30 Jan
2020
30 Jan
'20
1:38 p.m.
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