- NEST Users - NEST Initiative Mail

by gerlach.mi＠gmx.de

Hello, I am using Anaconda on a Mac OS X platform. I installed nest using homebrew by following the instructions on this page: https://nest-simulator.readthedocs.io/en/latest/installation/mac_install.ht… After finishing the installation, IPython first could not find the nest module, so I manually copied the nest folder that was created in /Users/name/opt/nest/lib/python3.7/site-packages/nest into /anaconda/lib/python3.7/site-packages/nest Now IPython can import the nest module, but returns an error message when I try to run a basic nest example: "module 'nest' has no attribute 'Create' ". I am sorry for failing at a very basic level here, but I tried for quite some time and could not get it running despite trying different instructions. I would greatly appreciate it if anyone could help me or give me a hint into the right direction, thanks in advance!

4 years, 11 months

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Where are the archive questions?

by Abolfazl Ziaeemehr

I remember before the new mailing list I had access to the archived questions and some times by digging into them I could find some answers to simple questions. Now I can not find them. Thank you let me know if there are still available. One more silly question. Do we have access to synaptic current in iaf psc alpha model. We can simply plot the post synaptic potential for two couple neuron (in tutorial <https://nest-simulator.readthedocs.io/en/latest/tutorials/pynest_tutorial/p…>), how about the I_syn? Excuse me if seems easy, and thanks for guide.

4 years, 11 months

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parallel computing on a shared cluster

by Jimmy Mulder

Hi everyone, For my masters thesis I'm using (py)NEST for the first time. I have some questions about parallel computing. first a short intro to give you the context: My research group has access to 4 clusters; 2 with a focus on RAM/CPU on 2 with focus on GPU. These are shared systems; resources are dynamically allocated depending on the number of users doing calculations. The way these clusters are set up allows me to simply set "local_num_threads" to a value of 10, and if no one else is using it the cluster manager will say I get 1000% CPU power, and the speed will increase about 8-fold as expected. (in case you find that number confusing: the manager rates 1 core as 100%, so 56 cores translates to 5600% CPU power) However, problems start to occur when others are using the cluster as well. I might get 500% CPU power one moment, and just 300% the next. At this point it is actually FASTER to only request 1 thread and get the full 100% power. I'm guessing this is due to the architecture; something with nodes A and B waiting on node C which has been temporarily allocated to my colleague? *So, the questions:* 1. Does NEST prefer CPU or GPU? Is it RAM intensive? I couldn't find this on your website, or anywhere really. Are there ballpark numbers for the memory required for 10^9 connections? 2. Am I abusing the "local_num_threads" mechanic by applying it to a cluster like this? Why is 1 thread sometimes faster than 10 threads? 3. Would switching to MPI help? 4. If so: the documentation says I need to run $NEST_SOURCE_DIR/configure -- with-mpi, but there is no "configure" folder or command to be found anywhere, and this line fails. What and where is this "configure"? Any help would be greatly appreciated. Thank you for your time. Kind regards, Jimmy Mulder

4 years, 11 months

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Open NEST Developer Video Conference Monday 3 June 2019 11.30 CET (UTC+2)

by Dennis Terhorst

Dear NEST Developers! I would like to invite you to our next bi-weekly Open NEST Developer Video Conference tomorrow Monday 3 June, 11.30-12.30 CET (UTC+2). This is the substitute for the postponed meeting from last week and the missing meeting next week (pentecost). See below for information about how to log into the meeting. The agenda for this meeting is also available online https://github.com/nest/nest-simulator/wiki/2019-06-03-Open-NEST-Developer-… 1. Welcome 2. New features in NEST3 / current developments 3. Review of NEST User Mailing List <https://www.nest-simulator.org/mailinglist/postorius/lists/users.nest-simul…> 4. Review of open Github Pull Request <https://github.com/nest/nest-simulator/pulls> 5. Review of open Github Issues <https://github.com/nest/nest-simulator/issues> See 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 * Enter your name and allow your browser to use camera and microphone * Click green video-call button to open the call panel * In the "Search to call" box at the top right enter *97938800* and connect * 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 -- 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

4 years, 11 months

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Open NEST Developer Video Conference Monday 27 May 2019 -- POSTPONED

by Dennis Terhorst

Dear NEST Developers! our next bi-weekly Open NEST Developer Video Conference would be today. However, due to many participants not being available and the next meeting falling on Pentecost Monday we decided to do one meeting on the out-of-phase Monday June 3rd. Monday 3 June, 11.30-12.30 CET (UTC+2). (note: out-of-phase) An invitation to that meeting will be sent separately. best, Dennis Terhorst -- 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

4 years, 11 months

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Passing options to recording backends via Python

by Simon Oehrl

Hello everyone, I am currently working on a custom recording backend based on the nestio branch of this fork: https://github.com/jougs/nest-simulator/. I want the user to be able to customize the behavior of my backend from their python code. I can see that the RecordingBackend class has the virtual functions set_status() and get_status() that would enable such a thing and I see that other recording backends implement them accordingly. However, I haven't found an example yet how to get access to the recording backend to call these functions. Can anyone give me hint on how to do that? Kind regards Simon

4 years, 11 months

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Fwd: Re: Nest Neuron Modelling - Tonic Neuron Input and Synaptic Weight Normalization

by Abigail Morrison

Dear Benedikt > 1) Are there any implementations for tonic neuron input, that means an > additional Neuron input channel that mulitplies with all synaptic inputs? We don't have an implementation that does this, but I don't see any reason why you can't make your own. The most effective way to do this is using NESTML, then you don't have to worry about C++ or numerics. A brief description of NESTML with links to publications and Github is here: https://www.fz-juelich.de/ias/jsc/EN/Expertise/SimLab/slns/research/nestml/… we are happy to support you in using this. > > 2) Can synaptic weights be normalized, in particular keeping the sum of > all inputs of a single neuron equal to 1? This is tricky. We did implement something close to this for a paper: https://www.frontiersin.org/articles/10.3389/fncom.2010.00160/full but we did not merge the infrastructure changes with master, because we felt it wasn't general enough. Making a general version would be a large, complicated job. As a workaround, you could consider running your simulation in small time segments, and after each segment you can read-out, sum and normalise the incoming weights for each neuron 'manually' from your simulation script. For a small network this will work fine, but it won't scale. All the best, Abigail -- Prof. Dr. Abigail Morrison IAS-6 / INM-6 / SimLab Neuroscience Jülich Research Center & Institute of Cognitive Neuroscience Ruhr-University Bochum http://www.fz-juelich.de/inm/inm-6 http://www.fz-juelich.de/ias/jsc/slns http://www.ikn.psy.ruhr-uni-bochum.de Office: +49 2461 61-9805 Fax # : +49 2461 61-9460 ------------------------------------------------------------------------------------------------ ------------------------------------------------------------------------------------------------ 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.-Ing. Harald Bolt, Prof. Dr. Sebastian M. Schmidt ------------------------------------------------------------------------------------------------ ------------------------------------------------------------------------------------------------

4 years, 11 months

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PhD scholarship within Data Science and Computational Neuroscience at the Norwegian University of Life Sciences (NMBU)

by Kristin Tøndel

The Faculty of Science and Technology at the Norwegian University of Life Sciences (NMBU) has a vacant 3-year PhD-position related to Data Science and Computational Neuroscience: https://www.jobbnorge.no/en/available-jobs/job/168816/phd-scholarship-withi… Please share with your network. Best regards, Kristin Tøndel

4 years, 12 months

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Open NEST Developer Video Conference Monday 13 May 2019 11.30 CET (UTC+2)

by Dennis Terhorst

Dear NEST Developers! I would like to invite you to our next bi-weekly Open NEST Developer Video Conference today Monday 13 May, 11.30-12.30 CET (UTC+2). See below for information about how to log into the meeting. The agenda for this meeting is also available online https://github.com/nest/nest-simulator/wiki/2019-05-13-Open-NEST-Developer-… 1. Welcome 2. NEST Initiative web services 3. Review of NEST User Mailing List <https://www.nest-simulator.org/mailinglist/postorius/lists/users.nest-simul…> 4. Review of open Github Pull Request <https://github.com/nest/nest-simulator/pulls> 5. Review of open Github Issues <https://github.com/nest/nest-simulator/issues> See 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 * Enter your name and allow your browser to use camera and microphone * Click green video-call button to open the call panel * In the "Search to call" box at the top right enter *97938800* and connect * 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 -- 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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Nest Neuron Modelling - Tonic Neuron Input and Synaptic Weight Normalization

by Benedikt Feldotto

Dear all, I am wondering about two specific neuron characteristics to be modelled in Nest. Since I did not really find documentation I want to ask about those features here: 1) Are there any implementations for tonic neuron input, that means an additional Neuron input channel that mulitplies with all synaptic inputs? 2) Can synaptic weights be normalized, in particular keeping the sum of all inputs of a single neuron equal to 1? On top, information on having those features modelled in PyNN would be a plus. Thank you very much in advance for any hints where to look, possible solutions, or developer support on how to implement these features! Best Regards, Benedikt

5 years

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