperkitty/list/users@nest-simul…) where I encountered segmentation faults while executing structural-plasticity-based simulations in NESTv3.8. Previously, I suspected that the crashes occurred due to presumed buggy installations of NEST on HPCs. The helpful comments on that post did not solve the issue, so I performed some tests and gathered feedback from other users testing structural plasticity (SP) in NESTv3.6+. My conclusion is that MPI-based simulations spontaneously crash when using structural plasticity. The probability of spontaneous crashes increases with the number of MPI processes. Below, I'll provide more details and also a link to a minimal code that reproduces the segmentation fault. Background: I use SP to perform large-scale network simulations on HPC. Hitherto, I've been using NESTv2.20.1 for various reasons. When I found that SP functionality in NESTv3.6 was finally equivalent to that of NESTv2.20.1, I decided to port my code to the latest release (v3.8). I installed v3.8 on my local machine with MPI support, and tested a scaled-down experiment as a sanity check---everything worked as expected. However, when I ran the full-scale network on HPCs (JUSUF at Jülich and NEMO at uni-freiburg), I got segmentation faults. HPC support couldn't help in resolving the issues. Reinstalling didn't help. At this point, I reached out with the aforementioned post on the mailing list ("MPI-based error on v3.8"). Current Status: I created a minimal pynest script that simulates an E-I network, where the E-->E connections are organised by structural plasticity. I believe this minimal example includes the necessary steps involved in any SP-based experiment. The script can be run by the following BASH call: `mpirun python minimal.py $RANDOM_SEED $TOTAL_NUM_VIRTUAL_PROCS # use srun, when required` The following table gives a summary of the segmentation-fault crashes for `minimal.py`: NEST version machine (MPI procs count) Crash v2.20.1 local (2) No v2.20.2 local (2) No v2.20.1 HPC-2 (upto 1024) No v2.20.2 HPC-1 (upto 1024) No v3.8 local (2) Yes (rarely) v3.8 HPC-1 (8) No v3.8 HPC-1 (16, 24, 32, 64, 128) Yes v3.8 HPC-2 (8) No v3.8 HPC-2 (16, 24, 32, 64, 128) Yes v3.6 HPC-1 (32, 64, 128, 256) Yes - machines: - local: Linux 5.4.0-204-generic x86_64; Intel Core i5-5300U; 16GB - HPC-2: NEMO (https://www.nemo.uni-freiburg.de/) - HPC-1: JUSUF (https://www.fz-juelich.de/en/ias/jsc/systems/supercomputers/jusuf) - NESTv2.20.1, v2.20.2, and v3.8 in all cases were installed manually. v3.6 was available as a preinstalled module in HPC-1 - The crashes do not occur if MPI is not used for SP simulations - The crashes do not occur in MPI-based simulations that do not involve SP Conclusion: - MPI-based crashes occur in SP simulations. - Perhaps how MPI-procs handle data in NESTv3.6+ leads to spontaneous segmentation faults. - MPI-proc count potentially correlates with segmention-fault frequency. It is possible that faults will occur, although rarely, with small no. of MPI procs Expectations from this post: Large no. of MPI-procs provide a very significant speed-up for SP-based simulations, therefore it is important that MPI is fully functional in NEST. - Kindly let me know if you can reproduce the same crash. If what I observe is indeed true, then this merits creating an issue on GitHub. - If you cannot reproduce the crashes, I would greatly appreciate any help and fixing the issue. Code: - You will find a formated version of this post with acocmpanying code and crash dumps on this GitLab page: https://gitlab.rz.uni-freiburg.de/as2013/minimal_share.git - minimal.py: https://gitlab.rz.uni-freiburg.de/as2013/minimal_share/-/blob/119e52d3552a7… Thanks! Best, Ady PS. Is it possible to add some sort of text formatting (HTML/markdown) to these posts?

2 1

Open NEST Developer Video Conference Monday January 13, at 11:30 CET (UTC+0100)
by Dennis Terhorst 13 Jan '25

13 Jan '25

Dear NEST Users & Developers! I would like to invite you to our next fortnightly Open NEST Developer Video Conference today *Monday January 13, 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/2025-01-13-Open-NEST-Developer-… <https://github.com/nest/nest-simulator/wiki/2025-01-13-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 ----------------------------------------------------------------------

1 0

Test message, please ignore
by Hans Ekkehard Plesser 09 Jan '25

09 Jan '25

This message is a test. -- 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

1 0

Test and a Happy New Year!
by Jochen Martin Eppler 07 Jan '25

07 Jan '25

Cheers Jochen!  

2 1

Assistance with Installing NESTML
by atiye nejadebrahim 26 Dec '24

26 Dec '24

Dear all, I have installed NEST from source in a conda environment and attempted to install NESTML both via conda and manually. However, I consistently encounter the following error: pynestml.exceptions.generated_code_build_exception.GeneratedCodeBuildException: Error occurred during 'make all'! More detailed error messages can be found in stderr. I have tried adding it to the path, but despite installing pynestml, it still cannot locate it. Could you please assist me in resolving this issue and successfully installing NESTML to create a new module? Thank you in advance for your help! Best regards,Atiyeh Atiyeh Nezhadebrahim,Scientific Researcher

2 3

Using nest server to run nestml models
by pabloabur＠gmail.com 17 Dec '24

17 Dec '24

Hi Everyone, Does nest server currently support nestml models? I couldn't find examples in the documentation (even though `nestml-server` binary exists in nest3.8 docker image). Ideally, I would like to run it with MPI too. I can run a simple example (`python test.py`) with `nest-server` running from a docker container, but the same code fails if I use `nestml-server`: ``` docker run -it --rm -e LOCAL_USER_ID=`id -u $USER` -p 52425:52425 nest/nest-simulator:3.8 nest-server start ``` works, but ``` docker run -it --rm -e LOCAL_USER_ID=`id -u $USER` -p 52426:52426 nest/nest-simulator:3.8 nestml-server start ``` fails with ``` Traceback (most recent call last): File "/usr/local/lib/python3.10/dist-packages/urllib3/connection.py", line 199, in _new_conn sock = connection.create_connection( File "/usr/local/lib/python3.10/dist-packages/urllib3/util/connection.py", line 85, in create_connection raise err File "/usr/local/lib/python3.10/dist-packages/urllib3/util/connection.py", line 73, in create_connection sock.connect(sa) ConnectionRefusedError: [Errno 111] Connection refused The above exception was the direct cause of the following exception: Traceback (most recent call last): File "/usr/local/lib/python3.10/dist-packages/urllib3/connectionpool.py", line 789, in urlopen response = self._make_request( File "/usr/local/lib/python3.10/dist-packages/urllib3/connectionpool.py", line 495, in _make_request conn.request( File "/usr/local/lib/python3.10/dist-packages/urllib3/connection.py", line 441, in request self.endheaders() File "/usr/lib/python3.10/http/client.py", line 1278, in endheaders self._send_output(message_body, encode_chunked=encode_chunked) File "/usr/lib/python3.10/http/client.py", line 1038, in _send_output self.send(msg) File "/usr/lib/python3.10/http/client.py", line 976, in send self.connect() File "/usr/local/lib/python3.10/dist-packages/urllib3/connection.py", line 279, in connect self.sock = self._new_conn() File "/usr/local/lib/python3.10/dist-packages/urllib3/connection.py", line 214, in _new_conn raise NewConnectionError( urllib3.exceptions.NewConnectionError: <urllib3.connection.HTTPConnection object at 0x7fb8b63ea440>: Failed to establish a new connection: [Errno 111] Connection refused The above exception was the direct cause of the following exception: Traceback (most recent call last): File "/usr/lib/python3/dist-packages/requests/adapters.py", line 439, in send resp = conn.urlopen( File "/usr/local/lib/python3.10/dist-packages/urllib3/connectionpool.py", line 843, in urlopen retries = retries.increment( File "/usr/local/lib/python3.10/dist-packages/urllib3/util/retry.py", line 519, in increment raise MaxRetryError(_pool, url, reason) from reason # type: ignore[arg-type] urllib3.exceptions.MaxRetryError: HTTPConnectionPool(host='localhost', port=52425): Max retries exceeded with url: /exec (Caused by NewConnectionError('<urllib3.connection.HTTPConnection object at 0x7fb8b63ea440>: Failed to establish a new connection: [Errno 111] Connection refused')) During handling of the above exception, another exception occurred: Traceback (most recent call last): File "/home/pablo/git/nest-client/test_server.py", line 4, in <module> response = nsc.from_file('examples/NESTClient_script.py', return_vars='n_events') File "/home/pablo/git/nest-client/nest_client/nest_client.py", line 68, in from_file return self.exec_script(script, return_vars) File "/home/pablo/git/nest-client/nest_client/nest_client.py", line 56, in exec_script response = requests.post(self.url + 'exec', json=params, headers=self.headers) File "/usr/lib/python3/dist-packages/requests/api.py", line 119, in post return request('post', url, data=data, json=json, **kwargs) File "/usr/lib/python3/dist-packages/requests/api.py", line 61, in request return session.request(method=method, url=url, **kwargs) File "/usr/lib/python3/dist-packages/requests/sessions.py", line 544, in request resp = self.send(prep, **send_kwargs) File "/usr/lib/python3/dist-packages/requests/sessions.py", line 657, in send r = adapter.send(request, **kwargs) File "/usr/lib/python3/dist-packages/requests/adapters.py", line 516, in send raise ConnectionError(e, request=request) requests.exceptions.ConnectionError: HTTPConnectionPool(host='localhost', port=52425): Max retries exceeded with url: /exec (Caused by NewConnectionError('<urllib3.connection.HTTPConnection object at 0x7fb8b63ea440>: Failed to establish a new connection: [Errno 111] Connection refused')) ``` The simple python code used is shown below. ``` from nest_client import NESTClient nsc = NESTClient() response = nsc.from_file('examples/NESTClient_script.py', return_vars='n_events') n_events = response['data'] print('Number of events:', n_events) ``` No nestml models are being tested for now because I don't know which functions should be used to generate code with `nest-client` e.g. ``` from pynestml.codegeneration.nest_code_generator_utils import NESTCodeGeneratorUtils module_name, neuron_model_name, synapse_model_name = \ NESTCodeGeneratorUtils.generate_code_for( "neuron.nestml", "synapse.nestml", post_ports=["post_spikes"], codegen_opts=codegen_opts ) ``` should be rewritten to use `from nest_client import NESTClient`. Thanks in advance, Pablo Alejandro

1 0

Open NEST Developer Video Conference Monday December 16, at 11:30 CET (UTC+0100)
by Dennis Terhorst 16 Dec '24

16 Dec '24

Dear NEST Users & Developers! I would like to invite you to our next fortnightly Open NEST Developer Video Conference today *Monday December 16, 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/2024-12-16-Open-NEST-Developer-… <https://github.com/nest/nest-simulator/wiki/2024-12-16-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 ----------------------------------------------------------------------

1 0

Issue In testing of a trained network
by Aditya Srivastava 10 Dec '24

10 Dec '24

I have built a nest model with a reverse stdp approach in which with time I'm trying to reduce the spikes in training data which is a normal bearing metal data and then during testing I'll try to test it on a anomalous data which should produce opposite results to that of training data so now firstly I made it in brian and it worked fine but here in nest after training the model when I have to test it then again the synaptic weights are changing which should not happen during testing. In brian I had put the learning rate as 0 thats why it was working fine but in Nest I am not able to find a way to test a model by freezing the weights. So I tried something which I'm not sure is the correct approach so can anyone please review this approach or if suggest a better approach for testing these kind of models. Also I want to mention one thing that with my current approach the weights are freezing but as I'm assigning input spikes from anomalous signal and start testing, the kernel is getting died which usually happens when there is a some issue in nest network. nest.ResetKernel() # Simulation parameters dt = 0.01 # Simulation time step in ms nest.SetKernelStatus({"resolution": dt}) N = 16 # Number of neurons gmax = 3 neuron_params = { "tau_m": 140.0, # Membrane time constant in ms "E_L": -70.6, # Resting potential (in mV) "V_th": -40.4, # Threshold potential (in mV) "V_reset": -70.6, # Reset potential (in mV) "V_m":0.0, } nest.CopyModel("stdp_synapse_hom", "stdp_synapse_exc", {"weight":gmax,"alpha":1,"Wmax":gmax, "tau_plus": 20.0,"lambda": -0.0005, "mu_minus": 0, "mu_plus": 0}) nest.CopyModel("stdp_synapse_hom", "stdp_synapse_inh", {"weight":-gmax/(N-1),"alpha":1,"Wmax":-gmax, "tau_plus": 20.0,"lambda": 0.005, "mu_minus": 0, "mu_plus": 0}) G_spike_gen = nest.Create("spike_generator", N) G_input = nest.Create("parrot_neuron", N) G_hidden = nest.Create("iaf_psc_delta", N,params=neuron_params) G_output = nest.Create("iaf_psc_delta", 1,params=neuron_params) S_in = nest.Connect(G_spike_gen, G_input, "one_to_one") # Connect input to hidden layer with excitatory STDP synapses S_exc = nest.Connect(G_input, G_hidden,"one_to_one",syn_spec = "stdp_synapse_exc") # Retrieve the neuron IDs for G_input and G_hidden input_ids = G_input.tolist() hidden_ids = G_hidden.tolist() # Get the existing excitatory connections and extract their source-target ID pairs exc_connections = nest.GetConnections(G_input, G_hidden) exc_connection_pairs = set(zip(exc_connections.get("source"), exc_connections.get("target"))) for i in input_ids: for h in hidden_ids: if (i, h) not in exc_connection_pairs: nc1 = nest.NodeCollection([i]) nc2 = nest.NodeCollection([h]) nest.Connect(nc1, nc2, syn_spec= "stdp_synapse_inh") S_out = nest.Connect(G_hidden, G_output,"all_to_all",syn_spec = {"weight": 40.4/N}) def train_net(signals, spike_tol=0): output_spike_recorder = nest.Create("spike_recorder") output_membrane_recorder = nest.Create("voltmeter", 1) nest.Connect(G_output, output_spike_recorder) # Record output layer spikes nest.Connect(output_membrane_recorder, G_output, "one_to_one") while True: recorder_for_epoch = nest.Create("spike_recorder") nest.Connect(G_output, recorder_for_epoch) for signal in signals: indices, times = process_signal(signal) # Get the indices and times offset = nest.GetKernelStatus()["biological_time"] for i in range(N): times_for_neuron = [t+offset for j,t in enumerate(times) if indices[j] == i] G_spike_gen[i].set(spike_times = times_for_neuron) nest.Simulate(len(signal)*(1/SAMPLE_RATE)*1000) output_spikes_num = len(recorder_for_epoch.get()["events"]["times"]) print("# of output spikes: " + str(output_spikes_num)) del recorder_for_epoch if output_spikes_num <= spike_tol: print("Training finished") break return output_membrane_recorder, output_spike_recorder def synapse_freeze(): conn = nest.GetConnections() sources = conn.get("source") targets = conn.get("target") weights = conn.get("weight") # Store as a list of tuples connections = list(zip(sources, targets, weights)) # Replace dynamic synapses with static synapses for s,t,w in connections: nc1 = nest.NodeCollection([s]) nc2 = nest.NodeCollection([t]) conn_t = nest.GetConnections(nc1,nc2) model=nest.GetConnections(nc1,nc2).get("synapse_model") if model=="stdp_synapse_exc": nest.Disconnect(nc1,nc2,syn_spec = {"synapse_model":"stdp_synapse_exc"}) nest.Connect(nc1,nc2,syn_spec = {"synapse_model":"static_synapse","weight":w}) if model=="stdp_synapse_inh": nest.Disconnect(nc1,nc2,syn_spec = {"synapse_model":"stdp_synapse_inh"}) nest.Connect(nc1,nc2,syn_spec = {"synapse_model":"static_synapse","weight":w}) print("Switched to static synapses with trained weights.") def inference(signal): output_spike_recorder_t = nest.Create("spike_recorder") output_membrane_recorder_t = nest.Create("voltmeter", 1) nest.Connect(G_output, output_spike_recorder_t) # Record output layer spikes nest.Connect(output_membrane_recorder_t, G_output, "one_to_one") indices, times = process_signal(signal) # Prepare test signal offset = nest.GetKernelStatus()["biological_time"] for i in range(N): times_for_neuron = [t+offset for j,t in enumerate(times) if indices[j] == i] G_spike_gen[i].set(spike_times = times_for_neuron) nest.Simulate(len(signal)*(1/SAMPLE_RATE)*1000) # Run simulation output_spikes_num = len(output_spike_recorder_t.get()["events"]["times"]) print("# of output spikes: " + str(output_spikes_num)) return output_membrane_recorder_t, output_spike_recorder_t

2 7

Request for Assistance with Synaptic Weight Normalization
by Peter Mason 02 Dec '24

02 Dec '24

I am currently working on a project involving synaptic weight normalization using the guidelines provided in the NEST simulator documentation. I have implemented the normalization process; however, I encountered some questions that I would appreciate your insights on. 1. Normalization Value: I found that the normalization value for a neuron with approximately 190 synapses is around 420, which I do not fully understand. This looks like the total weight of the neuron synapses. Could you provide clarification on how the normalisation value is determined? 2. Simulation State Preservation: I would like to save and restore the state of synaptic weights to maintain the simulation's behaviour across sessions. Below is the pseudocode I intend to use: Save synaptic weights: w = array of current weights of neuron connections normalization_factor = sum of absolute weights if normalization_factor != 0: normalized_weights = w / normalization_factor save normalized_weights to file Load synaptic weights: read normalized_weights from file assign loaded weights back to connection I would like to know if you have any suggestions for improving this pseudocode or if there are best practices I should consider. Thank you for your time and assistance. I look forward to your response.

3 4

Open NEST Developer Video Conference Monday December 2, at 11:30 CET (UTC+0100)
by Dennis Terhorst 02 Dec '24

02 Dec '24

Dear NEST Users & Developers! I would like to invite you to our next fortnightly Open NEST Developer Video Conference today *Monday December 2, 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/2024-12-02-Open-NEST-Developer-… <https://github.com/nest/nest-simulator/wiki/2024-12-02-Open-NEST-Developer-…> Today Jessica will be chairing the meeting. 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 ----------------------------------------------------------------------

1 0

Open NEST Developer Video Conference Monday November 18, at 11:30 CET (UTC+0100)
by Dennis Terhorst 02 Dec '24

02 Dec '24

Dear NEST Users & Developers! I would like to invite you to our next fortnightly Open NEST Developer Video Conference today *Monday November 18, 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/2024-11-18-Open-NEST-Developer-… <https://github.com/nest/nest-simulator/wiki/2024-11-18-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 ----------------------------------------------------------------------

2 1

About Resonate and Fire Neuron Model?
by Thanh Binh To 02 Dec '24

02 Dec '24

2 5

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

2 1

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

2 1

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

1 0

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 ----------------------------------------------------------------------

1 0

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

1 1

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

1 0

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 ------------------------------------------------------------------------------------------------ ------------------------------------------------------------------------------------------------

1 1

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 ----------------------------------------------------------------------

1 0

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

2 9

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

3 3

Open NEST Developer Video Conference Monday October 7, at 11:30 CEST (UTC+0200)
by Dennis Terhorst 07 Oct '24

07 Oct '24

Dear NEST Users & Developers! I would like to invite you to our next fortnightly Open NEST Developer Video Conference today *Monday October 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/2024-10-07-Open-NEST-Developer-… <https://github.com/nest/nest-simulator/wiki/2024-10-07-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/ 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 ----------------------------------------------------------------------

1 0

Enhancement of C++ implementation of DumpLayerConnections()
by Xavier Otazu 27 Sep '24

27 Sep '24

Hi! After using some PyNEST functions and modifying the C++ implementation of DumpLayerConnections(), I was thinking on a possible further improvement of this function (or creating a new function). But since I do not know the design and architecture of C++ nestkernel code, I prefer to ask. In my code I normalize the presynaptic connections of every neuron. To do this, I originally do something like for i in range(len(target_layer)) conn[i] = nest.GetConnections(source_layer, target_layer, synapse_model) normalize(conn) Since I am using MPI and the loop iterates over all the neurons, I modified the previous code to local_nodes = nest.GetLocalNodeCollection(target_layer) local_nodes = nest.NodeCollection(local_nodes) for i in range(len(local_nodes)) conn[i] = nest.GetConnections(source_layer, local_nodes, synapse_model) normalize(conn) This last code is faster that the previous one (I guess that local_nodes variable is local to every MPI process and, as a consequence, GetConnections() is more efficient because it only works with local nodes instead of with all of them). Using the idea of the GetLocalNodeCollection(), I was thinking it could be used into the C++ implementation of DumpLayerConnections(). Presently, this function obtain all the connections between source and target layers. Could it be possible to call the equivalent C++ implementation of GetLocalCollection()? I understand that the problem is that, since DumpLayerConnections() needs the spatial information of the layers, the node collections obtained with GetLocalNodeCollection() (I guess similarly its C++ implementation) does not have this spatial information. As a second possibility, I was thinking on adding a new method (GetSpatialInformation()) and enhancing DumpLayerConnections() (or add a new function). The GetSpatialInformation() function could return the spatial information of a collection of nodes (the ones obtained by GetLocalNodeCollection() ). The DumpLayerConnections() (or a new function) could be enhanced by changing the target layer parameter to a pair of parameters that contain the local nodes collection and their spatial information. Something like DumpLaterConnections(source_layer, local_nodes_collection, spatial_information, synapse_model). This way DumpLayerConnections() will only used local nodes and would be much faster. Sorry for the technical email. Xavier

3 7

Open NEST Developer Video Conference Monday September 23, at 11:30 CEST (UTC+0200)
by Dennis Terhorst 23 Sep '24

23 Sep '24

Dear NEST Users & Developers! I would like to invite you to our next fortnightly Open NEST Developer Video Conference today *Monday September 23, 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/2024-09-23-Open-NEST-Developer-… <https://github.com/nest/nest-simulator/wiki/2024-09-23-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 ----------------------------------------------------------------------

1 0

stdp synapse nestml erro
by Chris Huyck 20 Sep '24

20 Sep '24

I'm working with the nestml 7.0.2. I got the example models from https://github.com/nest/nestml/blob/v7.0.2/models/neurons/hill_tononi.nestml this git tree. I tried three different stdp models including stdp_triplet_naive.nestml. All give AssertionError: Synapses only support one spiking input port when I generate_target in python. -Chris

2 7

Discuss NEST @ Bernstein Conference in Frankfurt 29 Sep–2 Oct
by Hans Ekkehard Plesser 19 Sep '24

19 Sep '24

Dear NEST Users, I just wanted to let you know that I and a number of other NEST developers will attend the Bernstein Conference in Frankfurt from 29 September to 2 October this year. If you would like to discuss anything related to NEST, let me know so we can arrange to meet. You are also welcome to drop by the EBRAINS booth, where we will have NEST stickers 😊. If you are going to present work done with NEST, we’d appreciate it if you put a “nest::simulated()” logo on your slides or poster (see https://github.com/nest/nest-simulator/tree/master/doc/logos) and let us know about your talk/poster number in advance. Best Hans Ekkehard -- Prof. Dr. Hans Ekkehard Plesser Head of Research, 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

1 0

stp synapse nestml errror
by Chris Huyck 18 Sep '24

18 Sep '24

I'm trying to make a Hebbian Short Term plasticity model. I got the stdp_synapse working, and then tried to change that to stp. I kept getting the error stp_synapse not found in pynest. So, I just started from the static synapse, and modified that to get an stp_synapse that wasn't Hebbian. When I introduced the post_synaptic neuron into the model, the stp_synapse not found error returns. Oddly, in the generated files (.h, .cpp, in stp_synapse__with_iaf_cond_exp_neuron and iaf_cond_exp_neuron__with_stp_synapse) there is a function for register stdp_synapse. (If you want to duplicate this, just change the stdp_synapse model name to stp_synapse). -Chris

2 4

Regular LIF with adaptive threshold
by jona.m.scholz＠gmail.com 13 Sep '24

13 Sep '24

Hello everyone, just a quick question in case anybody knows: is there a LIF model that has an adaptive spike threshold in NEST? I know there's the GLIF model which can have a threshold, but it seems to bring other deviations from the conventional LIF model that I want to avoid. There's also the adaptive exponential integrate and fire model, but again I don't want the exponential part. It's not a problem if no such model exists in NEST, I am only asking so I don't reimplement an existing model. Any feedback would be appreciated. Kind regards, Jona

4 7

Open NEST Developer Video Conference Monday September 9, at 11:30 CEST (UTC+0200)
by Dennis Terhorst 09 Sep '24

09 Sep '24

Dear NEST Users & Developers! I would like to invite you to our next fortnightly Open NEST Developer Video Conference today *Monday September 9, 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/2024-09-09-Open-NEST-Developer-… <https://github.com/nest/nest-simulator/wiki/2024-09-09-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 ----------------------------------------------------------------------

1 0

Invitation for Article Submissions
by David Wack 05 Sep '24

05 Sep '24

Greetings Everyone, Paul John Werbos, Rajendra D Badgaiyan, Konstantinos Slavakis, and I are bringing key researchers together in a focused project on 'Modeling brain circuits as intelligent systems'. Here's a link to find out more about the project: https://www.frontiersin.org/researchtopic/64421. This topic is an extension of a US NSF push led by Dr. Werbos in 2007. We believe that members of this community would have much to offer and we would like to invite you to participate. If you are interested, please let me know directly, and I will send an invitation link: dswack(a)buffalo.edu<mailto:dswack@buffalo.edu> We are trying to finalize the leading group of participating authors in the next two weeks, so we can start publishing our work before the topic closes on 07 March 2025. Our Research Topic will be hosted in Frontiers in Systems Neuroscience Impact Factor: 3.1 Cite Score: 6.0 Frontiers will provide a team to help develop and promote our project, and we'll have a dedicated space in the journal to showcase our collective work and to amplify its impact and visibility. I'm looking forward to seeing your work and exploring this emerging topic together. I really think we can push this field forward as a team. All the best, dave David S. Wack, PhD dswack(a)buffalo.edu Associate Professor, Depts. of Nuclear Medicine and Biomedical Engineering University at Buffalo, USA P.S. Frontiers is a publisher created by scientists for scientists. We created Research Topics to give emerging research communities a platform. They bring together leading researchers to accelerate the development of cutting-edge research themes. As an open access publisher, Frontiers applies article publishing charges (APCs) to make research freely open and available for all. You can find more information here. If you encounter any technical issue, contact support(a)frontiersin.org<mailto:support@frontiersin.org>, with s0WY7RwlpCx5JEP as reference. David S. Wack, PhD Associate Professor Depts. of Nuclear Medicine And Biomedical Engineering University at Buffalo tel: 716 829-2648 cell: 716 319-4853 email: dswack(a)buffalo.edu or : dswack(a)gmail.com

1 0

Open NEST Developer Video Conference Monday August 26, at 11:30 CEST (UTC+0200)
by Dennis Terhorst 26 Aug '24

26 Aug '24

Dear NEST Users & Developers! I would like to invite you to our next fortnightly Open NEST Developer Video Conference today *Monday August 26, 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/2024-08-26-Open-NEST-Developer-… <https://github.com/nest/nest-simulator/wiki/2024-08-26-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 ----------------------------------------------------------------------

1 0

Open NEST Developer Video Conference Monday July 29, at 11:30 CEST (UTC+0200)
by Dennis Terhorst 12 Aug '24

12 Aug '24

Dear NEST Users & Developers! I would like to invite you to our next fortnightly Open NEST Developer Video Conference today *Monday July 29, 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/2024-07-29-Open-NEST-Developer-… <https://github.com/nest/nest-simulator/wiki/2024-07-29-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 ----------------------------------------------------------------------

2 1

Inject analog signal in a neuron
by Maryada Maryada 08 Aug '24

08 Aug '24

Dear NEST Users, Could anyone recommend the best way to inject a fluctuating current over time. A sample signal [image: image.png] -- Thanks and Regards *Maryada*

3 2

Order or Computation
by carriere.maxime93＠gmail.com 08 Aug '24

08 Aug '24

Hello everyone, I am trying to replicate our brain-constrained model to NEST. In our model the computation of the inhibition occurs before the inhibition. I believe it's the other way round in NEST. I was wondering, where the order of computation was implemented in NEST and if that was possible to change it. Best, Maxime

2 1

Open NEST Developer Video Conference Monday July 15, at 11:30 CEST (UTC+0200)
by Dennis Terhorst 24 Jul '24

24 Jul '24

Dear NEST Users & Developers! I would like to invite you to our next fortnightly Open NEST Developer Video Conference today *Monday July 15, 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/2024-07-15-Open-NEST-Developer-… <https://github.com/nest/nest-simulator/wiki/2024-07-15-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 ----------------------------------------------------------------------

3 3

nestml syntax problem
by Chris Huyck 19 Jul '24

19 Jul '24

I was using an old version of nest (3.5) and nestml. Someone sent me a nestml model, and that worked. I wanted to make my own model, but the tutorials had a different format. In particular, it seems like the first line of code in the tutorials start with model, and the old version started with neuron of synapse. So, I thought it was time to upgrade, so installed nest 3.7, and pip-ed nestml. (I also installed PyNN as that's the way I typically work.) When I imported generate_target (through python 3.12), I got the typical PyGSL warning; I think that's because I'm using python 3.12 not 3.11, and I don't think it matters in this case. Then I ran the generate_target and I got an error mismatched input 'model' expecting {newline, 'neuron', 'synapse} I expect there's something like a yacc table that specifies the syntax, and somehow I've got the old syntax. I've tried it with several version of nestml 7.0.2, 7.0.0, 6.0.0 and 5.0.0. I think 5.0.0 had the old syntax. I've tried several models from the library, and the Izhikevich tutorial. Any thoughts about how to fix it? -Chris

3 10

e-prop tutorial missing data file
by Xavier Otazu 04 Jul '24

04 Jul '24

Hi! Looking at the e-prop tutorial (https://nest-simulator.readthedocs.io/en/v3.7/auto_examples/eprop_plasticit…), the chaos_handwriting.txt datafile is needed. Where can I find this file? Thanks a lot in advance! Xavier

3 2

Open NEST Developer Video Conference Monday July 1, at 11:30 CEST (UTC+0200)
by Dennis Terhorst 01 Jul '24

01 Jul '24

Dear NEST Users & Developers! I would like to invite you to our next fortnightly Open NEST Developer Video Conference today *Monday July 1, 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/2024-07-01-Open-NEST-Developer-… <https://github.com/nest/nest-simulator/wiki/2024-07-01-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 ----------------------------------------------------------------------

1 0

Questions about Neuron Update Mechanism and Spike Event Handling in Source Code
by anh.phan＠tuni.fi 25 Jun '24

25 Jun '24

Hi, I've been trying to read through the source code to understand this, but I'm still having trouble figuring it out. From what I can see, the neurons are updated using a for loop, meaning each neuron is updated one at a time. The update function for each neuron can run for multiple timesteps, but I'm unclear on how its B_.input_buffer_ gets updated while the update function is running. If it doesn't get updated during this process, wouldn't it miss some spike events? Additionally, how does the code ensure that neurons updated one at a time for all simulation steps do not miss any spike events? Thank you for your help! Best regards, Anh Phan

3 4

Developers: Please pull Master to your branches / NumPy 2.0 changes
by Hans Ekkehard Plesser 20 Jun '24

20 Jun '24

Dear Colleagues, This mail is mainly for those of you who contribute to NEST Simulator development. NumPy 2.0, released last Sunday, has some minor changes that broke existing tests and examples. This has now been fixed in the master branch (PRs #3226, #3227). Please pull master into all your branches—otherwise, the testsuite will fail on Github and your contributions cannot be merged. Best, Hans Ekkehard -- Prof. Dr. Hans Ekkehard Plesser 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

1 0

Open NEST Developer Video Conference Monday June 3, at 11:30 CEST (UTC+0200)
by Dennis Terhorst 09 Jun '24

09 Jun '24

Dear NEST Users & Developers! I would like to invite you to our next fortnightly Open NEST Developer Video Conference today *Monday June 3, at 11:30 CEST (UTC+0200).* Despite many people attending conferences this week, we will briefly meet to offer attention also to smaller questions or more general topics that you may bring. The Project team round, might however be quite short today. Feel free to join the meeting and bring your own quick questions for direct discussion or just to hear what's going on in and around NEST. 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/2024-06-03-Open-NEST-Developer-… <https://github.com/nest/nest-simulator/wiki/2024-06-03-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 Juelich GmbH 52425 Juelich Sitz der Gesellschaft: Juelich Eingetragen im Handelsregister des Amtsgerichts Dueren Nr. HR B 3498 Vorsitzender des Aufsichtsrats: MinDir Stefan Müller Geschaeftsfuehrung: Prof. Dr. Astrid Lambrecht (Vorsitzende), Karsten Beneke (stellv. Vorsitzender), Dr. Ir. Pieter Jansens ----------------------------------------------------------------------

3 5

NEST Conference 2024 — Register by Friday!
by Hans Ekkehard Plesser 04 Jun '24

04 Jun '24

Dear NEST Users, We are looking forward to an exciting Virtual NEST Conference 2024 on Monday/Tuesday 17./18. June 2024. This years program includes keynotes by Tadashi Yamazaki, University of Electro-Communications, Japan Diversity and inclusion: Distributed simulation of multiple brain and body models in multiple simulators on multiple computers across multiple organizations Benedetta Gambosi, University of Pavia A multiarea model predicts the changes in thalamocortical beta oscillations caused by dopamine depletion in basal ganglia and cerebellum Tobias Gemmeke, RWTH Aachen Accelerated Simulation of Biological Neural Networks Behnam Ghazinouri, Ruhr-Universität Bochum The attractor dynamics of behavioral flexibility in spatial and reversal learning complemented by contributed talks, posters and a workshop Introducing Arbor. For the full program an to register, please see https://nest-simulator.org/conference. Registration deadline is this FRIDAY, 7 June 2024. We are looking forward to seeing you at the NEST Conference 2024! Hans Ekkehard Plesser -- Prof. Dr. Hans Ekkehard Plesser 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

1 0

About example structural plasticity?
by Thanh Binh To 21 May '24

21 May '24

1 0

Problem in STDP Windows tutorial notebook
by Ashraf Ul Islam Shihab 15 May '24

15 May '24

Hi, In nestml/doc/tutorials/stdp_windows notebook, in cell 3, I see an example of fetching model name, neuron name, and synapse name from nestml/models/neurons/iaf_psc_delta_neuron.nestml, which appears to have only model inside of it. It tries to extract the names from a format of 1. model <name>: 2. neuron <name>: 3. synapse <name>: But the iaf_psc_delta_neuron.nestml file from the latest build doesn't have any structure as neuron <name>: to my best knowledge. Please let me know if there is any fix for this problem. I went ahead and tried to edit the generate_code_for function from NESTCodeGeneratorUtils class. It can be found here <https://pastebin.com/Qz8JwinA>. But it gives an error as follows: > [6,GLOBAL, ERROR]: An error occurred while importing the `nest` module in > Python. Please check your NEST installation-related environment variables > and paths, or specify ``nest_version`` manually in the code generator > options. > An exception has occurred, use %tb to see the full traceback. Best, Ashraf Ul Islam Shihab Graduate Research Assistant Department of Electrical and Computer Engineering Boise State University (BSU) Boise, Idaho 83725 Email: ashrafshihab(a)u.boisestate.edu

2 5

gsl import error after update (plus: NEST on WSL)
by Patricio Orio 09 May '24

09 May '24

Hello, I have been trying NEST under the WSL in Windows and I am glad to say that it works! I think that getting NEST working correctly under the WSL may attract more users, to both NEST and the WSL. BTW (this is a side note), I have noticed that some Python codes (unrelated to NEST) run a little faster (15-20%) under the WSL than in Windows itself. Anyway, nest works perfectly on the WSL using either Spyder as IDE or JupyterLab. However, after a while the installation breaks. After doing any upgrade via "conda upgrade --all" (once it was NEST itself updated), when I try to import NEST I get the error transcribed below, which ends in "ImportError: libgsl.so.25: cannot open shared object file: No such file or directory". I have narrowed down the problem to this: when installing NEST, the package "conda-forge::gsl-2.7-he838d99_0" is installed along. Then, if I do any "conda update --all" (or I guess that if I install any other package that uses gsl), the package gets updated "conda-forge::gsl-2.7-he838d99_0 --> pkgs/main::gsl-2.7.1-h6e86dc7_1". Then here: https://nest-simulator.org/mailinglist/hyperkitty/list/users@nest-simulator… I found out that "If you upgrade your environment, you might have to cmake and compile NEST anew in order for it to pick up the new version.". So I thought that a force-reinstall of nest might do the trick, but it didn't. Moreover, I did the following: - start a new, clean environment - install gsl before nest (I got main::gsl-2.7.1-h6e86dc7_1) - then install nest-simulator. But the error appears again. FINALLY, I did "conda install conda-forge::gsl", it picked gsl-2.7-he838d99_0 and now NEST works again!! So it seems that the problem is specific with gsl-2.7.1 (and/or whatever version is in main?). I don't want to end up using NEST in a frozen environment where nothing can be added or changed, neither before nor after installing NEST. Although I found the workaround, I guess you may find a way of this not happening at all. Thank you and best regards Patricio. In [1]: import nest --------------------------------------------------------------------------- ImportError Traceback (most recent call last) Cell In[1], line 1 ----> 1 import nest File ~/miniconda3/lib/python3.12/site-packages/nest/__init__.py:64 61 import sys # noqa 62 import types # noqa ---> 64 from .ll_api_kernel_attributes import KernelAttribute # noqa 66 try: 67 import versionchecker # noqa: F401 File ~/miniconda3/lib/python3.12/site-packages/nest/ll_api_kernel_attributes.py:22 1 # -*- coding: utf-8 -*- 2 # 3 # ll_api_kernel_attributes.py (...) 19 # You should have received a copy of the GNU General Public License 20 # along with NEST. If not, see <http://www.gnu.org/licenses/>. ---> 22 from .ll_api import spp, sps, sr, stack_checker 25 class KernelAttribute: 26 """ 27 Descriptor that dispatches attribute access to the nest kernel. 28 """ File ~/miniconda3/lib/python3.12/site-packages/nest/ll_api.py:53 48 # Make MPI-enabled NEST import properly. The underlying problem is that the 49 # shared object pynestkernel dynamically opens other libraries that open 50 # yet other libraries. 51 sys.setdlopenflags(os.RTLD_NOW | os.RTLD_GLOBAL) ---> 53 from . import pynestkernel as kernel # noqa pylint: disable=no-name-in-module 55 __all__ = [ 56 "check_stack", 57 "connect_arrays", (...) 69 "take_array_index", 70 ] 73 engine = kernel.NESTEngine() ImportError: libgsl.so.25: cannot open shared object file: No such file or directory

1 0

Open NEST Developer Video Conference Monday May 6, at 11:30 CEST (UTC+0200)
by Dennis Terhorst 06 May '24

06 May '24

Dear NEST Users & Developers! I would like to invite you to our next fortnightly Open NEST Developer Video Conference today *Monday May 6, 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/2024-05-06-Open-NEST-Developer-… <https://github.com/nest/nest-simulator/wiki/2024-05-06-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 Juelich GmbH 52425 Juelich Sitz der Gesellschaft: Juelich Eingetragen im Handelsregister des Amtsgerichts Dueren Nr. HR B 3498 Vorsitzender des Aufsichtsrats: MinDir Stefan Müller Geschaeftsfuehrung: Prof. Dr. Astrid Lambrecht (Vorsitzende), Karsten Beneke (stellv. Vorsitzender), Dr. Ir. Pieter Jansens ----------------------------------------------------------------------

1 0

NEST on Google Colab?
by Alvin Spivey 03 May '24

03 May '24

I'm trying to install and use NEST on google Colab, but it's not importing: !pip install -Uqq nest !pip install -Uqq nestml !pip install -Uqq pysilsub import nest import nestml import numpy as np import matplotlib.pyplot as plt from pysilsub import observers from nestml.network import Network from nestml.models import ConeNakaRushton Am I able to use NEST on Google Colab? -- Alvin J. Spivey, Ph.D. (c) 843.267.8055

6 10

Open NEST Developer Video Conference Monday April 22, at 11:30 CEST (UTC+0200)
by Dennis Terhorst 22 Apr '24

22 Apr '24

Dear NEST Users & Developers! I would like to invite you to our next fortnightly Open NEST Developer Video Conference today *Monday April 22, 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/2024-04-22-Open-NEST-Developer-… <https://github.com/nest/nest-simulator/wiki/2024-04-22-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 Juelich GmbH 52425 Juelich Sitz der Gesellschaft: Juelich Eingetragen im Handelsregister des Amtsgerichts Dueren Nr. HR B 3498 Vorsitzender des Aufsichtsrats: MinDir Stefan Müller Geschaeftsfuehrung: Prof. Dr. Astrid Lambrecht (Vorsitzende), Karsten Beneke (stellv. Vorsitzender), Dr. Ir. Pieter Jansens ----------------------------------------------------------------------

1 0

NEST Conference 2024 - Extension of abstract submission deadline
by Hans Ekkehard Plesser 16 Apr '24

16 Apr '24

Dear all, The abstract submission deadline for the NEST Conference 2024 has been extended to 30 April. We are looking forward to your contributions! [Image] 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. This year's conference will again take place as a virtual conference on Monday/Tuesday 17/18 June 2024. We are inviting contributions to the conference, including talks, "posters" and workshops on specific topics. For more information on how to submit your contribution, register and participate, please visit the conference website https://nest-simulator.org/conference Important dates 26 April 2024 - Deadline for NEST Initiative membership applications eligible for fee reduction 30 April 2024 - Extended deadline for submission of contributions 08 May 2024 - Notification of acceptance 07 June 2024 - Registration deadline 17 June 2024 - NEST Conference 2024 starts We are looking forward to seeing you all in June! Hans Ekkehard Plesser and the conference organizing committee -- Prof. Dr. Hans Ekkehard Plesser 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

1 0

NEST Conference 2024 - reminder for abstract submission deadline on 15 April 2024
by Hans Ekkehard Plesser 09 Apr '24

09 Apr '24

Dear all, The abstract submission deadline for the virtual NEST Conference 2024 is approaching (15 April 2024). We are looking forward to your contributions! 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. This year's conference will again take place as a virtual conference on Monday/Tuesday 17/18 June 2024. We are inviting contributions to the conference, including talks, "posters" and workshops on specific topics. Important dates 15 April 2024 - Deadline for submission of contributions 26 April 2024 - Deadline for NEST Initiative membership applications eligible for fee reduction 08 May 2024 - Notification of acceptance 07 June 2024 - Registration deadline 17 June 2024 - NEST Conference 2024 starts For more information on how to submit your contribution, register and participate, please visit the conference website https://nest-simulator.org/conference We are looking forward to seeing you all in June! Hans Ekkehard Plesser and the conference organizing committee -- Prof. Dr. Hans Ekkehard Plesser 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

1 0

Open NEST Developer Video Conference Monday April 8, at 11:30 CEST (UTC+0200)
by Hans Ekkehard Plesser 08 Apr '24

08 Apr '24

Dear NEST Users & Developers! I would like to invite you to our next fortnightly Open NEST Developer Video Conference today Monday April 8, 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. Special topic today is the status of the upcoming NEST 3.7 release. 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 * NEST Conference 2024<http://www.nest-initiative.org/conference>: Submission Deadline 15 April 2024 * NEST 3.7 RC1 Status * Reduce number of warnings (see, e.g., https://github.com/nest/nest-simulator/actions/runs/8566897766) * Porting tests from SLI to Py The agenda for this meeting is also available online, see https://github.com/nest/nest-simulator/wiki/2024-03-25-Open-NEST-Developer-… Looking forward to seeing you soon! Cheers, Hans Ekkehard Plesser 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 * 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<tel:+493020097938800> For those who do not have a video conference system or suitable software, Polycom provides a pretty good free app for iOS and Android, so you can join from your tablet (Polycom RealPresence Mobile, available from AppStore/PlayStore). Note that firewalls may interfere with videoconferencing in various and sometimes confusing ways. For more technical information on logging in from various VC systems, please see http://vcc.zih.tu-dresden.de/index.php?linkid=1.1.3.4 -- Prof. Dr. Hans Ekkehard Plesser 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

1 0

Questions regarding the iaf_psc_exp model
by anh.phan＠tuni.fi 02 Apr '24

02 Apr '24

Hello, I have some questions regarding the iaf_psc_exp model. When it receives current from a current generator (with static synapse), does that current go to receptor_type 0 and not be filtered through an exponential kernel? Secondly, I would like to confirm if the exponential PSCs follow the exponential function:: i_syn(t) = (q / tau_syn) * exp(-t / tau_syn) * Θ(t) , where Θ(t) is the Heaviside step function defined as Θ(t) = 1 fot t >0 and Θ(t) = 0 otherwise. Additionally, is q chosen to be equal to tau_syn? Thank you very much! Best regards, Anh Phan

2 5

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

25 Mar '24

Dear NEST Users & Developers! I would like to invite you to our next fortnightly Open NEST Developer Video Conference today *Monday March 25, 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. Special topic today is the status of the /upcoming NEST 3.7 release/. 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/2024-03-25-Open-NEST-Developer-… <https://github.com/nest/nest-simulator/wiki/2024-03-25-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 Juelich GmbH 52425 Juelich Sitz der Gesellschaft: Juelich Eingetragen im Handelsregister des Amtsgerichts Dueren Nr. HR B 3498 Vorsitzender des Aufsichtsrats: MinDir Stefan Müller Geschaeftsfuehrung: Prof. Dr. Astrid Lambrecht (Vorsitzende), Karsten Beneke (stellv. Vorsitzender), Dr. Ir. Pieter Jansens ----------------------------------------------------------------------

1 0

NESTML sample random distributions - assertion failed
by chiara de luca 19 Mar '24

19 Mar '24

Dear NESTML community, I have a problem with random number generator in the new version of nestml. Specifically, I am using nest 3.6.0 nestml 7.0 This is what I would like to do: whenever creating a neuron with a set of parameters defined by the user, each parameter should be affected by a "gaussian error" with defined variability. I tried to use the internal random_normal() function but with the current version I am getting some issues there. Specifically, whenever trying to call such function from the "internals", "parameters", "state" blocks the model is correctly generated (no errors returned) but exits with en error whenever trying to "install". The error is the following Assertion failed: (tid < static_cast< size_t >( vp_specific_rngs_.size() )), function get_vp_specific_rng, file my/path/to/miniforge3/conda-bld/nest-simulator_1707218961774/work/nestkernel/random_manager.h, line 173. [1] 32875 abort python test.py Such problem does not exist for random_normal() called within the update and equations blocks. Attached some minimal code to reproduce the error. Best, Chiara

2 3

DumpLayerConnections() enhancement request
by Xavier Otazu 18 Mar '24

18 Mar '24

Hi! I am using DumpLayerConnections() with two layers with around 100x100 nodes each layer. Every layer node is connected to around 100 nodes on the other layer. Calling the DumpLayerConnections() takes around 10-15 minutes to save connections to file. I know it is a too general request, but it would be nice if this function is faster. In my particular case, I obtain these connections in a previous step using GetConnections(). I guess (hence I am probably wrong) that DumpLayerConnections() calls GetConnections(). If I am right, I believe it could be an interesting enhancement to implement a DumpLayerConnections() function with input parameters that are a set of connections, that is, something like: myconn = nest.GetConnections(layer1, layer2, ...) nest.DumpLayerConnections(myconn) Thanks a lot in advance! Xavier

3 9

ValueError: 'Wmax' is not allowed in syn_spec when connecting with mask or kernel
by anh.phan＠tuni.fi 14 Mar '24

14 Mar '24

I am working with a 2D spatially-structured neural network and aim to employ STDP synapses to establish connections between neurons. However, I encountered an error stating 'ValueError: 'Wmax' is not allowed in syn_spec when connecting with mask or kernel,' along with similar issues for parameters such as tau_plus, alpha, lambda, and others. Could you give me some guidance on how to properly configure these parameters? Thank you very much.

2 2

SelectNodesByMask() and DumpLayerConnections() combination problem
by Xavier Otazu 14 Mar '24

14 Mar '24

Hello, Looking at the documentation, I understand that the output of SelectNodesByMask() is a NodeCollection, and the 'layer' input parameters of DumpLayerConnections() is also a NodeCollection. Hence, I understand that I can combine these two parameters, but when I do it (see code below) I receive the error: nest.lib.hl_api_exceptions.LayerExpected: LayerExpected in SLI function DumpLayerConnections_os_g_g_l Am I missing something? Thanks a lot in advance! Xavier -------- import nest # Layers creation pos = nest.spatial.grid(shape = [100,100] ) input_l = nest.Create('iaf_psc_alpha', positions=pos) layer_0 = nest.Create('iaf_psc_alpha', positions=pos) conn_neur = {'rule':'pairwise_bernoulli', 'mask': {'grid':{'shape':[10,10]}} } syn_0 = {'synapse_model': 'static_synapse'} nest.Connect(input_l, layer_0, conn_neur, syn_0) # GetNodesByMask mask_specs = {'lower_left':[-0.25,-0.25], 'upper_right':[0.25,0.25]} mask_obj = nest.CreateMask(masktype='rectangular', specs=mask_specs, anchor=[0.0,0.0]) center_neur = nest.SelectNodesByMask(layer_0,[0.0,0.0],mask_obj) nest.DumpLayerConnections(input_l,center_neur, 'static_synapse', 'conn.txt')

3 2

Strange interaction between NEST and IPython
by Hans Ekkehard Plesser 12 Mar '24

12 Mar '24

Dear Python experts among the NEST Users! I just notice a strange interaction between NEST and Ipython. In a freshly started Ipython, I execute the following three statements import nest n = nest.Create('parrot_neuron', positions=nest.spatial.free([(x, 0) for x in range(10000)])) n The last one takes extraordinarily long, over 10 seconds, I think. But if I instead do print(n) it executes instantaneously. Also, if I do the same thing in python directly, just entering n shows the NodeCollection immediately. Can anyone reproduce this and does anyone have an idea what might be going on? I am on macOS 14.3.1 with Python 3.12.2, Ipython 8.22.2, and have checked with NEST 3.6 and a branch of recent master. Best, Hans Ekkehard -- Prof. Dr. Hans Ekkehard Plesser 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

4 6

Re: Problems in simulation restore
by Hans Ekkehard Plesser 11 Mar '24

11 Mar '24

Dear Petia, Please excuse my late reply to your questions about restoring NEST simulations. For some reason, your mail had disappeared from my computer. The behaviour you observe is as expected. When storing and then re-loading and continuing the simulation, a number of things will be different in the second part of the simulation: * Any spikes that were in transit from pre- to postsynaptic neuron are lost. * Random number generators re-start from a different point then where they stopped. * Internal properties of neuron models, such as the state of GSL-based ODE integrators for nonlinear neuron models. There is currently no way to avoid this loss of information. Best regards, Hans Ekkehard -- Prof. Dr. Hans Ekkehard Plesser 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

2 1

Opt out of MPI during an MPI run
by Robin Gilbert De Schepper 11 Mar '24

11 Mar '24

Hi! Is there a way to disable the following fatal error? Perhaps an environment variable to tell NEST not to try to initialize MPI: [FATAL] [2024.3.1 12:15:12 /home/robin/git/nest-simulator/nestkernel/mpi_manager.cpp:203 @ MPIManager::initialize()] : You seem to be using NEST via an MPI launcher like mpirun, mpiexec or srun although NEST was not compiled with MPI support. Please see the NEST documentation about parallel and distributed computing. Exiting. I know I could rebuild with MPI support, and set the communicator to a communicator containing just that rank, on each rank, but this is during unit testing where nest is just imported, so a quick opt-out would be less work. -- Robin De Schepper, PhD (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/

2 1

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

11 Mar '24

Dear NEST Users & Developers! I would like to invite you to our next fortnightly Open NEST Developer Video Conference today *Monday March 11, 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 o Todo's for the 3.7 release The agenda for this meeting is also available online, see https://github.com/nest/nest-simulator/wiki/2024-03-11-Open-NEST-Developer-… <https://github.com/nest/nest-simulator/wiki/2024-03-11-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 Juelich GmbH 52425 Juelich Sitz der Gesellschaft: Juelich Eingetragen im Handelsregister des Amtsgerichts Dueren Nr. HR B 3498 Vorsitzender des Aufsichtsrats: MinDir Stefan Müller Geschaeftsfuehrung: Prof. Dr. Astrid Lambrecht (Vorsitzende), Karsten Beneke (stellv. Vorsitzender), Dr. Ir. Pieter Jansens ----------------------------------------------------------------------

1 0

GetConnections() enhancement request
by Xavier Otazu 08 Mar '24

08 Mar '24

Hi! In order to perform connections weight normalization, I am using the GetConnections() function to obtain the input connections for every neuron. That is, I use a code like for i in range(number_of neurons) conn[i] = GetConnections(my_source, my_target[i], ...) Later in the code, I use conn[i].weight to perform my normalization. It implies that for big networks (number_of_neurons=10k) I have to call GetConnections() around 10k times. Hence, the execution time is huge. Could it be possible that you enhance GetConnections() (or define a new function) in order to return the connections for all the neurons in the target in array with the same longitude as the number of neurons in target instead of the number of connections? That is, indexed by neurons instead of indexed by connections. I understand that present implementation of GetConnections() visits all the connections and return only the input connections to target. I do not want to tell developers how to do it :-) but I believe it could be implemented by visiting all the connections (related to target) just ONCE and copy each one to the corresponding output array indexed by neuron. This way, it would be a single call to GetConnections() (plus the time needed to internally manage the assignment to the output array), instead of 10k times. It would be very much appreciated. Thanks a lot in advance! Xavier

2 3

Virtual NEST Conference 2024 / Abstract Submission and Registration Open
by Hans Ekkehard Plesser 05 Mar '24

05 Mar '24

Dear Colleagues, The NEST Initiative is excited to invite everyone interested in Neural Simulation Technology and the NESTSimulator to the NEST Conference 2024. 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. We explicitly encourage young scientists to participate in the conference! This year's conference will again take place as a virtual conference on Monday/Tuesday 17/18 June 2024. We are delighted to welcome * Tadashi Yamazaki (University of Electro-Communications, Tokyo) * Behnam Ghazinouri (Ruhr University Bochum) * Benedetta Gambosi (Politecnico di Milano) * Tobias Gemmeke (RWTH Aachen University) as keynote speakers at the conference. Registration and submission of contributions are now open! We are inviting contributions to the conference, including talks, "posters" and workshops on specific topics. Please register and submit your contribution(s) via the conference website https://nest-simulator.org/conference. Important dates 15 April 2024 - Deadline for submission of contributions 26 April 2024 - Deadline for NEST Initiative membership applications eligible for fee reduction 08 May 2024 - Notification of acceptance 07 June 2024 - Registration deadline 17 June 2024 - NEST Conference 2024 starts We are looking forward to seeing you all in June! Hans Ekkehard Plesser and the conference organizing committee [Image] -- Prof. Dr. Hans Ekkehard Plesser 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

1 0

Open NEST Developer Video Conference Monday February 26, at 11:30 CET (UTC+0100)
by Dennis Terhorst 26 Feb '24

26 Feb '24

Dear NEST Users & Developers! I would like to invite you to our next fortnightly Open NEST Developer Video Conference today *Monday February 26, 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 o MPI tests port to Python #3102 <https://github.com/nest/nest-simulator/pull/3102> The agenda for this meeting is also available online, see https://github.com/nest/nest-simulator/wiki/2024-02-26-Open-NEST-Developer-… <https://github.com/nest/nest-simulator/wiki/2024-02-26-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 Juelich GmbH 52425 Juelich Sitz der Gesellschaft: Juelich Eingetragen im Handelsregister des Amtsgerichts Dueren Nr. HR B 3498 Vorsitzender des Aufsichtsrats: MinDir Stefan Müller Geschaeftsfuehrung: Prof. Dr. Astrid Lambrecht (Vorsitzende), Karsten Beneke (stellv. Vorsitzender), Dr. Ir. Pieter Jansens ----------------------------------------------------------------------

1 0

SLIInterpreter --> Key '/Install' does not exist in dictionary
by Willem Wybo 21 Feb '24

21 Feb '24

Dear all, I’m trying to run nestml with the latest nest master branch commit (8e85268ca512e0f509240fb5ef06f62a4e61a67e) but I get an error when calling the `nest.Install()` function. -- Install configuration: "" -- Installing: /Users/wybo/miniconda3/envs/nest-multiscale/lib/nest/concmech_mockup_module.so Traceback (most recent call last): File "/Users/wybo/Code/NEST/nestml/tests/nest_compartmental_tests/compile_test.py", line 23, in <module> nest.Install("concmech_mockup_module") File "/Users/wybo/miniconda3/envs/nest-multiscale/lib/python3.12/site-packages/nest/ll_api.py", line 216, in stack_checker_func return f(*args, **kwargs) ^^^^^^^^^^^^^^^^^^ File "/Users/wybo/miniconda3/envs/nest-multiscale/lib/python3.12/site-packages/nest/lib/hl_api_simulation.py", line 332, in Install return sr("(%s) Install" % module_name) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/Users/wybo/miniconda3/envs/nest-multiscale/lib/python3.12/site-packages/nest/ll_api.py", line 103, in catching_sli_run raise exceptionCls(commandname, message) nest.lib.hl_api_exceptions.NESTErrors.DictError: DictError in SLI function SLIInterpreter::execute: Key '/Install' does not exist in dictionary. Did anybody experience the same problem, or know what might cause it? Best regards, Willem ---------------------- Dr. Willem Wybo 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), Karsten Beneke (stellv. Vorsitzender), Dr. Ir. Pieter Jansens ------------------------------------------------------------------------------------------------ ------------------------------------------------------------------------------------------------

3 4

Tripsitter: A Psychedelics, Ketamine, & Cannabis Encyclopedia
by Leon Vergara 21 Feb '24

21 Feb '24

In a world where the use of psychedelics, ketamine, and cannabis is increasing, it is important for individuals to have access to accurate and comprehensive information. Enter Tripsitter, a one-stop encyclopedia that provides all the necessary knowledge on these mind-altering substances. Whether you are a novice or an experienced user, this encyclopedia aims to guide you through the world of psychedelics, ketamine, and cannabis, ensuring you have the most informed and safe experiences possible. The Benefits of Education Education is the key to responsible and mindful engagement with psychedelics, ketamine, and cannabis. By understanding the effects, risks, and best practices of consumption, individuals can make informed decisions about their experiences. Tripsitter recognizes the importance of education and strives to empower its readers with accurate and up-to-date information. Understanding Psychedelics Psychedelics have been used for centuries for their mind-altering effects and potential therapeutic benefits. Tripsitter provides detailed explanations of different psychedelics such as LSD, magic mushrooms, and DMT, as well as their effects on the mind, body, and consciousness. This knowledge encourages individuals to approach these substances with mindfulness and respect. Exploring Ketamine Ketamine, originally developed as an anesthetic, has become known for its hallucinogenic properties and potential in treating depression and other psychiatric conditions. Tripsitter delves into the origins, effects, and risks associated with ketamine use. With this information, individuals can make informed choices about their mental health and well-being. Unveiling Cannabis Cannabis, a widely used recreational and medicinal plant, has a long history of human interaction and benefits. Tripsitter enlightens readers about the various strains, consumption methods, and potential therapeutic applications of cannabis. By unraveling the complexity of this plant, individuals can harness its benefits while minimizing potential risks. Addressing Safety Tripsitter places a strong focus on responsible and safe use of psychedelics, ketamine, and cannabis. It provides comprehensive harm reduction techniques, user guides, and precautions to ensure individuals' physical and mental well-being. By following these recommendations, readers can minimize the risks associated with these substances. Safe Environments for Experiences Creating a safe environment is crucial for positive and transformative experiences. Tripsitter guides readers on setting and preparation, emphasizing the importance of a trusted companion, a comfortable physical space, and appropriate mental and emotional states before engaging with psychedelics, ketamine, or cannabis. These guidelines promote safe and intentional exploration. Integrating Experiences Tripsitter recognizes that the journey doesn't end with the trip. The integration process is equally important for individuals to fully benefit from their experiences. With insights into mindfulness practices, journaling, and therapy, readers can embark on a deeper understanding and personal growth as a result of psychedelic, ketamine, or cannabis encounters. Final Recommendation Tripsitter serves as the ultimate resource for those seeking to explore psychedelics, ketamine, and cannabis. By covering a wide range of topics and embracing harm reduction principles, this encyclopedia educates, guides, and empowers readers to create safe and meaningful experiences. The comprehensive nature of Tripsitter allows individuals to approach these substances with a level of awareness that promotes personal growth and well-being. In a world where the use of psychedelics, ketamine, and cannabis is rapidly evolving, having access to accurate and reliable information is paramount. With Tripsitter, the journey becomes safer, more informed, and more transformative. Let this encyclopedia be your trusted companion on the exploration of new horizons within your mind and beyond Company Name: Tripsitter Magazine Company website: https://tripsitter.com/ Address: 4498 Main St Ste 4 #5040 Amherst, NY 14226, United States Phone: +1-716-839-4444 Email: high(a)tripsitter.com Tags: #psychedelics, #magicmushrooms, #ketamine, #mdma, #cannabis

1 0

Problems when using a mask inside the conn_dict on 3 or 4 MPI processes
by Kempter, Miriam 20 Feb '24

20 Feb '24

Dear NEST Community, while adapting my model to run on multiple MPI processes, I have been running into some problems connected with the usage of masks inside the connectivity dictionary for a 2D-spatially distributed population. You can find a minimal example containing further details in the attachments in the form of a .txt file. Please just change "txt" with "py" for execution. The following explanation also references to the example. My setup: - NEST version 3.4 - Python version 3.10 - Executed with mpirun inside a conda environment "mpirun -np 4 python3 minEx_4MPIprocesses_problem.py" - System: Ubuntu 22.04 - The same problem occurred when the model was executed on JURECA. Problem description: While using multiple MPI processes: 1. Create circular mask. See line 119 Create a spatial 2D-Population of neurons "neurons". See line 125-132 2. Select some of the neurons as source neurons. See line 154 3. Set up the connection dictionary with a mask inside. See line 157-163 4. For each source neuron: See line 173 Connect the source neurons with the neurons population using the connection dictionary See line 183 Where does the Problem occur?: The error occurs at the point when the nest.Connect(…) call is executed in the loop at line 183 when each source neuron is connected. When does the Problem occur?: Its occurrance depends on whether or not a mask is used inside the connection-dict given to the nest.Connect(...) function. If the mask is removed as in the conn-dict. in line 164-169, no error is produced in none of the used settings (however the result is not as desired). If the mask is used, the way the problem shows itself depends on the number of MPI processes used, and on the setting of the number of neurons, extent, mask radius, number of source neurons and if edge wrap is used. - For 1 and 2 MPI procs the model is running correctly, independent of the used conn-dict and setting. - For 3 MPI procs either the model runs but the distance between connected neurons does not correspond to the given mask dimensions. In other words: The established connections are longer/shorter than the mask should allow. Or execution leads to an error code output ("segmentation fault") from mpirun and job abortion. The terminal output for an example run can be seen in the attached file "minEx_4MPIprocesses_problem_error_output_3_MPI" - For 4 MPI procs either, the model runs correctly, or it leads to an error code output ("segmentation fault") and the model not terminating. (When executed in the terminal the keyboard command "str+c" is needed to stop the execution. The terminal output for an example run can be seen in the attached file "minEx_4MPIprocesses_problem_error_output_4_MPI" If the model is executed with the same setting on 3 and 4 MPI procs there are 3 possible combinations of above described problems. 1. The model runs and terminates on both, however the distances created on 3 MPI procs are wrong. 2. The model works with 4 MPI procs but creates the "segmentation fault" error on 3 MPI processes. 3. The model creates a "segmentation fault" error on both. Please keep in mind that whether an error occurs and in which form highly depends on the used setting. In the minimal example I provide different settings which represent the above described cases. However, it might not cover everything that can occur. Workaround: For my own use-case I found a rather computing-time consuming workaround. It involves applying nest.SelectNodesByMask() on every source neuron, and from the resulting set choosing the targets using the desired probability. This requires multiple additional loops and also communicating the position data of every neuron to every MPI process in the beginning. Using this approach, the connection distances seem to be correct and no error occurs while executing the model. However, while writing this I'm questioning if I actually tested it enough. So there might be some not yet discovered problems. Is there something that I overlooked or approached wrong when using masks in the connectivity dict on multiple MPI processes? Thanks in advance! Best, Miriam Kempter ------------------------------------------------------------------------------------------------ ------------------------------------------------------------------------------------------------ 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), Dr. Ir. Pieter Jansens ------------------------------------------------------------------------------------------------ ------------------------------------------------------------------------------------------------

2 4

2025

2024

2023

2022

2021

2020

2019

NEST Users