Hello Rachael,
Could you post a minimal script or Jupyter notebook reproducing the problem? Does the problem only occur on the Neurorobotics platform or can you reproduce it locally on your computer
as well?
Best regards,
Hans Ekkehard
--
Prof. Dr. Hans Ekkehard Plesser
Head, Department of Data Science
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
On 13/04/2022, 13:20, "Rachael Stentiford" <rachael.stentiford@brl.ac.uk> wrote:
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Apologies for so many emails. Looks like i jumped the gun a little and i am still having this issue. So if anyone does have any ideas, I would welcome the help.
Cheers,
Rachael
From: Rachael Stentiford <rachael.stentiford@brl.ac.uk>
Sent: Wednesday, April 13, 2022 11:46 AM
To: users@nest-simulator.org <users@nest-simulator.org>
Subject: Re: Kernel death when recording from 300+ cells for 2mins+
Looks like i have solved this issue now.
For those interested in the solution, i have switched from using the efficient method for splitting a simulation into multiple intervals
described in the docs, which has the clean up functions outside of the loop, to just using nest.Simulate() in the loop so the clean up functions are called each time.
Cheers,
Rachael
From: Rachael Stentiford <rachael.stentiford@brl.ac.uk>
Sent: Tuesday, April 12, 2022 6:32 PM
To: users@nest-simulator.org <users@nest-simulator.org>
Subject: [NEST Users] Kernel death when recording from 300+ cells for 2mins+
Dear all,
I hope you are doing well. I am having an issue using pyNEST which i haven't come across before and have been unable
to find answer to elsewhere. I am working with Python 3.8 and Nest 2.18 (which is the version currently used by the Neurorobotics platform).
I have a network of 6 x 360 neurons, and i am trying to record spikes from 360 of these. However, I am finding that
if i try to simulate for more than ~2 mins i run into problems. In jupyter notebooks I get a kernel death error, but even just running a standard python script NEST dies. I
can simulate for longer if i only record from a single neuron.
Previously I have used networks of 4 x 180 neurons and recorded from 180 for 10+ minutes without an issue.
I have tried splitting up the simulation into multiple intervals, as explained in the docs, and saving spikes in between.
This would mean there are fewer spikes to save each time, but this doesn't appear to help.
Ideally i would like to record from 360 cells for around 30 mins. Have any of you come across a similar issue in the
past, or have any suggestions for how I could fix this issue?
Thanks for your help!
Rachael
-------------------------
Dr Rachael Stentiford (she/her)
Research Associate in Neurobotics
Bristol Robotics Laboratory
University of the West of England
Bristol
BS16 1QY