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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?

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

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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

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