Dear nest developer,
Is there a pre-implemented nest model
allowing multiplicative aggregation of compartments/dendritic branches.
I am looking for a model that will allow
multiplicative aggregation of two dendritic branches at the soma.
I very much appreciate any support provided.
Best regards,
Benedikt
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
Dear NEST Users & Developers!
I would like to invite you to our next bi-weekly Open NEST Developer
Video Conference, today
Monday 17 February, 11.30-12.30 CET (UTC+1).
For details how to log in see below.
As usual the agenda for this meeting is also available online, see
https://github.com/nest/nest-simulator/wiki/2020-02-17-Open-NEST-Developer-…
Agenda
* Welcome
* Review of NEST User Mailing List
* Review of open Github Pull Request
* Review of open Github Issues
Looking forward to seeing you soon!
best,
Dennis Terhorst
------------------
Log-in information
------------------
We use a virtual conference room provided by DFN (Deutsches Forschungsnetz).
You can use the web client to connect. We however encourage everyone to
use a headset for better audio quality or even a proper video
conferencing system (see below) or software when available.
Web client
* Visit https://conf.dfn.de/webapp/conference/97938800
* Enter your name and allow your browser to use camera and microphone
* The conference does not need a PIN to join, just click join and you're in.
In case you see a dfnconf logo and the phrase "Auf den
Meetingveranstalter warten", just be patient, the meeting host needs to
join first (a voice will tell you).
VC system/software
How to log in with a video conferencing system, depends on you VC system
or software.
- Using the H.323 protocol (eg Polycom): vc.dfn.net##97938800 or
194.95.240.2##97938800
- Using the SIP protocol:97938800@vc.dfn.de
- By telephone: +49-30-200-97938800
For those who do not have a video conference system or suitable
software, Polycom provides a pretty good free app for iOS and Android,
so you can join from your tablet (Polycom RealPresence Mobile, available
from AppStore/PlayStore). Note that firewalls may interfere with
videoconferencing in various and sometimes confusing ways.
For more technical information on logging in from various VC systems,
please see
http://vcc.zih.tu-dresden.de/index.php?linkid=1.1.3.4
Hello NEST Users,
I wanted to create a neural network with generalized LIF Neurons. I do not want any exponential or alpha shaped PSCs. Since I cannot draw to describe its shape, I am posting a link from google images to help understand what I mean by a generalized LIF.
https://www.google.com/url?sa=i&url=https%3A%2F%2Fwww.researchgate.net%2Ffi…
Thanks in advance!
Hi NEST-Team,
To use the NEST-Simluator in an interactive installation, I would need to
1) have access to the spike in the network in realtime, and
2) send signals (spikes) to neurons in the simulation in realtime.
For 1), I could imagine writing the spike-times to a file and then reading that file while the simulation is running. However, I currently don’t see an option for 2). Then I heard that you are actually working on module that would enable realtime I/O-access. Is that the case? And, if so, is there a timeline?
Best,
Benjamin
-- -- --
Dr. Benjamin Staude | Paul-Lincke-Ufer 7 | 10999 Berlin | benjamin.staude(a)gmail.com
Hi,
I wanted to know how to stop printing the simulation details on my terminal window. For instance I can see the number of open mpi process, simulation time being printed every time I run a model. I do not want to see the details on my terminal screen, is there a way to do it?
Hi NEST-team,
I would like to run a simulation of > 1000 neurons, and to make my
computing time faster I am looking into how to use parallel computing with
NEST.
I have seen this <https://www.nest-simulator.org/parallel-computing/> page
but I can't seem to find anything about using the cloud (e.g. google cloud,
colab etc.) and the use of GPU's. I am quite new to this so it could be I
missed something.
- Is it possible to use a GPU for the nest simulations?
- Are the some resources I could learn from?
Thank you!
Best,
Daphne
Hello,
I have an issue regarding random generation in nest version 2.18 with
Python3.6.
I attach a small python script that replicates my issue (less than 50
lines).
In short, I am trying to create two Poisson generators and connect them to
the same neuron.
I noticed that if I reverse the order by which these Poisson generators are
created (using the nest.Create()) function, then I get a different membrane
potential response over time.
In the code, noise_exc is created before noise_inh. If that order is
reversed, the plot is different.
My hunch is that this has to do with how nest generates random numbers.
So I tried to force the creation of Poisson generators by providing a seed
(lines 15 and 18).
However this behavior persists.
Do you have any insights as to why this happens?
At the end of the script (lines 32-43) I provide a trivial case of the
desired behavior I am trying to replicate.
Thank you for your time
Angeliki
--
[image: Kth Logo]
Angeliki Papadimitriou
Research EngineerKTH Royal Institute of Technology
*School of Electrical Engineering and Computer Science (EECS)**Division of
Computational Science and Technology (CST)*
Computational Brain Science Unit
Room 4438, Floor 4, Lindstedtsvägen 5
11428 Stockholm, Sweden
angpap(a)kth.se <namn(a)kth.se>
Dear NEST Users & Developers!
I would like to invite you to this years first Open NEST Developer Video Conference, tomorrow
Monday 20 January, 11.30-12.30 CET (UTC+1).
As usual the agenda for this meeting is also available online, see https://github.com/nest/nest-simulator/wiki/2020-01-20-Open-NEST-Developer-…
For details how to log in see below.
Agenda
* Welcome
* Preparing NEST 2.20 release
* Preparing merge of nest-3 branch to master
* Review of NEST User Mailing List
* Review of open Github Pull Request
* Review of open Github Issues
Looking forward to seeing you soon!
Hans Ekkehard Plesser
------------------
Log-in information
------------------
We use a virtual conference room provided by DFN (Deutsches Forschungsnetz).
You can use the web client to connect. We however encourage everyone to use a headset for better audio quality or even a proper video conferencing system (see below) or software when available.
Web client
* Visit https://conf.dfn.de/webapp/conference/97938800
* Enter your name and allow your browser to use camera and microphone
* The conference does not need a PIN to join, just click join and you're in.
In case you see a dfnconf logo and the phrase "Auf den Meetingveranstalter warten", just be patient, the meeting host needs to join first (a voice will tell you).
VC system/software
How to log in with a video conferencing system, depends on you VC system or software.
- Using the H.323 protocol (eg Polycom): vc.dfn.net##97938800 or 194.95.240.2##97938800
- Using the SIP protocol:97938800@vc.dfn.de
- By telephone: +49-30-200-97938800
For those who do not have a video conference system or suitable
software, Polycom provides a pretty good free app for iOS and Android,
so you can join from your tablet (Polycom RealPresence Mobile, available
from AppStore/PlayStore). Note that firewalls may interfere with
videoconferencing in various and sometimes confusing ways.
For more technical information on logging in from various VC systems,
please see
http://vcc.zih.tu-dresden.de/index.php?linkid=1.1.3.4
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