September 2019 - NEST Users - NEST Initiative Mail

Realtime access to spikes in simulation
by Benjamin Staude 04 Feb '20

04 Feb '20

Hi NEST-Team, To use the NEST-Simluator in an interactive installation, I would need to 1) have access to the spike in the network in realtime, and 2) send signals (spikes) to neurons in the simulation in realtime. For 1), I could imagine writing the spike-times to a file and then reading that file while the simulation is running. However, I currently don’t see an option for 2). Then I heard that you are actually working on module that would enable realtime I/O-access. Is that the case? And, if so, is there a timeline? Best, Benjamin -- -- -- Dr. Benjamin Staude | Paul-Lincke-Ufer 7 | 10999 Berlin | benjamin.staude(a)gmail.com

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C/C++ interface
by Xavier Otazu 24 Oct '19

24 Oct '19

Hello, I would like to make a suggestion for future development. Now there is a Python interface, but some of us have been working with C/C++ for many years (and we have a lot of data processing software developed in this language). Please, could you include a C/C++ interface for NEST? Thanks a lot in advance! Xavier

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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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installation issue: make installcheck fail pynest tests
by Julian Martin Leslie Budd 03 Sep '19

03 Sep '19

Hi Please could someone suggest the most likely reason why current NEST (v2.16.0) appears to install ok (tutorials tested work) but fails during make installcheck for pynest tests: $ make installcheck ... Phase 7: Running PyNEST tests. ------------------------------ Using nosetests. [cajal:07463] Failing at address: 0x44000099 [cajal:07463] *** End of error message *** Segmentation fault (core dumped) PyNEST tests: Passed: 0 Skipped: 0 Failed: 0 /home/julianb/Documents/NEST/share/nest/extras/do_tests.sh: 790: /home/julianb/Documents/NEST/share/nest/extras/do_tests.sh: arithmetic expression: expecting primary: " 363 + " CMakeFiles/installcheck.dir/build.make:57: recipe for target 'CMakeFiles/installcheck' failed make[3]: *** [CMakeFiles/installcheck] Error 2 CMakeFiles/Makefile2:99: recipe for target 'CMakeFiles/installcheck.dir/all' failed make[2]: *** [CMakeFiles/installcheck.dir/all] Error 2 CMakeFiles/Makefile2:106: recipe for target 'CMakeFiles/installcheck.dir/rule' failed make[1]: *** [CMakeFiles/installcheck.dir/rule] Error 2 Makefile:208: recipe for target 'installcheck' failed make: *** [installcheck] Error 2 $ Current setup: ubuntu 16.04, python 2.7.12, and nose 1.3.7. Thanks.

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weigth recorder does not record recorded eligibility trace and neuromodulator concentration.
by anduls＠web.de 02 Sep '19

02 Sep '19

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NEST Users September 2019