- NEST Users - NEST Initiative Mail

local_num_threads, multiprocessing and topology.ConnectLayers
by Juan Manuel Vicente 06 May '20

06 May '20

Hi all, I'm trying to understand some inner workings of Nest. Rigth now I'm running simulations with close half millons elements, using mpirun in a cluster with 25 nodes. The problem I am having is that the "setup" (layer creation and connections) phase takes close to 8min and the simulation only takes 1min. So I tried to use python's multiprocessing package to speed it up, with the following code: nest.ResetKernel() nest.SetKernelStatus({"local_num_threads": 1}) #... connections = [ (layer1, layer1, conn_ee_dict, 1), (layer1, layer2, conn_ee_dict, 2), (layer2, layer2, conn_ee_dict, 3), (layer2, layer1, conn_ee_dict, 4) ] # Process the connections. def parallel_topology_connect(parameters): [pre, post, projection, number] = parameters print(f"Connection number: {number}") topology.ConnectLayers(pre, post, projection) pool = multiprocessing.Pool(processes=4) pool.map(parallel_topology_connect, connections) The above example takes around 0.9s, but if the last two to lines are changed for a sequential call, it takes 2.1s: for [pre, post, projection, number] in connections: print(f"Connection number: {number}") topology.ConnectLayers(pre, post, projection) So far the multiprocessing works great, the problem comes when the "local_num_threads" parameters is changed from 1 to 2 or more, in the cluster it could be 32. The code gets stuck in the topology.Connect without any error, after a while I just stopped it. Also I realised that the tolopoly.ConnectLayers just spawn one thread to connects layers despite the local_num_threads is setted more than one. Any idea what is going on? Thanks in advance Juan Manuel PD: The full example code is attached (60 lines of code). The local_num_threads and multiprocessing_flag variables change the behaviors of the code.

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Implementing Synaptic Failure Rate
by Joshua Stern 04 May '20

04 May '20

Hello, I hope everyone is well. I am working on replicating some results from Teremae et al 2012 <https://www.nature.com/articles/srep00485#Sec4> and have run into an area of uncertainty. The paper calls for there to be a synaptic weight-dependent failure rate of synaptic transmission: [image: image.png] Is there any way to implement this in Nest? If it would help, I am working on a custom neuron model built in Nestml. I can also write some C++ if it seems that there would be an easy way to add this functionality with a short function. Alternatively, are there canonical ways to alter network structure to account for such a failure rate if it cannot be implemented in Nest? Thank you and best wishes, Josh Stern

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NEST3 / Some thoughts on NodeCollections and Connect
by Hans Ekkehard Plesser 01 May '20

01 May '20

Dear Colleagues, This mail is mostly relevant for developers, but I would also like interested users to take a look and comment. In https://github.com/nest/nest-simulator/issues/1570#issuecomment-622380622 I have attempted to summarize a number of thoughts about the details of node representation and Connect() semantics. While a lot is in place, we still need to clarify some details in the near future, before we can release NEST 3. Your input is therefore welcome! If you haven't looked at NEST 3 yet, you may want to take a look at https://nest-simulator.readthedocs.io/en/latest/guides/nest2_to_nest3/nest2… first. Best regards, 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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NEST Conference 2020 goes virtual — Call for Contributions
by Anne Elfgen 30 Apr '20

30 Apr '20

Dear all, The NEST Initiative is excited to invite everyone interested in Neural Simulation Technology and the NEST Simulator to the NEST Conference 2020. The NEST Conference provides an opportunity for the NEST Community to meet, exchange success stories, swap advice, learn about current developments in and around NEST spiking network simulation and its application. This year's conference will take place as a *virtual conference* on *Monday/Tuesday 29/30 June 2020*. We are now inviting contributions to the conference, including plenary talks, "posters" and breakout sessions on specific topics. *Important dates* *01 June 2020* — Deadline for submission of contributions *08 June 2020* — Notification of acceptance *10 June 2020* — Deadline for NEST Initiative Membership applications (registration is free for members in 2020) *22 June 2020* — Registration deadline *29 June 2020* — NEST Conference 2020 starts For more information on how to submit your contribution, register and participate, please visit the conference website *https://nest-simulator.org/conference* We are looking forward to seeing you all in June! Hans Ekkehard Plesser, Susanne Kunkel, Dennis Terhorst, Anne Elfgen & many more

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error at installing nest2.20 from source code
by Abolfazl Ziaeemehr 29 Apr '20

29 Apr '20

Hello everyone, I used the source code to install nest simulator 2.20 from here <https://nest-simulator.readthedocs.io/en/stable/installation/linux_install.…> and did the following steps (I used to do the same steps for version 2.18 without error.) cmake -Dwith-python=3 -DCMAKE_INSTALL_PREFIX:PATH=</install/path> </path/to/NEST/src> make make install make installcheck I got this error from "make installcheck": Phase 1: Testing if SLI can execute scripts and report errors ------------------------------------------------------------- Running test 'selftests/test_pass.sli'... Running Apr 21 19:46:31 SLIStartup [Error]: NEST_DATA_DIR is not usable: Apr 21 19:46:31 SLIStartup [Error]: Directory '/usr/share/nest' does not exist. Apr 21 19:46:31 SLIStartup [Error]: I'm using the default: /home/abolfazl/prog/install-dir/nest-simulator-2.20.0_build/share/nest Apr 21 19:46:31 SLIStartup [Error]: NEST_DOC_DIR is not usable: Apr 21 19:46:31 SLIStartup [Error]: Directory '/usr/share/doc/nest' does not exist. Apr 21 19:46:31 SLIStartup [Error]: I'm using the default: /home/abolfazl/prog/install-dir/nest-simulator-2.20.0_build/share/doc/nest /usr/bin//bin/nest /usr/share/doc/nest/selftests/test_pass.sli /home/abolfazl/prog/install-dir/nest-simulator-2.20.0_build/bin/nest_serial: 20: /home/abolfazl/prog/install-dir/nest-simulator-2.20.0_build/bin/nest_serial: Apr: not found Failed: unexpected exit code 127 Running Apr 21 19:46:31 SLIStartup [Error]: NEST_DATA_DIR is not usable: Apr 21 19:46:31 SLIStartup [Error]: Directory '/usr/share/nest' does not exist. Apr 21 19:46:31 SLIStartup [Error]: I'm using the default: /home/abolfazl/prog/install-dir/nest-simulator-2.20.0_build/share/nest Apr 21 19:46:31 SLIStartup [Error]: NEST_DOC_DIR is not usable: Apr 21 19:46:31 SLIStartup [Error]: Directory '/usr/share/doc/nest' does not exist. Apr 21 19:46:31 SLIStartup [Error]: I'm using the default: /home/abolfazl/prog/install-dir/nest-simulator-2.20.0_build/share/doc/nest /usr/bin//bin/nest /usr/share/doc/nest/selftests/test_pass.sli /home/abolfazl/prog/install-dir/nest-simulator-2.20.0_build/bin/nest_serial: 20: /home/abolfazl/prog/install-dir/nest-simulator-2.20.0_build/bin/nest_serial: Apr: not found *** *** An unexpected exit code usually hints at a bug in the test suite! *** *** Please report the problem at *** https://github.com/nest/nest-simulator/issues *** *** To help us diagnose the problem, please attach the archived content *** of these directories to the issue: *** - '/home/abolfazl/prog/install-dir/nest-simulator-2.20.0_build/reports' *** - '/home/abolfazl/prog/install-dir/nest-simulator-2.20.0_build/reports/nest.CgbAi' *** CMakeFiles/installcheck.dir/build.make:57: recipe for target 'CMakeFiles/installcheck' failed make[3]: *** [CMakeFiles/installcheck] Error 2 CMakeFiles/Makefile2:99: recipe for target 'CMakeFiles/installcheck.dir/all' failed make[2]: *** [CMakeFiles/installcheck.dir/all] Error 2 CMakeFiles/Makefile2:106: recipe for target 'CMakeFiles/installcheck.dir/rule' failed make[1]: *** [CMakeFiles/installcheck.dir/rule] Error 2 Makefile:188: recipe for target 'installcheck' failed make: *** [installcheck] Error 2 -- regards, Abolfazl Ziaeemehr Department of Physics, PhD student in Computational Physics Institute for Advanced Studies in Basic Sciences (IASBS) Tel: 0919 607 4296 Page: iasbs.ac.ir/~a.ziaeemehr

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Reset while keeping network connections
by Daphne Cornelisse 27 Apr '20

27 Apr '20

Dear Nest community, I have a network of LIF neurons ('iaf_cond_alpha') and I would like to implement STDP synapses, rather than the standard 'static_synapse'. I would like to be able to set a subset of the network to STDP synapses (e.g. all excitatory ones) and leave the rest static. This is how have implemented that currently (see code). I am using a for loop because I want to see how STDP changes the activity over time (over many iterations), which leaves me with the following two questions: *1. Is this a correct way to implement STDP in nest? * *2. Is there a way to reset the network such that the connections are not lost? *ResetNetwork() and ResetKernel() both seem to destroy all the network connections. While I would like to keep them, so that the network becomes less and less randomly connected per simulation. Thank you! Best, Daphne *CODE* # define network connectivity conn_dict = {'rule': 'pairwise_bernoulli', 'p': 0.1} # define dicts for static synapses static_ex_params = {'model':'static_synapse','weight': 6.0, 'delay': 1.5} static_in_params = {'model':'static_synapse','weight': -96.0, 'delay': 1.5} if self.STDP == 'ALL': # all synapses should be stdp ones, make connections between the two populations: # from exc neurons to all neurons nest.Connect(neurons_all[:self.NE], neurons_all, conn_dict, self.syn_params_ex) # from interneurons to all neurons nest.Connect(neurons_all[self.NE:], neurons_all, conn_dict, self.syn_params_in) elif self.STDP == 'EXC': # keep the inhibitory synapses static # connections from exc neurons to all neurons nest.Connect(neurons_all[:self.NE], neurons_all, conn_dict, self.syn_params_ex) # connections from interneurons to all neurons nest.Connect(neurons_all[self.NE:], neurons_all, conn_dict, static_in_params) where synapse_params_in = { 'model':'stdp_synapse', 'lambda': 0.01, 'alpha': 1.0, 'delay': 1.5, 'weight':-95.0 }

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Open NEST Video Conference Satellite Event: A declarative front-end for network and simulation specifications
by Dennis Terhorst 24 Apr '20

24 Apr '20

Dear NEST Users & Developers! Additionally to the Open NEST Developers VC on Monday, we would like to announce a user contributed presentation of *A declarative front-end for network and simulation specifications* by /Tom Bugnon/ (Paris) and /Will Mayner/ (Wisconsin). on Monday 27 April, 16.00-17.00 CEST (UTC+2) / 9.00am CDT (UTC-5). This frontend to NEST allows to define the structure of more-or-less arbitrary simulations in a set of parameter files. Those let the user define network parameters (layers, neuron/synapse models, connections and nest.Topo "connection models", "input" layers etc.) and simulation parameters (set-up recorders, set-up "sessions", or units of simulations, for which the user can define specific inputs, changes in the state of some units, etc). This approach makes it easier to version-control the network and simulation specifications, share parameter files, perform parameter exploration, or run the same network in different conditions. We will meet in the same VC room, but due to the timezone difference of the presenters this had to be detached from the meeting in the morning. Connection details are given below. 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 -- 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 ------------------------------------------------------------------------------------- Forschungszentrum Juelich GmbH 52425 Juelich Sitz der Gesellschaft: Juelich Eingetragen im Handelsregister des Amtsgerichts Dueren Nr. HR B 3498 Vorsitzender des Aufsichtsrats: MinDir Volker Rieke Geschaeftsfuehrung: Prof. Dr.-Ing. Wolfgang Marquardt (Vorsitzender), Karsten Beneke (stellv. Vorsitzender), Prof. Dr.-Ing. Harald Bolt -------------------------------------------------------------------------------------

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Open NEST Developer Video Conference Monday 27 April 2020 11:30 CEST (UTC+2)
by Dennis Terhorst 24 Apr '20

24 Apr '20

Dear NEST Users & Developers! I would like to invite you to our next fortnightly Open NEST Developer Video Conference on Monday 27 April, 11.30-12.30 CEST (UTC+2). This VC will be in the updated format and we may do some more explanation than I'd expect in future meetings. In the Project team round, a contact person of each team will give a short statement summarizing ongoing work in the team and cross-cutting points that need discussion among the teams. The remainder of the meeting we would go into a more in-depth discussion suggested from the teams. Agenda Welcome Review of NEST User Mailing List Short introduction to Github project usage Project team round In-depth discussion The agenda for this meeting is also available online, see https://github.com/nest/nest-simulator/wiki/2020-04-27-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

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Re: SARS-CoV face mask sanitizing gels
by ywjingqing 23 Apr '20

23 Apr '20

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Question about MPI and multithreading
by kusch lionel 15 Apr '20

15 Apr '20

Dear all, I am actually working on the I/O for Nest with MPI. I am not aware of the solution of Nest for managing the communication between process and thread. I would like to learn more about it for adapting the interface with the actual solution. If someone can answer some of my questions : 1) By looking at the initialization of the MPI, I saw Nest use the /MPI_THREAD_FUNNELED /for the level of thread support. What is the reason for it? 2) This level of thread support surprise me because I suppose that it will overload one thread with all the MPI calls. Why do you do not choose the level /MPI_THREAD_SERIALIZED/? 3) I would like to have different levels for thread support. Do you think it's possible ? Thank you in advance for your answer, Kusch Lionel PS: The reference to the different MPI thread support : http://mpi.deino.net/mpi_functions/MPI_Init_thread.html

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GitHub Projects
by Dennis Terhorst 14 Apr '20

14 Apr '20

Dear NEST users and developers, some of you may already have noticed, that we recently updated a lot of issues and pull-requests in our repository. The changes are completely organizational and aim to provide a better overview and service to our community. In particular, we removed the "C:" category labels (Model, Kernel, PyNEST, Documentation, ...) and instead now make use of corresponding GitHub projects. There, issues and pull-requests are represented as "cards" on a Kanban-like board, which gives a comprehensive view on the current topics and enables dedicated discussions to focus more easily. For each project we assigned a contact person that will take care of organizing work for that subset of cards. You notice that also the "P:" progress labels have mostly been removed (except "blocked" and "won't fix"), as this is automatically tracked in the columns of the projects and is much easier to manage there. The change to GitHub projects enables us to discuss topics in a more focused fashion than detailed issue-by-issue, which will also be reflected in the Open NEST Developer Video Conference. Projects will give a general status update and can raise overarching questions into the discussion. The detailed issue-by-issue work on the other hand, is organized by the project groups separately and each group may decide to do separate meetings to discuss details. Besides the long-running projects corresponding to the category labels, larger short/mid-term activities are organized in "Feature-Projects". These projects aim to help developers to work on special or cross-cutting topics and are expected to be "finished" at some point. The open VC will cover them similar to the long-term projects if required. We hope these changes improve the overview over the work ongoing in all the many areas for users and developers, facilitate detailed discussions between relevant and interested people and make the work on the simulator more transparent. Best, Dennis

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Open NEST Developer Video Conference Monday 13 April 2020 SKIPPED (Easter Monday)
by Dennis Terhorst 13 Apr '20

13 Apr '20

Dear NEST Users & Developers! I would like to wish you all a happy Easter time and I hope you are all well despite the current circumstances. Since it is Easter Monday in some parts of the world, we will skip this meeting. I am looking forward to seeing you again in our next Open NEST Developer Video Conference on April 27th. Stay safe, best, Dennis Terhorst

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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 be able to control the dynamic of these inputs. However, I have not been able to find a way to do this. One idea I've had is to set the amplitude of a noise-generator to change according to a function of my choosing (going back to the previous example, it would be an exponential function). But this would require for this parameter to be changed mid-simulation, or to be assigned to a function and interpreted by NEST. Is any of this possible? Or alternatively, do you know of another way of accomplishing this? Thank you! Nicolas

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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 Projects & Branches Review of open Github Pull Request Review of open Github Issues The agenda for this meeting is also available online, see https://github.com/nest/nest-simulator/wiki/2020-03-30-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

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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,{'rule': 'all_to_all'}) # we can now query the synapses using GetConnections conns = nest.GetConnections(epop1,target = epop2) nest.GetStatus(conns,["target","weight"]) This runs fine for n < 5, but I get the following error with n >=5: Assertion failed: (source_lid < MAX_LID), function set_source_lid, file /usr/local/miniconda/conda-bld/nest-simulator_1583214474797/work/nestkernel/target_data.h, line 264. Abort trap: 6 I have run some of the example scripts like brunel_alpha_numpy with a few thousand neurons and they work just fine. Am I making an improper call to GetConnections here? And if so, what is a better way to dynamically check connectivity? Alternatively, might there be something wrong with my Nest environment? And if so, what should I look at to troubleshoot this? Thank you so much for your help. Best wishes, Josh

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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 CMakeLists.txt:106 (FILTER_HEADERS): Unknown CMake command "FILTER_HEADERS". CMake Warning (dev) in CMakeLists.txt: No cmake_minimum_required command is present. A line of code such as cmake_minimum_required(VERSION 3.13) should be added at the top of the file. The version specified may be lower if you wish to support older CMake versions for this project. For more information run "cmake --help-policy CMP0000". This warning is for project developers. Use -Wno-dev to suppress it. -- Configuring incomplete, errors occurred! See also "/home/bsvogler/Dokumente/nest-simulator/nestinstall/CMakeFiles/CMakeOutput.log". ======= I tried the master branch and the nest3 branch. I need a working nest 3 simulator. I managed to compile just yesterday but in the meantime, I reinstalled the operating system. Please help me out. Kind regards, Benedikt S. Vogler

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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 used in NEST guides (https://bit.ly/2xBNfpO). As I imagined, it didn’t work maybe because the output type of the music port doesn’t match the input type of the receptor type (’the following error’). Does anyone know how I can overcome this problem (that I can use ‘music_cont_in_proxy’ as current source)? Thank you very much in advance. ########ERROR######## Traceback (most recent call last): File "./conttest.py", line 39, in <module> nest.Connect(mcip, mc, 'one_to_one', {'receptor_type': 7}) File "/local/work/Projects/closed-loop-learning/NEST/lib/python3.7/site-packages/nest/ll_api.py", line 246, in stack_checker_func return f(*args, **kwargs) File "/local/work/Projects/closed-loop-learning/NEST/lib/python3.7/site-packages/nest/lib/hl_api_connections.py", line 362, in Connect sr('Connect') File "/local/work/Projects/closed-loop-learning/NEST/lib/python3.7/site-packages/nest/ll_api.py", line 132, in catching_sli_run raise exceptionCls(commandname, message) nest.ll_api.UnexpectedEvent: ('UnexpectedEvent in Connect_g_g_D_D: Node cannot handle received event.', 'UnexpectedEvent', <SLILiteral: Connect_g_g_D_D>, ': Node cannot handle received event.’) ########ERROR######## Best wishes, Mohammad -- Mohammadreza Mohagheghi Nejad Postdoctoral researcher in computational neuroscience, Institute of Neural Computation, Ruhr University Bochum, Germany https://www.ini.rub.de/the_institute/people/mohammadreza-mohagheghi_nejad/

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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 available. Does anybody have any idea where I can find it? Thank you very much in advance for your help, Best wishes, Mohammad -- Mohammadreza Mohagheghi Nejad Postdoctoral researcher in computational neuroscience, Institute of Neural Computation, Ruhr University Bochum, Germany https://www.ini.rub.de/the_institute/people/mohammadreza-mohagheghi_nejad/

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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 Review of NEST User Mailing List Review of open Github Pull Request Review of open Github Issues The agenda for this meeting is also available online, see https://github.com/nest/nest-simulator/wiki/2020-03-16-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

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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 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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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. Could you please advise what I should do to examine the problem? I am using NEST version 2.20 and NESTML version 3.0.post0.dev5 (pip-installed). Faithfully yours, Alex Serenko, graduate student at Kurchatov Institute, Moscow, Russia

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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 operator and could not find similar documentation as in the transition guide. My current workaround is to loop over each instance the list and call Set() on each instance/synapse. What is the recommended way to create a SynapseCollections from many? Is there somewhere more documentation covering nest 3 than the two pages covering the changes form nest 2 to 3? Kind regards, Benedikt S. Vogler

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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 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

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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 nestkernel/CMakeFiles/nestkernel.dir/connection_manage.cpp.o /home/visapy_and_dependencies/nest-simulator-2.20.0/nestkernel/connection_managercpp:419:1: error: prototype for ‘void nest::ConnectionManager::connect(nest::inde, nest::Node*, nest::thread, nest::synindex, const DictionaryDatum&, double, doube)’ does not match any in class ‘nest::ConnectionManager’ nest::ConnectionManager::connect( const index sgid, ^~~~ In file included from /home/visapy_and_dependencies/nest-simulator-2.20.0/nestkerel/connection_manager.cpp:23:0: /home/visapy_and_dependencies/nest-simulator-2.20.0/nestkernel/connection_managerh:135:8: error: candidates are: bool nest::ConnectionManager::connect(nest::inde nest::index, const DictionaryDatum&, nest::synindex) bool connect( const index sgid, const index target, const DictionaryDatum& parms, const synindex syn_id ); ^~~~~~~ /home/visapy_and_dependencies/nest-simulator-2.20.0/nestkernel/connection_managerh:117:8: error: void nest::ConnectionManager::connect(nest::index nest::Node*, nest::thread, nest::synindex, const DictionaryDatum&, double_t, doule_t) void connect( const index sgid, ^~~~~~~ /home/visapy_and_dependencies/nest-simulator-2.20.0/nestkernel/connection_managercpp:352:1: error: void nest::ConnectionManager::connect(const nes::GIDCollection&, const nest::GIDCollection&, const DictionaryDatum&, const DictinaryDatum&) nest::ConnectionManager::connect( const GIDCollection& sources, ^~~~ make[2]: *** [nestkernel/CMakeFiles/nestkernel.dir/connection_manager.cpp.o] Erro 1 make[1]: *** [nestkernel/CMakeFiles/nestkernel.dir/all] Error 2 make: *** [all] Error 2 I have no idea about this, I'd appreciate it if you could help me. and my cmake version 3.10.1, gcc version 7.4.0

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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 quite sure what it is trying to tell me. Thanks in advance, Lea ......................................................... M. Sc. Lea Steffen Wissenschaftlicher Mitarbeiter | Research Scientist Intelligent Systems and Production Engineering (ISPE) Interactive Diagnosis and Service Systems (IDS) FZI Forschungszentrum Informatik Haid-und-Neu-Str. 10–14 76131 Karlsruhe, Germany Tel.: +49 721 9654-218 steffen(a)fzi.de www.fzi.de/mitarbeiter/steffen ......................................................... FZI Forschungszentrum Informatik am Karlsruher Institut für Technologie Stiftung des bürgerlichen Rechts Stiftung Az: 14-0563.1 Regierungspräsidium Karlsruhe Vorstand: Prof. Dr. Andreas Oberweis, Jan Wiesenberger, Prof. Dr.-Ing. J. Marius Zöllner Vorsitzender des Kuratoriums: Ministerialdirigent Günther Leßnerkraus .........................................................

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