17 Feb
2020
17 Feb
'20
2:23 p.m.
Hi Charl,
Nice detective work.
I wonder why there are negative weight values? Is that due to negative weights being set
explicitly (not allowed for conductance-based multisynapse models) or do weights become
negative due to a plasticity mechanism?
For further comments, see https://github.com/nest/nest-simulator/issues/1432
Best,
Hans Ekkehard
On 17 Feb 2020, at 12:59, Charl Linssen
<nest-users@turingbirds.com<mailto:nest-users@turingbirds.com>> wrote:
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@kth.se<mailto:angpap@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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--
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(a)nmbu.no
Home http://arken.nmbu.no/~plesser