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Dennis Asked
by Chris Huyck 12 Oct '21

12 Oct '21

I've recently downloaded a new version of NEST, and I'm trying to make a new synaptic model, but am breaking down in building their default MyModule model. The process onhttps://nest.github.io/nest-simulator/extension_modules<https://eur02.safelinks.protection.outlook.com/?url=https%3A%2F%2Fnest.gith…> says to run bootstrap.sh, but I can't find a bootstrap.sh. Do you have a version you could send me? If not, who can I contact for help (and how)? -Chris

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Open NEST Developer Video Conference Monday 11 October 2021 11:30 CEST (UTC+2)
by Dennis Terhorst 11 Oct '21

11 Oct '21

Dear NEST Users & Developers! I would like to invite you to our next fortnightly Open NEST Developer Video Conference, today Monday 11 October, 11.30-12.30 CEST (UTC+2). Today we again have two possible topics for the in-depth discussion that you may be interested in: * Plasticity models via NESTML, and * NEST wheels (Python package mechanism). 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/2021-10-11-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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Open NEST Developer Video Conference Monday 27 September 2021 11:30 CEST (UTC+2)
by Dennis Terhorst 27 Sep '21

27 Sep '21

Dear NEST Users & Developers! I would like to invite you to our next fortnightly Open NEST Developer Video Conference, today Monday 27 September, 11.30-12.30 CEST (UTC+2). 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/2021-09-27-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 3.1 is there!
by Dennis Terhorst 15 Sep '21

15 Sep '21

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Open NEST Developer Video Conference Monday 13 September 2021 11:30 CEST (UTC+2)
by Dennis Terhorst 13 Sep '21

13 Sep '21

Dear NEST Users & Developers! I would like to invite you to our next fortnightly Open NEST Developer Video Conference, today Monday 13 September, 11.30-12.30 CEST (UTC+2). Today we have two topics for the in-depth discussion that you may be interested in. 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 * Failing assertions #2101 <https://github.com/nest/nest-simulator/issues/2101> * Naming of modules (see nest-connplotter:#2 <https://github.com/nest/nest-connplotter/pull/2>) The agenda for this meeting is also available online, see https://github.com/nest/nest-simulator/wiki/2021-09-13-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 3.0: Plot weight matrices example ERROR
by Ing Jyh Tsang 31 Aug '21

31 Aug '21

I think there is an error in https://nest-simulator.readthedocs.io/en/stable/auto_examples/plot_weight_m… * min(E_neurons)and min(I_neurons) should be replace to * min(E_neurons.tolist()) and min(I_neurons.tolist())or some other way to get the right values Suggestion: The file plot_weight_matrices.py just contain a def plot_weight_matrices(E_neurons, I_neurons). If it had a complete code to create nodes, assign weights then plot the weight matrixes, the error could have been caught automatically (CI/CD)? Best, Inton

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Problems after ubuntu installed nest-3.0 built on Aug 24 2021
by Ing Jyh Tsang 31 Aug '21

31 Aug '21

Hi, After my ubuntu upgraded nest. Whenever I run a program it does not seems to identify the nest module. For example, running the twoneuron.py example gives: Traceback (most recent call last): File "twoneurons.py", line 43, in <module> import nest.voltage_trace ModuleNotFoundError: No module named 'nest.voltage_trace' Please solution for this? I tried remove and reinstalling and did not work. I did not try building it. Thanks, Inton

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AttributeError: module 'nest' has no attribute 'SetKernelStatus'
by Alberto 31 Aug '21

31 Aug '21

Hi, suddenly, I am starting having this error. I have both PyNN and Nest installed. If it's more related to the PyNN community, I will forward this message to them, but at this moment I don't know if it's more related to Nest or PyNN side. Maybe some of you have met a similar issue. >>> import pyNN.nest as sim Traceback (most recent call last): File "<stdin>", line 1, in <module> File "/home/alberto/.local/lib/python3.8/site-packages/pyNN/nest/__init__.py", line 18, in <module> from . import simulator File "/home/alberto/.local/lib/python3.8/site-packages/pyNN/nest/simulator.py", line 261, in <module> state = _State() # a Singleton, so only a single instance ever exists File "/home/alberto/.local/lib/python3.8/site-packages/pyNN/nest/simulator.py", line 58, in __init__ self.spike_precision = "off_grid" File "/home/alberto/.local/lib/python3.8/site-packages/pyNN/nest/simulator.py", line 114, in _set_spike_precision nest.SetKernelStatus({'off_grid_spiking': True}) AttributeError: module 'nest' has no attribute 'SetKernelStatus' Thanks, Alberto

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Open NEST Developer Video Conference Monday 30 August 2021 11:30 CEST (UTC+2)
by Dennis Terhorst 30 Aug '21

30 Aug '21

Dear NEST Users & Developers! I would like to invite you to our next fortnightly Open NEST Developer Video Conference, today Monday 30 August, 11.30-12.30 CEST (UTC+2). 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 (optional) The agenda for this meeting is also available online, see https://github.com/nest/nest-simulator/wiki/2021-08-30-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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ISAV'21: In Situ Infrastructures for Enabling Extreme-scale Analysis and Visualization
by Tom Vierjahn 19 Aug '21

19 Aug '21

Dear all, for our in situ workshop at this year’s Supercomputing (https://vis.lbl.gov/events/ISAV2021/) we are still looking for submissions. So, if you are doing work on visualizing or analysing the results of a NEST simulation while it is running, you might consider submitting, quickly. The deadline will be extended to August 27. Please, find the CfP below. Cheers, Tom Vierjahn -- Tom Vierjahn Professor of Computer Science Dept. Business Studies and Information Technology Westphalian University of Applied Sciences Bocholt, Germany -- ISAV 2021: In Situ Infrastructures for Enabling Extreme-scale Analysis and Visualization # Workshop Theme The considerable interest in the HPC community regarding in situ analysis and visualization is due to several factors. First is an I/O cost savings, where data is analyzed/visualized while being generated, without first storing to a file system. Second is the potential for increased accuracy, where fine temporal sampling of transient analysis might expose some complex behavior missed in coarse temporal sampling. Third is the ability to use all available resources, CPUs and accelerators, in the computation of analysis products. The workshop brings together researchers, developers and practitioners from industry, academia, and government laboratories developing, applying, and deploying in situ methods in extreme-scale, high performance computing. The goal is to present research findings, lessons learned, and insights related to developing and applying in situ methods and infrastructure across a range of science and engineering applications in HPC environments; to discuss topics like opportunities presented by new architectures, existing infrastructure needs, requirements, and gaps, and experiences to foster and enable in situ analysis and visualization; to serve as a “center of gravity” for researchers, practitioners, and users/consumers of in situ methods and infrastructure in the HPC space. # Participation/Call for Papers We invite two types of submissions to ISAV 2021: (1) short, 4-page (+references) papers that present research results, that identify opportunities or challenges, and that present case studies/best practices for in situ methods/infrastructure in the areas of data management, analysis and visualization; (2) lightning presentation submissions, consisting of a 1- or 2-page (+references) submission, for a brief oral presentation at the workshop. Short papers will appear in the workshop proceedings and authors will be invited to give an oral presentation of 15 to 20 minutes; lightning round submissions invited to present at the workshop will have author names and titles included as part of the proceedings. Submissions of both types are welcome that fall within one or more areas of interest. Areas of interest for ISAV include, but are not limited to: - In situ infrastructures: Novel designs for systems and libraries; Opportunities; Gaps - System resources, hardware, and emerging architectures: Enabling Hardware; Hardware and architectures that provide opportunities for In situ processing, such as burst buffers, staging computations on I/O nodes, sharing cores within a node for both simulation and in situ processing; Efficient use of heterogeneous architectures. - Methods/algorithms: Best practices; Analysis: Feature detection, statistical methods, temporal methods, geometric and topological methods; Visualization: information visualization, scientific visualization, time-varying methods; Data reduction/compression. - Case Studies and Data Sources: Examples/case studies of solving a specific science challenge with in situ methods/infrastructure; In situ methods/systems applied to data from simulations and/or experiments/observations. - Simulation and Workflows: Integration, data modeling, software-engineering; Resilience: error detection, fault recovery; Workflows for supporting complex in situ processing pipelines. - Requirements and Usability: Reproducibility, provenance and metadata; Using in situ to enable rapid and flexible post-processing; Simplified access to extreme heterogeneous resources.

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