Thanks, Hans. I've tried running the microcircuit with python and iPython, so I'll provide both error messages below. Per the instructions, N_scaling and K_scaling are set to 0.1 in network_params.py (running locally).


- the version of NEST you installed with conda


nest-simulator 2.20.0 mpi_openmpi_py38h4b37503_6 conda-forge


- the commands you used to run the microcircuit example


$ python example.py


- all the output generated, including the full error message

[INFO] [2020.10.8 9:53:9 /home/conda/feedstock_root/build_artifacts/nest-simulator_1600101873508/work/nestkernel/rng_manager.cpp:217 @ Network::create_rngs_] : Creating default RNGs
[INFO] [2020.10.8 9:53:9 /home/conda/feedstock_root/build_artifacts/nest-simulator_1600101873508/work/nestkernel/rng_manager.cpp:260 @ Network::create_grng_] : Creating new default global RNG

              -- N E S T --
  Copyright (C) 2004 The NEST Initiative

 Version: nest-2.20.0
 Built: Sep 14 2020 16:48:48

 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.

data directory already exists
Data will be written to /home/dominic/Code/nest/microcircuit_example/data/
Time to initialize the network: 0.00 s

Oct 08 09:53:09 ModelManager::clear_models_ [Info]:
    Models will be cleared and parameters reset.

Oct 08 09:53:09 Network::create_rngs_ [Info]:
    Deleting existing random number generators

Oct 08 09:53:09 Network::create_rngs_ [Info]:
    Creating default RNGs

Oct 08 09:53:09 Network::create_grng_ [Info]:
    Creating new default global RNG
Master seed: 55

Oct 08 09:53:09 ModelManager::clear_models_ [Info]:
    Models will be cleared and parameters reset.

Oct 08 09:53:09 Network::create_rngs_ [Info]:
    Deleting existing random number generators

Oct 08 09:53:09 Network::create_rngs_ [Info]:
    Creating default RNGs

Oct 08 09:53:09 Network::create_grng_ [Info]:
    Creating new default global RNG
Number of total processes: 1
Seeds for random number generators of virtual processes: [57]
Global random number generator seed: 56

Oct 08 09:53:09 SimulationManager::set_status [Info]:
    Temporal resolution changed.
/home/dominic/Code/nest/microcircuit_example/helpers.py:133: FutureWarning:arrays to stack must be passed as a "sequence" type such as list or tuple. Support for non-sequence iterables such as generators is deprecated as of NumPy 1.16 and will raise an error in the future.
The number of neurons is scaled by a factor of: 0.10
The number of synapses is scaled by a factor of: 0.10
/home/dominic/miniconda3/envs/nest/lib/python3.8/site-packages/nest/lib/hl_api_helper.py:127: UserWarning:
GetNodes is deprecated and will be removed in NEST 3.0. Use             GIDCollection instead.

Oct 08 09:53:09 SLIInterpreter [Deprecated]:
    SLI function GetNodes_i_D_b_b is deprecated in NEST 3.0.
Spike detectors created
Thalamic input not provided
Poisson background input created
Recurrent connections are established
Poisson background input is connected
Spike detector connected
Time to create the connections: 1.30 s

Oct 08 09:53:10 NodeManager::prepare_nodes [Info]:
    Preparing 7729 nodes for simulation.
[dominic-Precision-7530:11593] *** Process received signal ***
[dominic-Precision-7530:11593] Signal: Segmentation fault (11)
[dominic-Precision-7530:11593] Signal code: Address not mapped (1)
[dominic-Precision-7530:11593] Failing at address: 0xfffffffffffffff8
[dominic-Precision-7530:11593] [ 0] /lib/x86_64-linux-gnu/libpthread.so.0(+0x128a0)[0x7fec5842d8a0]
[dominic-Precision-7530:11593] [ 1] /home/dominic/miniconda3/envs/nest/lib/python3.8/site-packages/nest/../../../libmodels.so(+0x4b5960)[0x7febf6cee960]
[dominic-Precision-7530:11593] [ 2] /home/dominic/miniconda3/envs/nest/lib/python3.8/site-packages/nest/../../../libmodels.so(+0x4b5f5e)[0x7febf6ceef5e]
[dominic-Precision-7530:11593] [ 3] /home/dominic/miniconda3/envs/nest/lib/python3.8/site-packages/nest/../../../libmodels.so(+0x4b5f5e)[0x7febf6ceef5e]
[dominic-Precision-7530:11593] [ 4] /home/dominic/miniconda3/envs/nest/lib/python3.8/site-packages/nest/../../../libmodels.so(+0x4b7936)[0x7febf6cf0936]
[dominic-Precision-7530:11593] [ 5] /home/dominic/miniconda3/envs/nest/lib/python3.8/site-packages/nest/../../../libmodels.so(+0x4b8882)[0x7febf6cf1882]
[dominic-Precision-7530:11593] [ 6] /home/dominic/miniconda3/envs/nest/lib/python3.8/site-packages/nest/../../../libmodels.so(+0x4b8ae4)[0x7febf6cf1ae4]
[dominic-Precision-7530:11593] [ 7] /home/dominic/miniconda3/envs/nest/lib/python3.8/site-packages/nest/../../../libmodels.so(_ZN4nest4sortINS_6SourceENS_16StaticConnectionINS_24TargetIdentifierPtrRportEEEEEvR11BlockVectorIT_ERS5_IT0_E+0x1d9)[0x7febf6cf1d19]
[dominic-Precision-7530:11593] [ 8] /home/dominic/miniconda3/envs/nest/lib/python3.8/site-packages/nest/../../../libnestkernel.so(_ZN4nest17ConnectionManager16sort_connectionsEi+0x99)[0x7febf66d3c19]
[dominic-Precision-7530:11593] [ 9] /home/dominic/miniconda3/envs/nest/lib/python3.8/site-packages/nest/../../../libnestkernel.so(_ZN4nest17SimulationManager32update_connection_infrastructureEi+0x1f2)[0x7febf66c6ae2]
[dominic-Precision-7530:11593] [10] /home/dominic/miniconda3/envs/nest/lib/python3.8/site-packages/nest/../../../libgomp.so.1(GOMP_parallel+0x42)[0x7febf6036e8c]
[dominic-Precision-7530:11593] [11] /home/dominic/miniconda3/envs/nest/lib/python3.8/site-packages/nest/../../../libnestkernel.so(_ZN4nest17SimulationManager7prepareEv+0x1be)[0x7febf66c5e4e]
[dominic-Precision-7530:11593] [12] /home/dominic/miniconda3/envs/nest/lib/python3.8/site-packages/nest/../../../libnestkernel.so(_ZN4nest17SimulationManager8simulateERKNS_4TimeE+0x12)[0x7febf66d1442]
[dominic-Precision-7530:11593] [13] /home/dominic/miniconda3/envs/nest/lib/python3.8/site-packages/nest/../../../libnestkernel.so(_ZN4nest8simulateERKd+0xc3)[0x7febf66b17d3]
[dominic-Precision-7530:11593] [14] /home/dominic/miniconda3/envs/nest/lib/python3.8/site-packages/nest/../../../libnestkernel.so(_ZNK4nest10NestModule16SimulateFunction7executeEP14SLIInterpreter+0x45)[0x7febf6684b05]
[dominic-Precision-7530:11593] [15] /home/dominic/miniconda3/envs/nest/lib/python3.8/site-packages/nest/../../../libsli.so(+0x743b3)[0x7febf63c93b3]
[dominic-Precision-7530:11593] [16] /home/dominic/miniconda3/envs/nest/lib/python3.8/site-packages/nest/../../../libsli.so(_ZN14SLIInterpreter8execute_Em+0x222)[0x7febf63cdc62]
[dominic-Precision-7530:11593] [17] /home/dominic/miniconda3/envs/nest/lib/python3.8/site-packages/nest/../../../libsli.so(_ZN14SLIInterpreter7executeERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEE+0x162)[0x7febf63ce202]
[dominic-Precision-7530:11593] [18] /home/dominic/miniconda3/envs/nest/lib/python3.8/site-packages/nest/pynestkernel.so(+0x29a5c)[0x7febf736aa5c]
[dominic-Precision-7530:11593] [19] python(+0x18166a)[0x556ade2dd66a]
[dominic-Precision-7530:11593] [20] python(_PyEval_EvalFrameDefault+0x4bf)[0x556ade33a42f]
[dominic-Precision-7530:11593] [21] python(_PyFunction_Vectorcall+0x1b7)[0x556ade3266a7]
[dominic-Precision-7530:11593] [22] python(_PyEval_EvalFrameDefault+0x71a)[0x556ade33a68a]
[dominic-Precision-7530:11593] [23] python(_PyFunction_Vectorcall+0x1b7)[0x556ade3266a7]
[dominic-Precision-7530:11593] [24] python(PyObject_Call+0x7d)[0x556ade29243d]
[dominic-Precision-7530:11593] [25] python(_PyEval_EvalFrameDefault+0x1f12)[0x556ade33be82]
[dominic-Precision-7530:11593] [26] python(_PyEval_EvalCodeWithName+0x929)[0x556ade325bc9]
[dominic-Precision-7530:11593] [27] python(_PyFunction_Vectorcall+0x594)[0x556ade326a84]
[dominic-Precision-7530:11593] [28] python(_PyEval_EvalFrameDefault+0x4fa1)[0x556ade33ef11]
[dominic-Precision-7530:11593] [29] python(_PyFunction_Vectorcall+0x1b7)[0x556ade3266a7]
[dominic-Precision-7530:11593] *** End of error message ***
Segmentation fault (core dumped)

--

With iPython -

- all the output generated, including the full error message

Python 3.8.5 | packaged by conda-forge | (default, Sep 24 2020, 16:55:52)
Type "copyright", "credits" or "license" for more information.

IPython 7.18.1 -- An enhanced Interactive Python.

runfile('/home/dominic/Code/nest/microcircuit_example/example.py', wdir='/home/dominic/Code/nest/microcircuit_example')
[INFO] [2020.10.8 10:10:23 /home/conda/feedstock_root/build_artifacts/nest-simulator_1600101873508/work/nestkernel/rng_manager.cpp:217 @ Network::create_rngs_] : Creating default RNGs
[INFO] [2020.10.8 10:10:23 /home/conda/feedstock_root/build_artifacts/nest-simulator_1600101873508/work/nestkernel/rng_manager.cpp:260 @ Network::create_grng_] : Creating new default global RNG

              -- N E S T --
  Copyright (C) 2004 The NEST Initiative

 Version: nest-2.20.0
 Built: Sep 14 2020 16:48:48

 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.

data directory already exists
Data will be written to /home/dominic/Code/nest/microcircuit_example/data/
Time to initialize the network: 0.00 s
Master seed: 55
Number of total processes: 1
Seeds for random number generators of virtual processes: [57]
Global random number generator seed: 56

Oct 08 10:10:23 ModelManager::clear_models_ [Info]:
    Models will be cleared and parameters reset.

Oct 08 10:10:23 Network::create_rngs_ [Info]:
    Deleting existing random number generators

Oct 08 10:10:23 Network::create_rngs_ [Info]:
    Creating default RNGs

Oct 08 10:10:23 Network::create_grng_ [Info]:
    Creating new default global RNG

Oct 08 10:10:23 ModelManager::clear_models_ [Info]:
    Models will be cleared and parameters reset.

Oct 08 10:10:23 Network::create_rngs_ [Info]:
    Deleting existing random number generators

Oct 08 10:10:23 Network::create_rngs_ [Info]:
    Creating default RNGs

Oct 08 10:10:23 Network::create_grng_ [Info]:
    Creating new default global RNG

Oct 08 10:10:23 SimulationManager::set_status [Info]:
    Temporal resolution changed.
The number of neurons is scaled by a factor of: 0.10
The number of synapses is scaled by a factor of: 0.10
/home/dominic/Code/nest/microcircuit_example/helpers.py:133: FutureWarning:arrays to stack must be passed as a "sequence" type such as list or tuple. Support for non-sequence iterables such as generators is deprecated as of NumPy 1.16 and will raise an error in the future.
/home/dominic/miniconda3/envs/nest/lib/python3.8/site-packages/nest/lib/hl_api_helper.py:127: UserWarning:
GetNodes is deprecated and will be removed in NEST 3.0. Use             GIDCollection instead.

Oct 08 10:10:23 SLIInterpreter [Deprecated]:
    SLI function GetNodes_i_D_b_b is deprecated in NEST 3.0.
Spike detectors created
Thalamic input not provided
Poisson background input created
Recurrent connections are established

Restarting kernel...

[SpyderKernelApp] WARNING | No such comm: f2c6ea32096f11eba0c4fc77749073f1

--

Best

Dominic

Dominic Standage, PhD
Marie Curie Senior Research Fellow
School of Psychology /
Centre for Computational Neuroscience and Cognitive Robotics
University of Birmingham
Birmingham, B15 2TT
United Kingdom
Email - d.standage@bham.ac.uk

From: hans.ekkehard.plesser@nmbu.no <hans.ekkehard.plesser@nmbu.no>
Sent: 08 October 2020 01:29:31
To: NEST User Mailing List
Subject: [NEST Users] Re: Microcircuit example, segmentation fault
 

Hi Dominic,

Brevity is appreciated, but we need more information in this case to understand the cause of the problem.

Could you provide

- the version of NEST you installed with conda
- the commands you used to run the microcircuit example
- all the output generated, including the full error message

Thanks,
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@nmbu.no
Home http://arken.nmbu.no/~plesser
 

´╗┐On 07/10/2020, 18:50, "d.standage@bham.ac.uk" <d.standage@bham.ac.uk> wrote:

    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
    _______________________________________________
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