April 2020 - NEST Users - NEST Initiative Mail

NEST network object
by alehr 20 Nov '20

20 Nov '20

Dear NEST developer, I would like to initialize a network with neurons and connections and then run many simulations with it. It would be great if I could build the network one time and then deepcopy (or something similar) for each simulation. Is something like this possible? Thanks, Andrew Lehr

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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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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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