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HBP event in Heidelberg
by Dennis Terhorst 17 Oct '19

17 Oct '19

Dear NEST colleagues, We like to inform you all about an event of the Human Brain Project, that will take place in Heidelberg on November 25-28. It will be comprised of introductory sessions on different types of infrastructure that is being built for the neuroscience community. Among these will be several NEST related sessions which may be of interest to you (see attached file). This is a combined event with a CodeJam and infrastructure trainings, which will take place in close space-time proximity: * 25 Nov: [Public event] EBRAINS - New enabling infrastructure for neuroscience * 26 Nov: How to increase the FAIRness of your research - an HBP training course about data sharing * *26-28 Nov: 2nd HPAC Platform Training * * *26-28 Nov: CodeJam#10 * The 2nd HPAC Platform Training will introduce the tools and services of the High-Performance Analysis and Computing Platform and Fenix, including an interactive session on how to apply for those resources. There will also be several sessions about the simulators with different resolutions being (co)developed in the HBP (Arbor, NEST and TVB). More info and registration can be found here: https://www.humanbrainproject.eu/en/education/participatecollaborate/infras… The registration is already open but requires an account to register. If you would like join the event please send an email to Maren Frings <m.frings(a)fz-juelich.de> so we can create a guest account for you. Then you can*register e.g. for the HPAC Training*. The events will have joint breaks and it will be possible to switch to another event for the one or the other session. You need to register only for the event you are most interested in. It would be great to see you there! :-) Best regards, Dennis & Maren

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MUSIC in nest-docker
by Benjamin Staude 17 Oct '19

17 Oct '19

Hi there, I tried to run the basic example from https://nest-simulator.readthedocs.io/en/latest/guides/using_nest_with_musi… <https://nest-simulator.readthedocs.io/en/latest/guides/using_nest_with_musi…> in the docker environment of NEST (https://github.com/nest/nest-docker <https://github.com/nest/nest-docker>) on my OSX host. To be precise, I create the files minimalmusicsetup.music, minimalmusicsetup_sendnest.py and minimalmusicsetup_receivenest.py in the root directory (~/nest-docker) of the host system, and then called mpirun -np 2 music minimalmusicsetup.music from within docker. The output was: MUSIC: Unable to determine process rank. MUSIC: Did you launch music using mpirun? MUSIC: If so, check the comments about porting in README. ------------------------------------------------------- Primary job terminated normally, but 1 process returned a non-zero exit code.. Per user-direction, the job has been aborted. ------------------------------------------------------- MUSIC: Unable to determine process rank. MUSIC: Did you launch music using mpirun? MUSIC: If so, check the comments about porting in README. -------------------------------------------------------------------------- mpirun detected that one or more processes exited with non-zero status, thus causing the job to be terminated. The first process to do so was: Process name: [[46746,1],0] Exit code: 1 Can anyone help? Thanks in advance, Benjamin -- -- -- Dr. Benjamin Staude | Paul-Lincke-Ufer 7 | 10999 Berlin | benjamin.staude(a)gmail.com

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+me for HBP members
by Dennis Terhorst 15 Oct '19

15 Oct '19

Dear HBP-NEST users! // This mail only regards people involved in the Human Brain Project (HBP). // For making your usage of NEST more visible to the HBP internal reporting, we would be happy to see you in the list of the so called /component users/. For this you just need to go to the NEST component page https://plus.humanbrainproject.org/components/209/ and do *three clicks*: 1. click the green [edit] button 2. click [+me] at "Component User Group", and finally 3. click [Save] at the bottom of the page. This ensures the continued support of many developers and helps to show the multitude of research using NEST simulations, and is highly appreciated. If you use or intend to use any number of the following specific NEST features, please feel free to also add yourself there, to show your appreciation to the respective developers: * optimizations for simulations on high-performance computing platforms https://plus.humanbrainproject.org/components/1666/ and https://plus.humanbrainproject.org/components/1667/ * models with continuous dynamics / gap-junctions https://plus.humanbrainproject.org/components/510/ * models with 3rd factor plasticity https://plus.humanbrainproject.org/components/2696/ * the NEST modeling language (NESTML) https://plus.humanbrainproject.org/components/2679/ * connection generation in very large networks https://plus.humanbrainproject.org/components/2678/ There are many other related components that you may also want to add yourself, like simulator-simulator interactions (e.g. 2693), visualization (e.g. 2697), and many more. Please contact me if you feel like you can't find something that you would like to "+me". 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

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Open NEST Developer Video Conference Monday 14 October 2019 11.30 CEST (UTC+2)
by Dennis Terhorst 14 Oct '19

14 Oct '19

Dear NEST Developers! I would like to invite you to our next bi-weekly Open NEST Developer Video Conference today (please excuse the late invitation) Monday 14 October, 11.30-12.30 CEST (UTC+2). See below for information about how to log into the meeting. The agenda for this meeting is also available online, see https://github.com/nest/nest-simulator/wiki/2019-10-14-Open-NEST-Developer-… Agenda • Welcome • Python 2 support in NEST3? • 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

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IF COND EXP Model
by vergani.aa＠gmail.com 17 Sep '19

17 Sep '19

Dear experts, do you have any suggestions where could I find the explicit model for the IF COND EXP neuron? I mean the mathematical formulation of the model. Thanks Alberto

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Poisson - crash when changing the rate and delay of rate change
by nest-simulator.org＠weinzierl.it 16 Sep '19

16 Sep '19

I use NEST (Version 2.16.0) by using PyNN. While using I came across the problem that NEST throws an error, when the rate of a SpikeSourcePoisson (in PyNN) is updated from any positive value to 0 and to any positive value again. In other words, once the rate is set to zero, it cannot be changed anymore. It seems like this issue is independant of the temporal location. The exception thrown is the following: > python2.7: /pathToNestSimulator/nest-simulator-2.16.0/nestkernel/event_delivery_manager.h:564: nest::delay nest::EventDeliveryManager::get_slice_modulo(nest::delay): Assertion `static_cast< std::vector< delay >::size_type >( d ) < slice_moduli_.size()' failed. Further, any rate change of a specific neuron is not applied before the next spike at the previous rate. This is problematic when dealing with low rates as spikes occur only rarely. For instance, with a rate of 1 it is not unlikely that there is not a spike for a few seconds. As a result, a rate change can and will be applied extremely delayed. I initially reported this at PyNN, but it seems to be a NEST issue: https://github.com/NeuralEnsemble/PyNN/issues/650 What would you advise?

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Open NEST Developer Video Conference Monday 16 September 2019 11.30 CEST (UTC+2)
by Dennis Terhorst 15 Sep '19

15 Sep '19

Dear NEST Developers! I would like to invite you to our next bi-weekly Open NEST Developer Video Conference tomorrow Monday 16 September, 11.30-12.30 CEST (UTC+2). See below for information about how to log into the meeting. The agenda for this meeting is also available online, see https://github.com/nest/nest-simulator/wiki/2019-09-16-Open-NEST-Developer-… 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

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installation issue PyNest: outdated libgsl.so.23 dependency on recent linux release
by samuel.bottani＠parisdescartes.fr 07 Sep '19

07 Sep '19

Hi, nestsimulator-2.18.0 fails PyNEST installation as requesting libgsl.so.23 while libgsl.so.25 is available (see brelow --1-- log of installcheck for PyNEST tests) cmake reports no errors with GSL (see bleow --2-- log extract of cmake output ) configuration: linux manjaro latest system update 2019-09-05 Sorry for my ignorance : is there a way to force linking with most recent gsl library ? Or is it necessary to install also the old library version somehow? If then how ? Thank you in advance for any help Samuel Bottani --1-- Phase 7: Running PyNEST tests. ------------------------------ Using nosetests. Failure: ImportError (libgsl.so.23: cannot open shared object file: No such file or directory) ... ERROR Failure: ImportError (libgsl.so.23: cannot open shared object file: No such file or directory) ... ERROR ERROR: Failure: ImportError (libgsl.so.23: cannot open shared object file: No such file or directory) File "/usr/lib/python3.7/site-packages/nose/failure.py", line 39, in runTest ImportError: libgsl.so.23: cannot open shared object file: No such file or directory ERROR: Failure: ImportError (libgsl.so.23: cannot open shared object file: No such file or directory) File "/usr/lib/python3.7/site-packages/nose/failure.py", line 39, in runTest ImportError: libgsl.so.23: cannot open shared object file: No such file or directory FAILED (errors=2) PyNEST tests: 2 Passed: 0 Skipped: 0 Failed: 2 --2-- Concerning GLS log : Use GSL : Yes (GSL 2.6) Includes : /usr/include Libraries : /usr/lib/libgsl.so;/usr/lib/libgslcblas.so

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get/set status conductance based synapses
by Mikkel Elle Lepperød 04 Sep '19

04 Sep '19

Hi! Is it possible to get and set the status of a neuron with conductance based synapses (iaf_cond_alpha)? I only see V_m after getting the status of the nodes, but I need to get/set the synapse states as well (g_ex, g_in). Best -- Mikkel Elle Lepperød <http://cinpla.org/people/> Centre for Integrative Neuroplasticity (CINPLA <http://cinpla.org>) University of Oslo (UiO <http://uio.no>) Kristine Bonnevies hus, room 2513

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problem loading pynn nest installed from live media
by Julian Martin Leslie Budd 04 Sep '19

04 Sep '19

Hi After installing NEST ubuntu 18.04 live media (lubuntu-18.04_nest-2.18.0.ova downloaded a few days ago), I get the following error message but a m able to import nest in python3 ok: nest@nestvm:~$ python3 Python 3.6.8 (default, Jan 14 2019, 11:02:34) [GCC 8.0.1 20180414 (experimental) [trunk revision 259383]] on linux Type "help", "copyright", "credits" or "license" for more information. >>> import pyNN.nest as sim [INFO] [2019.8.21 14:31:47 /home/nest/work/nest-simulator-2.18.0/nestkernel/rng_manager.cpp:217 @ Network::create_rngs_] : Creating default RNGs [INFO] [2019.8.21 14:31:47 /home/nest/work/nest-simulator-2.18.0/nestkernel/rng_manager.cpp:260 @ Network::create_grng_] : Creating new default global RNG -- N E S T -- Copyright (C) 2004 The NEST Initiative Version: nest-2.18.0 Built: Jul 2 2019 15:09:55 This program is provided AS IS and comes with NO WARRANTY. See the file LICENSE for details. Problems or suggestions? Visit https://www.nest-simulator.org Type 'nest.help()' to find out more about NEST. Traceback (most recent call last): File "<stdin>", line 1, in <module> File "/usr/local/lib/python3.6/dist-packages/pyNN/nest/__init__.py", line 18, in <module> from . import simulator File "/usr/local/lib/python3.6/dist-packages/pyNN/nest/simulator.py", line 257, in <module> state = _State() # a Singleton, so only a single instance ever exists File "/usr/local/lib/python3.6/dist-packages/pyNN/nest/simulator.py", line 59, in __init__ self.verbosity = "warning" File "/usr/local/lib/python3.6/dist-packages/pyNN/nest/simulator.py", line 120, in _set_verbosity nest.sli_run("M_%s setverbosity" % verbosity.upper()) AttributeError: module 'nest' has no attribute 'sli_run' >>> Any suggestions? Thanks.

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