May 2022 - NEST Users - NEST Initiative Mail

Assertion error during connection when using CopyModel and own neuron model
by Barna Zajzon 07 Oct '22

07 Oct '22

Dear all, I'm encountering the following error python: /home/zbarni/software/packages/nest/znest/nestkernel/model_manager.h:296: nest::Model* nest::ModelManager::get_node_model(nest::index) const: Assertion `m < node_models_.size()' failed. when using the following code: nest.SetKernelStatus({'total_num_virtual_procs':16, 'local_num_threads':16}) nest.Install('my_neuron_module') for iin range(16): nest.CopyModel('MyNeuron', f'MyNeuron_{i}') neurons = nest.Create('MyNeuron_0', 2) nest.Connect(neurons, neurons) The script uses a neuron model that I wrote in C++ and is loaded without errors. The error is thrown upon nest.Connect(), and goes away if I create the neurons using `MyNeuron` and not `MyNeuron_x` (copied) or if the #vp and #threads is 1. I've used the model with NEST 2.20.0 without problems, but I'd like to port the code to the latest version. Maybe I'm just missing something new functionality/API related to CopyModel and multiprocessing - have there been any critical changes in the model requirements? Any help would be greatly appreciated. Barni

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I can not install Nest 3.3 simulator in Ubuntu 18.04
by salvatore.taffara＠phd.unict.it 01 Jun '22

01 Jun '22

Hi to the community, In order to install Nest 3.3 in Ubuntu 18.04 WITHOUTH the Docker, I followed two ways: 1) I downloaded the source zip file from "https://github.com/nest/nest-simulator/tags", then I followed the guide in "https://nest-simulator.readthedocs.io/en/v3.3/installation/linux_install.ht…", in particular the "Installation from source without a virtual Python environment" version. What I obtain is an error in the terminal: salvo@salvo-Aspire-GX-781:~/Downloads/nest-simulator-3.3-build$ cmake -DCMAKE_INSTALL_PREFIX:PATH=/home/nest /home/salvo/Downloads/nest-simulator-3.3-build/ -- Host triple: x86_64-pc-linux -- Target triple: x86_64-pc-linux CMake Error at /usr/share/cmake-3.23/Modules/FindPackageHandleStandardArgs.cmake:230 (message): Could NOT find Python (missing: Python_INCLUDE_DIRS Python_LIBRARIES Development Development.Module Development.Embed) (found suitable version "3.8.13", minimum required is "3.8") Call Stack (most recent call first): /usr/share/cmake-3.23/Modules/FindPackageHandleStandardArgs.cmake:594 (_FPHSA_FAILURE_MESSAGE) /usr/share/cmake-3.23/Modules/FindPython/Support.cmake:3192 (find_package_handle_standard_args) /usr/share/cmake-3.23/Modules/FindPython.cmake:519 (include) cmake/ProcessOptions.cmake:367 (find_package) CMakeLists.txt:129 (nest_process_with_python) -- Configuring incomplete, errors occurred! See also "/home/salvo/Downloads/nest-simulator-3.3-build/CMakeFiles/CMakeOutput.log". See also "/home/salvo/Downloads/nest-simulator-3.3-build/CMakeFiles/CMakeError.log". salvo@salvo-Aspire-GX-781:~/Downloads/nest-simulator-3.3-build$ 2) I also tried to force the following Ubuntu commands to obtain, from the ppa repository, the Nest version that I need (this is the ppa nest site: https://launchpad.net/~nest-simulator/+archive/ubuntu/nest): sudo add-apt-repository ppa:nest-simulator/nest sudo apt-get update sudo apt-get install nest=3.2-0~202202100714~ubuntu18.04.1 But is seems that the only package that is downloaded from this ppa is nest 2.20, in particular: 2.20.1-0~202103121402~ubuntu18.04.1. What can I do to install Nest 3.3 in my Ubuntu 18.04? Best, Salvo

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CNS*2022 satellite tutorials: free online sessions: June 27--July 1
by Ankur Sinha 31 May '22

31 May '22

Dear all, Apologies for the cross posts. https://ocns.github.io/SoftwareWG/pages/software-wg-satellite-tutorials-at-… The INCF/OCNS Software working group is organising 5 days of free online satellite tutorials ahead of the CNS*2022 conference. These tutorials will run from June 27--July 1 and feature sessions on: - Arbor - Brian2 - Introduction to containers - EBRAINS - GeNN - Keras/TensorFlow - LFPy - MOOSE - Neo + Elephant - NEST - NetPyNE - NeuroLib - NeuroML - NEURON - OSBv2 - RateML More information on the schedule and (free) registration will be published in the next week or so. Please do mark your calendars and spread to word to your colleagues, students, and anyone else who these may interest. For more information on the INCF/OCNS Software working group and how you can join our community, please visit our website: https://ocns.github.io/SoftwareWG/ -- Thanks, Regards, Ankur Sinha (He / Him / His) | https://ankursinha.in Research Fellow at the Silver Lab, University College London | http://silverlab.org/ Free/Open source community volunteer at the NeuroFedora project | https://neuro.fedoraproject.org Time zone: Europe/London

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Integration between ROS node and NEST
by salvatore.taffara＠phd.unict.it 30 May '22

30 May '22

Dear Nest community, I should import numerical data (not spiking data) obtained from a dynamic simulator called CoppeliaSim (ex VRep) into a Nest script. To do this I thought of using a ROS subscriber node that receives the data using a topic. I ask you, how do I interface Nest with Ros in order to import the data? Greetings, Except

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Test NEST performance
by 512491013＠qq.com 30 May '22

30 May '22

Dear all, Recently, I've been trying to test NEST's performance(with and without MPI). But with PyNEST, it's hard to do more detailed testing with tools like Gprof. Only some print-time and memory methods can be inserted into the C++ source code for testing. Is there a C++ front-end interface that can call NEST C++ source code for testing? Of course, I used some of Python's performance testing tools, but only to the interface, not C++ in action. I'd appreciate any tips on how to test NEST's performance! Cong

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Open NEST Developer Video Conference Monday May 23 2022 11:30 CEST (UTC+2)
by Dennis Terhorst 22 May '22

22 May '22

Dear NEST Users & Developers! I would like to invite you to our next fortnightly Open NEST Developer Video Conference, tomorrow Monday May 23, 11.30-12.30 CEST (UTC+2). Feel free to join the meeting also if it's 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/2022-05-23-Open-NEST-Developer-… Since I will not be available for the meeting, Hans Ekkehard Plesser has kindly agreed to chair the meeting. Looking forward to seeing you again 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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NEST Conference 2022 - Extension of abstract submission deadline
by Hans Ekkehard Plesser 10 May '22

10 May '22

Dear all, The abstract submission deadline for the (virtual) NEST Conference 2022 has been extended to Wednesday, 25 May. 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 Thursday/Friday 23/24 June 2022. We are inviting contributions to the conference, including talks, "posters" and workshops on specific topics. Important dates 25 May 2022 — Deadline for submission of contributions 03 June 2022 — Notification of acceptance 17 June 2022 — Registration deadline 23 June 2022 — NEST Conference 2022 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 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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NEST Conference 2022 - Extension of abstract submission deadline
by Hans Ekkehard Plesser 10 May '22

10 May '22

Dear all, The abstract submission deadline for the (virtual) NEST Conference 2022 has been extended to Wednesday, 25 May. 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 Thursday/Friday 23/24 June 2022. We are inviting contributions to the conference, including talks, "posters" and workshops on specific topics. Important dates 25 May 2022 — Deadline for submission of contributions 03 June 2022 — Notification of acceptance 17 June 2022 — Registration deadline 23 June 2022 — NEST Conference 2022 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 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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Job opportunity
by Elena Pastorelli 09 May '22

09 May '22

Dear NEST developers, I would like to share with you a job opportunity that could be of interest for the community. APE Lab (Rome, Italy) is looking for a motivated and enthusiast candidate for activities aimed at system software development and application porting on advanced HPC platforms, in the framework of the RED-SEA <https://jobs.dsi.infn.it/borseassegni/pdf/getfile.php?filename=24338.pdf> project. Application submission details <https://jobs.dsi.infn.it/borseassegni/pdf/getfile.php?filename=24338.pdf> here (English version in the second part of the document), deadline: 20/05/2022 APE Lab is a INFN (National Institute of Nuclear Physic) initiative started in 1984 with the goal of connecting theoretical physics and technology through the development of custom distributed and parallel computing systems. Since then, APE Lab has generated unique know-how, enabling cutting-edge research in HPC (High Performance Computing) with leading roles in the HPC community. APE Lab has participated in several EU-funded projects, the last of which being RED-SEA. The RED-SEA project prepares a new-generation European Network Interconnect, capable of powering the EU Exascale systems to come, leveraging efficient European interconnect technology (BXI) associated with a standard and mature technology (Ethernet), in full coordination with other EU-funded initiatives. The INFN task in RED-SEA is two-fold: 1. to design and implement the network interface card (APEnetX) based on PCIe interface to communicate with CPU and GPU accelerators, and prototyped exploiting Xilinx Alveo FPGAs. 2. to support the co-design approach for network design activities focusing in particular on NEST application as a benchmark. Job Details Task: contribution to development of scalable network simulator based on Omnet++ framework as well as to the Linux Kernel Driver of the Network Interface Card. Requirements: 24 months of demonstrated experience in software development and knowledge/development of linux kernel driver. Knowledge of simulator architectures, coding and use of MPI framework would be an advantage. Best, Elena Pastorelli -- This email has been checked for viruses by Avast antivirus software. https://www.avast.com/antivirus

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Open NEST Developer Video Conference Monday May 9 2022 11:30 CEST (UTC+2)
by Dennis Terhorst 09 May '22

09 May '22

Dear NEST Users & Developers! I would like to invite you to our next fortnightly Open NEST Developer Video Conference, today Monday May 9, 11.30-12.30 CEST (UTC+2). 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/2022-05-09-Open-NEST-Developer-… Looking forward to seeing you soon! Cheers, Dennis Terhorst ------------------ Log-in information ------------------ We use a virtual conference room provided by DFN (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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