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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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C++ files for synapse models renamed
by Hans Ekkehard Plesser 12 Mar '21

12 Mar '21

Dear NEST Developers, With #1972, which I just merged into the master branch, the C++ file names for the synapse models have changed from xyz_connection.h to xyz_synapse.h to make them consistent with the model names we have on the user side. Please pull this change into your branches as soon as possible. This is purely a behind-the-scenes change which does not affect users. Best, 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<mailto:hans.ekkehard.plesser@nmbu.no> Home http://arken.nmbu.no/~plesser

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Writing an extension module with MyModule
by raymond.hawkins＠mail.utoronto.ca 11 Mar '21

11 Mar '21

Hello, I would like to add a kernel function to use with NEST topology, and am attempting to follow the instructions at http://nest.github.io/nest-simulator/extension_modules and https://nest-simulator.readthedocs.io/en/nest-2.20.1/topology/Topology_User…, which both mention the MyModule example in the examples folder of the NEST distributable. However, I can't find such an example in my local NEST files, or in the github repository (https://github.com/nest/nest-simulator). Is there another location I should be looking in for this example, or would someone be kind enough to send me the necessary files? Many thanks, Raymond Hawkins

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NEST performance assesment
by conrad.hillairet＠arm.com 09 Mar '21

09 Mar '21

Hello, I would like to assess the performances of NEST on different hardwares. And I have some questions if I may. I am thinking about reusing one of the benchmarks here : https://github.com/compneuronmbu/nest-benchmarks. Let's assume we have two nodes : A and B. A has N cores and B has M cores. I want to know if NEST runs faster for a particular test case on A or B. Hence I am fully filling the nodes with MPI ranks and OpenMP threads. If my understanding is correct, I need to set NVP = MPI ranks x OpenMP threads hence NVP = N on A and NVP = M on B. At this stage, for a lot of applications I would just say "The application runs faster on A or on B." . What worries me for NEST is that N and M might be different, hence different NVP for the simulation on A and B. From the documentation it says that for different NVP we have different results. So it gets me a bit worried to say that NEST is faster on A or B for a particular test case if I am not computing the same thing. I was wondering if you could confirm whether this is (or not) an issue and if you could give me some guidelines as regards benchmarking NEST please. That would be fantastic. This is also problematic if I want to do a strong scaling study on a single node for instance. I could run NEST on the smallest common multiple of N and M (let's call it P). This would mean P/N nodes of A and P/M nodes of B. I guess this would make sense for NEST. But this is not a single node comparison, this is more a core vs core comparison. Hope this makes sense. And please feel free to correct me if I said something wrong. I do not have a lot of experience with NEST. Best regards, Conrad Hillairet.

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Transcribing NEST mailing list questions?
by Robin Gilbert De Schepper 06 Mar '21

06 Mar '21

Hi, I have proposed the use of StackOverflow as a channel for questions. What does everyone think about it if I transcribe the mailing list questions and possibly their answers onto StackOverflow? (For fellow SO'ers, I will be making them Community Wiki questions as not to unfairly absorb all that future reputation 💸💰💵)

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Pull-request session
by Dennis Terhorst 01 Mar '21

01 Mar '21

Dear everyone, in today's meeting [1] we discussed the relations between the currently open pull-requests [2], and found that we would need a separate meeting to discuss some in more detail. To find an appropriate date I've put a few random slots into a poll [3]. Please fill your availability if you are interested to join, till tomorrow evening: --> https://nuudel.digitalcourage.de/zreAHis9t4BPC5Rl Anyone involved with any of the topics or interested to help testing/proof-reading/…, is very welcome to join. Feel free to have a look! Some discussions will – by their nature – however be quite developer oriented. I'll send connection details to participants when a suitable slot is found. Best, Dennis [1]: https://github.com/nest/nest-simulator/wiki/2021-03-01-Open-NEST-Developer-… [2]: https://github.com/nest/nest-simulator/pulls [3]: https://nuudel.digitalcourage.de/zreAHis9t4BPC5Rl -- 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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Restructured documentation build system: please update open PRs!
by Hans Ekkehard Plesser 01 Mar '21

01 Mar '21

Dear NEST Developers! With the merge of #1843 a few moments ago, we have implemented a significant change in the way NEST documentation is built (thank you, Jochen!). Please merge the current master in all open PRs to avoid complications. With the new setup, documentation can be built with `make doc` and will be built in the build directory and can also be installed. To build the documentation, you will need a range of Python packages. Please see doc/requirements.txt for what is needed. We will continue to make improvements to the documentation build system, but these will be minor. If you have any open PRs, please merge the current master as soon as possible into your branches. 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<mailto:hans.ekkehard.plesser@nmbu.no> Home http://arken.nmbu.no/~plesser

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Open NEST Developer Video Conference Monday 1 March 2021 11:30 CET (UTC+1)
by Dennis Terhorst 01 Mar '21

01 Mar '21

Dear NEST Users & Developers! I would like to invite you to our next fortnightly Open NEST Developer Video Conference, today Monday 1 March, 11.30-12.30 CET (UTC+1). As usual, 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. Today this would for example be a discussion about changing the minimum required Python version. Agenda Welcome Review of NEST User Mailing List Project team round In-depth discussion Raise minimal Python version required: hike to 3.7 or 3.8 (see #1932 <https://github.com/nest/nest-simulator/pull/1932#issuecomment-782710952>)? The agenda for this meeting is also available online, see https://github.com/nest/nest-simulator/wiki/2021-03-01-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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Error when plotting masks with azimuthal angle
by Arturo del Cerro Vergara 26 Feb '21

26 Feb '21

Hello, my name is Arturo and I think I found a bug when calling PlotTargets using the mask plot option with an azimuthal angle > 0. Below I give an example very easy to follow that shows that although the targets are plotted correctly, the mask is not. Correct me if I am doing anything wrong please. I attach an image of the results also. Thank you, Arturo. Code: l = topo.CreateLayer({'rows': 21, 'columns': 21, 'elements': 'iaf_psc_alpha'}) conndict = {'connection_type': 'divergent', 'mask': {'rectangular': {'lower_left': [-0.3, -0.12], 'upper_right': [-0.05, 0.12], 'azimuth_angle': 45.}}, 'kernel': 1.0} topo.ConnectLayers(l, l, conndict) fig = topo.PlotLayer(l, nodesize=40) ctr = topo.FindCenterElement(l) topo.PlotTargets(ctr, l, fig=fig, mask=conndict['mask'], src_size=250, tgt_color='red', tgt_size=20) [image: Captura.PNG]

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NEST Developers / Github Checks: Please merge master into open PRs/branches
by Hans Ekkehard Plesser 25 Feb '21

25 Feb '21

Dear NEST Developers! Thanks to Lekshmi's great work, we can now use Github checks for continuous integration testing. Please merge master into your open PRs/branches to make sure your contributions run the Github checks. We will run Github checks and Travis checks in parallel for now. Best 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<mailto:hans.ekkehard.plesser@nmbu.no> Home http://arken.nmbu.no/~plesser

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