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Custom input for neurons
by Nicolas Martorell 06 Apr '20

06 Apr '20

Dear all, I'm new at NEST, and I've been trying to recreate a neural system from my work. This involves an IAF neuron which receives two different stimuli (they would be represented by inputs to the neuron - increases in post-synaptic potential). Since these are stimuli I control in my experiments, I need to be able to control their dynamics as the simulation progresses (for example, one of the stimuli has an exponentially larger effect as time progresses). Therefore, it's important for me to … [View More]

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Open NEST Developer Video Conference Monday 30 March 2020 11:30 CEST (UTC+2)
by Dennis Terhorst 30 Mar '20

30 Mar '20

Dear NEST Users & Developers! I would like to invite you to our next bi-weekly Open NEST Developer Video Conference, today Monday 30 March, 11.30-12.30 CEST (UTC+2). Given the current circumstances today's meeting will be again via video conference only, so please do not meet in person! Stay safe! We discuss development status of relevant pull-requests/issues for the upcoming releases. Agenda Welcome Review of NEST User Mailing List &… [View More]

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Memory issues arising in small neural networks
by sternj＠college.harvard.edu 27 Mar '20

27 Mar '20

Hello all, Hope everyone is staying safe and well in these difficult times. I am an undergrad who is just getting started with this library, so I want to apologize in advance for the basic question. I am having issues I believe are memory-related when I call GetConnections on rather small networks. Here is my script: import nest # memory testing nest.ResetKernel() n = 5 # number of neurons epop1 = nest.Create("iaf_psc_alpha",n) epop2 = nest.Create("iaf_psc_alpha",n) nest.Connect(epop1,epop2,{… [View More]

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Error message when installing with cmake
by benedikt.s.vogler＠tum.de 22 Mar '20

22 Mar '20

Hello everyone! I tried installing nest using cmake version 3.14 on ubuntu. This is the command I tried from the nest-simulator directory: cmake -DCMAKE_INSTALL_PREFIX:PATH=/home/bsvogler/Dokumente/nest /home/bsvogler/Dokumente/nest-simulator/nest I get the following two error messages and cannot find any information on how to resolve this issue ========= CMake Error at CMakeLists.txt:97 (install): install TARGETS given no RUNTIME DESTINATION for executable target "nest". CMake Error at … [View More]

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Using music_cont_in_proxy as current source
by Mohammadreza Mohagheghi Nejad 16 Mar '20

16 Mar '20

Dear all, I would like to receive a continuous stream of data via ‘music_cont_in_proxy’ and use it as input current to a neuron. I used ‘iaf_cond_alpha_mc’ as model neuron because I could specify the input that should target the neuron via the receptor_type that accepts current {‘receptor_type’: 7} (’soma_curr’: 7) and connected the ‘music_cont_in_proxy’ via this receptor to the neuron. Currently, for testing purposes, I used ‘constsource’ music binary continuous data stream, which is also … [View More]

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MUSIC - music_cont_in/out_proxy - Guide
by Mohammadreza Mohagheghi Nejad 16 Mar '20

16 Mar '20

Dear all, I am trying to use music ports for my simulations, which requires continuous transmission of data to NEST. I would like to test them in a toy example before integrating them in my project to make sure I am using them as I should. So, under section "Receiving continuous data" in "Guides\Using NEST with MUSIC" ( https://nest-simulator.readthedocs.io/en/stable/guides/using_nest_with_musi…), I found a guide for this functionality of NEST, however, the binary "constsource" is not … [View More]

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Open NEST Developer Video Conference Monday 16 March 2020 11:30 CET (UTC+1)
by Dennis Terhorst 16 Mar '20

16 Mar '20

Dear NEST Users & Developers! I would like to invite you to our next bi-weekly Open NEST Developer Video Conference, today Monday 16 March, 11.30-12.30 CET (UTC+1). Given the current circumstances today's meeting will be *via VIDEO CONFERENCE**ONLY*, so please do not meet in person! We will focus on the organization of our now even more decentralized work and discuss development status of relevant pull-requests/issues for the upcoming releases. Agenda Welcome … [View More]

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Please merge master if you have open pull requests / Issue #1449
by Hans Ekkehard Plesser 12 Mar '20

12 Mar '20

Dear NEST Developers! If you currently have an open pull request against the NEST master branch on Github, please merge the most recent updates from master into your branch. A bug described in #1449 and fixed by #1458 lead to non-deterministic test suite failures. Once you have merged master into your branch, please push again to Github to re-run the tests on Travis. Best, Hans Ekkehard -- Prof. Dr. Hans Ekkehard Plesser Head, Data Science Section Faculty of Science and Technology … [View More]

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A question about NESTML: parameters inherited from Archiving Node aren't exposed to Get/SetStatus
by Alexey Serenko 06 Mar '20

06 Mar '20

Dear community, Sorry if this is off-topic for this list, but I am facing a problem with NESTML. After compiling any of the example neuron models present in the repository, the model seems not to have parameters inherited from ArchivingNode (such as, for instance, an STDP parameter tau_minus) available for GetStatus() or SetStatus(). Oddly enough, the model probably does possess these parameters, because can be connected to/from TDP synapses, but just does not expose them to Get/SetStatus. … [View More]

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nest3: How to create composite of SynapseCollections
by benedikt.s.vogler＠tum.de 03 Mar '20

03 Mar '20

Hello everyone! I am transitioning my Code from nest 2 to nest 3. In nest 2 I used a list of connections and could use this list with nest.Get/SetStatus(). With nest 3 I now have a list of SynapseCollections instances, where each synapse collection contains only one connection. For node collections, there seems to be an operator to create a composite (https://nest-simulator.readthedocs.io/en/latest/guides/from_nest2_to_nest3.…). For SynapseCollections, however, I was unable to use the plus … [View More]

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Open NEST Developer Video Conference Monday 2 March 2020 11:30 CET (UTC+1)
by Dennis Terhorst 02 Mar '20

02 Mar '20

Dear NEST Users & Developers! I would like to invite you to our next bi-weekly Open NEST Developer Video Conference, today Monday 2 March, 11.30-12.30 CET (UTC+1). In today's meeting we will focus on the development status of some critical pull-requests/issues. Agenda Welcome Review of NEST User Mailing List Critical issues Issue #1394, PR #1442 … [View More] Issue #1409, PR #1409 Issue #1449 Random numbers in NEST3 see Issue #1440 Review of open Github Pull Request Review of open Github Issues If you feel uncomfortable to join meetings in larger groups, consider to dial in via video from your desk (details how to log in are given below, as usual). The agenda for this meeting is also available online, see https://github.com/nest/nest-simulator/wiki/2020-03-02-Open-NEST-Developer-… 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 [View Less]

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Install nest-simulator-2.20.0 failed in Ubuntu 14.04
by 1033471810＠qq.com 01 Mar '20

01 Mar '20

Hello everyone, I followed the instructions to install nest-simulator-2.20.0 in my Ubuntu. When I do the things follow: ------------------------------------------------------------------------------- cmake -DCMAKE_INSTALL_PREFIX:PATH=/usr/bin/nest /home/visapy_and_dependencies/nest-simulator-2.20.0 make make install -------------------------------------------------------------------------------- Unfortunately, during "make" it reports some Error, see following: [ 49%] Building CXX object … [View More]

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warning: 'GetConnections' are now invalid
by Lea Steffen 28 Feb '20

28 Feb '20

Hi everybody, I switched from Nest 2.16 to 2.20 and now I get this warning message: ConnectionManager [Warning]: New connections created, connection descriptors previously obtained using 'GetConnections' are now invalid This happens at several parts in my code while building synapses with 'sim.Projection(...)'. I use a 'FromListConnector' and 'STDPMechanism' as synapse_type. I neversaw this warning in the previous Nest version, is it something to be concerned about? I am not … [View More]

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How to stimulate neurons in a network with different amplitudes
by Daphne Cornelisse 22 Feb '20

22 Feb '20

Dear nest community, I have a network of 'iaf_cond_alpha' neurons and want to use the 'dc_generator' to apply two different current amplitudes to the network. (see code below) - A subset of the neurons should receive a sub-threshold amplitude so that they won't spike. - A subset of the neurons should receive a suprathreshold amplitude, making them spike. I created a random number of indices of neurons that should receive a suprathreshold current, the rest of the neurons should … [View More]

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Re: Multi-compartmental models
by Benedikt Rank 20 Feb '20

20 Feb '20

Dear Charl, thank you for the specific pointers. This sounds very promising! Best, Benedikt

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Re: Multi-compartmental models
by Benedikt Rank 20 Feb '20

20 Feb '20

Dear Charl, thank you for the specific pointers. This sounds very promising! Best, Benedikt ⁣

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NEST3 is now the Master Branch
by Hans Ekkehard Plesser 20 Feb '20

20 Feb '20

Dear NEST Developers and Users! After more than two years of intense work, NEST 3 is sufficiently close to completion that we merged the nest-3 branch into the NEST master branch in Github yesterday, closing a large number of issues in the process. What does this mean for you? If you are a NEST User, you can continue to use an existing NEST release for now, ideally NEST 2.20.0, the most recent release. If you are a NEST User and feel just a little adventurous, or are a developer, we … [View More]

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Multi-compartmental models
by benediktr＠hotmail.de 19 Feb '20

19 Feb '20

Dear nest developer, Is there a pre-implemented nest model allowing multiplicative aggregation of compartments/dendritic branches. I am looking for a model that will allow multiplicative aggregation of two dendritic branches at the soma. I very much appreciate any support provided. Best regards, Benedikt

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nest::BadProperty error that behaves like a OOM error
by angpap＠kth.se 17 Feb '20

17 Feb '20

Hello, I am fairly new to NEST and I have been struggling with the following issue. Github repo: https://github.com/angpapadi/wm-net My simulation code consists of 3 python files: - sim.py, the main simulation script, where the model is built and the simulation program is specified - helpers.py a collection of helper functions - parameters.py a script where all parameters are specified. In order to be able to run the code successfully, I have to set certain parameters to unrealistic … [View More]values. If I try to move any of these parameters towards a more realistic regime, NEST crashes (see end of post for full error message). Most relevant is the fact that setting these parameters to more reasonable values, increases by a lot the amount of spikes that NEST has to keep track of. Examples of such parameters that currently have wrong values: > the DOWNSCALE_FACTOR, that essentially controls the neural network's size. Right now my network size is downscaled 95% of what I would want it to be. There are 2 hypercolumns with 4 minicolumns each. Each minicolumn consists of 4 neurons. > E_rev is a list of the reversal potential for each synaptic port. My neuron model has 3 synaptic ports for AMPA, NMDA and GABA, in that order. The Erev for GABA is correctly set but for AMPA and NMDA I cannot get it to work for values bigger than -25, when the correct reversal potential for both is 0. I cannot find the issue with my code, if there is any. When the simulation is very limited (the aforementioned parameters are set to unrealistic values), the code runs flawlessly and produces the expected plots and spike rasters. Also, if I allocate more resources by running on multiple mpi processes, I can be slightly closer to the correct parameter ranges before the nest::badproperty error occurs. To reproduce the error: 1. You can optionally first run the code as is to verify that it works (by running the sim.py script) 2. Then try setting one of the parameters mentioned above to a more plausible value. You can do so by going to the parameters.py file and either reducing the DOWNSCALE_FACTOR parameter (line 7) or increasing the first two entries of the E_rev list (line 203) that correspond to the AMPA and NMDA reversal potentials, or doing both if you 're feeling adventurous! The error is the following: terminate called after throwing an instance of 'nest::BadProperty' what(): BadProperty [59eb791543aa:00113] *** Process received signal *** [59eb791543aa:00113] Signal: Aborted (6) [59eb791543aa:00113] Signal code: (-6) [59eb791543aa:00113] [ 0] /lib/x86_64-linux-gnu/libc.so.6(+0x3ef20)[0x7f2c117b7f20] [59eb791543aa:00113] [ 1] /lib/x86_64-linux-gnu/libc.so.6(gsignal+0xc7)[0x7f2c117b7e97] [59eb791543aa:00113] [ 2] /lib/x86_64-linux-gnu/libc.so.6(abort+0x141)[0x7f2c117b9801] [59eb791543aa:00113] [ 3] /usr/lib/x86_64-linux-gnu/libstdc++.so.6(+0x8c957)[0x7f2c0a55a957] [59eb791543aa:00113] [ 4] /usr/lib/x86_64-linux-gnu/libstdc++.so.6(+0x92ab6)[0x7f2c0a560ab6] [59eb791543aa:00113] [ 5] /usr/lib/x86_64-linux-gnu/libstdc++.so.6(+0x91b19)[0x7f2c0a55fb19] [59eb791543aa:00113] [ 6] /usr/lib/x86_64-linux-gnu/libstdc++.so.6(__gxx_personality_v0+0x2a8)[0x7f2c0a560488] [59eb791543aa:00113] [ 7] /lib/x86_64-linux-gnu/libgcc_s.so.1(+0x10613)[0x7f2c0d6f1613] [59eb791543aa:00113] [ 8] /lib/x86_64-linux-gnu/libgcc_s.so.1(_Unwind_Resume+0x125)[0x7f2c0d6f1e95] [59eb791543aa:00113] [ 9] /opt/nest/lib/python3.6/site-packages/nest/../../../libnestkernel.so(_ZN4nest20EventDeliveryManager18gather_spike_data_INS_9SpikeDataEEEviRSt6vectorIT_SaIS4_EES7_+0x10ed)[0x7f2c0af0684d] [59eb791543aa:00113] [10] /opt/nest/lib/python3.6/site-packages/nest/../../../libnestkernel.so(+0xf4894)[0x7f2c0aee4894] [59eb791543aa:00113] [11] /usr/lib/x86_64-linux-gnu/libgomp.so.1(GOMP_parallel+0x3f)[0x7f2c08d79ecf] [59eb791543aa:00113] [12] /opt/nest/lib/python3.6/site-packages/nest/../../../libnestkernel.so(_ZN4nest17SimulationManager7update_Ev+0x151)[0x7f2c0aee0f61] [59eb791543aa:00113] [13] /opt/nest/lib/python3.6/site-packages/nest/../../../libnestkernel.so(_ZN4nest17SimulationManager12call_update_Ev+0x5a5)[0x7f2c0aee1915] [59eb791543aa:00113] [14] /opt/nest/lib/python3.6/site-packages/nest/../../../libnestkernel.so(_ZN4nest17SimulationManager3runERKNS_4TimeE+0x1d3)[0x7f2c0aee6713] [59eb791543aa:00113] [15] /opt/nest/lib/python3.6/site-packages/nest/../../../libnestkernel.so(_ZN4nest17SimulationManager8simulateERKNS_4TimeE+0x1c)[0x7f2c0aee699c] [59eb791543aa:00113] [16] /opt/nest/lib/python3.6/site-packages/nest/../../../libnestkernel.so(_ZN4nest8simulateERKd+0xc2)[0x7f2c0aecb972] [59eb791543aa:00113] [17] /opt/nest/lib/python3.6/site-packages/nest/../../../libnestkernel.so(_ZNK4nest10NestModule16SimulateFunction7executeEP14SLIInterpreter+0x43)[0x7f2c0ae97a53] [59eb791543aa:00113] [18] /opt/nest/lib/python3.6/site-packages/nest/../../../libsli.so(_ZN13FunctionDatum7executeEP14SLIInterpreter+0x43)[0x7f2c0a8e9063] [59eb791543aa:00113] [19] /opt/nest/lib/python3.6/site-packages/nest/../../../libsli.so(_ZN14SLIInterpreter8execute_Em+0x222)[0x7f2c0a8e6d42] [59eb791543aa:00113] [20] /opt/nest/lib/python3.6/site-packages/nest/../../../libsli.so(_ZN14SLIInterpreter7executeERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEE+0x15e)[0x7f2c0a8e72be] [59eb791543aa:00113] [21] /opt/nest/lib/python3.6/site-packages/nest/pynestkernel.so(+0x29ac8)[0x7f2c0c5caac8] [59eb791543aa:00113] [22] python[0x50a94c] [59eb791543aa:00113] [23] python(_PyEval_EvalFrameDefault+0x449)[0x50c5b9] [59eb791543aa:00113] [24] python[0x509d48] [59eb791543aa:00113] [25] python[0x50aa7d] [59eb791543aa:00113] [26] python(_PyEval_EvalFrameDefault+0x449)[0x50c5b9] [59eb791543aa:00113] [27] python[0x508245] [59eb791543aa:00113] [28] python[0x589471] [59eb791543aa:00113] [29] python(PyObject_Call+0x3e)[0x5a067e] [59eb791543aa:00113] *** End of error message *** Let me know if you need any additional information and I thank you for your time Angeliki [View Less]

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Open NEST Developer Video Conference Monday 17 February 2020 11:30 CET (UTC+1)
by Dennis Terhorst 17 Feb '20

17 Feb '20

Dear NEST Users & Developers! I would like to invite you to our next bi-weekly Open NEST Developer Video Conference, today Monday 17 February, 11.30-12.30 CET (UTC+1). For details how to log in see below. As usual the agenda for this meeting is also available online, see https://github.com/nest/nest-simulator/wiki/2020-02-17-Open-NEST-Developer-… Agenda * Welcome * Review of NEST User Mailing List * Review of open Github Pull Request * Review of open Github Issues Looking forward … [View More]

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Neuron Model for a Generalized LIF Neuron (No alpha or exponential shaped psc)
by shanka19＠purdue.edu 14 Feb '20

14 Feb '20

Hello NEST Users, I wanted to create a neural network with generalized LIF Neurons. I do not want any exponential or alpha shaped PSCs. Since I cannot draw to describe its shape, I am posting a link from google images to help understand what I mean by a generalized LIF. https://www.google.com/url?sa=i&url=https%3A%2F%2Fwww.researchgate.net%2Ffi… Thanks in advance!

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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, … [View More]

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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 … [View More]

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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/&… [View More]

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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 … [View More]

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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 … [View More]

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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/… [View More]

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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 … [View More]

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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 … [View More]

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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*… [View More]

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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 … [View More]

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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 … [View More]

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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 … [View More]

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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 … [View More]

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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 … [View More]

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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 … [View More]

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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 … [View More]

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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 … [View More]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 [View Less]

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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, … [View More]

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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 … [View More]

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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 … [View More]

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Re: parrot neurons PORT 1
by Charl Linssen 01 Nov '19

01 Nov '19

Dear Nikolas, Could the following example in NEST Simulator be what you're looking for? https://github.com/nest/nest-simulator/blob/f28b138f469354264f65c3b5c9d05e5… """Check STDP protocol between two parrot_neurons connected by a stdp_synapse. Exact pre- and post-synaptic spike times are set by spike_generators connected to each parrot neuron. Additional spikes sent through the stdp_synapse are explicitly ignored in the postsynaptic parrot_neuron by setting the stdp_synapse to connect to … [View More]port 1. """ With kind regards, Charl On Wed, Oct 30, 2019, at 11:58, Nikolaos Chrysanthidis wrote: > Hi Charl, > I want to test the weight change of a single synapse providing stimulation at 2 parrot neurons, so for that reason, > If I excite two pre-,post- parrot neurons (parrot_A,B) using port 0, then the parrot_A will excite the parrot_B as well, so the parrot_B will end up having more spikes than expected. > I think this can be overcome by using port1 of parrot_B in order to ignore the extra excitation from parrot_A. > Please, I'd be grateful if you could provide a way to avoid extra excitation from parrot_A onto parrot_B. > > Kind regards, > Nikolas > > *From:* Charl Linssen <nest-users(a)turingbirds.com> > *Sent:* 28 October 2019 12:11 > *To:* users(a)nest-simulator.org > *Subject:* [NEST Users] Re: parrot neurons PORT 1 > > Dear Nikolaos, > > I'm a little confused as to why you wish to use port 1 for this. A synapse is not aware of incoming or outgoing ports, so if you want to test a particular synapse model, you can connect it between port 0 of a presynaptic parrot neuron, and port 0 of a postsynaptic parrot neuron. Could you otherwise please clarify your use case a bit? > > With kind regards, > Charl > > > On Thu, Oct 17, 2019, at 17:00, Nikolaos Chrysanthidis wrote: >> Hi NEST users, >> >> I have a pre- and post-synaptic spike train and I want to impose these spike trains onto a plastic synapse to see the weight development. >> >> To this end, I thought of having 2 "parrot_neuron_ps" as pre- and post-synaptic neurons connected with the plastic synapse which uses AMPA receptor. >> By doing this, NEST yields the following error: "NESTError: UnknownReceptorType in Connect_g_g_D_D: Receptor type 1 is not available in parrot_neuron_ps." which in my case Receptor type 1 is the AMPA receptor. >> >> At the nest documentation about "parrot_neuron_ps" I found out that I can have the plastic synapse onto port 1 of the postsynaptic parrot neuron >> which I hope it will solve the error with the receptor. >> >> From nest documentation -> "Only spikes arriving on connections to port 0 will be repeated. Connections onto port 1 will be accepted, but spikes incoming >> through port 1 will be ignored. This allows setting exact pre- and post-synaptic spike times for STDP protocols by connecting >> >> two parrot neurons spiking at desired times by, e.g., a stdp_synapse onto port 1 on the post-synaptic parrot neuron." >> >> My query is, how to connect the 2 neurons using port 1 of the post synaptic neuron ? >> If this approach with parrot neurons doesn't seem the right choice, what is the most commonly used approach ? >> >> Thank you very much, >> Kind regards, >> Nikolas >> >> >> >> >> _______________________________________________ >> NEST Users mailing list -- users(a)nest-simulator.org >> To unsubscribe send an email to users-leave(a)nest-simulator.org >> > [View Less]

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Random balanced network with conductance based synapses
by Adam Haber 31 Oct '19

31 Oct '19

Hi, I'm trying to port to NEST this "conductance-based" network from Brian: https://brian2.readthedocs.io/en/stable/examples/frompapers.Stimberg_et_al_… I'm unable to reproduce their results (qualitatively - I'm not expecting identical results since I assume RNGs, solvers and other implementation details differ in many ways). Is there any publicly available example of a random balanced network with conductance based synapses? From what I've seen, all the brunel-style example networks are … [View More]

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parrot neurons PORT 1
by Nikolaos Chrysanthidis 28 Oct '19

28 Oct '19

Hi NEST users, I have a pre- and post-synaptic spike train and I want to impose these spike trains onto a plastic synapse to see the weight development. To this end, I thought of having 2 "parrot_neuron_ps" as pre- and post-synaptic neurons connected with the plastic synapse which uses AMPA receptor. By doing this, NEST yields the following error: "NESTError: UnknownReceptorType in Connect_g_g_D_D: Receptor type 1 is not available in parrot_neuron_ps." which in my case Receptor type 1 is … [View More]

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