I use NEST (Version 2.16.0) by using PyNN.
While using I came across the problem that NEST throws an error, when the rate of a SpikeSourcePoisson (in PyNN) is updated from any positive value to 0 and to any positive value again. In other words, once the rate is set to zero, it cannot be changed anymore. It seems like this issue is independant of the temporal location.
The exception thrown is the following:
python2.7: /pathToNestSimulator/nest-simulator-2.16.0/nestkernel/event_delivery_manager.h:564: nest::delay nest::EventDeliveryManager::get_slice_modulo(nest::delay): Assertion `static_cast< std::vector< delay >::size_type >( d ) < slice_moduli_.size()' failed.
Further, any rate change of a specific neuron is not applied before the next spike at the previous rate. This is problematic when dealing with low rates as spikes occur only rarely. For instance, with a rate of 1 it is not unlikely that there is not a spike for a few seconds. As a result, a rate change can and will be applied extremely delayed.
I initially reported this at PyNN, but it seems to be a NEST issue: https://github.com/NeuralEnsemble/PyNN/issues/650
What would you advise?
Dear Weinzierl,
this (both) looks like genuine bugs that should be fixed. Could you open two issues in the github tracker (https://github.com/nest/nest-simulator/issues), so we can properly track it and collect more detailed information.
We would need a minimal reproducer, ideally in NEST itself, to understand what is happening.
best, Dennis
Dear all,
Please note that I created two issues two weeks ago in response to PyNN #560.
poisson_generator_ps causes segmentation fault after setting rate from 0 to positive value nest/nest-simulator#1278https://github.com/nest/nest-simulator/issues/1278 poisson_generator_ps does not handle rate change correctly nest/nest-simulator#1279https://github.com/nest/nest-simulator/issues/1279
and a PR is already availabe
https://github.com/nest/nest-simulator/pull/1280
Both issues are linked from PyNN #560.
Best, Hans Ekkehard
On 16 Sep 2019, at 11:40, Dennis Terhorst <d.terhorst@fz-juelich.demailto:d.terhorst@fz-juelich.de> wrote:
Dear Weinzierl,
this (both) looks like genuine bugs that should be fixed. Could you open two issues in the github tracker (https://github.com/nest/nest-simulator/issues), so we can properly track it and collect more detailed information.
We would need a minimal reproducer, ideally in NEST itself, to understand what is happening.
best, Dennis
-- Dipl.-Phys. Dennis Terhorst Coordinator Software Development
Institute of Neuroscience and Medicine (INM-6) Computational and Systems Neuroscience & Theoretical Neuroscience, Institute for Advanced Simulation (IAS-6) Jülich Research Centre, Member of the Helmholz Association and JARA 52425 Jülich, Germany
Building 15.22 Room 4004 Phone +49 2461 61-85062 Fax +49 2461 61- 9460 d.terhorst@fz-juelich.demailto:d.terhorst@fz-juelich.de
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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@nmbu.no Home http://arken.nmbu.no/~plesser