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Segmentation Fault loading custom nest module

by Benedikt Feldotto

Dear all, I tried to install a custom module into Nest first using the MyModule example as described here https://nest.github.io/nest-simulator/extension_modules The installation works fine without errors, however when I try to load the model into pynest with import nest import('mymodule') I get a "Segmentation fault (core dumped)". The last traceback of debbugging with python pdb is the following: -> engine.run('{%s} runprotected' % decode(cmd)) (Pdb) s --Call-- > /home/user/.local/lib/python2.7/site-packages/nest/__init__.py(107)decode() -> def decode(s): (Pdb) s > /home/user/.local/lib/python2.7/site-packages/nest/__init__.py(108)decode() -> return s.decode('utf-8') (Pdb) s --Call-- > /usr/lib/python2.7/encodings/utf_8.py(15)decode() -> def decode(input, errors='strict'): (Pdb) s > /usr/lib/python2.7/encodings/utf_8.py(16)decode() -> return codecs.utf_8_decode(input, errors, True) (Pdb) s --Return-- > /usr/lib/python2.7/encodings/utf_8.py(16)decode()->(u'(cereb... Install', 26) -> return codecs.utf_8_decode(input, errors, True) (Pdb) s --Return-- > /home/user/.local/lib/python2.7/site-packages/nest/__init__.py(108)decode()->u'(mymod... Install' -> return s.decode('utf-8') (Pdb) s Segmentation fault (core dumped) I already added the model path to my LD_LIBRARY_PATH variable so that the module can be found, but now it cannot be loaded. It looks like a decoding issue, but I don't know what went wrong during the installation. Do you have any idea what could be the issue? I am using python 2.7 and NEST 2.3.1 Thanks! Benedikt Feldotto -- 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

4 years, 11 months

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NEST Creating a simple network

by shanka19＠purdue.edu

Hello everyone, Happy New Year! I want to create a simple neural network consisting of a single neuron connected by multiple inputs (spike generators). I am aware that I can create single spike generators and then connect them but it becomes infeasible as the size of input grows. Is there a way to create a network of maybe 100 spike generators connected to a single LIF Neuron without explicitly creating 100 of them? Once the connections are made is there a way that the network is updated when the weights are updated. I want the network to get updated as I update the weights. Now, I update the weights and reset the network to create it again with new weights. Any help would be appreciated. Thanks in advance!

4 years, 11 months

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nest user in nest-docker entrypoint file

by bignamini＠cscs.ch

Hi all, I have a question about nest user creation/usage in nest docker entrypoint file: I am working with Sarus and Singularity and due to some permission limits I can't create a new user inside a container. I have tried to modify the entrypoint.sh file as follows https://github.com/ChristopherBignamini/nest-docker/blob/no_nest_user_creat… in order to skip the creation of the nest user. I am not a nest expert but everything seems to work, at least if I try to run a couple of examples like one_neuron.py and twoneurons.py. My question is: what is the reason behind the creation and usage of the nest user? Thank you in advance. Cheers Christopher

4 years, 11 months

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Error when compiling MyModule, the example extension module

by eben.cowley42＠gmail.com

Hi, I'm on Ubuntu 18.10 and I've successfully installed nest to `/usr`. I'm interested in writing my own synapse models and found these instructions for getting started: https://nest.github.io/nest-simulator/extension_modules The configuration step, `cmake -Dwith-nest=/usr/bin/nest-config ../MyModule` works fine. However, when I ran `make` I received the following compiler error: ``` ~/Projects/NEST/MyModule/mymodule.cpp: In member function ‘virtual void mynest::MyModule::init(SLIInterpreter*)’: ~/Projects/NEST/MyModule/mymodule.cpp:128:24: error: no matching function for call to ‘nest::ModelManager::register_connection_model<mynest::DropOddSpikeConnection<nest::TargetIdentifierPtrRport> >(const char [17])’ "drop_odd_synapse" ); ^ In file included from /usr/include/nest/kernel_manager.h:31, from /usr/include/nest/connector_base_impl.h:26, from /usr/include/nest/connection.h:29, from /home/ebanflo/Projects/NEST/MyModule/drop_odd_spike_connection.h:27, from /home/ebanflo/Projects/NEST/MyModule/mymodule.cpp:29: /usr/include/nest/model_manager.h:197:8: note: candidate: ‘template<template<class targetidentifierT> class ConnectionT> void nest::ModelManager::register_connection_model(const string&, nest::RegisterConnectionModelFlags)’ void register_connection_model( const std::string& name, ^~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/nest/model_manager.h:197:8: note: template argument deduction/substitution failed: make[2]: *** [CMakeFiles/mymodule_module.dir/build.make:63: CMakeFiles/mymodule_module.dir/mymodule.cpp.o] Error 1 make[1]: *** [CMakeFiles/Makefile2:73: CMakeFiles/mymodule_module.dir/all] Error 2 make: *** [Makefile:152: all] Error 2 ``` I am not sure how to deal with this, and any help would be appreciated. Thank you!

4 years, 11 months

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Issue review VC Friday 10 Jan 10-13

by Hans Ekkehard Plesser

Dear all! We are going to have a NEST issue review VC tomorrow morning (Friday 10 Jan 10-13 CET) in the usual VC room for developer VCs (https://github.com/nest/nest-simulator/wiki/Connection-Details). The main aim is to review open issues in preparation of the NEST 3 merge and (eventually) release. Excuse the short notice, still booting up for 2020. Best, Hans Ekkehard -- Prof. Dr. Hans Ekkehard Plesser Head, Data Science Section 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 Home http://arken.nmbu.no/~plesser

4 years, 11 months

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Open NEST Developer Video Conference Monday 6 January 2020 11:30 CET (UTC+1)

by Dennis Terhorst

Dear NEST Users & Developers! Happy new year 2020! I would like to invite you to this years first Open NEST Developer Video Conference, tomorrow Monday 6 January, 11.30-12.30 CET (UTC+1). As usual the agenda for this meeting is also available online, see https://github.com/nest/nest-simulator/wiki/2020-01-06-Open-NEST-Developer-… For details how to log in see below. Agenda * Welcome * Review of NEST User Mailing List * Review of open Github Pull Request * Review of open Github Issues 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

4 years, 11 months

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NO open NEST Developer Video Conference on 23 December 2019

by Dennis Terhorst

Dear NEST Developers! Best of seasons greetings to everyone! Since many people will not be available today we will skip the video conference. Our next regular meeting will be on January 6th. Merry Christmas to everyone! Enjoy the last days of 2019 and have a nice new-years! Looking forward to seeing all of you again in 2020! best, Dennis Terhorst https://github.com/nest/nest-simulator/wiki/Open-NEST-Developer-Video-Confe…

4 years, 12 months

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NEST Conference 2020 — Save the Date: 29/30 June 2020 at Ås, Norway

by Hans Ekkehard Plesser

Dear NEST Users, We are happy to announce that the NEST Conference 2020 will again be held on NMBU's beautiful campus in Ås, Norway on 29 / 30 June 2020 followed by a NEST Hackathon until 3 July. More information will follow in a few weeks. Save the date & see you in the summer! Hans Ekkehard -- Prof. Dr. Hans Ekkehard Plesser Head, Data Science Section 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 Home http://arken.nmbu.no/~plesser

5 years

1
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Hackathon on CEREBELLUM MODELLING

by Dennis Terhorst

Dear simulation enthusiasts, The group in Pavia is preparing an event around CEREBELLUM MODELLING, in which you can see NEST and other simulators put to use on larger scale. It will be a nice occasion to meet with many other users, exchange experience and learn about model construction. Egidio, Claudia, Simona and team are organising this as a hackathon: Hackathon on CEREBELLUM MODELLING 13-15 January 2020, in Pavia. If you are interested in joining, please drop Simona Tritto an email:simona.tritto@unipv.it<mailto:simona.tritto@unipv.it> You can find the program attached. best, Dennis -- Dipl.-Phys. Dennis Terhorst Coordinator Software Development Institute of Neuroscience and Medicine (INM-6) Computational and Systems Neuroscience & Theoretical Neuroscience, Institute for Advanced Simulation (IAS-6) Jülich Research Centre, Member of the Helmholz Association and JARA 52425 Jülich, Germany Building 15.22 Room 4004 Phone +49 2461 61-85062 Fax +49 2461 61- 9460 d.terhorst(a)fz-juelich.de

5 years

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Reset Network with to_file

by Maryada Maryada

Hi all, I am currently using nest.ResetNetwork() with to_file option and when I reset the network, seemingly it also deletes everything recorded so far by connected probes (spike detector, for instance). Any suggestions on how to avoid the deletion of previously written data on files. -- Thanks and Regards *Maryada*

5 years

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