Dear NEST Users & Developers!
I would like to invite you to our next fortnightly Open NEST Developer Video Conference today
*Monday November 18, at 11:30 CET (UTC+0100).*
As usual, in the Project team round, a contact person of each team will give a short statement summarizing ongoing and planned work in the team and highlight cross-cutting points that need discussion among the teams. The remainder of the meeting we would go into a more in-depth discussion of topics that came up on the mailing list or that are suggested by the teams.
Feel free to join the meeting also if it’s just to bring your own quick questions for direct discussion in the in-depth section.
Agenda
* Welcome
* Review of NEST User Mailing List
* Project team round
* In-depth discussion
The agenda for this meeting is also available online, see https://github.com/nest/nest-simulator/wiki/2024-11-18-Open-NEST-Developer-… <https://github.com/nest/nest-simulator/wiki/2024-11-18-Open-NEST-Developer-…>
Looking forward to seeing you soon!
Cheers,
Dennis Terhorst
Log-in information
We use a virtual conference room provided by DFN <https://www.dfn.de/en/> (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 <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 <mailto: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 <http://vcc.zih.tu-dresden.de/index.php?linkid=1.1.3.4>
--
Dipl.-Phys. Dennis Terhorst
Coordinator Software Development
Institute for Advanced Simulation (IAS-6)
Computational and Systems Neuroscience
&
JARA-Institute Brain Structure-Function Relationships (INM-10)
Institute of Neuroscience and Medicine
Jülich Research Center, Member of the Helmholz Association
52425 Jülich, Germany
http://www.csn.fz-juelich.de/
Phone +49 2461 61-85062
----------------------------------------------------------------------
Forschungszentrum Jülich GmbH
52425 Jülich
Sitz der Gesellschaft: Jülich
Eingetragen im Handelsregister des Amtsgerichts Düren Nr. HR B 3498
Vorsitzender des Aufsichtsrats: MinDir Stefan Müller
Geschäftsführung: Prof. Dr. Astrid Lambrecht (Vorsitzende),
Karsten Beneke (stellv. Vorsitzender), Prof. Dr. Ir. Pieter Jansens
----------------------------------------------------------------------
Hello everyone,
I am Shavika Rastogi, a PhD student at the International Centre for
Neuromorphic Systems, Western Sydney University, Australia. I currently use
NEST and NESTML to write and test any arbitrary neuron model. Before
writing my own neuron model, I wanted to test neuron models already
existing in NESTML. I am using NEST and NESTML using docker.
I am running the Izhikevich tutorial available in the documentation (
https://nestml.readthedocs.io/en/latest/tutorials/izhikevich/nestml_izhikev…).
As per this tutorial, we can generate and build code using the following
statement :
"module_name,neuron_model_name=NESTCodeGeneratorUtils.generate_code_for("izhikevich_solution.nestml")"
When I am using this function, I get the following error :
"AttributeError: 'NESTCodeGeneratorUtils' object has no attribute
'generate_code_for'"
Does anyone know whether the generate_code_for() function exists in
the NESTCodeGeneratorUtils package? If not, what could be the alternative
function we can use for generating and building neuron models ?
Thanks in advance.
With Warm Regards
Shavika Rastogi, Research Scholar (Dual Award PhD)
International Centre for Neuromorphic Systems
The MARCS Institute of Brain, Behaviour and Development
Western Sydney University
Sydney, Australia
&
Biocomputation Research Group
University of Hertfordshire, UK
Hello everyone,
quick update on my problem: I was using the latest .nestml models from the
main branch with NESTML version 8.0.0-rc3. There is a slight difference
between these and apparently that caused it.
It works now and I hope everyone has a great weekend.
Kind regards,
Jona
Dear NESTML enthusiasts,
I'm trying to do the NESTML dopamine-modulated STDP synapse tutorial (
https://nestml.readthedocs.io/en/latest/tutorials/stdp_dopa_synapse/stdp_do…)
and get an error during the first code generation (see bottom of the
message). This is the line where it fails:
NESTCodeGeneratorUtils.generate_code_for("../../../models/neurons/iaf_psc_delta_neuron.nestml",
nestml_stdp_dopa_model, ...)
I am running the tutorial notebook as is, except for a change in the neuron
model path. I changed it like this:
NESTCodeGeneratorUtils.generate_code_for("iaf_psc_delta_neuron.nestml",
nestml_stdp_dopa_model, ...)
With this model
https://github.com/nest/nestml/blob/master/models/neurons/iaf_psc_delta_neu…
in
the same folder as the notebook.
I am using NESTML version 8.0.0rc3 and Nest 3.8.
If I only generate code for the neuron model everything is fine.
module_name, neuron_model_name = NESTCodeGeneratorUtils.generate_code_for(
"iaf_psc_delta_neuron.nestml")
[100%] Built target
nestml_24dea23d173448c9b2a52d4f6a232dbd_module_module Install
the project...
Additionally, in the SFA tutorial I am able to change the neuron model and
run it without any problems (
https://nestml.readthedocs.io/en/latest/tutorials/spike_frequency_adaptatio…
).
With all of that said, here is the error:
[1,GLOBAL, INFO]: List of files that will be processed:
[2,GLOBAL, INFO]: /home/jona/rstdp-gym/iaf_psc_delta_neuron.nestml
[3,GLOBAL, INFO]: /home/jona/rstdp-gym/neuromodulated_stdp_synapse.nestml
[4,GLOBAL, INFO]: Target platform code will be generated in directory:
'/home/jona/rstdp-gym/target'
[5,GLOBAL, INFO]: Target platform code will be installed in directory:
'/tmp/nestml_target_8uqeeze7'
-- N E S T --
Copyright (C) 2004 The NEST Initiative
Version: 3.8.0
Built: Aug 27 2024 04:33:09
This program is provided AS IS and comes with
NO WARRANTY. See the file LICENSE for details.
Problems or suggestions?
Visit https://www.nest-simulator.org
Type 'nest.help()' to find out more about NEST.
[6,GLOBAL, INFO]: The NEST Simulator version was automatically detected as:
v3.8.0
[7,GLOBAL, INFO]: Given template root path is not an absolute path.
Creating the absolute path with default templates directory
'/home/jona/mambaforge/envs/neuro/lib/python3.11/site-packages/pynestml/codegeneration/resources_nest/point_neuron'
[8,GLOBAL, INFO]: Given template root path is not an absolute path.
Creating the absolute path with default templates directory
'/home/jona/mambaforge/envs/neuro/lib/python3.11/site-packages/pynestml/codegeneration/resources_nest/point_neuron'
[9,GLOBAL, INFO]: Given template root path is not an absolute path.
Creating the absolute path with default templates directory
'/home/jona/mambaforge/envs/neuro/lib/python3.11/site-packages/pynestml/codegeneration/resources_nest/point_neuron'
[10,GLOBAL, INFO]: The NEST Simulator installation path was automatically
detected as: /home/jona/mambaforge/envs/neuro
[11,GLOBAL, INFO]: Start processing
'/home/jona/rstdp-gym/iaf_psc_delta_neuron.nestml'!
[13,GLOBAL, INFO]: Start processing
'/home/jona/rstdp-gym/neuromodulated_stdp_synapse.nestml'!
[14,GLOBAL, ERROR]: Error occurred during parsing: abort
[15,iaf_psc_delta_neuron_nestml, WARNING, [43:0;85:0]]: Model
'iaf_psc_delta_neuron_nestml' contains errors. No code generated!
line 37:13 mismatched input '(' expecting NEWLINE
line 39:4 extraneous input 'onReceive' expecting {<EOF>, NEWLINE, 'model'}
line 40:8 extraneous input ' ' expecting {<EOF>, NEWLINE, 'model'}
line 40:4 extraneous input ' ' expecting {<EOF>, NEWLINE, 'model'}
line 43:8 extraneous input ' ' expecting {<EOF>, NEWLINE, 'model'}
line 46:8 extraneous input 'c' expecting {<EOF>, NEWLINE, 'model'}
line 46:4 extraneous input ' ' expecting {<EOF>, NEWLINE, 'model'}
line 49:8 extraneous input ' ' expecting {<EOF>, NEWLINE, 'model'}
line 52:8 extraneous input 'c' expecting {<EOF>, NEWLINE, 'model'}
line 55:8 extraneous input 'emit_spike' expecting {<EOF>, NEWLINE, 'model'}
line 55:4 extraneous input ' ' expecting {<EOF>, NEWLINE, 'model'}
line 59:8 extraneous input ' ' expecting {<EOF>, NEWLINE, 'model'}
line 63:8 extraneous input 'w' expecting {<EOF>, NEWLINE, 'model'}
line 64:8 extraneous input 'w' expecting {<EOF>, NEWLINE, 'model'}
line 65:8 extraneous input 'c' expecting {<EOF>, NEWLINE, 'model'}
line 66:8 extraneous input 'n' expecting {<EOF>, NEWLINE, 'model'}
line 66:0 extraneous input '\n' expecting {<EOF>, NEWLINE, 'model'}
Any help is appreciated.
Kind regards,
Jona
Dear NEST Users & Developers!
I would like to invite you to our next fortnightly Open NEST Developer Video Conference today
*Monday November 4, at 11:30 CET (UTC+0100).*
As usual, in the Project team round, a contact person of each team will give a short statement summarizing ongoing and planned work in the team and highlight cross-cutting points that need discussion among the teams. The remainder of the meeting we would go into a more in-depth discussion of topics that came up on the mailing list or that are suggested by the teams.
Feel free to join the meeting also if it’s just to bring your own quick questions for direct discussion in the in-depth section.
Agenda
* Welcome
* Review of NEST User Mailing List
* Project team round
* In-depth discussion
The agenda for this meeting is also available online, see https://github.com/nest/nest-simulator/wiki/2024-11-04-Open-NEST-Developer-… <https://github.com/nest/nest-simulator/wiki/2024-11-04-Open-NEST-Developer-…>
Looking forward to seeing you soon!
Cheers,
Dennis Terhorst
Log-in information
We use a virtual conference room provided by DFN <https://www.dfn.de/en/> (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 <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 <mailto: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 <http://vcc.zih.tu-dresden.de/index.php?linkid=1.1.3.4>
--
Dipl.-Phys. Dennis Terhorst
Coordinator Software Development
Institute for Advanced Simulation (IAS-6)
Computational and Systems Neuroscience
&
JARA-Institute Brain Structure-Function Relationships (INM-10)
Institute of Neuroscience and Medicine
Jülich Research Center, Member of the Helmholz Association
52425 Jülich, Germany
http://www.csn.fz-juelich.de/
Phone +49 2461 61-85062
----------------------------------------------------------------------
Forschungszentrum Jülich GmbH
52425 Jülich
Sitz der Gesellschaft: Jülich
Eingetragen im Handelsregister des Amtsgerichts Düren Nr. HR B 3498
Vorsitzender des Aufsichtsrats: MinDir Stefan Müller
Geschäftsführung: Prof. Dr. Astrid Lambrecht (Vorsitzende),
Karsten Beneke (stellv. Vorsitzender), Prof. Dr. Ir. Pieter Jansens
----------------------------------------------------------------------
The simulation of C.elegans now is implemented in a multi processing
environment. The simulation of each individual object and various
observation tools such as visualisation, matplotlib spike data plotting and
configuration of the simulation parameters have their own process.
An issue has arisen with only one object being simulated in that the
execution 'time' for the constant 'simulation step time', increases with
subsequent call to pynn.nest.Simulate(self.simulation_step).
I presume nest continues the simulation from the previous iteration state.
A crude plot suggests that the time increase is linear. Eventually the
simulation stalls.
I have a recorder connected to each of the 302 nodes and multiple recorders
connected to some of the nodes. These use multiprocessor queues and a
manged list to transfer data and as far as I can tell they do not overflow.
I have disabled the recorders by not connecting them to the neurons and the
phenomenon persists. It looks as if the issue is in the nest simulation.
I have increased the process priority to -1. It does not help.
Also does anyone know of the work of Ramin Hasani at Wien. He seems to have
done the same thing and is now using 19 neurons to steer a car. How can I
get a copy of the report of work done by him and his students?
Peter Mason
