17 Feb
2020
17 Feb
'20
12:59 p.m.
Hi,
Sorry for the delay in reply. I've been able to reproduce your error. Fundamentally,
there is an issue here that when BadProperty is raised from the C++ level, the message
that is (usually) supplied as part of it is lost when the exception makes it up to the
Python level. I will create an issue for this on our GitHub repository.
Sidestepping this issue for now, by simply printing the message when the exception object
is instantiated in C++ (add a print statement on line 558 of nestkernel/exceptions.h),
I'm getting "Synaptic weights for conductance-based multisynapse models must be
positive." Could you check this in your model?
If, after this, you are still experiencing issues, could you please first upgrade to the
latest release (NEST 2.20) and provide a (very!) minimal script that reproduces the
issue?
Thanks, kind regards,
Charl Linssen
On Thu, Jan 30, 2020, at 13:38, angpap(a)kth.se wrote:
> Hello,
>
> I am fairly new to NEST and I have been struggling with the following issue.
>
> Github repo: https://github.com/angpapadi/wm-net
>
> My simulation code consists of 3 python files:
> - sim.py, the main simulation script, where the model is built and the
> simulation program is specified
> - helpers.py a collection of helper functions
> - parameters.py a script where all parameters are specified.
>
> In order to be able to run the code successfully, I have to set certain
> parameters to unrealistic values. If I try to move any of these
> parameters towards a more realistic regime, NEST crashes (see end of
> post for full error message). Most relevant is the fact that setting
> these parameters to more reasonable values, increases by a lot the
> amount of spikes that NEST has to keep track of.
>
> Examples of such parameters that currently have wrong values:
> > the DOWNSCALE_FACTOR, that essentially controls the neural network's size.
Right now my network size is downscaled 95% of what I would want it to be. There are 2
hypercolumns with 4 minicolumns each. Each minicolumn consists of 4 neurons.
>
> > E_rev is a list of the reversal potential for each synaptic port. My neuron
model has 3 synaptic ports for AMPA, NMDA and GABA, in that order. The Erev for GABA is
correctly set but for AMPA and NMDA I cannot get it to work for values bigger than -25,
when the correct reversal potential for both is 0.
>
> I cannot find the issue with my code, if there is any. When the
> simulation is very limited (the aforementioned parameters are set to
> unrealistic values), the code runs flawlessly and produces the expected
> plots and spike rasters. Also, if I allocate more resources by running
> on multiple mpi processes, I can be slightly closer to the correct
> parameter ranges before the nest::badproperty error occurs.
>
> To reproduce the error:
> 1. You can optionally first run the code as is to verify that it works
> (by running the sim.py script)
> 2. Then try setting one of the parameters mentioned above to a more
> plausible value. You can do so by going to the parameters.py file and
> either reducing the DOWNSCALE_FACTOR parameter (line 7) or increasing
> the first two entries of the E_rev list (line 203) that correspond to
> the AMPA and NMDA reversal potentials, or doing both if you 're feeling
> adventurous!
>
> The error is the following:
>
> terminate called after throwing an instance of 'nest::BadProperty'
> what(): BadProperty
> [59eb791543aa:00113] *** Process received signal ***
> [59eb791543aa:00113] Signal: Aborted (6)
> [59eb791543aa:00113] Signal code: (-6)
> [59eb791543aa:00113] [ 0]
> /lib/x86_64-linux-gnu/libc.so.6(+0x3ef20)[0x7f2c117b7f20]
> [59eb791543aa:00113] [ 1]
> /lib/x86_64-linux-gnu/libc.so.6(gsignal+0xc7)[0x7f2c117b7e97]
> [59eb791543aa:00113] [ 2]
> /lib/x86_64-linux-gnu/libc.so.6(abort+0x141)[0x7f2c117b9801]
> [59eb791543aa:00113] [ 3]
> /usr/lib/x86_64-linux-gnu/libstdc++.so.6(+0x8c957)[0x7f2c0a55a957]
> [59eb791543aa:00113] [ 4]
> /usr/lib/x86_64-linux-gnu/libstdc++.so.6(+0x92ab6)[0x7f2c0a560ab6]
> [59eb791543aa:00113] [ 5]
> /usr/lib/x86_64-linux-gnu/libstdc++.so.6(+0x91b19)[0x7f2c0a55fb19]
> [59eb791543aa:00113] [ 6]
> /usr/lib/x86_64-linux-gnu/libstdc++.so.6(__gxx_personality_v0+0x2a8)[0x7f2c0a560488]
> [59eb791543aa:00113] [ 7]
> /lib/x86_64-linux-gnu/libgcc_s.so.1(+0x10613)[0x7f2c0d6f1613]
> [59eb791543aa:00113] [ 8]
> /lib/x86_64-linux-gnu/libgcc_s.so.1(_Unwind_Resume+0x125)[0x7f2c0d6f1e95]
> [59eb791543aa:00113] [ 9]
>
/opt/nest/lib/python3.6/site-packages/nest/../../../libnestkernel.so(_ZN4nest20EventDeliveryManager18gather_spike_data_INS_9SpikeDataEEEviRSt6vectorIT_SaIS4_EES7_+0x10ed)[0x7f2c0af0684d]
> [59eb791543aa:00113] [10]
>
/opt/nest/lib/python3.6/site-packages/nest/../../../libnestkernel.so(+0xf4894)[0x7f2c0aee4894]
> [59eb791543aa:00113] [11]
> /usr/lib/x86_64-linux-gnu/libgomp.so.1(GOMP_parallel+0x3f)[0x7f2c08d79ecf]
> [59eb791543aa:00113] [12]
>
/opt/nest/lib/python3.6/site-packages/nest/../../../libnestkernel.so(_ZN4nest17SimulationManager7update_Ev+0x151)[0x7f2c0aee0f61]
> [59eb791543aa:00113] [13]
>
/opt/nest/lib/python3.6/site-packages/nest/../../../libnestkernel.so(_ZN4nest17SimulationManager12call_update_Ev+0x5a5)[0x7f2c0aee1915]
> [59eb791543aa:00113] [14]
>
/opt/nest/lib/python3.6/site-packages/nest/../../../libnestkernel.so(_ZN4nest17SimulationManager3runERKNS_4TimeE+0x1d3)[0x7f2c0aee6713]
> [59eb791543aa:00113] [15]
>
/opt/nest/lib/python3.6/site-packages/nest/../../../libnestkernel.so(_ZN4nest17SimulationManager8simulateERKNS_4TimeE+0x1c)[0x7f2c0aee699c]
> [59eb791543aa:00113] [16]
>
/opt/nest/lib/python3.6/site-packages/nest/../../../libnestkernel.so(_ZN4nest8simulateERKd+0xc2)[0x7f2c0aecb972]
> [59eb791543aa:00113] [17]
>
/opt/nest/lib/python3.6/site-packages/nest/../../../libnestkernel.so(_ZNK4nest10NestModule16SimulateFunction7executeEP14SLIInterpreter+0x43)[0x7f2c0ae97a53]
> [59eb791543aa:00113] [18]
>
/opt/nest/lib/python3.6/site-packages/nest/../../../libsli.so(_ZN13FunctionDatum7executeEP14SLIInterpreter+0x43)[0x7f2c0a8e9063]
> [59eb791543aa:00113] [19]
>
/opt/nest/lib/python3.6/site-packages/nest/../../../libsli.so(_ZN14SLIInterpreter8execute_Em+0x222)[0x7f2c0a8e6d42]
> [59eb791543aa:00113] [20]
>
/opt/nest/lib/python3.6/site-packages/nest/../../../libsli.so(_ZN14SLIInterpreter7executeERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEE+0x15e)[0x7f2c0a8e72be]
> [59eb791543aa:00113] [21]
> /opt/nest/lib/python3.6/site-packages/nest/pynestkernel.so(+0x29ac8)[0x7f2c0c5caac8]
> [59eb791543aa:00113] [22] python[0x50a94c]
> [59eb791543aa:00113] [23]
> python(_PyEval_EvalFrameDefault+0x449)[0x50c5b9]
> [59eb791543aa:00113] [24] python[0x509d48]
> [59eb791543aa:00113] [25] python[0x50aa7d]
> [59eb791543aa:00113] [26]
> python(_PyEval_EvalFrameDefault+0x449)[0x50c5b9]
> [59eb791543aa:00113] [27] python[0x508245]
> [59eb791543aa:00113] [28] python[0x589471]
> [59eb791543aa:00113] [29] python(PyObject_Call+0x3e)[0x5a067e]
> [59eb791543aa:00113] *** End of error message ***
>
> Let me know if you need any additional information and I thank you for your time
>
> Angeliki
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