- NEST Users - NEST Initiative Mail

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

1 0

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>

3 3

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

2 2

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

1 0

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

1 0

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 ------------------------------------------------------------------------------------------------ ------------------------------------------------------------------------------------------------

2 1

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 ------------------------------------------------------------------------------------------------ ------------------------------------------------------------------------------------------------

1 0

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

1 0

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

2 2

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

1 0

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

2 4

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]

3 4

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

1 0

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

2 3

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.

3 2

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 💸💰💵)

1 0

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 -------------------------------------------------------------------------------------

1 0

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

1 0

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

1 0

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]

2 1

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

1 0

Help on models from the command line?
by Hans Ekkehard Plesser 24 Feb '21

24 Feb '21

Hi! Just a question, I may have ovelooked something. If I use NEST help to get information about a neuron model, I get the message that there is no help: In [28]: nest.help('iaf_psc_alpha') Sorry, there is no help for 'iaf_psc_alpha'. But we have all the nice model documentation. Have I overlooked something or do we need to upgrade help()? 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

2 1

Re: Nest on parallel computer
by Hans Ekkehard Plesser 20 Feb '21

20 Feb '21

Dear Johan, You do not tell us what the “result” number is that you print out. But I notice that the value you get when running with 10 MPI processes on PDC, is about 10 times smaller than the value you see with one process on your PC. I’ll venture a guess and assume you have a network of N neurons which you connect to one spike detector. You simulate, read out the number of spikes and convert it into a firing rate, dividing number of spikes by N * simtime. In an MPI-parallel simulation, the spike detector on each MPI process only gets the spikes of neurons simulated on that MPI process. If you still divide by the full number of neurons to compute the rate, one would expect exactly the behavior you observe. In the future, please provide more details about what you are doing, so we can provide more pointed 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 19/02/2021, 22:20, "JOHAN LILJEFORS" <JOHAN(a)liljefors.eu<mailto:JOHAN@liljefors.eu>> wrote: Dear Nest users, I am fairly new to Nest having used it only for a few months and it has been working without any problems on my PC running Linux. Recently I was given access to a PDC where I have been submitting jobs but I am encountering a problem with my model. I'm running Python 3.7.3 and Nest 2.18. On both my PC and on the PDC, I run the following python script: ------------------------------ import Nest For counter in range(0,10): nest.resetkernel() ___run___script print(result) ------------------------------ I execute this with "srun -n=1 python3 run.py" This outputs 10 numbers, ranging from 0.35-0.4. On the PDC, i run the same scripts but without the for loop: ------------------------------ import Nest nest.resetkernel() ___run___script print(result) ------------------------------ I execute this with "srun -n=10 python3 run.py" this outputs 10 numbers, but this time much smaller around 0.04. I am not doing any file operations, nor any MPI communication between the tasks and I am genuinely confused as to how submitting multiple tasks can yield a different result than a single task. Has anyone encountered anything similar? Regards Johan Liljefors

2 1

Nest on parallel computer
by JOHAN LILJEFORS 19 Feb '21

19 Feb '21

Dear Nest users, I am fairly new to Nest having used it only for a few months and it has been working without any problems on my PC running Linux. Recently I was given access to a PDC where I have been submitting jobs but I am encountering a problem with my model. I'm running Python 3.7.3 and Nest 2.18. On both my PC and on the PDC, I run the following python script: ------------------------------ import Nest For counter in range(0,10): nest.resetkernel() ___run___script print(result) ------------------------------ I execute this with "srun -n=1 python3 run.py" This outputs 10 numbers, ranging from 0.35-0.4. On the PDC, i run the same scripts but without the for loop: ------------------------------ import Nest nest.resetkernel() ___run___script print(result) ------------------------------ I execute this with "srun -n=10 python3 run.py" this outputs 10 numbers, but this time much smaller around 0.04. I am not doing any file operations, nor any MPI communication between the tasks and I am genuinely confused as to how submitting multiple tasks can yield a different result than a single task. Has anyone encountered anything similar? Regards Johan Liljefors

1 0

SAVE THE DATE for the virtual NEST Conference 2021
by Anne Elfgen 18 Feb '21

18 Feb '21

Dear Colleagues, 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 willagaintake place as a *virtual conference*on Monday/Tuesday *28**/**29 June **2021*followed by a virtual NESTUserHackathon until Friday 2 July, whichoffers the opportunity to deep-dive your own code with expert developers at your fingertips. For more information please visit the conference website _*https://nest-simulator.org/conference*_ <https://nest-simulator.org/conference> We are looking forward to seeing you all in June! Hans EkkehardPlesser, Dennis Terhorst & Anne Elfgen

1 0

Nest compile on Piz-Daint
by Sergio Solinas 17 Feb '21

17 Feb '21

Dear NEST Users, I'm trying to get NEST up and running on Piz-Daint. I could manage to have it fully compiled and installed with python bindings, MPI, GSL and Boost. However, simulations start but get killed returning a std::bad_alloc. make installcheck also fails. Did anyone managed to have it installed on this HPC? Best regards, Sergio MG Solinas Dip. di Scienze Biomediche Università di Sassari Viale San Pietro 23 07100 - Sassari The NEURON School <https://www.neuronschool.org/> -- -- *Dona il 5x1000* all'Università degli Studi di Sassaricodice fiscale: 00196350904

2 1

neuron parameter as array?
by Cristiano Alessandro 16 Feb '21

16 Feb '21

Hi all, I am writing a new neuron model using nestml and then I modify the C++ code. I am having a hard time defining an input parameter of the neuron as an array of numbers. Is this even possible? Thanks. Regards Cristiano

3 2

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

15 Feb '21

Alaaf!¹ Dear NEST Users & Developers! I would like to invite you to our next fortnightly Open NEST Developer Video Conference, today Monday 15 February, 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. 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/2021-02-15-Open-NEST-Developer-… Looking forward to seeing you soon! best, Dennis Terhorst ¹) "Alaaf" is the traditional chant in this particular southern region of the Rheinland for this particular day. See https://en.wikipedia.org/wiki/Rosenmontag ------------------ 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

1 1

Master branch Doxygen location
by Itaru Kitayama 08 Feb '21

08 Feb '21

Hi, The NEST "Read the Docs" tells us how to invoke doxygen, but I am wondering if the community continuously builds Doxygen db every time a series is committed to master and put it somewhere.

2 1

Registration to the mailing list
by Vittorio De Falco 04 Feb '21

04 Feb '21

Dear NEST users, I tried to inscribe to the mailing list with this e-mail account deltafi.mat(a)live.it. I completed the registration, but I did not receive any link. Could you please help me? Thanks for your support. Best, Vittorio *************************************************************** * Postdoctoral Researcher in Mathematics * University of Naples "Federico II" * Department of Mathematics and Application "R. Caccioppoli" * Via Cintia, IT-80126 Naples, Italy * CELL: +39 340 544 70 15 ****************************************************************

1 0

Spike Event Multiplicity
by Benedikt Feldotto 04 Feb '21

04 Feb '21

Dear all, I realized that spikes that pass synapses (e.g. stdp_connection) are not processing a "multiplicity" value. However, some other nodes e.g. spikes delivered from the volume_transmitter into the stdp_dopa_connection include such a value. Does this mean, the multiplicity for spike events that pass a synapse is always equal to 1? 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

3 3

Turn Off NEST Warnings
by Benedikt Feldotto 03 Feb '21

03 Feb '21

Dear all, is there a possibility to turn off NEST warnings such as: It does not influence my experiments per se, but we are currently recording videos for our review and it just doesnt make a good impression to have warnings popping up :) Thanks, 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

2 2

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

01 Feb '21

Dear NEST Users & Developers! I would like to invite you to our next fortnightly Open NEST Developer Video Conference, today Monday 1 February, 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. 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/2021-02-01-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

1 0

CBD Online
by brielleyoung31＠gmail.com 20 Jan '21

20 Jan '21

If you are thinking of starting a CBD product business, then you should get to know the different CBD products on the market. Cannabidiol, also called cannabidiol, is a powerful phytochemical found in nature. It's one of only 47 known compounds that produce delta-9-tetrahydrocannabinol (THC) in plants. The good news is that scientists have successfully bred several strains of plants that contain cannabidiol and made it usable as a food supplement. Some of these strains are even available online, which makes it easier for people to try out new products that they haven't tried before. Unfortunately, not every CBD product is created equal. It's important to understand the differences between these strains so that you can get a better understanding of which ones will be the most effective when used as dietary supplements. Take some time to learn more about these CBD products, because there is an abundance of information available at https://goldbee.com/. A good way to start is by looking at the ingredients. Most of the CBD products available today are derived from a variety of different sources. Some sources include hemp, the leaves of hemp, and other plants. Other sources are not as reliable, such as hemp seed oil, hemp hurd, and other plant parts. Take the time to learn about the various components of each CBD product so that you can make a more informed decision. One of the best natural compounds found in CBD products is cannabidiol. This substance is often used interchangeably with cannabigerol. While cannabidiol has been shown to have a number of health benefits, it has also been shown to produce some of the same side effects as other substances. In some instances, it has been shown to cause depression, and it has also been linked to memory loss and muscle weakness. This substance has also been banned in several countries because of its possible side effects. It's important to note that some clinical trials have shown positive results with this compound. However, there are still many questions surrounding this herb. It's important that you understand why it is important to have clinical trials conducted on CBD products. If the medical community is able to determine the full potential for CBD, then it will help them come up with better medications. There may come a time when it will be possible to develop a CBD pill that produces the same positive results without the dangerous side effects. With that said, it's important that you research different CBD products so that you're ready to enter the world of natural medicine. There are a lot of different options out there that offer great products that can help you combat a wide range of conditions. Take some time to get familiar with all of your options, and then you will be ready to get started.

1 0

CBD Products Online
by brielleyoung31＠gmail.com 20 Jan '21

20 Jan '21

If you are thinking of starting a CBD product business, then you should get to know the different CBD products on the market. Cannabidiol, also called cannabidiol, is a powerful phytochemical found in nature. It's one of only 47 known compounds that produce delta-9-tetrahydrocannabinol (THC) in plants. The good news is that scientists have successfully bred several strains of plants that contain cannabidiol and made it usable as a food supplement. Some of these strains are even available online, which makes it easier for people to try out new products that they haven't tried before. Unfortunately, not every CBD product is created equal. It's important to understand the differences between these strains so that you can get a better understanding of which ones will be the most effective when used as dietary supplements. Take some time to learn more about these CBD products, because there is an abundance of information available. A good way to start is by looking at the ingredients. Most of the CBD products available today are derived from a variety of different sources. Some sources include hemp, the leaves of hemp, and other plants. Other sources are not as reliable, such as hemp seed oil, hemp hurd, and other plant parts. Take the time to learn about the various components of each CBD product so that you can make a more informed decision. One of the best natural compounds found in CBD products is cannabidiol. This substance is often used interchangeably with cannabidiol. While cannabidiol has been shown to have a number of health benefits, it has also been shown to produce some of the same side effects as other substances. In some instances, it has been shown to cause depression, and it has also been linked to memory loss and muscle weakness. This substance has also been banned in several countries because of its possible side effects. It's important to note that some clinical trials have shown positive results with this compound. However, there are still many questions surrounding this herb. It's important that you understand why it is important to have clinical trials conducted on CBD products. If the medical community is able to determine the full potential for CBD, then it will help them come up with better medications. There may come a time when it will be possible to develop a CBD pill that produces the same positive results without the dangerous side effects. With that said, it's important that you research different CBD products so that you're ready to enter the world of natural medicine. There are a lot of different options out there that offer great products that can help you combat a wide range of conditions. Take some time to get familiar with all of your options, and then you will be ready to get started.

1 0

Plot weight matrices example
by Ing Jyh Tsang 19 Jan '21

19 Jan '21

HI, I may be mistaken, but isn't the EI and IE index switched (https://nest-simulator.readthedocs.io/en/stable/auto_examples/plot_weight_m…) ? a_EI = nest.GetConnections(I_neurons, E_neurons) c_EI = nest.GetStatus(a_EI, keys='weight') a_IE = nest.GetConnections(E_neurons, I_neurons) c_IE = nest.GetStatus(a_IE, keys='weight') for idx, n in enumerate(a_EI): W_EI[n[0] - min(I_neurons), n[1] - min(E_neurons)] += c_EI[idx] for idx, n in enumerate(a_IE): W_IE[n[0] - min(E_neurons), n[1] - min(I_neurons)] += c_IE[idx] Thanks,

5 5

Re: NEST installation error on Mac
by Hans Ekkehard Plesser 18 Jan '21

18 Jan '21

Hi Pooja, Over the weekend, I did a brief test on a Mac with Big Sur an built NEST successfully. Below is a detailed description of my setup and steps I have taken. I hope this helps. Best, Hans Ekkehard System: Mac Book Air with INTEL CPU, Big Sur 11.1 Apple Command Line Tools % xcode-select --print-path /Library/Developer/CommandLineTools Homebrew packages (explicitly installed; see below for full list) % brew leaves boost cmake git gsl imagemagick open-mpi scipy wget Conda packages (base installation is miniconda3; this shows only explicitly installed packages, full list below) % conda create -n nest_dev nomkl numpy scipy matplotlib ipython cython nose % conda activate nest_dev % pip install junitparser % conda export --from-history name: nest_dev channels: - defaults dependencies: - nomkl - numpy - nose - matplotlib - cython - ipython - scipy Additionally via pip: junitparser CMake invocation and report % cmake -DCMAKE_INSTALL_PREFIX:PATH=`pwd`/install -Dwith-mpi=ON ../src -- NEST version: master@0e6cd2819 -------------------------------------------------------------------------------- NEST Configuration Summary -------------------------------------------------------------------------------- Build type : Target System : Darwin Cross Compiling : FALSE C compiler : AppleClang 12.0.0.12000032 (/Library/Developer/CommandLineTools/usr/bin/cc) C compiler flags : -O2 -Wall -Xclang -fopenmp C++ compiler : AppleClang 12.0.0.12000032 (/Library/Developer/CommandLineTools/usr/bin/c++) C++ compiler flags : -std=c++11 -O2 -Wall -Xclang -fopenmp Build dynamic : ON Built-in modules : models User modules : None Python bindings : Yes (Python 3.8.5: /Users/hep/opt/miniconda3/envs/nest_dev/bin/python3) Includes : /Users/hep/opt/miniconda3/envs/nest_dev/include/python3.8 Libraries : /Users/hep/opt/miniconda3/envs/nest_dev/lib/libpython3.8.dylib Cython bindings : Yes (Cython 0.29.21: /Users/hep/opt/miniconda3/envs/nest_dev/bin/cython) MPI4PY header : NO Use threading : Yes (OpenMP: -Xclang -fopenmp) Use GSL : Yes (GSL 2.6) Includes : /usr/local/Cellar/gsl/2.6/include Libraries : /usr/local/Cellar/gsl/2.6/lib/libgsl.dylib;/usr/local/Cellar/gsl/2.6/lib/libgslcblas.dylib Use Readline : No Use libltdl : Yes (LTDL 2.4.6) Includes : /usr/local/include Libraries : /usr/local/lib/libltdl.dylib Use doxygen : No Use MPI : Yes (MPI: /usr/local/bin/mpicxx) FLAGS : Includes : /usr/local/Cellar/open-mpi/4.0.5/include Link Flags : -L/usr/local/Cellar/libevent/2.1.12/lib Libraries : /usr/local/Cellar/open-mpi/4.0.5/lib/libmpi.dylib Use MUSIC : No Use libneurosim : No Use Boost : Yes (Boost 1.75.0) Includes : /usr/local/include Libraries : Use recording backend Arbor : No Use SIONlib : No ———————————————————————————————————————— Results from testsuite % make -j4 install % make installcheck ---------------------------------------------------------------------- NEST Testsuite Results ---------------------------------------------------------------------- Phase Tests Skipped Failures Errors Time ---------------------------------------------------------------------- 01 basetests 6 0 0 0 12.0 02 selftests 8 4 0 0 24.0 03 unittests 185 1 0 0 208.0 04 regressiontests 94 7 0 0 142.0 05 mpitests 79 0 0 0 258.0 07 pynesttests 796 11 0 0 144.2 08 cpptests 29 0 0 0 0.0 ---------------------------------------------------------------------- Total 1197 23 0 0 788.2 ---------------------------------------------------------------------- Complete list of Brew packages % brew list aom 2.0.1 boost 1.75.0_1 cmake 3.19.3 docbook 5.1_1 docbook-xsl 1.79.2_1 freetype 2.10.4 gcc 10.2.0_2 gdbm 1.18.1_1 gettext 0.21 ghostscript 9.53.3_1 git 2.30.0 glib 2.66.4_1 gmp 6.2.1 gnu-getopt 2.36.1 gsl 2.6 hwloc 2.4.0 icu4c 67.1 ilmbase 2.5.4 imagemagick 7.0.10-57 isl 0.23 jpeg 9d libde265 1.0.8 libevent 2.1.12 libffi 3.3_2 libheif 1.10.0 libidn2 2.3.0 liblqr 0.4.2_1 libmpc 1.2.1 libomp 11.0.1 libpng 1.6.37 libtiff 4.2.0 libtool 2.4.6_2 libunistring 0.9.10 little-cms2 2.11 mpfr 4.1.0 numpy 1.19.5 open-mpi 4.0.5 openblas 0.3.13 openexr 2.5.4 openjpeg 2.3.1 openssl(a)1.1<mailto:openssl@1.1> 1.1.1i pcre 8.44 pcre2 10.36 pybind11 2.6.1_1 python(a)3.8<mailto:python@3.8> 3.8.7 python(a)3.9<mailto:python@3.9> 3.9.1_6 readline 8.1 scipy 1.6.0 shared-mime-info 2.1 sqlite 3.34.0 tcl-tk 8.6.11 webp 1.1.0 wget 1.21 x265 3.4_2 xmlto 0.0.28 xz 5.2.5 Complete list of Conda packages in nest_dev % conda activate nest_dev % conda env export name: nest_dev channels: - defaults dependencies: - appnope=0.1.2=py38hecd8cb5_1001 - backcall=0.2.0=py_0 - blas=1.0=openblas - ca-certificates=2020.12.8=hecd8cb5_0 - certifi=2020.12.5=py38hecd8cb5_0 - cycler=0.10.0=py38_0 - cython=0.29.21=py38h23ab428_0 - decorator=4.4.2=py_0 - freetype=2.10.4=ha233b18_0 - ipython=7.19.0=py38h01d92e1_1 - ipython_genutils=0.2.0=pyhd3eb1b0_1 - jedi=0.17.2=py38hecd8cb5_1 - jpeg=9b=he5867d9_2 - kiwisolver=1.3.0=py38h23ab428_0 - lcms2=2.11=h92f6f08_0 - libcxx=10.0.0=1 - libedit=3.1.20191231=h1de35cc_1 - libffi=3.3=hb1e8313_2 - libgfortran=3.0.1=h93005f0_2 - libopenblas=0.3.10=h0794777_0 - libpng=1.6.37=ha441bb4_0 - libtiff=4.1.0=hcb84e12_1 - lz4-c=1.9.2=h79c402e_3 - matplotlib=3.3.2=hecd8cb5_0 - matplotlib-base=3.3.2=py38h181983e_0 - ncurses=6.2=h0a44026_1 - nomkl=3.0=0 - nose=1.3.7=pyhd3eb1b0_1006 - numpy=1.19.2=py38h63973fd_0 - numpy-base=1.19.2=py38h68fea81_0 - olefile=0.46=py_0 - openssl=1.1.1i=h9ed2024_0 - parso=0.7.0=py_0 - pexpect=4.8.0=pyhd3eb1b0_3 - pickleshare=0.7.5=pyhd3eb1b0_1003 - pillow=8.1.0=py38h5270095_0 - pip=20.3.3=py38hecd8cb5_0 - prompt-toolkit=3.0.8=py_0 - ptyprocess=0.7.0=pyhd3eb1b0_2 - pygments=2.7.4=pyhd3eb1b0_0 - pyparsing=2.4.7=py_0 - python=3.8.5=h26836e1_1 - python-dateutil=2.8.1=py_0 - readline=8.0=h1de35cc_0 - scipy=1.5.2=py38h4420a3a_0 - setuptools=51.1.2=py38hecd8cb5_4 - six=1.15.0=py38hecd8cb5_0 - sqlite=3.33.0=hffcf06c_0 - tk=8.6.10=hb0a8c7a_0 - tornado=6.1=py38h9ed2024_0 - traitlets=5.0.5=py_0 - wcwidth=0.2.5=py_0 - wheel=0.36.2=pyhd3eb1b0_0 - xz=5.2.5=h1de35cc_0 - zlib=1.2.11=h1de35cc_3 - zstd=1.4.5=h41d2c2f_0 - pip: - future==0.18.2 - junitparser==1.6.2 -- 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 15/01/2021, 15:48, "Babu, Pooja" <p.babu(a)fz-juelich.de<mailto:p.babu@fz-juelich.de>> wrote: Hello everyone, I have a Mac with Big Sur and I tried installing NEST with a Conda environment as mentioned here<https://www.nest-initiative.org/mailinglist/hyperkitty/list/users@nest-simu…> by pulling in the latest code from Github. My commands look like this conda create -n nestml_dev nomkl numpy scipy matplotlib ipython cython nose pytest conda activate nestml_dev <Pull the latest code from github> mkdir nest-simulator-build cd nest-simulator-build cmake -DCMAKE_INSTALL_PREFIX:PATH=<nest_path> -DCMAKE_C_COMPILER=gcc-10 -DCMAKE_CXX_COMPILER=g++-10 <nest_src> make -j4 make install After this, if I try to import nest in python or run nest from the command line, I get the following error OMP: Error #13: Assertion failure at kmp_csupport.cpp(590). OMP: Hint Please submit a bug report with this message, compile and run commands used, and machine configuration info including native compiler and operating system versions. Faster response will be obtained by including all program sources. For information on submitting this issue, please see http://www.intel.com/software/products/support/. Abort trap: 6 Has anyone else seen this error? Any pointers on this would be helpful. Thank you, Pooja ------------------------------------------------------------------------------------------------ ------------------------------------------------------------------------------------------------ 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 ------------------------------------------------------------------------------------------------ ------------------------------------------------------------------------------------------------

2 2

V_act_NMDA and S_act_NMDA parameter in ht_neuron
by Maryada Maryada 18 Jan '21

18 Jan '21

Dear all, I am looking for the details of ht_neuron model and referred to DOI: https://doi.org/10.1152/jn.00915.2004 for details. However, I couldn't find information on V_act_NMDA and S_act_NMDA. Can anyone please point me in the specific paragraph/table in the paper or share a one line explanation. I have attached a screenshot of the equation from the example notebook and also the complete notebook for quick reference -- Thanks and Regards *Maryada*

2 3

Open NEST Developer Video Conference Monday 18 January 2021 11:30 CET (UTC+1)
by Dennis Terhorst 18 Jan '21

18 Jan '21

Dear NEST Users & Developers! I would like to invite you to our next fortnightly Open NEST Developer Video Conference, today Monday 18 January, 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. 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/2021-01-18-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

1 0

NEST installation error on Mac
by Babu, Pooja 15 Jan '21

15 Jan '21

Hello everyone, I have a Mac with Big Sur and I tried installing NEST with a Conda environment as mentioned here<https://www.nest-initiative.org/mailinglist/hyperkitty/list/users@nest-simu…> by pulling in the latest code from Github. My commands look like this conda create -n nestml_dev nomkl numpy scipy matplotlib ipython cython nose pytest conda activate nestml_dev <Pull the latest code from github> mkdir nest-simulator-build cd nest-simulator-build cmake -DCMAKE_INSTALL_PREFIX:PATH=<nest_path> -DCMAKE_C_COMPILER=gcc-10 -DCMAKE_CXX_COMPILER=g++-10 <nest_src> make -j4 make install After this, if I try to import nest in python or run nest from the command line, I get the following error OMP: Error #13: Assertion failure at kmp_csupport.cpp(590). OMP: Hint Please submit a bug report with this message, compile and run commands used, and machine configuration info including native compiler and operating system versions. Faster response will be obtained by including all program sources. For information on submitting this issue, please see http://www.intel.com/software/products/support/. Abort trap: 6 Has anyone else seen this error? Any pointers on this would be helpful. Thank you, Pooja ------------------------------------------------------------------------------------------------ ------------------------------------------------------------------------------------------------ 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 ------------------------------------------------------------------------------------------------ ------------------------------------------------------------------------------------------------

1 0

Error in Simulate
by Petia Koprinkova 15 Jan '21

15 Jan '21

We have encountered the following error: Traceback (most recent call last): File "all_v2.py", line 364, in <module> nest.Simulate(sim_time) File"/opt/soft/nest-2.18.0/lib64/python3.6/site-packages/nest/ll_api.py",line 246, in stack_checker_func return f(*args, **kwargs) File"/opt/soft/nest-2.18.0/lib64/python3.6/site-packages/nest/lib/hl_api_simulation.py",line 66, in Simulate sr('ms Simulate') File"/opt/soft/nest-2.18.0/lib64/python3.6/site-packages/nest/ll_api.py",line 132, in catching_sli_run raise exceptionCls(commandname, message) nest.ll_api.C++Exception: ('C++Exception in Simulate_d:std::bad_alloc', 'C++Exception', <SLILiteral: Simulate_d>, ':std::bad_alloc') Could you help to resolve it? Best regards,Petia Koprinkova-Hristova

2 3

Trouble about the spiking time will increase and get so bigger with the simulation epoch increasing.
by enguang zhou 13 Jan '21

13 Jan '21

Deal all, I am recording the spiking time of neurons after every simulation, and I find that the time beginning of every simulation isn't all 0 except the first simulation. So how can I set to recording spiking time beginning from 0 during all simulations? By now I am processing that for every simulation spiking time recording by deleting all the time used before a specific simulation epoch. Hope for your answer,thanks! Enguang

4 5

Problems with installation of NEST on MAC
by Vittorio De Falco 12 Jan '21

12 Jan '21

Dear Users of NEST, I have downloaded and installed nest on my MAC. I was able to configure it. When I launch make I receive the following error Undefined symbols for architecture x86_64: "___kmpc_critical", referenced from: SLIInterpreter::message(int, char const*, char const*, char const*) const in interpret.cc.o "___kmpc_end_critical", referenced from: SLIInterpreter::message(int, char const*, char const*, char const*) const in interpret.cc.o "___kmpc_global_thread_num", referenced from: SLIInterpreter::message(int, char const*, char const*, char const*) const in interpret.cc.o "_omp_in_parallel", referenced from: Name::insert(std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> > const&) in name.cc.o ld: symbol(s) not found for architecture x86_64 clang: error: linker command failed with exit code 1 (use -v to see invocation) make[2]: *** [sli/libsli.dylib] Error 1 make[1]: *** [sli/CMakeFiles/sli_lib.dir/all] Error 2 make: *** [all] Error 2 I have already installed it successfully the previous week, but for example I have problem when I launch an example code from NEST (one_neuron.py), because import nest is recognised, while "import nest.voltage_trace" is not found ModuleNotFoundError: No module named 'nest.voltage_trace' Sorry I am a little bit confused. When I try to launch a code in a folder different from the nest-simulator folder "import nest" is not recognised. Could you please explain me better how to solve such an issue? Thank you very much for your support. Best, Vittorio *************************************************************** * Postdoctoral Researcher in Mathematics * University of Naples "Federico II" * Department of Mathematics and Application "R. Caccioppoli" * Via Cintia, IT-80126 Naples, Italy * CELL: +39 340 544 70 15 ****************************************************************

2 1

spatiotemporal Poisson generator
by Abolfazl Ziaeemehr 08 Jan '21

08 Jan '21

Hello everyone, Is it possible to include a *spatiotemporal poisson generator* in the simulation? I am trying to apply a current to a population of neurons which is something like this? [image: Selection_001.png] where `i` is the index of the neuron and `t` is the current time of the simulation. Thank you for any guidance. best, -- Abolfazl Ziaeemehr PhD in Computational Neuroscience Institute for Advanced Studies in Basic Sciences (IASBS) Page: iasbs.ac.ir/~a.ziaeemehr https://github.com/Ziaeemehr

2 1

I want to know the derivative equation of iaf_psc_alpha neuron model to design some algorithms for neural network
by enguang zhou 06 Jan '21

06 Jan '21

Hi everyone, I have a very big problem now again for the iaf neuron(such as iaf_psc_alpha), which is I don't know know differential equation for the neuron model, so I can't get the derivative of voltage about some other variable, such as derivative of voltage versus synapse weight. The point is I do need to know the derivative equation of iaf_psc_alpha neuron model to design some algorithm for neural network. For the paper mentioned below, I still can't figure out the exact derivative equation of voltage or voltage state equation. https://link.springer.com/article/10.1007/s004220050570 By the way, At last meeting, I wanted to ask that but my device had trouble when host asked, so awkward. Hope for your answer. Thank you. Enguang

2 2

How does the synapse weight influence 'iaf_psc_alpha' neuron(or any other neuron you know) to send a spike?
by enguang zhou 04 Jan '21

04 Jan '21

Hello everyone, As the title says, can someone help me answer this? I am really confused about this. Because I need to know how to control the neuron spiking from the mathematical formula, and I check out the iaf_psc_alpha.cpp and its .h file, and I can't get a clue how does the synapse weight value influence the neuron spiking. I would be appreciate if you can tell me how to check out the code in nest_simualator. Thank you. Enguang

2 5

Open NEST Developer Video Conference Monday 4 January 2021 11:30 CET (UTC+1)
by Dennis Terhorst 04 Jan '21

04 Jan '21

Dear NEST Users & Developers! I would like to wish you all a Happy New Year and invite you to our first fortnightly Open NEST Developer Video Conference of this year, today Monday 4 January, 11.30-12.30 CET (UTC+1). Today we have a special feature discussion on * Python module installation Additionally, 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. Agenda Welcome Review of NEST User Mailing List Project team round In-depth discussion Python module installation The agenda for this meeting is also available online, see https://github.com/nest/nest-simulator/wiki/2021-01-04-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

1 0

Thank you for 2020
by Hans Ekkehard Plesser 23 Dec '20

23 Dec '20

Dear NEST Users! I would like to thank all of you in the NEST Community for you efforts and interest in NEST in 2020, which has been a special year for us all. We have achieved a lot and I am very confident that 2021 will finally see the official release of NEST 3 as the culmination of several years work with significant benefits for users. After the good experiences with the virtual NEST conference this year, the NEST Initiative has decided to hold the conference as a digital conference also in 2021, as this allows a much wider range of users to participate. The conference will take place at its usual time in the end of June. I wish you all happy holidays and all the best for 2021! Hans Ekkehard Plesser President, The NEST Initiative -- 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

2 1

Open NEST Developer Video Conference Monday 21 December 2020 11:30 CET (UTC+1)
by Dennis Terhorst 21 Dec '20

21 Dec '20

Dear NEST Users & Developers! I would like to invite you to our last fortnightly Open NEST Developer Video Conference of this year, today Monday 21 December, 11.30-12.30 CET (UTC+1). Today we have a special feature discussion on *NeuronGPU *by Bruno Golosio, bringing GPU acceleration to spiking neural networks. Additionally, 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. Agenda Welcome Review of NEST User Mailing List Project team round In-depth discussion NeuronGPU The agenda for this meeting is also available online, see https://github.com/nest/nest-simulator/wiki/2020-12-21-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

1 0

Multi-node parallel simulation error
by jiadu xie 17 Dec '20

17 Dec '20

I want to run neuron simulations in parallel on multiple servers in OpenMPI. I've installed Nest through conda: conda install -c conda-forge nest-simulator. multi_test.pycode show as below： from nest import * SetKernelStatus({"total_num_virtual_procs": 4}) pg = Create("poisson_generator", params={"rate": 50000.0}) n = Create("iaf_psc_alpha", 4) sd = Create("spike_detector", params={"to_file": True}) print("work01,My Rank is :{}".format(Rank())) #print("Processes Number is :{}".format(NumProcesses()) #print("Processor Name is :{}".format(ProcessorName()) Connect(pg, [n[0]], syn_spec={'weight': 1000.0, 'delay': 1.0}) Connect([n[0]], [n[1]], syn_spec={'weight': 1000.0, 'delay': 1.0}) Connect([n[1]], [n[2]], syn_spec={'weight': 1000.0, 'delay': 1.0}) Connect([n[2]], [n[3]], syn_spec={'weight': 1000.0, 'delay': 1.0}) Connect(n, sd) Simulate(100.0) To Reproduce Steps to reproduce the behavior: (pynest) work@work01:~/xiejiadu/nest_multi_test$ /home/work/anaconda3/envs/pynest/bin/mpirun -np 2 -host work01:1,work02:1 /home/work/anaconda3/envs/pynest/bin/python3 /home/work/xiejiadu/nest_multi_test/multi_test.py [INFO] [2020.11.23 3:57:6 /home/conda/feedstock_root/build_artifacts/nest-simulator_1580129123254/work/nestkernel/rng_manager.cpp:217 @ Network::create_rngs_] : Creating default RNGs [INFO] [2020.11.23 3:57:6 /home/conda/feedstock_root/build_artifacts/nest-simulator_1580129123254/work/nestkernel/rng_manager.cpp:260 @ Network::create_grng_] : Creating new default global RNG [INFO] [2020.11.23 3:57:6 /home/conda/feedstock_root/build_artifacts/nest-simulator_1580129123254/work/nestkernel/rng_manager.cpp:217 @ Network::create_rngs_] : Creating default RNGs [INFO] [2020.11.23 3:57:6 /home/conda/feedstock_root/build_artifacts/nest-simulator_1580129123254/work/nestkernel/rng_manager.cpp:260 @ Network::create_grng_] : Creating new default global RNG python3: /home/conda/feedstock_root/build_artifacts/nest-simulator_1580129123254/work/sli/scanner.cc:581: bool Scanner::operator()(Token&): Assertion `in->good()' failed. [work02:95945] *** Process received signal *** [work02:95945] Signal: Aborted (6) [work02:95945] Signal code: (-6) [work02:95945] [ 0] /lib/x86_64-linux-gnu/libpthread.so.0(+0x12730)[0x7fc94a207730] [work02:95945] [ 1] /lib/x86_64-linux-gnu/libc.so.6(gsignal+0x10b)[0x7fc94a0697bb] [work02:95945] [ 2] /lib/x86_64-linux-gnu/libc.so.6(abort+0x121)[0x7fc94a054535] [work02:95945] [ 3] /lib/x86_64-linux-gnu/libc.so.6(+0x2240f)[0x7fc94a05440f] [work02:95945] [ 4] /lib/x86_64-linux-gnu/libc.so.6(+0x30102)[0x7fc94a062102] [work02:95945] [ 5] /home/work/anaconda3/envs/pynest/lib/python3.8/site-packages/nest/../../../libsli.so(_ZN7ScannerclER5Token+0x1489)[0x7fc93cf3ceb9] [work02:95945] [ 6] /home/work/anaconda3/envs/pynest/lib/python3.8/site-packages/nest/../../../libsli.so(_ZN6ParserclER5Token+0x49)[0x7fc93cf2f229] [work02:95945] [ 7] /home/work/anaconda3/envs/pynest/lib/python3.8/site-packages/nest/../../../libsli.so(_ZNK14IparseFunction7executeEP14SLIInterpreter+0x96)[0x7fc93cf66666] [work02:95945] [ 8] /home/work/anaconda3/envs/pynest/lib/python3.8/site-packages/nest/../../../libsli.so(+0x74193)[0x7fc93cf25193] [work02:95945] [ 9] /home/work/anaconda3/envs/pynest/lib/python3.8/site-packages/nest/../../../libsli.so(_ZN14SLIInterpreter8execute_Em+0x222)[0x7fc93cf29a32] [work02:95945] [10] /home/work/anaconda3/envs/pynest/lib/python3.8/site-packages/nest/../../../libsli.so(_ZN14SLIInterpreter7startupEv+0x27)[0x7fc93cf29e57] [work02:95945] [11] /home/work/anaconda3/envs/pynest/lib/python3.8/site-packages/nest/../../../libnest.so(_Z11neststartupPiPPPcR14SLIInterpreterNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEE+0x1ea0)[0x7fc93d97ba40] [work02:95945] [12] /home/work/anaconda3/envs/pynest/lib/python3.8/site-packages/nest/pynestkernel.so(+0x444dc)[0x7fc93dd774dc] [work02:95945] [13] /home/work/anaconda3/envs/pynest/bin/python3(+0x1b4924)[0x55e5ae205924] [work02:95945] [14] /home/work/anaconda3/envs/pynest/bin/python3(_PyEval_EvalFrameDefault+0x4bf)[0x55e5ae22dbcf] [work02:95945] [15] /home/work/anaconda3/envs/pynest/bin/python3(_PyFunction_Vectorcall+0x1b7)[0x55e5ae21a637] [work02:95945] [16] /home/work/anaconda3/envs/pynest/bin/python3(_PyEval_EvalFrameDefault+0x71a)[0x55e5ae22de2a] [work02:95945] [17] /home/work/anaconda3/envs/pynest/bin/python3(_PyEval_EvalCodeWithName+0x260)[0x55e5ae219490] [work02:95945] [18] /home/work/anaconda3/envs/pynest/bin/python3(+0x1f6bb9)[0x55e5ae247bb9] [work02:95945] [19] /home/work/anaconda3/envs/pynest/bin/python3(+0x13a23d)[0x55e5ae18b23d] [work02:95945] [20] /home/work/anaconda3/envs/pynest/bin/python3(PyVectorcall_Call+0x6f)[0x55e5ae1aef2f] [work02:95945] [21] /home/work/anaconda3/envs/pynest/bin/python3(_PyEval_EvalFrameDefault+0x5fc1)[0x55e5ae2336d1] [work02:95945] [22] /home/work/anaconda3/envs/pynest/bin/python3(_PyEval_EvalCodeWithName+0x260)[0x55e5ae219490] [work02:95945] [23] /home/work/anaconda3/envs/pynest/bin/python3(_PyFunction_Vectorcall+0x594)[0x55e5ae21aa14] [work02:95945] [24] /home/work/anaconda3/envs/pynest/bin/python3(_PyEval_EvalFrameDefault+0x4e73)[0x55e5ae232583] [work02:95945] [25] /home/work/anaconda3/envs/pynest/bin/python3(_PyFunction_Vectorcall+0x1b7)[0x55e5ae21a637] [work02:95945] [26] /home/work/anaconda3/envs/pynest/bin/python3(_PyEval_EvalFrameDefault+0x4bf)[0x55e5ae22dbcf] [work02:95945] [27] /home/work/anaconda3/envs/pynest/bin/python3(_PyFunction_Vectorcall+0x1b7)[0x55e5ae21a637] [work02:95945] [28] /home/work/anaconda3/envs/pynest/bin/python3(_PyEval_EvalFrameDefault+0x71a)[0x55e5ae22de2a] [work02:95945] [29] /home/work/anaconda3/envs/pynest/bin/python3(_PyFunction_Vectorcall+0x1b7)[0x55e5ae21a637] [work02:95945] *** End of error message *** -------------------------------------------------------------------------- Primary job terminated normally, but 1 process returned a non-zero exit code. Per user-direction, the job has been aborted. -------------------------------------------------------------------------- -------------------------------------------------------------------------- WARNING: Open MPI failed to TCP connect to a peer MPI process. This should not happen. Your Open MPI job may now hang or fail. Local host: work01 PID: 114620 Message: connect() to 192.168.204.122:1024 failed Error: Operation now in progress (115) -------------------------------------------------------------------------- [work01:114615] PMIX ERROR: UNREACHABLE in file server/pmix_server.c at line 2193 -- N E S T -- Copyright (C) 2004 The NEST Initiative Version: nest-2.18.0 Built: Jan 27 2020 12:49:17 This program is provided AS IS and comes with NO WARRANTY. See the file LICENSE for details. Problems or suggestions? Visit https://www.nest-simulator.org Type 'nest.help()' to find out more about NEST. Nov 23 03:57:06 ModelManager::clear_models_ [Info]: Models will be cleared and parameters reset. Nov 23 03:57:06 Network::create_rngs_ [Info]: Deleting existing random number generators Nov 23 03:57:06 Network::create_rngs_ [Info]: Creating default RNGs Nov 23 03:57:06 Network::create_grng_ [Info]: Creating new default global RNG Nov 23 03:57:06 RecordingDevice::set_status [Info]: Data will be recorded to file and to memory. work01,My Rank is :0 -------------------------------------------------------------------------- mpirun noticed that process rank 1 with PID 95945 on node work02 exited on signal 6 (Aborted). -------------------------------------------------------------------------- Command to run /home/work/anaconda3/envs/pynest/bin/mpirun -np 2 -host work01:1,work02:1 /home/work/anaconda3/envs/pynest/bin/python3 /home/work/xiejiadu/nest_multi_test/multi_test.py Expected behavior A clear and concise description of what you expected to happen. Screenshots If applicable, add screenshots to help explain your problem. Desktop/Environment: OS: Debain-10.0 Shell: conda4.8.3 Python-Version: Python 3.8.6 NEST-Version: nest-2.18 Installation:conda packet, with MPI Best jiaduxie

2 2

NEST Spack package maintainers
by itaru.kitayama＠gmail.com 15 Dec '20

15 Dec '20

I am updating the package.py script a bit so that it can build; though I wonder who are the maintainers of the Spack package currently?

1 1

NEST developer documentation
by Cristiano Alessandro 11 Dec '20

11 Dec '20

Dear all, I am new to developing NEST neuron models. I am aware I should use NEST-ML and I started that way, but I now need to modify the (successfully) generated C++ code. To do so, I would like to understand the details of the C++ implementation, including the overall logic of the class NEST-ML created (what is the functionality of the methods and attributes). Where can I find documentation about this? I would also like to take a look at the description of the NEST C++ developers library. I could not find these aspects in the Nest Developer Space. Thank you in advance. Best Cristiano

3 3

NEST developer documentation
by Cristiano Alessandro 11 Dec '20

11 Dec '20

Dear all, I am new to developing NEST neuron models. I am aware I should use NEST-ML and I started that way, but I now need to modify the (successfully) generated C++ code. To do so, I would like to understand the details of the C++ implementation, including the overall logic of the class NEST-ML created (what is the functionality of the methods and attributes). Where can I find documentation about this? I would also like to take a look at the description of the NEST C++ developers library. I could not find these aspects in the Nest Developer Space. Thank you in advance. Best Cristiano

1 0

Open NEST Developer Video Conference Monday 07 December 2020 11:30 CET (UTC+1)
by Dennis Terhorst 07 Dec '20

07 Dec '20

Dear NEST Users & Developers! I would like to invite you to our next fortnightly Open NEST Developer Video Conference today Monday 07 December, 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 To squash, or not to squash The agenda for this meeting is also available online, see https://github.com/nest/nest-simulator/wiki/2020-12-07-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

1 0

Combining neuron model features
by d.standage＠bham.ac.uk 03 Dec '20

03 Dec '20

Hi all - I'm aiming to run simulations using Izhikevich's neuron model (or another efficient model with spike generation), two dendritic compartments, two glutamate receptor subtypes, and temporal synaptic dynamics. My understanding is that Nest supports the Izhikevich neuron model with instantaneous current injection (i.e. no synaptic dynamics), the iaf_cond_alpha_mc neuron model for multiple compartments, the aeif_cond_alpha_multisynapse model for multiple receptor subtypes, and any of the _psc_ or _cond_ neuron models for synaptic dynamics. Am I looking at multiple choice here? I.e. I can't use a single neuron model with all of these features? If so, does anyone know of any Nest add-ons that efficiently handle all the features above? I'd be grateful for any advice. Best Dominic

3 2

Technical Editor – European Research Infrastructures for Neuroscience (EBRAINS)
by Hans Ekkehard Plesser 03 Dec '20

03 Dec '20

Dear colleagues, The Computational Neuroscience Group at the Norwegian University of Life Sciences (www.nmbu.no<http://www.nmbu.no/>) aims to recruit a technical editor in a senior engineer position. The position is part of our contribution to the Human Brain Project (www.humanbrainproject.eu<http://www.humanbrainproject.eu/>) in building the European EBRAINS research infrastructures for neuroscience. This full-time position is available immediately and limited until 31 March 2023. As technical editor, you will be part of the EBRAINS High-Level Service Team and be responsible for coordinating and supervising the production and provision of documentation and tutorial materials for EBRAINS service offerings with the pertaining EBRAINS partners. We are looking for applicants with a master's, preferably a doctoral, degree in a STEM discipline, ideally with experience in technical writing, documentation generation systems, and neuroscience. Closing date for applications is 4 January 2021. For more information about the position and to submit your application, please see https://www.jobbnorge.no/en/available-jobs/job/196909/technical-editor-seni… Please contact Prof Hans Ekkehard Plesser (hans.ekkehard.plesser(a)nmbu.no<mailto:hans.ekkehard.plesser@nmbu.no>) if you have any questions concerning the position. 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

1 0

Reset Spike Detector
by feldotto 03 Dec '20

03 Dec '20

Dear all,I am running a large simulation where I need to evaluate the spike frequency of large populations in several elapsed time frames. In order to keep this procedure efficient and memory efficient, is it possible to reset the spikeDetector (delete all events)?Thanks in advance!Best,Benedikt

3 2

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.)

2 1

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

1 0

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

7 13

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

3 3

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

1 0

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

1 0

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

1 0

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?

2 1

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

3 2

because of the spike time stored in unordered time, so I get problem ablout the use of stdp_synapse.
by 1240288839＠qq.com 27 Oct '20

27 Oct '20

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.

3 4

Open NEST Developer Video Conference Monday 26 October 2020 11:30 CET (UTC+1)
by Dennis Terhorst 26 Oct '20

26 Oct '20

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

1 0

V_th Issue in Izhikevich Neuron Model
by Allen Rabayda 17 Oct '20

17 Oct '20

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

3 4

test failures on nest master@6997cae6c on Fedora 32 with Intel Prallel Studio XE 2020 update 2
by Nilton Liuji Kamiji 16 Oct '20

16 Oct '20

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

2 2

Running NEST with SIONlib
by Itaru Kitayama 14 Oct '20

14 Oct '20

Hi, Has anyone explored the external library support? I am on Fugaku and the jobs can create casually tens of thousands of files in a single directory; this aborts jobs. Itaru.

2 5

Open NEST Developer Video Conference Monday 12 October 2020 11:30 CEST (UTC+2)
by Dennis Terhorst 12 Oct '20

12 Oct '20

Dear NEST Users & Developers! I would like to invite you to our next fortnightly Open NEST Developer Video Conference today Monday 12 October, 11.30-12.30 CEST (UTC+2). 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 * HBP CodeJam #11 <https://www.humanbrainproject.eu/en/education/participatecollaborate/infras…> * Extension Module System <https://github.com/nest/nest-simulator/projects/22> * Issue #1773 <https://github.com/nest/nest-simulator/issues/1773>: wrapper around |Prepare| and |Run| The agenda for this meeting is also available online, see https://github.com/nest/nest-simulator/wiki/2020-10-12-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

1 0

Open NEST Developer Video Conference Monday 28 September 2020 11:30 CEST (UTC+2)
by Dennis Terhorst 28 Sep '20

28 Sep '20

Dear NEST Users & Developers! I would like to invite you to our next fortnightly Open NEST Developer Video Conference today Monday 28 September, 11.30-12.30 CEST (UTC+2). 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 Benchmarking setups for CoSim and the NRP-NEST coupling. Special guests will be Kim Sontheimer and Cristian Jimenez-Romero of the SimLab Neuroscience The agenda for this meeting is also available online, see https://github.com/nest/nest-simulator/wiki/2020-09-28-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

1 0

Is there a developer meeting soon?
by Robin Gilbert De Schepper 23 Sep '20

23 Sep '20

Hi! It seems to have been a while since an invitation to the bi-weekly meeting has been sent out. Will they resume soon? I would like to discuss the topic of extension modules and feel like the meeting is great place to get informed. Best regards -- Robin De Schepper, MSc Department of Brain and Behavioral Sciences Unit of Neurophysiology University of Pavia, Italy Via Forlanini 6, 27100 Pavia - Italy Tel: (+39) 038298-7607 http://www-5.unipv.it/dangelo/

1 0

Open NEST Developer Video Conference Monday 14 September 2020 11:30 CEST (UTC+2)
by Dennis Terhorst 14 Sep '20

14 Sep '20

Dear NEST Users & Developers! I would like to invite you to our next fortnightly Open NEST Developer Video Conference today Monday 14 September, 11.30-12.30 CEST (UTC+2). 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. The ongoing hackathon this week will be one of the topics and a quick overview will be discussed. 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/2020-09-14-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

1 0

error when making
by Carlos Gutierrez 05 Sep '20

05 Sep '20

Dear All, I get the following error when making NEST 2.20 on my desktop, any idea where is the problem?. Thanks, Carlos. [ 99%] Building CXX object pynest/CMakeFiles/pynestkernel.dir/pynestkernel.cxx.o [100%] Linking CXX shared module pynestkernel.so /usr/bin/ld: /usr/local/lib/libpython3.8.a(abstract.o): relocation R_X86_64_PC32 against symbol `_Py_NotImplementedStruct' can not be used when making a shared object; recompile with -fPIC /usr/bin/ld: final link failed: bad value collect2: error: ld returned 1 exit status make[2]: *** [pynest/CMakeFiles/pynestkernel.dir/build.make:103: pynest/pynestkernel.so] Error 1 make[1]: *** [CMakeFiles/Makefile2:1030: pynest/CMakeFiles/pynestkernel.dir/all] Error 2 make: *** [Makefile:141: all] Error 2 ######## -------------------------------------------------------------------------------- NEST Configuration Summary -------------------------------------------------------------------------------- Build type : Target System : Linux Cross Compiling : FALSE C compiler : GNU 9.3.0 (/usr/bin/cc) C compiler flags : -fPIC -fopenmp -pthread -fdiagnostics-color=auto C++ compiler : GNU 9.3.0 (/usr/bin/c++) C++ compiler flags : -std=c++11 -fPIC -fopenmp -pthread -fdiagnostics-color=auto Build dynamic : ON Built-in modules : models;precise;topology User modules : None Python bindings : Yes (Python 3.8: /usr/local/bin/python3) Includes : /usr/local/include/python3.8 Libraries : /usr/local/lib/libpython3.8.a Cython bindings : Yes (Cython 0.29.21: /usr/local/bin/cython) Use threading : Yes (OpenMP: -fopenmp) Use GSL : Yes (GSL 2.5) Includes : /usr/include Libraries : /usr/lib/x86_64-linux-gnu/libgsl.so;/usr/lib/x86_64-linux-gnu/libgslcblas.so Use Readline : Yes (GNU Readline 8.0) Includes : /usr/include Libraries : /usr/lib/x86_64-linux-gnu/libreadline.so;/usr/lib/x86_64-linux-gnu/libncurses.so Use libltdl : Yes (LTDL ) Includes : /usr/include Libraries : /usr/lib/x86_64-linux-gnu/libltdl.so Use doxygen : No Use MPI : Yes (MPI: /usr/bin/mpicxx) FLAGS : -pthread Includes : /usr/lib/x86_64-linux-gnu/openmpi/include/openmpi;/usr/lib/x86_64-linux-gnu/openmpi/include Link Flags : -pthread Libraries : /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi_cxx.so;/usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so Use MUSIC : No Use libneurosim : No Use Boost : No --------------------------------------------------------------------------------

2 3

Open NEST Developer Video Conference Monday 31 August 2020 11:30 CEST (UTC+2)
by Dennis Terhorst 31 Aug '20

31 Aug '20

Dear NEST Users & Developers! I would like to invite you to our next fortnightly Open NEST Developer Video Conference today Monday 31 August, 11.30-12.30 CEST (UTC+2). 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/2020-08-31-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

1 0

Re: Issue with NEST Live Media 2.20
by Steffen Graber 27 Aug '20

27 Aug '20

Hi Maryada I just tested the VM with Windows 10 Home (Version 1903) and with Virtualbox 6.12. No problems at startup. The network does not seem to start in your installation. If not done yet I would first delete the VM completely and reinstall it. Then deactivate the network in the settings of the VM and restart it again. Hope this helps. Best Steffen Am 26.08.20 um 11:08 schrieb Maryada Maryada: > Sorry for the late reply. > Here you go. I hope this helps. > > On Tue, Aug 25, 2020 at 2:16 PM Steffen Graber <s.graber(a)fz-juelich.de > <mailto:s.graber@fz-juelich.de>> wrote: > > Hi, > > That's ok. Could you send me the log of the VM? > Highlight the VM in the manager and press CTRL+L. > > Best > > Steffen > > Am 25.08.20 um 13:01 schrieb Maryada Maryada: > > Hey, > > The latest one, 6.1.12 > > > > On Tue, Aug 25, 2020 at 12:52 PM Steffen Graber > <s.graber(a)fz-juelich.de <mailto:s.graber@fz-juelich.de> > > <mailto:s.graber@fz-juelich.de <mailto:s.graber@fz-juelich.de>>> > wrote: > > > > Hi, > > > > Do you have the ExtensionPack installed? In which version? > > > > Best > > > > Steffen > > > > Am 25.08.20 um 12:39 schrieb Maryada Maryada: > > > Hi Steffen, > > > I am using Windows 10 as my host OS and Oracle Virtual Box 6.1 > > > > > > On Tue, Aug 25, 2020 at 12:34 PM Steffen Graber > > <s.graber(a)fz-juelich.de <mailto:s.graber@fz-juelich.de> > <mailto:s.graber@fz-juelich.de <mailto:s.graber@fz-juelich.de>> > > > <mailto:s.graber@fz-juelich.de > <mailto:s.graber@fz-juelich.de> <mailto:s.graber@fz-juelich.de > <mailto:s.graber@fz-juelich.de>>>> > > wrote: > > > > > > Hi Maryada, > > > > > > Just tried Live Media 2.20 under Ubuntu 20.04 with > Virtualbox 6.1. > > > Starting the VM worked fine for me. > > > > > > Which operating system and which version of Virtualbox > do you use? > > > > > > Best > > > > > > Steffen > > > > > > Am 25.08.20 um 11:40 schrieb Maryada Maryada: > > > > Hi, > > > > I am trying to import Live Media 2.20 however the VM > > virtualbox is > > > > always get stuck immediately > > > > as it starts (see attachment). I also tried to import the > > 2.18 version > > > > just to be sure if it's an issue on my side. However, > that's > > working > > > > perfectly fine. > > > > > > > > Is there an additional requirement that I might be > missing? > > > > -- > > > > Thanks and Regards > > > > > > > > *Maryada* > > > > > > > > > > > > _______________________________________________ > > > > NEST Users mailing list -- users(a)nest-simulator.org > <mailto:users@nest-simulator.org> > > <mailto:users@nest-simulator.org > <mailto:users@nest-simulator.org>> > > > <mailto:users@nest-simulator.org > <mailto:users@nest-simulator.org> > > <mailto:users@nest-simulator.org > <mailto:users@nest-simulator.org>>> > > > > To unsubscribe send an email to > > users-leave(a)nest-simulator.org > <mailto:users-leave@nest-simulator.org> > <mailto:users-leave@nest-simulator.org > <mailto:users-leave@nest-simulator.org>> > > > <mailto:users-leave@nest-simulator.org > <mailto:users-leave@nest-simulator.org> > > <mailto:users-leave@nest-simulator.org > <mailto:users-leave@nest-simulator.org>>> > > > > > > > > > > -- > > > > > > ------------------------------------------------------------------------------------- > > > Steffen Graber > > > SimLab Neuroscience > > > Division HPC in Neuroscience > > > Jülich Supercomputing Centre > > > Institute for Advanced Simulation > > > Forschungszentrum Jülich GmbH > > > E-mail: s.graber(a)fz-juelich.de > <mailto:s.graber@fz-juelich.de> <mailto:s.graber@fz-juelich.de > <mailto:s.graber@fz-juelich.de>> > > <mailto:s.graber@fz-juelich.de <mailto:s.graber@fz-juelich.de> > <mailto:s.graber@fz-juelich.de <mailto:s.graber@fz-juelich.de>>> > > > Phone: +49 2461 61 85457 > > > http://www.fz-juelich.de/ias/jsc > > > > > > Institute of Neuroscience and Medicine (INM-6) > > > Computational and Systems Neuroscience & > > > Institute for Advanced Simulation (IAS-6) > > > Theoretical Neuroscience & > > > JARA Institute Brain Structure-Function Relationships > (INM-10) > > > Forschungszentrum Jülich GmbH > > > http://www.csn.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 > > > > > > ------------------------------------------------------------------------------------- > > > > > > > > > > > > -- > > > Thanks and Regards > > > > > > *Maryada* > > > > > > > > > _______________________________________________ > > > NEST Users mailing list -- users(a)nest-simulator.org > <mailto:users@nest-simulator.org> > > <mailto:users@nest-simulator.org > <mailto:users@nest-simulator.org>> > > > To unsubscribe send an email to > users-leave(a)nest-simulator.org <mailto:users-leave@nest-simulator.org> > > <mailto:users-leave@nest-simulator.org > <mailto:users-leave@nest-simulator.org>> > > > > > > > -- > > > ------------------------------------------------------------------------------------- > > Steffen Graber > > SimLab Neuroscience > > Division HPC in Neuroscience > > Jülich Supercomputing Centre > > Institute for Advanced Simulation > > Forschungszentrum Jülich GmbH > > E-mail: s.graber(a)fz-juelich.de <mailto:s.graber@fz-juelich.de> > <mailto:s.graber@fz-juelich.de <mailto:s.graber@fz-juelich.de>> > > Phone: +49 2461 61 85457 > > http://www.fz-juelich.de/ias/jsc > > > > Institute of Neuroscience and Medicine (INM-6) > > Computational and Systems Neuroscience & > > Institute for Advanced Simulation (IAS-6) > > Theoretical Neuroscience & > > JARA Institute Brain Structure-Function Relationships (INM-10) > > Forschungszentrum Jülich GmbH > > http://www.csn.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 > > > ------------------------------------------------------------------------------------- > > > > > > > > -- > > Thanks and Regards > > > > *Maryada* > > > > -- > ------------------------------------------------------------------------------------- > Steffen Graber > SimLab Neuroscience > Division HPC in Neuroscience > Jülich Supercomputing Centre > Institute for Advanced Simulation > Forschungszentrum Jülich GmbH > E-mail: s.graber(a)fz-juelich.de <mailto:s.graber@fz-juelich.de> > Phone: +49 2461 61 85457 > http://www.fz-juelich.de/ias/jsc > > Institute of Neuroscience and Medicine (INM-6) > Computational and Systems Neuroscience & > Institute for Advanced Simulation (IAS-6) > Theoretical Neuroscience & > JARA Institute Brain Structure-Function Relationships (INM-10) > Forschungszentrum Jülich GmbH > http://www.csn.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 > ------------------------------------------------------------------------------------- > > > > -- > Thanks and Regards > > *Maryada* > -- ------------------------------------------------------------------------------------- Steffen Graber SimLab Neuroscience Division HPC in Neuroscience Jülich Supercomputing Centre Institute for Advanced Simulation Forschungszentrum Jülich GmbH E-mail: s.graber(a)fz-juelich.de Phone: +49 2461 61 85457 http://www.fz-juelich.de/ias/jsc Institute of Neuroscience and Medicine (INM-6) Computational and Systems Neuroscience & Institute for Advanced Simulation (IAS-6) Theoretical Neuroscience & JARA Institute Brain Structure-Function Relationships (INM-10) Forschungszentrum Jülich GmbH http://www.csn.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 -------------------------------------------------------------------------------------

1 0

Issue with NEST Live Media 2.20
by Maryada Maryada 25 Aug '20

25 Aug '20

Hi, I am trying to import Live Media 2.20 however the VM virtualbox is always get stuck immediately as it starts (see attachment). I also tried to import the 2.18 version just to be sure if it's an issue on my side. However, that's working perfectly fine. Is there an additional requirement that I might be missing? -- Thanks and Regards *Maryada*

2 5

Random refractory period
by giovannidisarra 18 Aug '20

18 Aug '20

How can I set a random refractory period (different for every neuron) in a population with SetDefaults()?

2 1

Open NEST Developer Video Conference Monday 17 August 2020 11:30 CEST (UTC+2)
by Dennis Terhorst 17 Aug '20

17 Aug '20

Dear NEST Users & Developers! I would like to invite you to our next fortnightly Open NEST Developer Video Conference today Monday 17 August, 11.30-12.30 CEST (UTC+2). 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/2020-08-17-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

1 0

Saving and loading entire network
by LOW, SOCK CHING 05 Aug '20

05 Aug '20

Hi, I am new to pynest and am using it to implement a liquid state machine. It works marvelously for generating the network. My workflow is as follows: - Initialise kernel - Get stimulation episodes - Create neurons (including spike generators) - Connect neurons - nest.Simulate() - nest.GetStatus(recording_neurons) for readout at relevant timepoints I would like to save the network so I can run nest.Simulate() on other episodes in a real-time application, is there a straight-forward way to do so? I have tried pickling conn = nest.GetConnections() but to my knowledge that does not include a lot of details about the connection, like the weight. It also does not return where there is *no* connections, which means simply using nest.SetConnections(conn) prior to nest.Simulate() will not work to reproduce the previously generated network even if I initialise with all the same variables. I have found the functions GetNetwork() and GetNodes() but I'm not sure how I can use them, or if they are even useful for what I need. Cheers, Sock Ching

6 7

Open NEST Developer Video Conference Monday 3 August 2020 11:30 CEST (UTC+2)
by Dennis Terhorst 03 Aug '20

03 Aug '20

Dear NEST Users & Developers! I would like to invite you to our next fortnightly Open NEST Developer Video Conference today Monday 3 August, 11.30-12.30 CEST (UTC+2). 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/2020-08-03-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

1 0

Open NEST Developer Video Conference Monday 20 July 2020 11:30 CEST (UTC+2)
by Dennis Terhorst 20 Jul '20

20 Jul '20

Dear NEST Users & Developers! I would like to invite you to our next fortnightly Open NEST Developer Video Conference today Monday 20 July, 11.30-12.30 CEST (UTC+2). 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/2020-07-20-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

1 0

Open NEST Developer Video Conference Monday 6 July 2020 11:30 CEST (UTC+2)
by Dennis Terhorst 06 Jul '20

06 Jul '20

Dear NEST Users & Developers! I would like to invite you to our next fortnightly Open NEST Developer Video Conference today Monday 6 July, 11.30-12.30 CEST (UTC+2). 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: Hackathon Wrap-up The agenda for this meeting is also available online, see https://github.com/nest/nest-simulator/wiki/2020-07-06-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

1 0

How to normalize incoming/outgoing synaptic weights
by Keiko Fujii 29 Jun '20

29 Jun '20

Hello everyone, I would like to ask how to normalize synaptic weights during STDP learning. What I want to do is keeping the total amount of synaptic weights to/from each neuron constant. I try to describe my goal a bit more precisely: i: The index of a pre-synaptic neuron. j: The index of a post-synaptic neuron. w_ij(t): The synaptic weight from i-th neuron to j-th neuron at time=t. s_i(t): the sum of all incoming synaptic weights to i-th neuron at time=t. i.e. the sum of w_ij(t) over j. The goal is to set the sum of incoming weights (s_i(*)) to 1 by normalization (1 is just for simplicity). By STDP, we can get updated synaptic weight matrix w_ij(t+1), and the sum s_i(t+1) is not necessarily 1. So, I want to set w_ij(t+1) <- w_ij(t+1) / s_i(t+1) I briefly read the documentation for synaptic models( https://nest-simulator.readthedocs.io/en/stable/models/synapses.html). I am not very confident if my understanding is correct, but it seems that existing synaptic models handle only one synaptic weight. How can I gather data of all incoming(or outgoing as well) weights to a neuron and use the summation value inside of the STDP synapse model? Best regards, Keiko Fujii

2 1

Error: UnknownModelName
by Allen Rabayda 27 Jun '20

27 Jun '20

Dear Nest Community, Would anyone have insight into why I'm getting an UnknownModelName error? I'm new to Nest and am using Nest 18.0 on Lubuntu Virtual Box (Windows 10 OS). Thanks for any help. Best Regards, --Allen **** Error Message--additional details attached ****** raise exceptionCls(commandname, message) nest.ll_api.UnknownModelName: ('UnknownModelName in CopyModel_l_l_D: /stdp_izh_bitwise_correct_connection is not a known model name. Please check the modeldict for a list of available models.', 'UnknownModelName', <SLILiteral: CopyModel_l_l_D>, ': /stdp_izh_bitwise_correct_connection is not a known model name. Please check the modeldict for a list of available models.') ********************************************************

5 16

Install nest via homebrew
by Tammo Ippen 22 Jun '20

22 Jun '20

Hello nest users with a mac, From now on, it is possible to install nest via homebrew from the default homebrew-core tap: https://formulae.brew.sh/formula/nest#default [1] You get nest 2.20.0 with OpenMP and PyNEST bindings with python 3.8 delivered as a 'bottle' (prebuild binary package) in a couple of seconds - with all dependencies. Go to https://brew.sh/ [2] and follow the installation of homebrew. When brew is installed, just type: brew install nest And you should see something like: $ brew install nest ==> Downloading https://homebrew.bintray.com/bottles/nest-2.20.0_1.catalina.bottle.tar.gz ==> Downloading from https://akamai.bintray.com/38/38bfd492f381cd059a495122d1c3342e8fb5095501c04… ######################################################################## 100.0% ==> Pouring nest-2.20.0_1.catalina.bottle.tar.gz Warning: nest dependency gcc was built with a different C++ standard library (libstdc++ from clang). This may cause problems at runtime. ==> Caveats The PyNEST bindings and its dependencies are installed with the python(a)3.8 formula. If you want to use PyNEST, use the Python interpreter from this path: /usr/local/opt/python(a)3.8/bin You may want to add this to your PATH. ==> Summary 🍺 /usr/local/Cellar/nest/2.20.0_1: 1,290 files, 21.2MB Now you can run nest like: $ nest -- N E S T -- Copyright (C) 2004 The NEST Initiative Version: nest-2.20.0 Built: Jun 22 2020 13:38:00 This program is provided AS IS and comes with NO WARRANTY. See the file LICENSE for details. Problems or suggestions? Visit https://www.nest-simulator.org Type 'help' to get more information. Type 'quit' or press CTRL-D to quit. SLI ] If you want to use PyNEST, you have to use the python(a)3.8 formula python - the dependencies numpy, scipy, etc. are also delivered via homebrew and they are build with the python(a)3.8 formula, which is keg-only [3]. Add the opt-bin path to your PATH variable like: export PATH=/usr/local/opt/python@3.8/bin:$PATH and you can start with: $ python3.8 -c 'import nest' -- N E S T -- Copyright (C) 2004 The NEST Initiative Version: nest-2.20.0 Built: Jun 22 2020 13:38:00 This program is provided AS IS and comes with NO WARRANTY. See the file LICENSE for details. Problems or suggestions? Visit https://www.nest-simulator.org Type 'nest.help()' to find out more about NEST. Best, Tammo Links: ------ [1] https://formulae.brew.sh/formula/nest#default [2] https://brew.sh/ [3] https://docs.brew.sh/How-to-Build-Software-Outside-Homebrew-with-Homebrew-k…

1 0

Feature discussion: STDP and delays
by Dennis Terhorst 22 Jun '20

22 Jun '20

Dear NEST enthusiasts! In the NEST Meeting on May 25th <https://github.com/nest/nest-simulator/wiki/2020-05-25-Open-NEST-Developer-…> [1] there was a very interesting discussion of handling of delays in networks with STDP in NEST. It became obvious, that this topic requires a more in-depth discussion and it was decided to do a separate VC for this discussion, which will happen this week on * Thursday, June 25, 2020 - 13:30 CEST with the connection details <https://github.com/nest/nest-simulator/wiki/Connection-Details> [2] as usual. Best, Dennis [1]: https://github.com/nest/nest-simulator/wiki/2020-05-25-Open-NEST-Developer-… [2]: https://github.com/nest/nest-simulator/wiki/Connection-Details i.e. https://conf.dfn.de/webapp/conference/97938800 -- 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 -------------------------------------------------------------------------------------

1 0

Open NEST Developer Video Conference Monday 22 June 2020 11:30 CEST (UTC+2)
by Dennis Terhorst 22 Jun '20

22 Jun '20

Dear NEST Users & Developers! I would like to invite you to our next fortnightly Open NEST Developer Video Conference on Monday 22 June, 11.30-12.30 CEST (UTC+2). 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/2020-06-22-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

1 0

Installation on supercomputer failed
by Petia Koprinkova 19 Jun '20

19 Jun '20

Hi, We are trying to install NEST on supercomputer Ahitohol but we were unable to manage with some errors. Here attached is a screenshot with last reported errors. Could you help to resolve it?Regards,Petia

5 10

LIF neuron with both current based and conductance based synapses
by Hartmut Schmidt 18 Jun '20

18 Jun '20

Dear all, I am trying to implement a network consisting of LIF neurons with mixed current based and conductance based synaptic connections. Eg. one LIF neuron which gets two inputs from which one is treated as current input and the other as conductance input. That means, how to treat the input should be encoded in the synapse and not in the type of the postsynaptic neuron. Is such a neuron model already implemented or is there a way to implement this? Thanks for your help. Best, Hartmut

3 2

pipnest
by Robin Gilbert De Schepper 17 Jun '20

17 Jun '20

Hi, I created a little tool that provides packaging for NEST extension modules into python packages that can be `pip installed` on the target machine. https://pip-nest.readthedocs.io/en/latest/ First off, is this interesting to the community? It certainly seems easier to `pip install some-module` than to provide installation instructions, and I can now specify my modules as dependencies in code I distribute. Secondly, there are some shortcomings based on the fact that the pip install only reliably produces the build artifacts into python's site-packages and nest doesn't look for them there. This can probably only be elegantly solved by adding an `entry_point` to the nest python module so that these pip nest modules can announce themselves there? -- Robin De Schepper, MSc Department of Brain and Behavioral Sciences Unit of Neurophysiology University of Pavia, Italy Via Forlanini 6, 27100 Pavia - Italy Tel: (+39) 038298-7607 http://www-5.unipv.it/dangelo/

2 2

NEST Conference 2020 Program — Registration Deadline Monday 22 June 2020
by Hans Ekkehard Plesser 16 Jun '20

16 Jun '20

Dear Colleagues! The virtual NEST Conference 2020 on 29/30 June is less than two weeks away and we are happy to invite you to an exciting program of presentations and workshops, which you will find below. The conference will be single track to facilitate interactions and include virtual coffee breakouts to mix and mingle. Please don't forget to register by MONDAY, 22 June 2020 at https://www.nest-simulator.org/conference. Please note that we now also accept PayPal as a payment method. See you at the NEST Conference 2020! Hans Ekkehard Plesser & Susanne Kunkel Monday 29 June, 2020 (all times are CEST) * 09:00 — Welcome & Introduction (Susanne Kunkel) * 09:15 — NEST user-level documentation: Why, how and what’s next? (Sara Konradi) * 09:35 — Exploring new Fenix resources using NEST (Alexander Patronis) * 09:55 — Minibreak * 10:00 — Toward a possible integration of NeuronGPU in NEST (Bruno Golosio) * 10:45 — Coffee breakout * 11:15 — Workshop: NEST multiscale co-simulation (Wouter Klijn) * 12:15 — Lunch break * 13:15 — Thalamo-cortical spiking model of incremental learning combining perception, context and NREM-sleep-mediated noise-resilience (Chiara De Luca) * 14:00 — Minibreak * 14:05 — An Integrated Model of Visual Perception and Reinforcement(Petia Koprinkova-Hristova) * 14:25 — Partial Information Decomposition Contextual Neurons in NEST(Sepehr Mahmoudian) * 14:45 — Coffee breakout * 15:15 — deNEST: a declarative frontend for specifying networks and running simulations in NEST (Tom Bugnon) * 15:35 — Primate perisylvian cortex in NEST: from reflex to small world (Harry Howard) * 15:55 — Minibreak * 16:00 — Modeling robust and efficient coding in the mouse primary visual cortex using computational perturbations (Stefan Mihalas) * 16:45 — Wrap-up (Hans Ekkehard Plesser) * 17:00 — Mingle Tuesday 30 June, 2020 (all times are CEST) * 09:00 — A spiking neural network builder for systematic data-to-model workflow(Carlos E Gutierrez) * 09:20 — Insite: A Generalized Pipeline for In-transit Visualization and Analysis(Simon Oehrl) * 09:40 — Minibreak * 09:45 — NEST Component for Modeling Spiking Neuron-Astrocyte Networks(Jugoslava Aćimović) * 10:30 — Coffee breakout * 11:00 — Atlas-mapped reconstruction and simulation of the cerebellar Lingula in NEST (Alice Geminiani) * 11:20 — Cerebro-cerebellar loops for sensorimotor adaptation (Alberto Antonietti) * 11:40 — Minibreak * 11:45 — Modeling plasticity inducing stimulation protocols in recurrent neuronal networks with homeostatic structural plasticity (Swathi Anil) * 12:30 — Lunch break * 13:30 — Dendrites in NEST (Willem Wybo) * 13:50 — Just-in-time compilation for NESTML models in NEST Simulator (Charl Linssen) * 14:10 — NEST Desktop: A web-based GUI for the NEST Simulator (Sebastian Spreizer) * 14:30 — Minibreak * 14:40 — Evolving interpretable plasticity rules using NEST (Jakob Jordan) * 15:25 — Coffee breakout * 15:45 — Workshop: deNEST: a declarative frontend for specifying networks and running simulations in NEST (Tom Bugnon & William Mayner) * 16:45 — Closing Remarks -- Prof. Dr. Hans Ekkehard Plesser Head, Data Science Section 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

1 0

Training SNNs with PyNEST
by s.kraemer96＠gmx.net 15 Jun '20

15 Jun '20

Dear all, I´m writing a master thesis on spiking neural networks and how transparent they are. For that I need to implement a SNN network and train it. So I started with Brian but that is much to complex and I don´t need something special. So I decided to use PyNest. I did all the tutorials but I´m missing a tutorial how to train the network. I don´t know how to put in a dataset to train the model. I haven´t found anything to this topic. So my questions are: 1. Can PyNest train set up a SNN and train it trough data and if not is there another simulator who can do this? 2. How do I do it? Is there anything I missed to read or can someone send me an example? This would be very helpful. Thanks for your help. Best, Sonja

7 6

Open NEST Developer Video Conference Monday 8 June 2020 11:30 CEST (UTC+2)
by Dennis Terhorst 08 Jun '20

08 Jun '20

Dear NEST Users & Developers! I would like to invite you to our next fortnightly Open NEST Developer Video Conference on Monday 8 June, 11.30-12.30 CEST (UTC+2). 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. In-depth discussions will cover updates on the ongoing discussion around #1604 (STDP and delays) and proposed refactoring of the testing framework. 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/2020-06-08-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

1 0

[NEST users] Docker container with NEST3 and music
by Benjamin Staude 05 Jun '20

05 Jun '20

Hi NEST users, Does anyone know if there is a Docker container available that has NEST3 and the MUSIC interface installed? Best regards, Benjamin -- -- -- Dr. Benjamin Staude | Paul-Lincke-Ufer 7 | 10999 Berlin | benjamin.staude(a)gmail.com

2 4

NEST Conference 2020 Registration now open
by Dennis Terhorst 04 Jun '20

04 Jun '20

The NEST Conference organization team would like to share the following exciting news: Dear Colleagues! The NEST Conference Website is open again on https://nest-simulator.org/conference and we have now opened for registration as well. Registration by 22 June 2020 is required for attendance. Only registered users will receive log-in information for the conference. Registration to the conference is * free of charge for members of the NEST Initiative * 35 CHF for non-members To qualify for the member rate, you must apply for membership in the NEST Initiative by 10 June. See http://www.nest-initiative.org/membership/ for information on how to join. Membership is currently free of charge for students, including PhD students, and 25 CHF annually for everyone else. We are looking forward to seeing you on 29/30 June! Hans Ekkehard -- Prof. Dr. Hans Ekkehard Plesser Head, Data Science Section 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

1 0

NEST Conference 2020 Registration now open
by Hans Ekkehard Plesser 03 Jun '20

03 Jun '20

Dear Colleagues! The NEST Conference Website is open again on https://nest-simulator.org/conference and we have now opened for registration as well. Registration by 22 June 2020 is required for attendance. Only registered users will receive log-in information for the conference. Registration to the conference is * free of charge for members of the NEST Initiative * 35 CHF for non-members To qualify for the member rate, you must apply for membership in the NEST Initiative by 10 June. See http://www.nest-initiative.org/membership/ for information on how to join. Membership is currently free of charge for students, including PhD students, and 25 CHF annually for everyone else. We are looking forward to seeing you on 29/30 June! Hans Ekkehard -- Prof. Dr. Hans Ekkehard Plesser Head, Data Science Section 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

1 0

NEST Conference Abstract Submission via EMAIL
by Hans Ekkehard Plesser 02 Jun '20

02 Jun '20

Dear Colleagues, Regrettably, the website for the NEST Conference 2020 became unavailable shortly before the abstract submission deadline. We are currently working to restore the website. In the meantime, please submit your abstract BY EMAIL to conference(a)nest-initiative.org using the attached template (DOCX). Please also find an example abstract with detailed instructions attached. We extend the deadline to 2 June 2020. Best regards, Hans Ekkehard

2 1

2025

2024

2023

2022

2021

2020

2019

NEST Users