November 2020 - NEST Users - NEST Initiative Mail

error std::bad_alloc: virtualbox
by Allen Rabayda 12 Mar '21

12 Mar '21

Dear Nest Community, Has anyone encountered a "bad_alloc" error like the one below and if so, any recommendations? It appears to be a VM memory issue but only using 21% of harddrive space (ref: below). My simulation successfully completes for 200,000 ms but errors out at 98% complete for 230,000 ms, 75% for 300,000 ms and 56% for 400,000 ms. I'm running on NEST 2.18.0 VirtualBox lubuntu 18.04 (ref: image of settings below). Thank you for any suggestions. Best Regards, --Allen ********************************************** **** Error Message ***** >> # SIMULATION >> nest.Simulate(300000) Nov 21 17:10:28 NodeManager::prepare_nodes [Info]: Preparing 684 nodes for simulation. Nov 21 17:10:28 MUSICManager::enter_runtime [Info]: Entering MUSIC runtime with tick = 1 ms Nov 21 17:10:28 SimulationManager::start_updating_ [Info]: Number of local nodes: 684 Simulation time (ms): 300000 Number of OpenMP threads: 2 Number of MPI processes: 1 75 %: network time: 223698.0 ms, realtime factor: 0.6277Traceback (most recent call last): File "<stdin>", line 3, in <module> File "/home/nest/work/nest-install/lib/python3.6/site-packages/nest/ll_api.py", line 246, in stack_checker_func return f(*args, **kwargs) File "/home/nest/work/nest-install/lib/python3.6/site-packages/nest/lib/hl_api_simulation.py", line 66, in Simulate sr('ms Simulate') File "/home/nest/work/nest-install/lib/python3.6/site-packages/nest/ll_api.py", line 132, in catching_sli_run raise exceptionCls(commandname, message) nest.ll_api.std::bad_alloc: ('std::bad_alloc in Simulate_d: C++ exception: std::bad_alloc', 'std::bad_alloc', <SLILiteral: Simulate_d>, ': C++ exception: std::bad_alloc') ******************************************** **** Folder Space on VirtualBox after Error **** nest@nestvm:~$ df -h Filesystem Size Used Avail Use% Mounted on udev 5.2G 0 5.2G 0% /dev tmpfs 1.1G 1.1M 1.1G 1% /run /dev/sda1 99G 20G 76G 21% / tmpfs 5.2G 0 5.2G 0% /dev/shm tmpfs 5.0M 4.0K 5.0M 1% /run/lock tmpfs 5.2G 0 5.2G 0% /sys/fs/cgroup SharedNest2 917G 447G 470G 49% /media/sf_SharedNest2 tmpfs 1.1G 16K 1.1G 1% /run/user/1000 /dev/sr0 74M 74M 0 100% /media/nest/VBox_GAs_6.0.10 *********************************** **** VirtualBox Settings ******* [image: image.png]

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Getting single neuron spiking
by nosratullah mohammadi 30 Nov '20

30 Nov '20

Dear NEST Users, I wonder how to get single neuron spikes out of spike detector that record all of the neurons in the network. Best, Nosratullah Mohammadi (Mr.)

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Open NEST Developer Video Conference Monday 23 November 2020 11:30 CET (UTC+1)
by Dennis Terhorst 23 Nov '20

23 Nov '20

Dear NEST Users & Developers! I would like to invite you to our next fortnightly Open NEST Developer Video Conference today Monday 23 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 For the in-depth discussion the topic of "/Compiler variants vs. MPI implementations/" was proposed, as this is recently causing headache on some setups. The agenda for this meeting is also available online, see https://github.com/nest/nest-simulator/wiki/2020-11-23-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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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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Microcircuit example, segmentation fault
by d.standage＠bham.ac.uk 17 Nov '20

17 Nov '20

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

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Re: NEST on macOS 11 Big Sur
by Joris Dolderer 14 Nov '20

14 Nov '20

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 > > ------------------------------------------------------------------------------------------------ > > ------------------------------------------------------------------------------------------------ > >

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NEST on macOS 11 Big Sur
by Hans Ekkehard Plesser 14 Nov '20

14 Nov '20

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

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Open NEST Developer Video Conference Monday 9 November 2020 11:30 CET (UTC+1)
by Dennis Terhorst 09 Nov '20

09 Nov '20

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

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Configuration of multi-node parallel environment
by 1323504842＠qq.com 05 Nov '20

05 Nov '20

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?

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Data-handling with NEST-MPI
by swathi anil 03 Nov '20

03 Nov '20

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

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NEST Users November 2020