December 2020 - 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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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

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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

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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

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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

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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

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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

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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?

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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

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NEST Users December 2020