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Error in NESTML when I run the 'NESTML Izhikevich tutorial'
by Salvo T 28 Feb '22

28 Feb '22

Dear NESTML Users, In the last post I fixed a problem that was related to the fact that in the 'izhikevich_solution.nestml' the first line was commented. Now, after following the guide in "https://nestml.readthedocs.io/en/latest/installation.html" related to the NESTML installation, I tried to follow the NESTML Izhikevich tutorial in "https://nestml.readthedocs.io/en/latest/tutorials/izhikevich/nestml_izhikev…". After installing the cmake with "pip install cmake", when I execute the following part of the tutorial: generate_nest_target(input_path="izhikevich_solution.nestml", target_path="/tmp/nestml-component", logging_level="ERROR", codegen_opts={"nest_path": NEST_SIMULATOR_INSTALL_LOCATION}) I obtain the following error: Warning: PyGSL is not available. The stiffness test will be skipped. Warning: No module named 'pygsl' Option "nest_path" does not exist in builder --------------------------------------------------------------------------- CalledProcessError Traceback (most recent call last) /opt/data/nestml/pynestml/codegeneration/nest_builder.py in build(self) 149 try: --> 150 subprocess.check_call(make_all_cmd, stderr=subprocess.STDOUT, shell=shell, 151 cwd=str(os.path.join(target_path))) /usr/lib/python3.8/subprocess.py in check_call(*popenargs, **kwargs) 363 cmd = popenargs[0] --> 364 raise CalledProcessError(retcode, cmd) 365 return 0 CalledProcessError: Command '['make', 'all']' returned non-zero exit status 2. During handling of the above exception, another exception occurred: GeneratedCodeBuildException Traceback (most recent call last) <ipython-input-2-f0909be085f4> in <module> ----> 1 generate_nest_target(input_path="izhikevich_solution.nestml", 2 target_path="/tmp/nestml-component", 3 module_name="nestml_izhikevich_module", 4 suffix="_nestml", 5 logging_level="ERROR", /opt/data/nestml/pynestml/frontend/pynestml_frontend.py in generate_nest_target(input_path, target_path, install_path, logging_level, module_name, store_log, suffix, dev, codegen_opts) 181 A dictionary containing additional options for the target code generator. 182 """ --> 183 generate_target(input_path, target_platform="NEST", target_path=target_path, logging_level=logging_level, 184 module_name=module_name, store_log=store_log, suffix=suffix, install_path=install_path, 185 dev=dev, codegen_opts=codegen_opts) /opt/data/nestml/pynestml/frontend/pynestml_frontend.py in generate_target(input_path, target_platform, target_path, install_path, logging_level, module_name, store_log, suffix, dev, codegen_opts) 150 FrontendConfiguration.set_codegen_opts(codegen_opts) 151 --> 152 if not process() == 0: 153 raise Exception("Error(s) occurred while processing the model") 154 /opt/data/nestml/pynestml/frontend/pynestml_frontend.py in process() 278 options=FrontendConfiguration.get_codegen_opts()) 279 if _builder is not None: --> 280 _builder.build() 281 282 if FrontendConfiguration.store_log: /opt/data/nestml/pynestml/codegeneration/nest_builder.py in build(self) 151 cwd=str(os.path.join(target_path))) 152 except subprocess.CalledProcessError as e: --> 153 raise GeneratedCodeBuildException('Error occurred during \'make all\'! More detailed error messages can be found in stdout.') 154 155 # finally execute make install GeneratedCodeBuildException: Error occurred during 'make all'! More detailed error messages can be found in stdout. So, the "nest_path" keyword does not exist. Can anyone help me? Best, Salvo

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Error in NESTML when I run the 'NESTML Izhikevich tutorial'
by Salvo T 28 Feb '22

28 Feb '22

Hi, after following the guide in "https://nestml.readthedocs.io/en/latest/installation.html" related to the NESTML installation, I tried to follow the NESTML Izhikevich tutorial in "https://nestml.readthedocs.io/en/latest/tutorials/izhikevich/nestml_izhikev…". After installing the cmake with "pip install cmake", when I execute the following part of the tutorial: generate_nest_target(input_path="izhikevich_solution.nestml", target_path="/tmp/nestml-component", logging_level="ERROR", codegen_opts={"nest_path": NEST_SIMULATOR_INSTALL_LOCATION}) I obtain the following error: line 3:2 extraneous input 'state' expecting {<EOF>, NEWLINE, 'neuron', 'synapse'} line 4:4 extraneous input 'v' expecting {<EOF>, NEWLINE, 'neuron', 'synapse'} line 8:2 extraneous input 'equations' expecting {<EOF>, NEWLINE, 'neuron', 'synapse'} line 9:4 extraneous input 'v' expecting {<EOF>, NEWLINE, 'neuron', 'synapse'} line 10:4 extraneous input 'u' expecting {<EOF>, NEWLINE, 'neuron', 'synapse'} line 11:2 extraneous input 'end' expecting {<EOF>, NEWLINE, 'neuron', 'synapse'} line 13:2 extraneous input 'parameters' expecting {<EOF>, NEWLINE, 'neuron', 'synapse'} line 14:4 extraneous input 'a' expecting {<EOF>, NEWLINE, 'neuron', 'synapse'} line 20:2 extraneous input 'input' expecting {<EOF>, NEWLINE, 'neuron', 'synapse'} line 21:4 extraneous input 'spikes' expecting {<EOF>, NEWLINE, 'neuron', 'synapse'} line 22:4 extraneous input 'I_e' expecting {<EOF>, NEWLINE, 'neuron', 'synapse'} line 23:2 extraneous input 'end' expecting {<EOF>, NEWLINE, 'neuron', 'synapse'} line 25:2 extraneous input 'output' expecting {<EOF>, NEWLINE, 'neuron', 'synapse'} line 27:2 extraneous input 'update' expecting {<EOF>, NEWLINE, 'neuron', 'synapse'} line 28:4 extraneous input 'integrate_odes' expecting {<EOF>, NEWLINE, 'neuron', 'synapse'} line 31:4 extraneous input 'v' expecting {<EOF>, NEWLINE, 'neuron', 'synapse'} line 34:4 extraneous input 'if' expecting {<EOF>, NEWLINE, 'neuron', 'synapse'} line 35:6 extraneous input 'v' expecting {<EOF>, NEWLINE, 'neuron', 'synapse'} line 36:6 extraneous input 'u' expecting {<EOF>, NEWLINE, 'neuron', 'synapse'} line 37:6 extraneous input 'emit_spike' expecting {<EOF>, NEWLINE, 'neuron', 'synapse'} line 38:4 extraneous input 'end' expecting {<EOF>, NEWLINE, 'neuron', 'synapse'} line 40:2 extraneous input 'end' expecting {<EOF>, NEWLINE, 'neuron', 'synapse'} line 42:0 extraneous input 'end' expecting {<EOF>, NEWLINE, 'neuron', 'synapse'} [5,GLOBAL, ERROR]: Error occurred during parsing: abort --------------------------------------------------------------------------- CalledProcessError Traceback (most recent call last) /opt/data/nestml/pynestml/codegeneration/nest_builder.py in build(self) 149 try: --> 150 subprocess.check_call(make_all_cmd, stderr=subprocess.STDOUT, shell=shell, 151 cwd=str(os.path.join(target_path))) /usr/lib/python3.8/subprocess.py in check_call(*popenargs, **kwargs) 363 cmd = popenargs[0] --> 364 raise CalledProcessError(retcode, cmd) 365 return 0 CalledProcessError: Command '['make', 'all']' returned non-zero exit status 2. During handling of the above exception, another exception occurred: GeneratedCodeBuildException Traceback (most recent call last) <ipython-input-5-5d459438a659> in <module> ----> 1 generate_nest_target(input_path="izhikevich_solution.nestml", 2 target_path="/tmp/nestml-component", 3 logging_level="ERROR", 4 codegen_opts={"nest_path": NEST_SIMULATOR_INSTALL_LOCATION}) /opt/data/nestml/pynestml/frontend/pynestml_frontend.py in generate_nest_target(input_path, target_path, install_path, logging_level, module_name, store_log, suffix, dev, codegen_opts) 181 A dictionary containing additional options for the target code generator. 182 """ --> 183 generate_target(input_path, target_platform="NEST", target_path=target_path, logging_level=logging_level, 184 module_name=module_name, store_log=store_log, suffix=suffix, install_path=install_path, 185 dev=dev, codegen_opts=codegen_opts) /opt/data/nestml/pynestml/frontend/pynestml_frontend.py in generate_target(input_path, target_platform, target_path, install_path, logging_level, module_name, store_log, suffix, dev, codegen_opts) 150 FrontendConfiguration.set_codegen_opts(codegen_opts) 151 --> 152 if not process() == 0: 153 raise Exception("Error(s) occurred while processing the model") 154 /opt/data/nestml/pynestml/frontend/pynestml_frontend.py in process() 278 options=FrontendConfiguration.get_codegen_opts()) 279 if _builder is not None: --> 280 _builder.build() 281 282 if FrontendConfiguration.store_log: /opt/data/nestml/pynestml/codegeneration/nest_builder.py in build(self) 151 cwd=str(os.path.join(target_path))) 152 except subprocess.CalledProcessError as e: --> 153 raise GeneratedCodeBuildException('Error occurred during \'make all\'! More detailed error messages can be found in stdout.') 154 155 # finally execute make install GeneratedCodeBuildException: Error occurred during 'make all'! More detailed error messages can be found in stdout. I can't solve it. Can anyone help me?

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Open NEST Developer Video Conference Monday February 28 2022 11:30 CET (UTC+1)
by Dennis Terhorst 28 Feb '22

28 Feb '22

Dear NEST Users & Developers! I would like to invite you to our next fortnightly Open NEST Developer Video Conference, today Monday February 28, 11.30-12.30 CET (UTC+1). Feel free to join the meeting also just to bring your own questions for direct discussion in the in-depth section. As usual, in the Project team round, a contact person of each team will give a short statement summarizing ongoing work in the team and cross-cutting points that need discussion among the teams. The remainder of the meeting we would go into a more in-depth discussion of topics that came up on the mailing list or that are suggested by the teams. Agenda * Welcome * Review of NEST User Mailing List * Project team round * In-depth discussion The agenda for this meeting is also available online, see https://github.com/nest/nest-simulator/wiki/2022-02-28-Open-NEST-Developer-… Looking forward to seeing you soon! Cheers, Dennis Terhorst ------------------ Log-in information ------------------ We use a virtual conference room provided by DFN (Deutsches Forschungsnetz). You can use the web client to connect. We however encourage everyone to use a headset for better audio quality or even a proper video conferencing system (see below) or software when available. Web client * Visit https://conf.dfn.de/webapp/conference/97938800 * Enter your name and allow your browser to use camera and microphone * The conference does not need a PIN to join, just click join and you're in. In case you see a dfnconf logo and the phrase "Auf den Meetingveranstalter warten", just be patient, the meeting host needs to join first (a voice will tell you). VC system/software How to log in with a video conferencing system, depends on you VC system or software. - Using the H.323 protocol (eg Polycom): vc.dfn.net##97938800 or 194.95.240.2##97938800 - Using the SIP protocol:97938800@vc.dfn.de - By telephone: +49-30-200-97938800 For those who do not have a video conference system or suitable software, Polycom provides a pretty good free app for iOS and Android, so you can join from your tablet (Polycom RealPresence Mobile, available from AppStore/PlayStore). Note that firewalls may interfere with videoconferencing in various and sometimes confusing ways. For more technical information on logging in from various VC systems, please see http://vcc.zih.tu-dresden.de/index.php?linkid=1.1.3.4

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Retrieving states and parameters variables from NodeCollection
by m.benelhedi＠fz-juelich.de 28 Feb '22

28 Feb '22

Hey Nest Team, Calling "NodeCollection.get" returns a dictionary containing the user declared "States" and "Parameters" with other keys such as "global_id", "recordables", and "synaptic_elements". In this context, I want to ask if there is a function in "nest" that returns exactly only the model declared "States" or "Parameters" without having these extra keys, and of course without having a prior knowledge of the "nestml" file from which the model was originated. Best, Ayssar

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Use of std::thread in rand generators in NEST
by Itaru Kitayama 28 Feb '22

28 Feb '22

Hi, Am I correct in thinking that all rand generators provided for NEST use std::thread? If I am not mistaken, it's an extension of POSIX threads and I'd like to avoid it for my target offloading work. Thanks, Itaru.

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Neuron models with Tsodyks synapse
by Alexander Kozlov 21 Feb '22

21 Feb '22

Hello, Documentation for `tsodyks_synapse` says it is only compatible with `iaf_psc_exp` or `iaf_psc_exp_htum` neuron models. Would it be possible to use it with other `_exp`-type models with postsynaptic currents or conductances with exponential decay (for example, `aeif_cond_exp`)? If not, what could be a work around? With best regards, Alexander Kozlov, CST EECS KTH.

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NEST Conference 2022 - registration is open
by Hans Ekkehard Plesser 17 Feb '22

17 Feb '22

Dear Colleagues, The NEST Initiative is excited to invite everyone interested in Neural Simulation Technology and the NEST Simulator to the NEST Conference 2022. 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 particularly encourage young scientists to participate in the conference! This year's conference will again take place as a virtual event on Thursday/Friday 23/24 June 2022. Register now! For more information please visit the conference website https://nest-simulator.org/conference We are looking forward to seeing you all in June! Hans Ekkehard Plesser and colleagues -- Prof. Dr. Hans Ekkehard Plesser Head, Department of Data Science Faculty of Science and Technology Norwegian University of Life Sciences PO Box 5003, 1432 Aas, Norway Phone +47 6723 1560 Email hans.ekkehard.plesser(a)nmbu.no<mailto:hans.ekkehard.plesser@nmbu.no> Home http://arken.nmbu.no/~plesser

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Neuron models with NMDA channels
by cagnol＠ksvi.mff.cuni.cz 15 Feb '22

15 Feb '22

Hello, We would like to use neurons models with NMDA channels in our spiking neuron model. We're still unsure whether we will use a native neuron model in Nest or whether we will implement our own one in NESTML. My understanding is that the only model in Nest which does that is the Hill - Tononi model, which seems rather complex. How fast would you roughly expect a Hill - Tononi neuron network to run compared to a network made of aeif_cond_exp neurons? Do you know by any chance any example of adex NESTML models which implement NMDA and Gaba_B channels? Also, one last question not really related to the previous ones: Is there any way to model synaptic reliability in Nest? Thanks a lot, Remy,

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WOIV'22: Extended Deadline -- 6th International Workshop on In Situ Visualization
by Tom Vierjahn 14 Feb '22

14 Feb '22

Hi all, we have extended the submission deadline for WOIV’22 until March 7. And we have added a 3rd submission type: lightning presentations (2 to 4 pages, published via Zenodo). Please find the updated CfP below and on the webpage https://woiv.gitlab.io Cheers, Tom ----- # WOIV'22: 6th International Workshop on In Situ Visualization * Held in conjunction with ISC 2022 * Hamburg, Germany, June 2, 2022 ## Scope Large-scale HPC simulations with their inherent I/O bottleneck have made in situ visualization an essential approach for data analysis, although the idea of in situ visualization dates back to the golden era of coprocessing in the 1990s. In situ coupling of analysis and visualization to a live simulation circumvents writing raw data to disk for post-mortem analysis – an approach that is already inefficient for today’s very large simulation codes. Instead, with in situ visualization, data abstracts are generated that provide a much higher level of expressiveness per byte. Therefore, more details can be computed and stored for later analysis, providing more insight than traditional methods. We encourage contributed talks on methods and workflows that have been used for large-scale parallel visualization, with a particular focus on the in situ case. Presentations on codes that closely couple numerical methods and visualization are particularly welcome. Speakers should detail if and how the application drove abstractions or other kinds of data reductions and how these interacted with the expressiveness and flexibility of the visualization for exploratory analysis. Presentations on codes that closely couple numerical methods and visualization are particularly welcome. Speakers should detail frameworks used and data reductions applied. They should also indicate how these impacted the flexibility of the visualization for exploratory analysis. Of particular interest to WOIV and its attendees are recent developments for in situ libraries and software. Submissions documenting recent additions to existing in situ software or new in situ platforms are highly encouraged. WOIV is an excellent place to connect providers of in situ solutions with potential customers. For the submissions we are not only looking for success stories, but are also particularly interested in those experiments that started with a certain goal or idea in mind, but later got shattered by reality or insufficient hardware/software. Areas of interest for WOIV include, but are not limited to: * Techniques and paradigms for in situ visualization. * Algorithms relevant to in situ visualization. These could include algorithms empowered by in situ visualization or algorithms that overcome limitations of in situ visualization. * Systems and software implementing in situ visualization. These include both general purpose and bespoke implementations. This also includes updates to existing software as well as new software. * Workflow management. * Use of in situ visualization for application science or other examples of using in situ visualization. * Performance studies of in situ systems. Comparisons between in situ systems or techniques or comparisons between in situ and alternatives (such as post hoc) are particularly encouraged. * The impact of hardware changes on in situ visualization. * The online visualization of experimental data. * Reports of in situ visualization failures. * Emerging issues with in situ visualization. ## Submissions We accept submissions of short papers (6 to 8 pages), full papers (10 to 12 pages) and lightning presentations (2 to 4 pages) in Springer single column LNCS style. Please find LaTeX and Word templates at https://woiv.gitlab.io/woiv22/template. `Submissions are exclusively handled via EasyChair: https://woiv.gitlab.io/woiv22/submit. The review process is single or double blind, we leave it to the discretion of the authors whether they want to disclose their identity in their submissions. All submissions will be peer-reviewed by experts in the field, and will be evaluated according to relevance to the workshop theme, technical soundness, thoroughness of success/failure comparison, and impactfulness of method/results. Accepted short and full papers will appear as post-conference workshop proceedings in the Springer Lecture Notes in Computer Science (LNCS) series; lightning presentations will be published via Zenodo. The submitted versions will be made available to workshop participants during ISC. ## Important Dates * Submission deadline (extended): March 7, 2022, anywhere on earth * Notification of acceptance: April 15, 2022 * Final presentation slides due: May 10, 2012, anywhere on earth (subject to change) * Workshop: June 2, 2022 * Camera-ready version due: July 1, 2022 (subject to change, extrapolated from previous years) ## Chairs * Peter Messmer, NVIDIA * Tom Vierjahn, Westphalian University of Applied Sciences, Bocholt, Germany ## Steering Committee * Steffen Frey, University of Groningen, The Netherlands * Kenneth Moreland, Oak Ridge National Laboratory, USA * Thomas Theussl, KAUST, Saudi Arabia * Guido Reina, University of Stuttgart, Germany * Tom Vierjahn, Westphalian University of Applied Sciences, Bocholt, Germany ## Website, Venue, Registration * Website: https://woiv.gitlab.io * Submission system: https://woiv.gitlab.io/woiv22/submit * Template: https://woiv.gitlab.io/woiv22/template * Venue: https://www.isc-hpc.com (ISC 2022) * Workshop registration: https://woiv.gitlab.io/woiv22/register ## Contact E-Mail: woiv(a)googlegroups.com

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Open NEST Developer Video Conference Monday February 14 2022 11:30 CET (UTC+1)
by Dennis Terhorst 14 Feb '22

14 Feb '22

Dear NEST Users & Developers! I would like to invite you to our next fortnightly Open NEST Developer Video Conference, today Monday February 14, 11.30-12.30 CET (UTC+1). Feel free to join the meeting also just to bring your own questions for direct discussion in the in-depth section. As usual, in the Project team round, a contact person of each team will give a short statement summarizing ongoing work in the team and cross-cutting points that need discussion among the teams. The remainder of the meeting we would go into a more in-depth discussion of topics that came up on the mailing list or that are suggested by the teams. Agenda * Welcome * Review of NEST User Mailing List * Project team round * In-depth discussion The agenda for this meeting is also available online, see https://github.com/nest/nest-simulator/wiki/2022-02-14-Open-NEST-Developer-… Looking forward to seeing you soon! Cheers, Dennis Terhorst ------------------ Log-in information ------------------ We use a virtual conference room provided by DFN (Deutsches Forschungsnetz). You can use the web client to connect. We however encourage everyone to use a headset for better audio quality or even a proper video conferencing system (see below) or software when available. Web client * Visit https://conf.dfn.de/webapp/conference/97938800 * Enter your name and allow your browser to use camera and microphone * The conference does not need a PIN to join, just click join and you're in. In case you see a dfnconf logo and the phrase "Auf den Meetingveranstalter warten", just be patient, the meeting host needs to join first (a voice will tell you). VC system/software How to log in with a video conferencing system, depends on you VC system or software. - Using the H.323 protocol (eg Polycom): vc.dfn.net##97938800 or 194.95.240.2##97938800 - Using the SIP protocol:97938800@vc.dfn.de - By telephone: +49-30-200-97938800 For those who do not have a video conference system or suitable software, Polycom provides a pretty good free app for iOS and Android, so you can join from your tablet (Polycom RealPresence Mobile, available from AppStore/PlayStore). Note that firewalls may interfere with videoconferencing in various and sometimes confusing ways. For more technical information on logging in from various VC systems, please see http://vcc.zih.tu-dresden.de/index.php?linkid=1.1.3.4

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Webinar Invitation: ""Embodied Large Scale Spiking Neural Networks in the Neurorobotics Platform"
by Benedikt Feldotto 09 Feb '22

09 Feb '22

Dear all, NEST is a powerful tool to simulate biologically derived spiking Neural Networks. Besides the ever improving model details, learning paradigms and computational complexity, there are two complementary components necessary in order to simulate a (full) biologically plausible mammalian brain: Running simulations at large scale and embodying the brain simulation in a (virtual) body. In frame of the Fenix Infrastructure Webinar series I am going to present "Embodied large scale spiking neural networks in the Neurorobotics Platform" with a focus on the deployment on High Performance Computing Infrastructure next week Thursday. The presentation showcases the joint work of developers from NEST and the Neurorobotics Platform, the CSCS Swiss National Supercomputing centre and researchers in the RoboBrain project. Check out the details and registration at: https://fenix-ri.eu/events/14th-fenix-infrastructure-webinar-ebrains-servic… Looking forward to see you there, Benedikt -- Benedikt Feldotto M.Sc. Research Assistant Human Brain Project - Neurorobotics Technical University of Munich Department of Informatics Chair of Robotics, Artificial Intelligence and Real-Time Systems Room HB 2.02.20 Parkring 13 D-85748 Garching b. München Tel.: +49 89 289 17628 Mail: feldotto(a)in.tum.de https://www6.in.tum.de/en/people/benedikt-feldotto-msc/ www.neurorobotics.net

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Synapse labels and connection rules
by Barna Zajzon 02 Feb '22

02 Feb '22

Dear NEST community, When trying to pass a `synapse_label` parameter in the syn_spec dictionary, in conjunction with the `one_to_one` rule and node ids passed as arrays, I get the following error with NEST 3.0: File "/home/zbarni/code/projects/lif_sorn_seqlearn/lif-sorn-nest-implementation/remote/test_nestml_multith.py", line 29, in <module> nest.Connect([1], [2], conn_spec={'rule': 'one_to_one'}, syn_spec={'synapse_model': 'static_synapse_lbl', 'synapse_label': 1}) File "/home/zbarni/software/installed/miniconda3/envs/del-lif-sorn-nestml-check_py390/lib/python3.9/site-packages/nest/ll_api.py", line 228, in stack_checker_func return f(*args, **kwargs) File "/home/zbarni/software/installed/miniconda3/envs/del-lif-sorn-nestml-check_py390/lib/python3.9/site-packages/nest/lib/hl_api_connections.py", line 255, in Connect connect_arrays(pre, post, weights, delays, synapse_model, syn_param_keys, syn_param_values) File "pynestkernel.pyx", line 360, in pynestkernel.NESTEngine.connect_arrays nest.lib.hl_api_exceptions.TypeMismatch: TypeMismatch in SLI function connect_arrays It works when using the `all_to_all` rule. Is this the expected behavior or for some reason it's not possible to use synapse_label and the one_to_one rule (yet)? Thank you, Barna

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Open NEST Developer Video Conference Monday January 31 2022 11:30 CET (UTC+1)
by Dennis Terhorst 31 Jan '22

31 Jan '22

Dear NEST Users & Developers! I would like to invite you to our next fortnightly Open NEST Developer Video Conference, today Monday January 31, 11.30-12.30 CET (UTC+1). Feel free to join the meeting also just to bring your own questions for direct discussion in the in-depth section. As usual, in the Project team round, a contact person of each team will give a short statement summarizing ongoing work in the team and cross-cutting points that need discussion among the teams. The remainder of the meeting we would go into a more in-depth discussion of topics that came up on the mailing list or that are suggested by the teams. Agenda * Welcome * Review of NEST User Mailing List * Project team round * In-depth discussion The agenda for this meeting is also available online, see https://github.com/nest/nest-simulator/wiki/2022-01-31-Open-NEST-Developer-… Looking forward to seeing you soon! Cheers, Dennis Terhorst ------------------ Log-in information ------------------ We use a virtual conference room provided by DFN (Deutsches Forschungsnetz). You can use the web client to connect. We however encourage everyone to use a headset for better audio quality or even a proper video conferencing system (see below) or software when available. Web client * Visit https://conf.dfn.de/webapp/conference/97938800 * Enter your name and allow your browser to use camera and microphone * The conference does not need a PIN to join, just click join and you're in. In case you see a dfnconf logo and the phrase "Auf den Meetingveranstalter warten", just be patient, the meeting host needs to join first (a voice will tell you). VC system/software How to log in with a video conferencing system, depends on you VC system or software. - Using the H.323 protocol (eg Polycom): vc.dfn.net##97938800 or 194.95.240.2##97938800 - Using the SIP protocol:97938800@vc.dfn.de - By telephone: +49-30-200-97938800 For those who do not have a video conference system or suitable software, Polycom provides a pretty good free app for iOS and Android, so you can join from your tablet (Polycom RealPresence Mobile, available from AppStore/PlayStore). Note that firewalls may interfere with videoconferencing in various and sometimes confusing ways. For more technical information on logging in from various VC systems, please see http://vcc.zih.tu-dresden.de/index.php?linkid=1.1.3.4

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NMBU / Associate Professors in Machine Learning and Scientific Computing / Deadline 15 Feb 2022
by Hans Ekkehard Plesser 27 Jan '22

27 Jan '22

Dear Colleagues, The Department of Data Science at NMBU is currently looking for two full-time permanent associate professors in machine learning and scientific computing, respectively. We are also looking for adjunct professors (20%, 4 years) to cover ethical and legal aspects of data science and data security, respectively. I'd appreciate if you would pass this information on to colleagues who may be interested in any of the positions. As we currently are mostly male faculty members, we'd in particular appreciate applications by women. * Associate professor in Data Science (Machine Learning) - Deadline: Tuesday, February 15, 2022<https://www.jobbnorge.no/en/available-jobs/job/217579/associate-professor-i…> * Associate professor in Scientific Computing - Deadline: Tuesday, February 15, 2022<https://www.jobbnorge.no/en/available-jobs/job/217590/associate-professor-i…> * Professor II/Associate professor II in Ethics and Law of Data Science - Deadline: Tuesday, February 15, 2022<https://www.jobbnorge.no/en/available-jobs/job/217629/professor-ii-associat…> * Professor II/Associate professor II in Data Security - Deadline: Tuesday, February 15, 2022<https://www.jobbnorge.no/en/available-jobs/job/217607/professor-ii-associat…> Best regards, Hans Ekkehard -- Prof. Dr. Hans Ekkehard Plesser Head, Department of Data Science Faculty of Science and Technology Norwegian University of Life Sciences PO Box 5003, 1432 Aas, Norway Phone +47 6723 1560 Email hans.ekkehard.plesser(a)nmbu.no<mailto:hans.ekkehard.plesser@nmbu.no> Home http://arken.nmbu.no/~plesser

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log data into data_path
by Benedikt Feldotto 21 Jan '22

21 Jan '22

Dear all, quick question about data logging to a specified folder: with nest.SetKernelStatus({"data_path": '/opt/data/log'}) I can specify the path, where data is logged to. If I do not specify a path, where does data get saved, or is it not saved to file if I do not specify 'data_path'? Thanks! Benedikt -- Benedikt Feldotto M.Sc. Research Assistant Human Brain Project - Neurorobotics Technical University of Munich Department of Informatics Chair of Robotics, Artificial Intelligence and Real-Time Systems Room HB 2.02.20 Parkring 13 D-85748 Garching b. München Tel.: +49 89 289 17628 Mail: feldotto(a)in.tum.de https://www6.in.tum.de/en/people/benedikt-feldotto-msc/ www.neurorobotics.net

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Open NEST Developer Video Conference Monday January 17 2021 11:30 CET (UTC+1)
by Dennis Terhorst 17 Jan '22

17 Jan '22

Dear NEST Users & Developers! I would like to invite you to our next fortnightly Open NEST Developer Video Conference, today Monday January 17, 11.30-12.30 CET (UTC+1). Feel free to join the meeting also just to bring your own questions for direct discussion in the in-depth section. As usual, in the Project team round, a contact person of each team will give a short statement summarizing ongoing work in the team and cross-cutting points that need discussion among the teams. The remainder of the meeting we would go into a more in-depth discussion of topics that came up on the mailing list or that are suggested by the teams. Agenda * Welcome * Review of NEST User Mailing List * Project team round * In-depth discussion The agenda for this meeting is also available online, see https://github.com/nest/nest-simulator/wiki/2022-01-17-Open-NEST-Developer-… Looking forward to seeing you soon! Cheers, Dennis Terhorst ------------------ Log-in information ------------------ We use a virtual conference room provided by DFN (Deutsches Forschungsnetz). You can use the web client to connect. We however encourage everyone to use a headset for better audio quality or even a proper video conferencing system (see below) or software when available. Web client * Visit https://conf.dfn.de/webapp/conference/97938800 * Enter your name and allow your browser to use camera and microphone * The conference does not need a PIN to join, just click join and you're in. In case you see a dfnconf logo and the phrase "Auf den Meetingveranstalter warten", just be patient, the meeting host needs to join first (a voice will tell you). VC system/software How to log in with a video conferencing system, depends on you VC system or software. - Using the H.323 protocol (eg Polycom): vc.dfn.net##97938800 or 194.95.240.2##97938800 - Using the SIP protocol:97938800@vc.dfn.de - By telephone: +49-30-200-97938800 For those who do not have a video conference system or suitable software, Polycom provides a pretty good free app for iOS and Android, so you can join from your tablet (Polycom RealPresence Mobile, available from AppStore/PlayStore). Note that firewalls may interfere with videoconferencing in various and sometimes confusing ways. For more technical information on logging in from various VC systems, please see http://vcc.zih.tu-dresden.de/index.php?linkid=1.1.3.4

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how do I record events emitted by "sinusoidal_poisson_generator"
by thierry nieus 03 Jan '22

03 Jan '22

Dear all, first of all, happy new year! I am using nest 2.2 (installed by conda) and I have set up a simple network of 20-100 neurons based on the ht_neuron model. I am delivering some noise to all neurons with the sinusoidal_poisson_generator (I can switch to another) and the simulation produces the results I am looking for. However I would like now to have a look at the spikes entering the network and therefore I need to access all events generated by the random generator. A sample of my code is: import nest receptors=nest.GetDefaults('ht_neuron')['receptor_types'] nest.CopyModel("sinusoidal_poisson_generator",'sin_pois',{'amplitude':50.,'rate':15.0 }) nest.CopyModel("static_synapse","AMPAnoise",{"receptor_type":receptors["AMPA"],"weight":10. }) neurons=nest.Create("ht_neuron",1) noise=nest.Create('sin_pois',1) g = nest.Create('sin_pois', 1) # current pulse dc_gen = nest.Create("dc_generator") nest.SetStatus(dc_gen, {"amplitude": 20., "start": 400, "stop": 1050}) nest.Connect(dc_gen, neurons, 'one_to_one') # recorders detect_noise = nest.Create('spike_detector', 1) nest.Connect(noise, neurons, 'one_to_one', syn_spec="AMPAnoise") nest.Connect(noise, detect_noise, 'one_to_one') ''' the latest does not work Creation of connection is not possible because: All outgoing connections from a device must use the same synapse type. ''' Is there a way to record those spikes ? Thanks in advance for any help Best

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Thank you for 2021!
by Hans Ekkehard Plesser 22 Dec '21

22 Dec '21

Dear NEST Users and Developers! I would like to thank you all for your engagement for high-quality computational neuroscience and research software in 2021. We have made some major steps forward with the release of NEST 3, NEST Desktop 3 and NESTML 4. A few days ago, PyNN 0.10 also brought support for NEST 3, nicely wrapping up the year of NEST 3. We also moved to quarterly releases with the release of NEST 3.0. If you wonder what happened to NEST 3.2 in that scheme of things don't worry, it will come in Januar. The combination of holiday season, new COVID restrictions and an important reporting deadline in the Human Brain Project—the major source of funding for NEST development in recent years—unfortunately left too little time to wrap everything up in time. 2022 promises to be an exciting year for NEST, including the deeper integration of NEST Desktop (so far mainly developed by Sebastian Spreizer) and NEST GPU (so far mainly developed by Bruno Golosio as NeuronGPU) into the NEST development process and community. Don't forget to block out 23/24 June in your calendars for the NEST Conference 2022 (this time on a Thursday and Friday)! On behalf of the NEST Initiative, I wish you happy holidays and all the best for 2022! Hans Ekkehard -- Prof. Dr. Hans Ekkehard Plesser Head, Department of Data Science Faculty of Science and Technology Norwegian University of Life Sciences PO Box 5003, 1432 Aas, Norway Phone +47 6723 1560 Email hans.ekkehard.plesser(a)nmbu.no<mailto:hans.ekkehard.plesser@nmbu.no> Home http://arken.nmbu.no/~plesser

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Call for Papers: WOIV'22: 6th International Workshop on In Situ Visualization
by Tom Vierjahn 20 Dec '21

20 Dec '21

Hi all, we will organise another edition of the in situ visualization workshop (https://woiv.gitlab.io) at ISC (https://isc-hpc.com). If you are working on visualizing results of neural simulations while these are still running, you might want to consider submitting your work to the workshop … Please find the CfP below. Cheers, Tom ----- # WOIV'22: 6th International Workshop on In Situ Visualization * Held in conjunction with ISC 2022 * Hamburg, Germany, June 2, 2022 ## Scope Large-scale HPC simulations with their inherent I/O bottleneck have made in situ visualization an essential approach for data analysis, although the idea of in situ visualization dates back to the golden era of coprocessing in the 1990s. In situ coupling of analysis and visualization to a live simulation circumvents writing raw data to disk for post-mortem analysis – an approach that is already inefficient for today’s very large simulation codes. Instead, with in situ visualization, data abstracts are generated that provide a much higher level of expressiveness per byte. Therefore, more details can be computed and stored for later analysis, providing more insight than traditional methods. We encourage contributed talks on methods and workflows that have been used for large-scale parallel visualization, with a particular focus on the in situ case. Presentations on codes that closely couple numerical methods and visualization are particularly welcome. Speakers should detail if and how the application drove abstractions or other kinds of data reductions and how these interacted with the expressiveness and flexibility of the visualization for exploratory analysis. Presentations on codes that closely couple numerical methods and visualization are particularly welcome. Speakers should detail frameworks used and data reductions applied. They should also indicate how these impacted the flexibility of the visualization for exploratory analysis. Of particular interest to WOIV and its attendees are recent developments for in situ libraries and software. Submissions documenting recent additions to existing in situ software or new in situ platforms are highly encouraged. WOIV is an excellent place to connect providers of in situ solutions with potential customers. For the submissions we are not only looking for success stories, but are also particularly interested in those experiments that started with a certain goal or idea in mind, but later got shattered by reality or insufficient hardware/software. Areas of interest for WOIV include, but are not limited to: * Techniques and paradigms for in situ visualization. * Algorithms relevant to in situ visualization. These could include algorithms empowered by in situ visualization or algorithms that overcome limitations of in situ visualization. * Systems and software implementing in situ visualization. These include both general purpose and bespoke implementations. This also includes updates to existing software as well as new software. * Workflow management. * Use of in situ visualization for application science or other examples of using in situ visualization. * Performance studies of in situ systems. Comparisons between in situ systems or techniques or comparisons between in situ and alternatives (such as post hoc) are particularly encouraged. * The impact of hardware changes on in situ visualization. * The online visualization of experimental data. * Reports of in situ visualization failures. * Emerging issues with in situ visualization. ## Submissions We accept submissions of short papers (6 to 8 pages) and full papers (10 to 12 pages) in Springer single column LNCS style. Please find LaTeX and Word templates at https://woiv.gitlab.io/woiv22/template. Submissions are exclusively handled via EasyChair: https://woiv.gitlab.io/woiv22/submit. The review process is single or double blind, we leave it to the discretion of the authors whether they want to disclose their identity in their submissions. All submissions will be peer-reviewed by experts in the field, and will be evaluated according to relevance to the workshop theme, technical soundness, thoroughness of success/failure comparison, and impactfulness of method/results. Accepted papers will appear as post-conference workshop proceedings in the Springer Lecture Notes in Computer Science (LNCS) series. The submitted versions will be made available to workshop participants during ISC. ## Important Dates * Submission deadline: February 13, 2022, anywhere on earth * Notification of acceptance: April 15, 2022 * Final presentation slides due: May 10, 2012, anywhere on earth (subject to change) * Workshop: June 2, 2022 * Camera-ready version due: July 1, 2022 (subject to change, extrapolated from previous years) ## Chairs * Peter Messmer, NVIDIA * Tom Vierjahn, Westphalian University of Applied Sciences, Bocholt, Germany ## Steering Committee * Steffen Frey, University of Groningen, The Netherlands * Kenneth Moreland, Sandia National Labs, USA * Thomas Theussl, KAUST, Saudi Arabia * Guido Reina, University of Stuttgart, Germany * Tom Vierjahn, Westphalian University of Applied Sciences, Bocholt, Germany ## Website, Venue, Registration * Website: https://woiv.gitlab.io * Submission system: https://woiv.gitlab.io/woiv22/submit * Template: https://woiv.gitlab.io/woiv22/template * Venue: https://www.isc-hpc.com (ISC 2022) * Workshop registration: https://woiv.gitlab.io/woiv22/register ## Contact E-Mail: woiv(a)googlegroups.com

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Open NEST Developer Video Conference Monday December 20 2021 11:30 CET (UTC+1)
by Jochen Martin Eppler 20 Dec '21

20 Dec '21

Dear NEST Users & Developers! I would like to invite you to our next fortnightly Open NEST Developer Video Conference, today Monday December 20, 11.30-12.30 CET (UTC+1). Feel free to join the meeting also just to bring your own questions for direct discussion in the in-depth section. As usual, in the Project team round, a contact person of each team will give a short statement summarizing ongoing work in the team and cross-cutting points that need discussion among the teams. The remainder of the meeting we would go into a more in-depth discussion of topics that came up on the mailing list or that are suggested by the teams. Agenda * Welcome * Review of NEST User Mailing List * Project team round * In-depth discussion The agenda for this meeting is also available online, see https://github.com/nest/nest-simulator/wiki/2021-12-20-Open-NEST-Developer-… Looking forward to seeing you soon! Cheers, Jochen Martin Eppler! ------------------ Log-in information ------------------ We use a virtual conference room provided by DFN (Deutsches Forschungsnetz). You can use the web client to connect. We however encourage everyone to use a headset for better audio quality or even a proper video conferencing system (see below) or software when available. Web client * Visit https://conf.dfn.de/webapp/conference/97938800 * Enter your name and allow your browser to use camera and microphone * The conference does not need a PIN to join, just click join and you're in. In case you see a dfnconf logo and the phrase "Auf den Meetingveranstalter warten", just be patient, the meeting host needs to join first (a voice will tell you). VC system/software How to log in with a video conferencing system, depends on you VC system or software. - Using the H.323 protocol (eg Polycom): vc.dfn.net##97938800 or 194.95.240.2##97938800 - Using the SIP protocol:97938800@vc.dfn.de - By telephone: +49-30-200-97938800 For those who do not have a video conference system or suitable software, Polycom provides a pretty good free app for iOS and Android, so you can join from your tablet (Polycom RealPresence Mobile, available from AppStore/PlayStore). Note that firewalls may interfere with videoconferencing in various and sometimes confusing ways. For more technical information on logging in from various VC systems, please see http://vcc.zih.tu-dresden.de/index.php?linkid=1.1.3.4 -- Dr. Jochen Martin Eppler Phone: +49(2461)61-96653 ---------------------------------- Simulation Laboratory Neuroscience Jülich Supercomputing Centre Institute for Advanced Simulation ------------------------------------------------------------------------------------------------ ------------------------------------------------------------------------------------------------ Forschungszentrum Juelich GmbH 52425 Juelich Sitz der Gesellschaft: Juelich Eingetragen im Handelsregister des Amtsgerichts Dueren Nr. HR B 3498 Vorsitzender des Aufsichtsrats: MinDir Volker Rieke Geschaeftsfuehrung: Prof. Dr.-Ing. Wolfgang Marquardt (Vorsitzender), Karsten Beneke (stellv. Vorsitzender), Prof. Dr. Astrid Lambrecht, Prof. Dr. Frauke Melchior ------------------------------------------------------------------------------------------------ ------------------------------------------------------------------------------------------------

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NESTML: neuron/synapse model with differential dynamics for computing post synaptic currents
by barthelemy 16 Dec '21

16 Dec '21

Dear all, I am a new NEST user. I have a question concerning the range of neuron/synapses model possibilities of NEST. I would like to implement my own neuron/synapse model with NESTML, but I am unsure that it would be possible. Indeed, in my model, synaptic currents are not only relying on pre-synaptic spikes. To compute synaptic currents, the opening probability of pre-synaptic channel receptors are required. Those pre-synaptic channel receptors opening probabilities are evolving according to differential equations involving second order dynamics, with specific decays and taking into account the pre-synaptic spikes arrivals times at this specific synapse. Those differential equations for the opening probabilities are relying on different parameters, according to the neurotransmitter type (GABA A,GABA B, NMDA, AMPA ). Furthermore, additionally to the input spikes and the pre-synaptic channel receptors opening probabilities, the current membrane potential of the post-synaptic neuron is also required to compute the synaptic currents. Do you know if one of the NEST models implement similar dynamics? Is it possible to compute such synaptic dynamics with NESTML by creating a synapse or (and) a neuron model? Or is it not, due to specific limitations? Thank you, Best regards, JB

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NEST Developers — Failing macOS checks solved
by Hans Ekkehard Plesser 08 Dec '21

08 Dec '21

Dear NEST Developers, You may have observed that Github checks failed on macOS in recent days. This is due to even more pedantic checking of standard compliance by the newest version of Clang. The issue is fixed in master now (#2231), so if you experience trouble with failing macOS tests, you should update your branch. Best, Hans Ekkehard -- Prof. Dr. Hans Ekkehard Plesser Head, Department of Data Science Faculty of Science and Technology Norwegian University of Life Sciences PO Box 5003, 1432 Aas, Norway Phone +47 6723 1560 Email hans.ekkehard.plesser(a)nmbu.no<mailto:hans.ekkehard.plesser@nmbu.no> Home http://arken.nmbu.no/~plesser

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Set 'grng' seed
by Benedikt Feldotto 06 Dec '21

06 Dec '21

Dear all, in a previous version of NEST I used to set the RNG seeds like this: nest.SetKernelStatus({'grng_seed' : value_grngseed}) nest.SetKernelStatus({'rng_seeds' : value_rngseed)}) I already found in newer NEST versions I can set the RNG seed like: nest.rng_seed = value_rngseed Is there also a possibility to set the Global RNG seed 'grng' with newer NEST versions? Thanks! Benedikt -- Benedikt Feldotto M.Sc. Research Assistant Human Brain Project - Neurorobotics Technical University of Munich Department of Informatics Chair of Robotics, Artificial Intelligence and Real-Time Systems Room HB 2.02.20 Parkring 13 D-85748 Garching b. München Tel.: +49 89 289 17628 Mail: feldotto(a)in.tum.de https://www6.in.tum.de/en/people/benedikt-feldotto-msc/ www.neurorobotics.net

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Open NEST Developer Video Conference Monday 6 December 2021 11:30 CET (UTC+1)
by Dennis Terhorst 06 Dec '21

06 Dec '21

Dear NEST Users & Developers! I would like to invite you to our next fortnightly Open NEST Developer Video Conference, today Monday 06 December, 11.30-12.30 CET (UTC+1). Feel free to join the meeting also just to bring your own questions for direct discussion in the in-depth section. As usual, in the Project team round, a contact person of each team will give a short statement summarizing ongoing work in the team and cross-cutting points that need discussion among the teams. The remainder of the meeting we would go into a more in-depth discussion of topics that came up on the mailing list or that are suggested by the teams. Agenda * Welcome * Review of NEST User Mailing List * Project team round * In-depth discussion The agenda for this meeting is also available online, see https://github.com/nest/nest-simulator/wiki/2021-12-06-Open-NEST-Developer-… Looking forward to seeing you soon! best, Dennis Terhorst ------------------ Log-in information ------------------ We use a virtual conference room provided by DFN (Deutsches Forschungsnetz). You can use the web client to connect. We however encourage everyone to use a headset for better audio quality or even a proper video conferencing system (see below) or software when available. Web client * Visit https://conf.dfn.de/webapp/conference/97938800 * Enter your name and allow your browser to use camera and microphone * The conference does not need a PIN to join, just click join and you're in. In case you see a dfnconf logo and the phrase "Auf den Meetingveranstalter warten", just be patient, the meeting host needs to join first (a voice will tell you). VC system/software How to log in with a video conferencing system, depends on you VC system or software. - Using the H.323 protocol (eg Polycom): vc.dfn.net##97938800 or 194.95.240.2##97938800 - Using the SIP protocol:97938800@vc.dfn.de - By telephone: +49-30-200-97938800 For those who do not have a video conference system or suitable software, Polycom provides a pretty good free app for iOS and Android, so you can join from your tablet (Polycom RealPresence Mobile, available from AppStore/PlayStore). Note that firewalls may interfere with videoconferencing in various and sometimes confusing ways. For more technical information on logging in from various VC systems, please see http://vcc.zih.tu-dresden.de/index.php?linkid=1.1.3.4

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NEST v3.1: Missing data for spike_recorder (ascii)
by Maryada Maryada 30 Nov '21

30 Nov '21

Dear NEST users, I am trying to debug my network and I found that my spike_recorder with *ascii* option isn't working as expected. I am simulating a network for a few milliseconds (say 1000. ms) and then do some structure changes and then re-run for another phase of a few ms (say 4000. ms) In the compact version, I am trying to see how this sample code would work. import nest nest.ResetKernel() nest.SetKernelStatus({ "overwrite_files": True, "data_path": './Debug-Log', "data_prefix": 'DEBUG-SPIKE-REC', }) noise_device = nest.Create("poisson_generator",params={'start': 0.,'rate' : 100.}) sd_params = { "record_to": 'ascii', "label": "Input_spike_recorder" } Input_SD = nest.Create("spike_recorder",1, params=sd_params) nest.Connect(noise_device,Input_SD) nest.Simulate(100.) # do something here nest.Simulate(100.) *Issue:* I only get the data recorded from 100th millisecond but for memory, I get all the data from 0-200 ms. This behavior is consistent for both overwrite_files as True and False. In the previous version (v2.20) I also used the same approach and had no issues. Is there a newer way to do such a simulation paradigm? I didn't find anything on this on the comparison page of NESTv2.x and NESTv3.x Am I missing something? It's really important for my work, I hope I could find a solution. -- Thanks and Regards *Maryada*

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