[NEST Users] Re: Error running tutorial notebook

5 Aug 2019

Hi Filip,

Sorry for the late reply.
I've tried a lot and can reproduce your bugs.
That's why I opened an issue on GitHub:

https://github.com/nest/nest-simulator/issues/1265

If you have found a solution or a workaround by now, it would be nice to
hear from you.

Best

Steffen

Am 13.07.19 um 11:11 schrieb Filip Vercruysse:
...
  At the NEST tutorial in CNS
 (https://github.com/AlexVanMeegen/CNS2019_NEST_Tutorial) I have tried
 NEST 2.18 (2.16 also failed but with different error) using Mac with
 Mojave 10.14.1 and anaconda 3

 Kind regards

 Filip Vercruysse

 On Sat, Jul 13, 2019 at 11:07 AM Filip Vercruysse
 &lt;filipvercruysse(a)gmail.com <mailto:filipvercruysse@gmail.com>> wrote:

     (CNS2019_NEST) Filips-MacBook-Pro:CNS2019_NEST_Tutorial filip$
     jupyter-notebook

     [I 11:01:50.427 NotebookApp]The port 8888 is already in use,
     trying another port.

     [I 11:01:50.439 NotebookApp]Serving notebooks from local
     directory: /Users/filip/Desktop/Research/Conferences/CNS
     Barcelona/NEST tutorial/CNS2019_NEST_Tutorial

     [I 11:01:50.439 NotebookApp]The Jupyter Notebook is running at:

     [I 11:01:50.439

NotebookApp]http://localhost:8889/?token=f4b50440467ee8d87607f84e947be0022dbd7aa394a0b4c9

     [I 11:01:50.439 NotebookApp]Use Control-C to stop this server and
     shut down all kernels (twice to skip confirmation).

     [C 11:01:50.445 NotebookApp] 

         To access the notebook, open this file in a browser:

     file:///Users/filip/Library/Jupyter/runtime/nbserver-31158-open.html

         Or copy and paste one of these URLs:

     http://localhost:8889/?token=f4b50440467ee8d87607f84e947be0022dbd7aa394a0b4…

     [I 11:01:57.768 NotebookApp]Kernel started:
     103ab68f-95af-4961-8f9d-3756f2192fd2

     [I 11:01:58.401 NotebookApp]Adapting to protocol v5.1 for kernel
     103ab68f-95af-4961-8f9d-3756f2192fd2

     [INFO] [2019.7.13 11:2:4

/usr/local/miniconda/conda-bld/nest-simulator_1562094389587/work/nestkernel/rng_manager.cpp:217
     @ Network::create_rngs_] : Creating default RNGs

     [INFO] [2019.7.13 11:2:4

/usr/local/miniconda/conda-bld/nest-simulator_1562094389587/work/nestkernel/rng_manager.cpp:260
     @ Network::create_grng_] : Creating new default global RNG

     Assertion failed: (out != NULL), function execute, file
     /usr/local/miniconda/conda-bld/nest-simulator_1562094389587/work/sli/sli_io.cc,
     line 422.

     [Filips-MacBook-Pro:31166] *** Process received signal ***

     [Filips-MacBook-Pro:31166] Signal: Abort trap: 6 (6)

     [Filips-MacBook-Pro:31166] Signal code:  (0)

     [Filips-MacBook-Pro:31166] [ 0] 0   libsystem_platform.dylib     
           0x00007fff791bfb3d _sigtramp + 29

     [Filips-MacBook-Pro:31166] [ 1] 0   ???                          
           0x0000000000000001 0x0 + 1

     [Filips-MacBook-Pro:31166] [ 2] 0   libsystem_c.dylib            
           0x00007fff7907e1c9 abort + 127

     [Filips-MacBook-Pro:31166] [ 3] 0   libsystem_c.dylib            
           0x00007fff79046868 basename_r + 0

     [Filips-MacBook-Pro:31166] [ 4] 0   libsli.dylib                 
           0x0000000110a01077
     _ZNK18StrSStreamFunction7executeEP14SLIInterpreter + 759

     [Filips-MacBook-Pro:31166] [ 5] 0   libsli.dylib                 
           0x00000001109edb2e
     _ZN13FunctionDatum7executeEP14SLIInterpreter + 446

     [Filips-MacBook-Pro:31166] [ 6] 0   libsli.dylib                 
           0x00000001109ebe42 _ZN14SLIInterpreter8execute_Em + 466

     [Filips-MacBook-Pro:31166] [ 7] 0   libsli.dylib                 
           0x00000001109ebc58 _ZN14SLIInterpreter7startupEv + 40

     [Filips-MacBook-Pro:31166] [ 8] 0   libnest.dylib                
           0x0000000110031ffa

_Z11neststartupPiPPPcR14SLIInterpreterNSt3__112basic_stringIcNS5_11char_traitsIcEENS5_9allocatorIcEEEE
     + 3306

     [Filips-MacBook-Pro:31166] [ 9] 0   pynestkernel.so              
           0x000000010ffd5cb8
     _ZL42__pyx_pw_12pynestkernel_10NESTEngine_5initP7_objectS0_S0_ + 3464

     [Filips-MacBook-Pro:31166] [10] 0   python                       
           0x00000001025a948a _PyCFunction_FastCallDict + 362

     [Filips-MacBook-Pro:31166] [11] 0   python                       
           0x000000010268042f call_function + 143

     [Filips-MacBook-Pro:31166] [12] 0   python                       
           0x000000010267dfc2 _PyEval_EvalFrameDefault + 46802

     [Filips-MacBook-Pro:31166] [13] 0   python                       
           0x00000001026807ec fast_function + 188

     [Filips-MacBook-Pro:31166] [14] 0   python                       
           0x000000010268048c call_function + 236

     [Filips-MacBook-Pro:31166] [15] 0   python                       
           0x000000010267dfc2 _PyEval_EvalFrameDefault + 46802

     [Filips-MacBook-Pro:31166] [16] 0   python                       
           0x0000000102671729 _PyEval_EvalCodeWithName + 425

     [Filips-MacBook-Pro:31166] [17] 0   python                       
           0x000000010266bf99 builtin_exec + 345

     [Filips-MacBook-Pro:31166] [18] 0   python                       
           0x00000001025a8dd2 PyCFunction_Call + 66

     [Filips-MacBook-Pro:31166] [19] 0   python                       
           0x000000010267e2b2 _PyEval_EvalFrameDefault + 47554

     [Filips-MacBook-Pro:31166] [20] 0   python                       
           0x0000000102671729 _PyEval_EvalCodeWithName + 425

     [Filips-MacBook-Pro:31166] [21] 0   python                       
           0x000000010268089a fast_function + 362

     [Filips-MacBook-Pro:31166] [22] 0   python                       
           0x000000010268048c call_function + 236

     [Filips-MacBook-Pro:31166] [23] 0   python                       
           0x000000010267dfc2 _PyEval_EvalFrameDefault + 46802

     [Filips-MacBook-Pro:31166] [24] 0   python                       
           0x00000001026807ec fast_function + 188

     [Filips-MacBook-Pro:31166] [25] 0   python                       
           0x000000010268048c call_function + 236

     [Filips-MacBook-Pro:31166] [26] 0   python                       
           0x000000010267dfc2 _PyEval_EvalFrameDefault + 46802

     [Filips-MacBook-Pro:31166] [27] 0   python                       
           0x00000001026807ec fast_function + 188

     [Filips-MacBook-Pro:31166] [28] 0   python                       
           0x000000010268048c call_function + 236

     [Filips-MacBook-Pro:31166] [29] 0   python                       
           0x000000010267dfc2 _PyEval_EvalFrameDefault + 46802

     [Filips-MacBook-Pro:31166] *** End of error message ***

     [I 11:02:06.763 NotebookApp]KernelRestarter: restarting kernel
     (1/5), keep random ports

     WARNING:root:kernel 103ab68f-95af-4961-8f9d-3756f2192fd2 restarted

     [I 11:03:57.801 NotebookApp]Saving file at
     /part1_NEST/0_hello_world.ipynb

 _______________________________________________
 NEST Users mailing list -- users(a)nest-simulator.org
 To unsubscribe send an email to users-leave(a)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>
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

2024

2023

2022

2021

2020

2019

[NEST Users] Re: Error running tutorial notebook