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Open NEST Developer Video Conference Monday 26 April 2021 11:30 CEST (UTC+2)
by Dennis Terhorst 26 Apr '21

26 Apr '21

Dear NEST Users & Developers! I would like to invite you to our next fortnightly Open NEST Developer Video Conference, today Monday 26 April, 11.30-12.30 CEST (UTC+2). 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 there will be an update and discussion about style guides for documentation and code. Agenda Welcome Review of NEST User Mailing List Project team round In-depth discussion * NEST Documentation Style Guide (#1986 <https://github.com/nest/nest-simulator/pull/1986>) * Single vs double quotes for Python strings? See also this discussion <https://github.com/nest/nest-simulator/pull/1986#discussion_r610373605> * Which well-established style guide to build on? See also this discussion <https://github.com/nest/nest-simulator/pull/1986#discussion_r613510749> The agenda for this meeting is also available online, see https://github.com/nest/nest-simulator/wiki/2021-04-26-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

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New NEST Random Number Generators in Master
by Hans Ekkehard Plesser 23 Apr '21

23 Apr '21

Dear NEST Users and Developers! After a long and demanding process, we merged pull request #1549 into the NEST master branch earlier this afternoon. It replaces the old random number generator suite in NEST completely with a new one based on the C++ Standard Library and also providing generators from the Random123 library, including cryptographic generators. The most important change for users is that you can now much more easily seed generators and change the type of random number generator used. To seed, you only need a single seed—NEST will take care of everything else: nest.SetKernelStatus({'rng_seed': 12345}) is all it takes. To select a different RNG type, use nest.SetKernelStatus({'rng_type': 'mt19937'}) To see all available RNG types, use nest.GetKernelStatus('rng_types') For more information, see https://nest-simulator.readthedocs.io/en/latest/guides/nest2_to_nest3/nest2…. I hope this change will motivate everyone to even more systematically explore their models with a wide range of seeds and with different random number generator types. Existing simulation scripts, which otherwise are compatible with NEST master will only need to change the part of the script related to seeding and RNG selection. Because we now use a completely different internal architecture to provide random numbers, the actual sequence of random numbers provided will be different from before. This means that it is not possible to exactly reproduce spike trains obtained with the old RNG setup. Statistically, though, results shall be identical. If you should observe any unexpected deviations in results after switching to the new RNG scheme, please contact us! I would like to thank everyone who has contributed to this effort over a long time, especially Håkon and Jochen for their design and development work, and Johanna and Jasper for generating a lot of test data. With the new RNGs, the last major component for NEST3 is now integrated into the NEST master branch and we are very optimistic to finally make the NEST3 release before this summer. 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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Iaf - psc - delta neurons data
by Parva Alavian 16 Apr '21

16 Apr '21

Dear developers/users of nest, I am using the iaf-psc-delta neurons in my network and I need to access the information on the amount of excitatory and inhibitory input that each neuron is receiving in time in order to study balance.(so not just I-e but also the inputs that it is getting from other neurons in the randomly connected network). Can you please help me with this? It would also help if I knew where to find the indices of all the neurons that are presynaptic to a given neuron (a connectivity matrix). I would then be able to calculate the input current myself. Looking forward to hearing from you! Kind regards, Parva

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Triplets STDP model
by Julia Gallinaro 14 Apr '21

14 Apr '21

Dear NEST community, I am working with the triplets STDP connection on NEST simulations, and I am interested in how the weight dynamics change when the spike trains are altered in some specific ways. In order to do that, I run a network simulation using NEST and the triplets STDP rule and save the full spike trains of two neurons which are synaptically connected (one pre and one post). I then recreate the weight changes on a code outside the NEST loop, so that I can manipulate the spike trains and observe what happens to the synaptic weights. Trying to validate this approach, though, I find that my code (outside NEST loop) generates different weight values than the NEST simulation when using the same spike trains generated during the simulation. I guess I have some error in my implementation of the triplets rule. I thought it could be something with the implementation of the delays, or the moment when the weights are measured in the simulation, but I have had no success trying to fix it yet. I know this is not exactly a NEST issue, but I thought I would give it a try and ask here at the list. In case someone has already worked with the triplets rule and could point me out to what is/could be wrong in my implementation, I would very much appreciate it :) Thanks! best, Júlia

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CreateLayer problem with dictionary
by xotazu＠cvc.uab.es 13 Apr '21

13 Apr '21

Hello, I am having a basic problem creating layers with topology (pyhton 3.6 and NEST 2.20.1). It always complains about the dictionary sent to CreateLayer, telling it is a number. The code below correctly prints <class 'dict'> but prints this error: Traceback (most recent call last): File "test/binary_gdf.py", line 9, in <module> kk=tp.CreateLayer({'extent': [1, 1],'rows': 20, 'columns': 20,'elements' : 'izhikevich','edge_wrap':True}) File "/home/neurobit/local/nest-py3/lib64/python3.6/site-packages/nest/topology/hl_api.py", line 650, in CreateLayer return topology_func('{ CreateLayer } Map', specs) File "/home/neurobit/local/nest-py3/lib64/python3.6/site-packages/nest/topology/ll_api.py", line 61, in topology_func return nest.ll_api.sli_func(slifunc, *args) File "/home/neurobit/local/nest-py3/lib64/python3.6/site-packages/nest/ll_api.py", line 182, in sli_func sli_run(slifun) # SLI support code to execute s on args File "/home/neurobit/local/nest-py3/lib64/python3.6/site-packages/nest/ll_api.py", line 132, in catching_sli_run raise exceptionCls(commandname, message) nest.lib.hl_api_exceptions.TypeMismatch: ('TypeMismatch in CreateLayer_D: Expected datatype: doubletype\nProvided datatype: integertype', 'TypeMismatch', <SLILiteral: CreateLayer_D>, ': Expected datatype: doubletype\nProvided datatype: integertype') Any help would be nice :-) Xavier ---- import nest import nest.topology as tp nest.SetKernelStatus({"overwrite_files": True}) my_dict = {'extent': [1, 1],'rows': 20, 'columns': 20,'elements' : 'izhikevich','edge_wrap':True} print(type(my_dict)) kk=tp.CreateLayer(my_dict)

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NEST Conference 2021 goes virtual — registration & call for contributions open
by Hans Ekkehard Plesser 13 Apr '21

13 Apr '21

Dear all, The NEST Initiative is excited to invite everyone interested in Neural Simulation Technology and the NEST Simulator to the NEST Conference 2021. 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 again take place as a virtual conference on Monday/Tuesday 28/29 June 2021 followed by a virtual NEST User Hackathon until Friday 2 July, which offers the opportunity to deep-dive your own code with expert developers at your fingertips. Registration and submission of contributions are now open! We are inviting contributions to the conference, including plenary talks, "posters", breakout sessions and workshops on specific topics. Please register and submit your contribution(s) via the conference website https://nest-simulator.org/conference. Important dates 16 May 2021 — Deadline for submission of contributions and for NEST Initiative Membership applications 08 June 2021 — Notification of acceptance 21 June 2021 — Registration deadline 28 June 2021 — NEST Conference 2021 starts We are looking forward to seeing you all in June! Hans Ekkehard Plesser, Dennis Terhorst & Anne Elfgen -- 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 gdf files in binary format
by Xavier Otazu 13 Apr '21

13 Apr '21

Hello, I am trying to write spikedector data into .gdf files in binary format, but I cannot. I am setting the 'binary' param of the spikedetector to True (I checked it using nest.GetStatus) but files are written in ASCII. Do I need some special python package? I am using python 2.7.5 and NEST 2.18. Thanks in advance. Xavier Computer Vision Center<http://www.cvc.uab.cat> CONFIDENTIALITY WARNING<http://www.cvc.uab.es/?page_id=7475>

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Data Science Morning Coffee
by Hans Ekkehard Plesser 12 Apr '21

12 Apr '21

Dear all! Here the morning coffees are back in Outlook. We meet at https://nmbu.zoom.us/j/940209461. Best, Hans Ekkehard

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Canceled: Data Science Morning Coffee
by Hans Ekkehard Plesser 12 Apr '21

12 Apr '21

Dear all! Here the morning coffees are back in Outlook. We meet at https://nmbu.zoom.us/j/940209461. Best, Hans Ekkehard

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Canceled: Data Science Morning Coffee
by Hans Ekkehard Plesser 12 Apr '21

12 Apr '21

Dear all! Here the morning coffees are back in Outlook. We meet at https://nmbu.zoom.us/j/940209461. Best, Hans Ekkehard

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Re: Spatial grid + jitter
by Hans Ekkehard Plesser 07 Apr '21

07 Apr '21

Dear Jasper, In NEST 3, this should be possible. Stine or Håkon, could you provide some advice? 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 On 06/04/2021, 12:05, "Albers, Jasper" <j.albers(a)fz-juelich.de<mailto:j.albers@fz-juelich.de>> wrote: Dear all, a colleague of mine (in CC) and myself are implementing a spatially structured network in NEST (using current NEST master). We are wondering how to generate a population of neurons that are distributed on a regular grid plus a random jitter. This means that we want to end up with a spatial distribution as can be seen in Figure 8 in the tutorial for creating spatially structured networks<https://nest-simulator.readthedocs.io/en/latest/tutorials/pynest_tutorial/p…>. Below that figure one finds a code snippet; however, we believe that this does not correspond to the distribution of Figure 8. In the documentation of NEST 2.20.1 we did find a code snippet that produces a jittered grid: import numpy as np # grid with jitter jit = 0.03 xs = np.arange(-0.5,.501,0.1) poss = [[x,y] for y in xs for x in xs] poss = [[p[0]+np.random.uniform(-jit,jit),p[1]+np.random.uniform(-jit,jit)] for p in poss] layer_dict_ex = {"positions": poss, "extent" : [1.1,1.1], "elements" : "iaf_psc_alpha"} As is apparent, this code does not make use of NEST internal random number generation but rather produces a list of positions that is then passed to a layer. Thus our question is: is it possible to create a jittered grid natively in NEST master? Best regards, Jasper and Anno ------------------------------------------------------------------------------------------------ ------------------------------------------------------------------------------------------------ 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, Prof. Dr. Frauke Melchior ------------------------------------------------------------------------------------------------ ------------------------------------------------------------------------------------------------

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Spatial grid + jitter
by Albers, Jasper 06 Apr '21

06 Apr '21

Dear all, a colleague of mine (in CC) and myself are implementing a spatially structured network in NEST (using current NEST master). We are wondering how to generate a population of neurons that are distributed on a regular grid plus a random jitter. This means that we want to end up with a spatial distribution as can be seen in Figure 8 in the tutorial for creating spatially structured networks<https://nest-simulator.readthedocs.io/en/latest/tutorials/pynest_tutorial/p…>. Below that figure one finds a code snippet; however, we believe that this does not correspond to the distribution of Figure 8. In the documentation of NEST 2.20.1 we did find a code snippet that produces a jittered grid: import numpy as np # grid with jitter jit = 0.03 xs = np.arange(-0.5,.501,0.1) poss = [[x,y] for y in xs for x in xs] poss = [[p[0]+np.random.uniform(-jit,jit),p[1]+np.random.uniform(-jit,jit)] for p in poss] layer_dict_ex = {"positions": poss, "extent" : [1.1,1.1], "elements" : "iaf_psc_alpha"} As is apparent, this code does not make use of NEST internal random number generation but rather produces a list of positions that is then passed to a layer. Thus our question is: is it possible to create a jittered grid natively in NEST master? Best regards, Jasper and Anno ------------------------------------------------------------------------------------------------ ------------------------------------------------------------------------------------------------ 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, Prof. Dr. Frauke Melchior ------------------------------------------------------------------------------------------------ ------------------------------------------------------------------------------------------------

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Open NEST Developer Video Conference Monday 29 March 2021 11:30 CEST (UTC+2)
by Dennis Terhorst 29 Mar '21

29 Mar '21

Dear NEST Users & Developers! I would like to invite you to our next fortnightly Open NEST Developer Video Conference, today Monday 29 March, 11.30-12.30 CEST (UTC+2). 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 we have two potential topics for the in-depth discussion. The first is probably not that much to discuss, but we'd be interested in everyone's point of view. The second one touches many areas of the simulator and new scientific use-cases. Agenda Welcome Review of NEST User Mailing List Project team round In-depth discussion * CMake targets vs. CMake flags #1905 Microhackathon * Discuss dump/reload of connectivity (/not/ checkpointing!) The agenda for this meeting is also available online, see https://github.com/nest/nest-simulator/wiki/2021-03-29-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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Weight Recorder after network creation
by Benedikt Feldotto 16 Mar '21

16 Mar '21

Dear all, is it possible to assign the weight recorder to a synapse /after /the network is created? In the Neurorobotics Platform we allow the user to add devices (this can be additional nodes, or current inputs via SetStatus) after the creation of the network and it would be nice to also add recorders/readouts for spikes and weights. For spike recorders and multimeters this is possible as just a new node with a new connection is added. Thanks! Best Regards, Benedikt -- Benedikt Feldotto M.Sc. Research Assistant Human Brain Project - Neurorobotics Technical University of Munich Department of Informatics Chair of Robotics, Artificial Intelligence and Real-Time Systems Room HB 2.02.20 Parkring 13 D-85748 Garching b. München Tel.: +49 89 289 17628 Mail: feldotto(a)in.tum.de https://www6.in.tum.de/en/people/benedikt-feldotto-msc/ www.neurorobotics.net

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Open NEST Developer Video Conference Monday 15 March 2021 11:30 CET (UTC+1)
by Dennis Terhorst 15 Mar '21

15 Mar '21

Dear NEST Users & Developers! I would like to invite you to our next fortnightly Open NEST Developer Video Conference, today Monday 15 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 the mechanisms of the Python module installation. Agenda Welcome Review of NEST User Mailing List Project team round In-depth discussion * Python installation of NEST, see [#1948](https://github.com/nest/nest-simulator/issues/1948), [#1959](https://github.com/nest/nest-simulator/pull/1959) The agenda for this meeting is also available online, see https://github.com/nest/nest-simulator/wiki/2021-03-15-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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Spike Frequency Generator
by Benedikt Feldotto 13 Mar '21

13 Mar '21

Dear all, maybe I am overlooking something, I am searching for a spike frequency generator without noise. I was looking at the poisson generator, but as far as I can see there is no parameter to adjust/remove the noise. Is there any node available that takes as input a frequency and outputs spikes at this given frequency? Thanks! Best, Benedikt -- Benedikt Feldotto M.Sc. Research Assistant Human Brain Project - Neurorobotics Technical University of Munich Department of Informatics Chair of Robotics, Artificial Intelligence and Real-Time Systems Room HB 2.02.20 Parkring 13 D-85748 Garching b. München Tel.: +49 89 289 17628 Mail: feldotto(a)in.tum.de https://www6.in.tum.de/en/people/benedikt-feldotto-msc/ www.neurorobotics.net

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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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