- NEST Users - NEST Initiative Mail

Stop Printing Simulation Details on Terminal (NEST)
by shanka19＠purdue.edu 04 Feb '20

04 Feb '20

Hi, I wanted to know how to stop printing the simulation details on my terminal window. For instance I can see the number of open mpi process, simulation time being printed every time I run a model. I do not want to see the details on my terminal screen, is there a way to do it?

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Using GPU's to run NEST simulaton
by Daphne Cornelisse 04 Feb '20

04 Feb '20

Hi NEST-team, I would like to run a simulation of > 1000 neurons, and to make my computing time faster I am looking into how to use parallel computing with NEST. I have seen this <https://www.nest-simulator.org/parallel-computing/> page but I can't seem to find anything about using the cloud (e.g. google cloud, colab etc.) and the use of GPU's. I am quite new to this so it could be I missed something. - Is it possible to use a GPU for the nest simulations? - Are the some resources I could learn from? Thank you! Best, Daphne

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NEST 2.20.0 released / Issue 1394 / NEST 3 to become Master Branch soon
by Hans Ekkehard Plesser 31 Jan '20

31 Jan '20

Dear NEST Users! We are very excited about the release of NEST 2.20.0 earlier today, including 454 commits in 82 pull requests by 25 developers since NEST 2.18.0. NEST 2.20.0 brings a wide range of improvements, including * generalized leaky integrate-and-fire neuron models developed by the Allen Institute (Teeter et al, 2018) * STDP synapses with nearest-neighbor spike paring schemes * improved documentation on Read The Docs<https://nest-simulator.readthedocs.io/en/latest/>. Please see below for a complete list of changes. NEST 2.20.0 is available for download from https://github.com/nest/nest-simulator/releases/tag/v2.20.0 To cite NEST 2.20.0, please refer to the Zenodo entry at https://doi.org/10.5281/zenodo.3605514 WARNING: NEST 2.20.0 is affected by issue #1394<https://github.com/nest/nest-simulator/issues/1394>, which may lead to incorrect results under certain circumstances when simulating very large networks across many MPI processes and threads. Simulations using only MPI parallelism, but no threads, work correctly according to our tests. The same holds for simulations using only thread-parallelism. The issue also affects NEST 2.18.0 and 2.16.0, but not 2.14.0. According to our analysis, in affected simulations, a very small number of connections is not created correctly. This happens under random cirucmstances, so that in one series of tests, out of ten identical simulations, five simulations produced correct results, while the remaining five simulations produced different results. For details, please follow the issue on GitHub. We are currently working hard to identify the cause of this issue and hope to be able to provide a fix soon. The next big step forward in NEST development will be the merge of the nest-3 development branch into the master branch on GitHub. NEST 3 will bring major improvements to the user interface and considerable changes under the hood. Please see https://nest-simulator.readthedocs.io/en/nest-3/guides/from_nest2_to_nest3.… https://nest-simulator.readthedocs.io/en/nest-3/ref_material/nest2_vs_3.html for more information on changes to come and modifications required to existing scripts. Best regards, Hans Ekkehard Plesser President, The NEST Initiative ------------------------------------------------ NEST 2.20.0<https://doi.org/10.5281/zenodo.3605514> is the result of 454 commits in 82 pull requests by 25 developers since NEST 2.18.0<https://doi.org/10.5281/zenodo.2605422> which was released on June 7, 2019. This release wraps up the 2.x series of NEST and contains many improvements and bug fixes. Highlights are the addition of the generalized leaky integrate-and-fire neuron models by the Allen Institute<https://portal.brain-map.org/explore/models/glif-single-neuron>, STDP synapses with nearest-neighbor spike pairing schemes and improved documentation, available on Read The Docs<https://nest-simulator.readthedocs.io/en/latest/>. Following is a list of all merged pull requests: Enhancements Models * Add STDP synapses with nearest-neighbor spike pairing schemes<https://github.com/nest/nest-simulator/pull/865> * Add generalized leaky integrate-and-fire (GLIF) neuron models by Allen Institute<https://github.com/nest/nest-simulator/pull/1126> * Add iaf_psc_alpha_ps neuron model<https://github.com/nest/nest-simulator/pull/1169> Installation * Add conda-forge installation documentation for Linux and MacOSX<https://github.com/nest/nest-simulator/pull/1204> * Add Fugaku platform CMake file<https://github.com/nest/nest-simulator/pull/1231> * Clean the build process for the NEST Debian packages<https://github.com/nest/nest-simulator/pull/1316> * Hike minimum required CMake to 3.12 and add support for OpenMP with Apple Clang<https://github.com/nest/nest-simulator/pull/1386> * More informative compiler information in CMake summary<https://github.com/nest/nest-simulator/pull/1403> Documentation * Added initial membrane potential options to microcircuit example<https://github.com/nest/nest-simulator/pull/1206> * Add initial membrane potential options to microcircuit example<https://github.com/nest/nest-simulator/pull/1260> * Add new options for installation and improve instructions for NEST<https://github.com/nest/nest-simulator/pull/1262> * Updated/extended macOS install instructions<https://github.com/nest/nest-simulator/pull/1297> * Update DOI and release buttons in README; add Zenodo reference to NEST 2.18.0<https://github.com/nest/nest-simulator/pull/1314> * Add link on website to new PyNEST templates and update citations<https://github.com/nest/nest-simulator/pull/1351> * Provide guidelines to writing to mailing list in documentation<https://github.com/nest/nest-simulator/pull/1368> Kernel * Introduce time-driven spiking connections<https://github.com/nest/nest-simulator/pull/1160> * Add support for sending secondary events to and from devices<https://github.com/nest/nest-simulator/pull/1244> * Add warning about invalid connection descriptors when new connections are created<https://github.com/nest/nest-simulator/pull/1250> * Use an unsigned data type for thread in spike data<https://github.com/nest/nest-simulator/pull/1308> Infrastructure * Fast static check in Travis CI<https://github.com/nest/nest-simulator/pull/1267> PyNEST * New templates for pynest examples and api<https://github.com/nest/nest-simulator/pull/1139> * Add getattr/setattr to GIDCollection<https://github.com/nest/nest-simulator/pull/1249> * Allow specifying arrays of values in the synapse specification when connecting with fixed_total_number<https://github.com/nest/nest-simulator/pull/1266> * Use shape as argument instead of columns/rows/depth and update topology examples to NEST3<https://github.com/nest/nest-simulator/pull/1287> Bug fixes Models * Fix uninitialized variable in iaf_psc_exp<https://github.com/nest/nest-simulator/pull/1225> * Fix handling of rate change in poisson_generator_ps<https://github.com/nest/nest-simulator/pull/1280> Documentation * Remove spurious brackets from code example in tutorial<https://github.com/nest/nest-simulator/pull/1270> * Fix MUSIC example<https://github.com/nest/nest-simulator/pull/1312> Kernel * Fix multiple definition of rho build complain observed on AArch64 with FCC<https://github.com/nest/nest-simulator/pull/1233> * Fix GetConnections to correctly get connections where the target is a global receiving device<https://github.com/nest/nest-simulator/pull/1251> * Fix logical error in elseif-statements in connect functions<https://github.com/nest/nest-simulator/pull/1254> * Check variables of GSL binomial random generator where they are set<https://github.com/nest/nest-simulator/pull/1299> * Ensure number of connections for fixed total number is properly set<https://github.com/nest/nest-simulator/pull/1367> * Fix MyModule by incorporating modelsmodule refactoring from #1069<https://github.com/nest/nest-simulator/pull/1383> * Avoid segfault when using a weight recorder with a probabilistic synapse<https://github.com/nest/nest-simulator/pull/1402> Infrastructure * Fix cppcheck in Travis CI testsuite<https://github.com/nest/nest-simulator/pull/1306> Maintenance Models * Fix namespaces in Hodgkin-Huxley neuron models<https://github.com/nest/nest-simulator/pull/1256> * Make multimeter and voltmeter class names lower case<https://github.com/nest/nest-simulator/pull/1345> Installation * Fix nest_vars in case of undefined PYTHONPATH<https://github.com/nest/nest-simulator/pull/1218> * Cleanup for the K computer specific CMake file for v2.18<https://github.com/nest/nest-simulator/pull/1228> * Fix up dependencies in Ubuntu install instructions<https://github.com/nest/nest-simulator/pull/1230> * Files needed to build Debian packages (.deb)<https://github.com/nest/nest-simulator/pull/1255> * Fix extraction of version number if sources are inside another Git repository<https://github.com/nest/nest-simulator/pull/1362> * Let uninstall of NEST Debian package also delete script in profile.d<https://github.com/nest/nest-simulator/pull/1363> Interpreter * Remove handling of external POSIX signals sent to NEST<https://github.com/nest/nest-simulator/pull/1385> Documentation * Convert topology user manual to ReStructuredText<https://github.com/nest/nest-simulator/pull/1214> * Update links to model directory in docs<https://github.com/nest/nest-simulator/pull/1227> * Documentation update pertaining to maximum line length<https://github.com/nest/nest-simulator/pull/1234> * Fix PyNEST installation instructions<https://github.com/nest/nest-simulator/pull/1240> * Update download page for 2.18 and conda-forge<https://github.com/nest/nest-simulator/pull/1247> * Correct typo in random number documentation<https://github.com/nest/nest-simulator/pull/1268> * Fix PyNEST API generation for documentation using mock<https://github.com/nest/nest-simulator/pull/1274> * Add updated NEST examples to Read The Docs <https://github.com/nest/nest-simulator/pull/1277> * Replace iaf_neuron by iaf_psc_alpha in MUSIC tutorial<https://github.com/nest/nest-simulator/pull/1330> * Autogenerate PyNEST examples from source with sphinx_gallery<https://github.com/nest/nest-simulator/pull/1336> * Update syntax formatting for terms in documentation<https://github.com/nest/nest-simulator/pull/1343> * Fix broken CSS style<https://github.com/nest/nest-simulator/pull/1344> * Update mailing list email address<https://github.com/nest/nest-simulator/pull/1346> * Small typographical updates to user documentation<https://github.com/nest/nest-simulator/pull/1397> Kernel * Refactor registration of models in modelsmodule<https://github.com/nest/nest-simulator/pull/1069> * Increase maximum line length in source code formatting style from 80 to 120<https://github.com/nest/nest-simulator/pull/1177> * Unify coeffarray_as_d and coeffarray_as_uint via union<https://github.com/nest/nest-simulator/pull/1243> * Add missing include of sys/time.h<https://github.com/nest/nest-simulator/pull/1273> * Fix threading issue when connecting<https://github.com/nest/nest-simulator/pull/1276> * Remove spurious thread_local_connectors update<https://github.com/nest/nest-simulator/pull/1333> * Fix rounding issue when setting small resolution<https://github.com/nest/nest-simulator/pull/1356> * Improve information given by error messages typically triggered by Connect<https://github.com/nest/nest-simulator/pull/1399> Infrastructure * Add tests for libnestutil/streamers.h<https://github.com/nest/nest-simulator/pull/1219> * Make version information consistent<https://github.com/nest/nest-simulator/pull/1223> * Update FindLibNeurosim to take Python version into account<https://github.com/nest/nest-simulator/pull/1235> * Remove the remaining markdown config in docs<https://github.com/nest/nest-simulator/pull/1263> * Skip deployment in Travis CI testsuite when not running a build<https://github.com/nest/nest-simulator/pull/1300> * Deploy build artifacts only when the build flag is set in the reply section<https://github.com/nest/nest-simulator/pull/1302> * Change the deployment branch to master<https://github.com/nest/nest-simulator/pull/1304> * Fix cppcheck usage in Travis CI testsuite<https://github.com/nest/nest-simulator/pull/1307> * Switch to GCC8 as default in continuous integration tests on Travis<https://github.com/nest/nest-simulator/pull/1310> * Fix formatting in test_stdp_nn_synapses.py<https://github.com/nest/nest-simulator/pull/1311> * Add security guidelines<https://github.com/nest/nest-simulator/pull/1329> * Moving to Python3.x on OsX<https://github.com/nest/nest-simulator/pull/1335> * Replace Python version by newest available on Travis<https://github.com/nest/nest-simulator/pull/1342> PyNEST * Fix warnings when Cythonizing pynestkernel.pyx<https://github.com/nest/nest-simulator/pull/1322> * Allow installation with Python 3.8<https://github.com/nest/nest-simulator/pull/1340> -- 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

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Issue with NEST 2.18.0/python 3.6
by Angeliki Papadimitriou 20 Jan '20

20 Jan '20

Hello, I have an issue regarding random generation in nest version 2.18 with Python3.6. I attach a small python script that replicates my issue (less than 50 lines). In short, I am trying to create two Poisson generators and connect them to the same neuron. I noticed that if I reverse the order by which these Poisson generators are created (using the nest.Create()) function, then I get a different membrane potential response over time. In the code, noise_exc is created before noise_inh. If that order is reversed, the plot is different. My hunch is that this has to do with how nest generates random numbers. So I tried to force the creation of Poisson generators by providing a seed (lines 15 and 18). However this behavior persists. Do you have any insights as to why this happens? At the end of the script (lines 32-43) I provide a trivial case of the desired behavior I am trying to replicate. Thank you for your time Angeliki -- [image: Kth Logo] Angeliki Papadimitriou Research EngineerKTH Royal Institute of Technology *School of Electrical Engineering and Computer Science (EECS)**Division of Computational Science and Technology (CST)* Computational Brain Science Unit Room 4438, Floor 4, Lindstedtsvägen 5 11428 Stockholm, Sweden angpap(a)kth.se <namn(a)kth.se>

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Open NEST Developer Video Conference Monday 20 January 2020 11:30 CET (UTC+1)
by Hans Ekkehard Plesser 19 Jan '20

19 Jan '20

Dear NEST Users & Developers! I would like to invite you to this years first Open NEST Developer Video Conference, tomorrow Monday 20 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/2020-01-20-Open-NEST-Developer-… For details how to log in see below. Agenda * Welcome * Preparing NEST 2.20 release * Preparing merge of nest-3 branch to master * Review of NEST User Mailing List * Review of open Github Pull Request * Review of open Github Issues Looking forward to seeing you soon! Hans Ekkehard Plesser ------------------ 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 _______________________________________________ NEST Users mailing list -- users(a)nest-simulator.org To unsubscribe send an email to users-leave(a)nest-simulator.org

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Segmentation Fault loading custom nest module
by Benedikt Feldotto 17 Jan '20

17 Jan '20

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

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NEST Creating a simple network
by shanka19＠purdue.edu 16 Jan '20

16 Jan '20

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!

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nest user in nest-docker entrypoint file
by bignamini＠cscs.ch 14 Jan '20

14 Jan '20

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

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Error when compiling MyModule, the example extension module
by eben.cowley42＠gmail.com 10 Jan '20

10 Jan '20

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!

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Issue review VC Friday 10 Jan 10-13
by Hans Ekkehard Plesser 09 Jan '20

09 Jan '20

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

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Open NEST Developer Video Conference Monday 6 January 2020 11:30 CET (UTC+1)
by Dennis Terhorst 05 Jan '20

05 Jan '20

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

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NO open NEST Developer Video Conference on 23 December 2019
by Dennis Terhorst 23 Dec '19

23 Dec '19

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…

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NEST Conference 2020 — Save the Date: 29/30 June 2020 at Ås, Norway
by Hans Ekkehard Plesser 17 Dec '19

17 Dec '19

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

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Hackathon on CEREBELLUM MODELLING
by Dennis Terhorst 17 Dec '19

17 Dec '19

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

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Reset Network with to_file
by Maryada Maryada 08 Dec '19

08 Dec '19

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*

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NEST 3 merge outlook
by Itaru Kitayama 06 Dec '19

06 Dec '19

Can somebody comment on this plan? I’m using the nest-3 branch heavily on FUGAKU and am wondering when it’ll be merged in the master.

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Multiplicity value + presynaptic spike history
by Benedikt Feldotto 27 Nov '19

27 Nov '19

Dear all, I have two questions that arise when implementing my adapted C++ synapse model. 1) Postsynaptic spikes have a "multiplicity" variable. Am I correct that if I receive a single spike object with a multiplicity value of 3, I actually receive 3 spikes? Since I do only get one time, what are the exact spike times of the other spikes? 2) For the postsynaptic spikes I can easily access the spike history and search for spikes in a certain time range, as for example done in the STDP synapse. Is it possible to also access the overall spike history of presynaptic spikes? So far I only found that in the std_dopamine synapse as an example the last spike time is stored manually. Thank you very much ! Best Regards, 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

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NO Open NEST Developer Video Conference Monday 25 November 2019
by Dennis Terhorst 23 Nov '19

23 Nov '19

Dear NEST Developers! On Monday there will be no Open NEST Developer Video Conference, since many of the NEST users and developers are traveling at that time to join the HBP CodeJam#10 and adjoined events. As usual, if you would have something you want to add to the agenda, please don't hesitate to contact me anyway. I will then add it in the the following meeting. Looking forward to seeing you soon! best, Dennis Terhorst https://github.com/nest/nest-simulator/wiki/Open-NEST-Developer-Video-Confe…

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About the spike_detector records
by zhe.sun.vk＠riken.jp 18 Nov '19

18 Nov '19

Dear all, Recently I always have an error when I tried to keep the spike_detector information into files. ********************** Nov 18 19:22:09 RecordingDevice::calibrate() [Error]: I/O error while opening file '0-94476-15.gdf'. This may be caused by too many open files in networks with many recording devices and threads. ********************** And I also found most of the gdf files are empty. Do you have any idea to solve this issue? And do you know how to avoid to keeping empty gdf files. Best wishes Sun

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Open NEST Developer Video Conference Monday 11 November 2019 11:30 CET (UTC+1)
by Dennis Terhorst 10 Nov '19

10 Nov '19

Dear NEST Developers! I would like to invite you to our next bi-weekly Open NEST Developer Video Conference tomorrow Monday 11 November, 11.30-12.30 CET (UTC+1). 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/2019-11-11-Open-NEST-Developer-… Agenda * Welcome * Review of NEST User Mailing List3 * 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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Re: Issues with make under OSX
by Hans Ekkehard Plesser 08 Nov '19

08 Nov '19

Hi Benjamin, It is curious that MPI is not found on your system. Could you double check that you have installed open-mpi via Homebrew? What does which mpicxx return on your system? Best, Hans Ekkehard On 26 Oct 2019, at 17:04, Benjamin Staude <benjamin.staude(a)gmail.com<mailto:benjamin.staude@gmail.com>> wrote: Hi Hans-Ekkehard, Thanks for the support, that solved one issue. But now, I get the same for OPEN_MPI: -- Could NOT find MPI_C (missing: MPI_C_WORKS) -- Could NOT find MPI_CXX (missing: MPI_CXX_WORKS) -- Could NOT find MPI (missing: MPI_C_FOUND MPI_CXX_FOUND) (I need open_mpi because I need the MUSIC interface). This is my cmake-call: cmake \ -DCMAKE_C_COMPILER=gcc-9 \ -DCMAKE_CXX_COMPILER=g++-9 \ -Dwith-music=ON \ -Dwith-mpi=ON \ -Dwith-openmp=ON \ -DCMAKE_INSTALL_PREFIX=/Users/staude/.pyenv/versions/3.7.2/ \ /Users/staude/Projekte/RainerDunkel/SensoryNetwork/Skripte/snn/NEST/nest-simulator-2.18.0 And the output: -- The CXX compiler identification is GNU 9.2.0 -- The C compiler identification is GNU 9.2.0 -- Checking whether CXX compiler has -isysroot -- Checking whether CXX compiler has -isysroot - yes -- Checking whether CXX compiler supports OSX deployment target flag -- Checking whether CXX compiler supports OSX deployment target flag - yes -- Check for working CXX compiler: /usr/local/bin/g++-9 -- Check for working CXX compiler: /usr/local/bin/g++-9 -- works -- Detecting CXX compiler ABI info -- Detecting CXX compiler ABI info - done -- Detecting CXX compile features -- Detecting CXX compile features - done -- Checking whether C compiler has -isysroot -- Checking whether C compiler has -isysroot - yes -- Checking whether C compiler supports OSX deployment target flag -- Checking whether C compiler supports OSX deployment target flag - yes -- Check for working C compiler: /usr/local/bin/gcc-9 -- Check for working C compiler: /usr/local/bin/gcc-9 -- works -- Detecting C compiler ABI info -- Detecting C compiler ABI info - done -- Detecting C compile features -- Detecting C compile features - done -- Could NOT find Doxygen (missing: DOXYGEN_EXECUTABLE) -- Looking for include file inttypes.h -- Looking for include file inttypes.h - found -- Looking for include file mach-o/dyld.h -- Looking for include file mach-o/dyld.h - found -- Looking for include file mach/mach.h -- Looking for include file mach/mach.h - found -- Looking for include file memory.h -- Looking for include file memory.h - found -- Looking for include file stdint.h -- Looking for include file stdint.h - found -- Looking for include file sys/types.h -- Looking for include file sys/types.h - found -- Looking for C++ include istream -- Looking for C++ include istream - not found -- Looking for C++ include ostream -- Looking for C++ include ostream - not found -- Looking for C++ include sstream -- Looking for C++ include sstream - not found -- Looking for stddef.h -- Looking for stddef.h - found -- Check size of long long -- Check size of long long - done -- Check size of u_int16_t -- Check size of u_int16_t - done -- Check size of uint16_t -- Check size of uint16_t - done -- Check size of u_int64_t -- Check size of u_int64_t - done -- Check size of uint64_t -- Check size of uint64_t - done -- Looking for NAN -- Looking for NAN - found -- Looking for isnan -- Looking for isnan - found -- Looking for M_E -- Looking for M_E - found -- Looking for M_PI -- Looking for M_PI - found -- Looking for expm1 -- Looking for expm1 - found -- Host triple: x86_64-apple-darwin -- Target triple: x86_64-apple-darwin -- Found LTDL: /usr/local/lib/libltdl.dylib (found version "2.4.6") -- Found Readline: /usr/lib/libreadline.dylib (found version "4.2") -- Found PkgConfig: /usr/local/bin/pkg-config (found version "0.29.2") -- Found GSL: /usr/local/Cellar/gsl/2.6/include (found version "2.6") -- Found PythonInterp: /Users/staude/.pyenv/shims/python (found version "3.7.2") -- Found PythonLibs: /Users/staude/.pyenv/versions/3.7.2/lib/libpython3.7m.a (found suitable exact version "3.7.2") -- Found Cython: /Users/staude/.pyenv/shims/cython (found version "0.29.13") -- Found OpenMP_C: -fopenmp -- Found OpenMP_CXX: -fopenmp -- Found OpenMP: TRUE -- Could NOT find MPI_C (missing: MPI_C_WORKS) -- Could NOT find MPI_CXX (missing: MPI_CXX_WORKS) -- Could NOT find MPI (missing: MPI_C_FOUND MPI_CXX_FOUND) CMake Error at cmake/ProcessOptions.cmake:528 (message): MUSIC requires -Dwith-mpi=ON. Call Stack (most recent call first): CMakeLists.txt:167 (nest_process_with_music) And the cmake-version: cmake --version cmake version 3.15.3 On 26. Oct 2019, at 14:11, Hans Ekkehard Plesser <hans.ekkehard.plesser(a)nmbu.no<mailto:hans.ekkehard.plesser@nmbu.no>> wrote: Hi Benjamin, The CMake output shows that you are using the AppleClang compiler, which does not support OpenMP. If you want to use that compiler, you need to turn off OpenMP with -Dwith-openmp=OFF. If you want NEST with OpenMP on the Mac, I would recommend using the GCC compiler installed via Homebrew, see https://nest-simulator.readthedocs.io/en/latest/installation/mac_install.ht… for instructions. Best, Hans Ekkehard On 25 Oct 2019, at 18:12, Benjamin Staude <benjamin.staude(a)gmail.com> wrote: Hi there, I am trying to install nest under OSX Mojave and run into the following cmake-error (see below for a full trace): -- Could NOT find OpenMP_C (missing: OpenMP_C_FLAGS OpenMP_C_LIB_NAMES) -- Could NOT find OpenMP_CXX (missing: OpenMP_CXX_FLAGS OpenMP_CXX_LIB_NAMES) -- Could NOT find OpenMP (missing: OpenMP_C_FOUND OpenMP_CXX_FOUND) I already tried various tricks (http://stechschulte.net/2016/03/20/openmp-osx-cmake.html, https://stackoverflow.com/questions/48825416/missing-openmp-c-flags-openmp-…), but had no success. Does anybody have experience? Thanks in advance, Benjamin ######################################################### -- The CXX compiler identification is AppleClang 9.0.0.9000038 -- The C compiler identification is AppleClang 9.0.0.9000038 -- Check for working CXX compiler: /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/c++ -- Check for working CXX compiler: /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/c++ -- works -- Detecting CXX compiler ABI info -- Detecting CXX compiler ABI info - done -- Detecting CXX compile features -- Detecting CXX compile features - done -- Check for working C compiler: /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/cc -- Check for working C compiler: /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/cc -- works -- Detecting C compiler ABI info -- Detecting C compiler ABI info - done -- Detecting C compile features -- Detecting C compile features - done -- Could NOT find Doxygen (missing: DOXYGEN_EXECUTABLE) -- Looking for include file inttypes.h -- Looking for include file inttypes.h - found -- Looking for include file mach-o/dyld.h -- Looking for include file mach-o/dyld.h - found -- Looking for include file mach/mach.h -- Looking for include file mach/mach.h - found -- Looking for include file memory.h -- Looking for include file memory.h - found -- Looking for include file stdint.h -- Looking for include file stdint.h - found -- Looking for include file sys/types.h -- Looking for include file sys/types.h - found -- Looking for C++ include istream -- Looking for C++ include istream - found -- Looking for C++ include ostream -- Looking for C++ include ostream - found -- Looking for C++ include sstream -- Looking for C++ include sstream - found -- Looking for stddef.h -- Looking for stddef.h - found -- Check size of long long -- Check size of long long - done -- Check size of u_int16_t -- Check size of u_int16_t - done -- Check size of uint16_t -- Check size of uint16_t - done -- Check size of u_int64_t -- Check size of u_int64_t - done -- Check size of uint64_t -- Check size of uint64_t - done -- Looking for NAN -- Looking for NAN - found -- Looking for isnan -- Looking for isnan - found -- Looking for M_E -- Looking for M_E - found -- Looking for M_PI -- Looking for M_PI - found -- Looking for expm1 -- Looking for expm1 - found -- Host triple: x86_64-apple-darwin -- Target triple: x86_64-apple-darwin -- Found LTDL: /usr/local/lib/libltdl.dylib (found version "2.4.6") -- Found Readline: /usr/lib/libreadline.dylib (found version "4.2") -- Found PkgConfig: /usr/local/bin/pkg-config (found version "0.29.2") -- Found GSL: /usr/local/Cellar/gsl/2.6/include (found version "2.6") -- Found PythonInterp: /Users/staude/.pyenv/shims/python (found version "3.7.2") -- Found PythonLibs: /Users/staude/.pyenv/versions/3.7.2/lib/libpython3.7m.a (found suitable exact version "3.7.2") -- Found Cython: /Users/staude/.pyenv/shims/cython (found version "0.29.13") -- Could NOT find OpenMP_C (missing: OpenMP_C_FLAGS OpenMP_C_LIB_NAMES) -- Could NOT find OpenMP_CXX (missing: OpenMP_CXX_FLAGS OpenMP_CXX_LIB_NAMES) -- Could NOT find OpenMP (missing: OpenMP_C_FOUND OpenMP_CXX_FOUND) CMake Error at cmake/ProcessOptions.cmake:452 (message): CMake can not find OpenMP. Call Stack (most recent call first): CMakeLists.txt:164 (nest_process_with_openmp) _______________________________________________ NEST Users mailing list -- users(a)nest-simulator.org To unsubscribe send an email to users-leave(a)nest-simulator.org -- 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 -- -- -- Dr. Benjamin Staude | Paul-Lincke-Ufer 7 | 10999 Berlin | benjamin.staude(a)gmail.com<mailto:benjamin.staude@gmail.com> -- 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

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VoIP Engineers jobs
by fieldengineer77＠gmail.com 06 Nov '19

06 Nov '19

Available in the Field Engineer marketplace are experts with Voice over Internet Protocol (VoIP) skills, which is a mix of voice, video, and knowledge on one network. VoIP allows people to make telephone calls over broadband Internet connections rather than analog landlines. A VoIP engineer designs, tests, installs and maintains both local VoIP systems in business and large networks that cover entire regions. VoIP Engineers use their experience with computer science, digital audio hardware, and VoIP software to install cutting-edge technologies. They also work with information technology (IT) professionals and system administrators to explain the functionality of VoIP. Many industries employ VoIP engineers to complete telecommunications work on a full-time or contract basis. More info: https://www.fieldengineer.com/skills/voip-engineer

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Educational qualifications and other certifications for Apple Certified Technical Coordinators
by kaitlyn.kristy9494＠gmail.com 06 Nov '19

06 Nov '19

A High school diploma or equivalent along with an Apple Certified Technical Coordinator certification is necessary. An A + certification from CompTIA gives candidates an edge over other aspirants. They should be conversant with various network configurations and hardware devices. Salaries for Apple Certified Technical Coordinators Payscale.com reveals that the average salary of an Apple Certified Technical Coordinator is $65,000 per year in the United States. If they freelance, they will earn $26 per hour. Read More: https://www.fieldengineer.com/skills/apple-certified-technical-coordinator

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PC Technician
by ashaikfe＠gmail.com 06 Nov '19

06 Nov '19

A PC technician often referred to as a computer technician or PC repair technician is responsible for identifying, troubleshooting and resolving computer issues. They are experienced and knowledgeable professionals with hands-on experience with different tools of repair and maintaining computer hardware, software and network/Internet issues. Read More: https://www.fieldengineer.com/skills/what-is-a-pc-technician

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Newbie questions
by Roman Kalivoda 04 Nov '19

04 Nov '19

Hello Nest users, I recently started to work on my bachelor thesis and the first step is to find existing simulators of neural networks and analyze them. Regarding that, I have some questions about the Nest to which I cannot find answers. Is there some graphical interface for Nest? I have found a GitHub project called nest-desktop (https://github.com/babsey/nest-desktop), but I could not find it being mentioned anywhere in the nest simulator documentation. Does anyone have some experience with this? Is it reliable? What is it capable of? If there is not any official Nest GUI, how do you typically work on new simulations? Do you just write plain python scripts for PyNest interface? The last request is directed more to the developers, but maybe someone can lead me in the right way. My thesis lead would like to see some schema of the Nest architecture or some overview of how the simulator is designed. Thank you very much, Roman Kalivoda

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