February 2021 - NEST Users - NEST Initiative Mail

Triplets STDP model
by Julia Gallinaro 14 Apr '21

14 Apr '21

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

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

12 Mar '21

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

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

11 Mar '21

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

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Error when plotting masks with azimuthal angle
by Arturo del Cerro Vergara 26 Feb '21

26 Feb '21

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

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

25 Feb '21

Dear NEST Developers! Thanks to Lekshmi's great work, we can now use Github checks for continuous integration testing. Please merge master into your open PRs/branches to make sure your contributions run the Github checks. We will run Github checks and Travis checks in parallel for now. Best Hans Ekkehard -- Prof. Dr. Hans Ekkehard Plesser Head, Department of Data Science Faculty of Science and Technology Norwegian University of Life Sciences PO Box 5003, 1432 Aas, Norway Phone +47 6723 1560 Email hans.ekkehard.plesser(a)nmbu.no<mailto:hans.ekkehard.plesser@nmbu.no> Home http://arken.nmbu.no/~plesser

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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

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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

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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

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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

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NEST Users February 2021