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Microcircuit example, segmentation fault

by d.standage＠bham.ac.uk

Hi all - I'm running NEST on Ubuntu 18.04, installed with Conda. I can run the example networks in the user documentation, except the Microcircuit Example (having downloaded all the files). It causes a segmentation fault during the call to Simulate( ). I can provide the full error message, but in the interest of brevity - Signal: Segmentation fault (11) Signal code: Address not mapped (1) ... [ 0] /lib/x86_64-linux-gnu/libpthread.so.0(+0x128a0)[0x7feb38d5f8a0] ... Segmentation fault (core dumped) Has anyone else had this issue? I'd be grateful for any help you can provide. Best Dominic

4 years, 1 month

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Re: NEST on macOS 11 Big Sur

by Joris Dolderer

Thank you for your very useful e-mail! You wrote a lot, but you also had something to say. On Sat, 14 Nov 2020, 13:35 Hans Ekkehard Plesser, < hans.ekkehard.plesser(a)nmbu.no> wrote: > > Dear all, > > I am happy to report that NEST seems to work find under macOS 11 Big Sur. > So far, I have only tested on Intel hardware, a system with the Apple M1 > chip is on its way. > > Specifcially, I proceeded as follows: > > 1. After upgrading to Big Sur, run "brew doctor" and follow the > instructions to update the Apple Command Line Tools. If you encounter > problems, see > https://stackoverflow.com/questions/64821648/homebrew-fails-on-macos-big-sur > > 2. Run "brew update" and "brew upgrade". > > 3. For safety's sake, I then ran "brew uninstall nest" and then "brew > install nest". This gave me a working NEST 2.20.0 installation. > > > To build NEST myself, I first performed steps 1 and 2 above and then > > 3. conda update conda > conda create -n nest_dev nomkl numpy scipy matplotlib ipython cython > nose > conda activate nest_dev > pip install junitparser > > The nomkl package ensures that NumPy does not use Intel's MKL, which can > lead to conflicting OpenMP libraries. > Junitparser is needed to handle testsuite results and is only available > from PyPI. > > 4. Pull latest sources from NEST master branch to src > > 5. mkdir bld > cd bld > cmake -DCMAKE_INSTALL_PREFIX:PATH=<install path> -Dwith-mpi=ON ../src > make -j4 install && make installcheck > > All tests pass. If many MPI tests fail, you may need to add > --oversubscribe to the mpirun command in your .nestrc file. C++ tests will > only run if you have installed boost, e.g., with "brew install boost". > > Best regards, > Hans Ekkehard > > -- > > > Prof. Dr. Hans Ekkehard Plesser > Head, Department of Data Science > > 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 > > > _______________________________________________ > NEST Users mailing list -- users(a)nest-simulator.org > To unsubscribe send an email to users-leave(a)nest-simulator.org > > > > ------------------------------------------------------------------------------------------------ > > ------------------------------------------------------------------------------------------------ > 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 > > ------------------------------------------------------------------------------------------------ > > ------------------------------------------------------------------------------------------------ > >

4 years, 1 month

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NEST on macOS 11 Big Sur

by Hans Ekkehard Plesser

Dear all, I am happy to report that NEST seems to work find under macOS 11 Big Sur. So far, I have only tested on Intel hardware, a system with the Apple M1 chip is on its way. Specifcially, I proceeded as follows: 1. After upgrading to Big Sur, run "brew doctor" and follow the instructions to update the Apple Command Line Tools. If you encounter problems, see https://stackoverflow.com/questions/64821648/homebrew-fails-on-macos-big-sur 2. Run "brew update" and "brew upgrade". 3. For safety's sake, I then ran "brew uninstall nest" and then "brew install nest". This gave me a working NEST 2.20.0 installation. To build NEST myself, I first performed steps 1 and 2 above and then 3. conda update conda conda create -n nest_dev nomkl numpy scipy matplotlib ipython cython nose conda activate nest_dev pip install junitparser The nomkl package ensures that NumPy does not use Intel's MKL, which can lead to conflicting OpenMP libraries. Junitparser is needed to handle testsuite results and is only available from PyPI. 4. Pull latest sources from NEST master branch to src 5. mkdir bld cd bld cmake -DCMAKE_INSTALL_PREFIX:PATH=<install path> -Dwith-mpi=ON ../src make -j4 install && make installcheck All tests pass. If many MPI tests fail, you may need to add --oversubscribe to the mpirun command in your .nestrc file. C++ tests will only run if you have installed boost, e.g., with "brew install boost". Best regards, Hans Ekkehard -- Prof. Dr. Hans Ekkehard Plesser Head, Department of Data Science 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

4 years, 1 month

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Open NEST Developer Video Conference Monday 9 November 2020 11:30 CET (UTC+1)

by Dennis Terhorst

Dear NEST Users & Developers! I would like to invite you to our next fortnightly Open NEST Developer Video Conference today Monday 9 November, 11.30-12.30 CET (UTC+1). 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 of topics that came up on the mailing list or that are suggested by the teams. Agenda Welcome Review of NEST User Mailing List Project team round In-depth discussion The agenda for this meeting is also available online, see https://github.com/nest/nest-simulator/wiki/2020-11-09-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

4 years, 1 month

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Configuration of multi-node parallel environment

by 1323504842＠qq.com

Hi,I am now simulating a small network for testing on two machines, and run it with the following command. It seems that the two machines run by themselves without interaction,running your own. mpirun -np 2 -host work0,work1 python ./multi_test.py Can nest simulate a network in a multi-node cluster environment? If yes, how do the nodes exchange data? Do you know about the configuration of a parallel cluster environment? I installed NEST under ANCCONDA? Can anyone share some experience?

4 years, 1 month

2
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Data-handling with NEST-MPI

by swathi anil

Hello all, I use NEST with OpenMPI on a high performance cluster to run plasticity related network simulations. So far I have divided my whole job into: phase 1: data collection (data collected: senders, times, sources, targets for each time point) phase 2: data anaylsis (refers to spike count and connectivity calculation) I face an issue with data-handling. In phase 1, the data pertaining to each of the four variables is saved in X different files (X = number of virtual processes), rank-wise. This means that the total number of files generated goes [ n(time-points)*X*4 ], which surpasses the chunk file storage limit, per user for the cluster. Each file here is an ndarray saved as a *.npy file. I wonder if there is a way to retrieve the data from each of the X processes while collecting data, concatenating and then saving them? So instead of X number of files, I can save the concatenated version. This probably involves recruiting a single VP to collect and concatenate and save the datapoints, but i am not quite sure how to execute this using NEST. Any help would be highly appreciated! Thanks in advance! Best, Swathi

4 years, 1 month

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because of the spike time stored in unordered time, so I get problem ablout the use of stdp_synapse.

by 1240288839＠qq.com

Dear all! I want to know how to use stdp_synapse correctly but I noticed there is a sentence 'Another important point is that spikes do NOT pass the Connection object in correct order of biological arrival time—they are unordered in time' about the overview of stdp_synapse; it's the last part of spike handling at website https://nest.github.io/nest-simulator/synapses_overview. So if these spike time are unordered, whether the stdp_synapse function would mimic properly.

4 years, 1 month

3
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Open NEST Developer Video Conference Monday 26 October 2020 11:30 CET (UTC+1)

by Dennis Terhorst

Dear NEST Users & Developers! I would like to invite you to our next fortnightly Open NEST Developer Video Conference today Monday 26 October, 11.30-12.30 CET (UTC+1). Please note that we changed to winter time (UTC+1). 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 of topics that came up on the mailing list or that are suggested by the teams. Agenda Welcome Review of NEST User Mailing List Project team round In-depth discussion We will continue discussion on some of the topics of last time: * Issue #1773 <https://github.com/nest/nest-simulator/issues/1773>: wrapper around |Prepare| and |Run| (postponed from last time) * organizing HBP CodeJam#11 activities <https://www.humanbrainproject.eu/en/education/participatecollaborate/infras…> The agenda for this meeting is also available online, see https://github.com/nest/nest-simulator/wiki/2020-10-26-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

4 years, 1 month

1
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0 0

V_th Issue in Izhikevich Neuron Model

by Allen Rabayda

Dear Nest Community, When trying to reproduce Izhikevich's Simple Neuron Model with NEST Izhikevich Neuron Model, it is spiking before reaching my V_th potential threshold setting of 30 mV, producing results inconsistent with the publication. Would anybody have insight as to why the neuron is spiking early? Did I perhaps not include a relevant NEST setting? I compared it to an explicit implementation of the ODEs, attached, for your reference of expected neuron response. Thank you for any suggestions. Best Regards, --Allen

4 years, 2 months

3
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test failures on nest master@6997cae6c on Fedora 32 with Intel Prallel Studio XE 2020 update 2

by Nilton Liuji Kamiji

Dear all, I have compiled NEST master@6997cae6c onFedora 32 with both, 1- gcc (10.2.1) and OpenMPI (4.0.4): the default on this distro 2 - Intel Parallel Studio XE update 2 with GSL compiled from source using the same compiler using same configuration (-Dwith-mpi=ON, -Dwith-boost=ON) . On Intel, -Dwith-gsl=${GSL_DIR} was added to point to the GSL built with the Intel Compiler. On the gcc configuration, all tests worked fine (I defined OMPI_MCA_rmaps_base_oversubscribe=1 to avoid oversubscription error as reported in issue #1758). On the other hand, on the Intel configuration, several MPI tests have failed as described in the attached files. (To allow oversubscription the following variables were defined: I_MPI_WAIT_MODE=1 and I_MPI_THREAD_YIELD=3) I report it here as it is probably not directly a NEST code issue, but hope that someone in the community could have the answer. If I should submit it as an issue on GitHub, please let me know. Attached files: cmake_command_summary.txt : cmake command invocation and summary installcheck.log : make installcheck log reports.tar.gz : reports folder created by make installcheck; it also contains the instalcheck.log file above Best, Nilton -- Nilton Liuji Kamiji University of Sao Paulo Department of Physics, FFCLRP Laboratory of Neural Systems Phone: +55 16 3315 3859

4 years, 2 months

2
2
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