I was using an old version of nest (3.5) and nestml. Someone sent me a nestml model, and that worked. I wanted to make my own model, but the tutorials had a different format. In particular, it seems like the first line of code in the tutorials start with model, and the old version started with neuron of synapse.
So, I thought it was time to upgrade, so installed nest 3.7, and pip-ed nestml. (I also installed PyNN as that's the way I typically work.) When I imported generate_target (through python 3.12), I got the typical PyGSL warning; I think that's because I'm using python 3.12 not 3.11, and I don't think it matters in this case.
Then I ran the generate_target and I got an error mismatched input 'model' expecting {newline, 'neuron', 'synapse}
I expect there's something like a yacc table that specifies the syntax, and somehow I've got the old syntax.
I've tried it with several version of nestml 7.0.2, 7.0.0, 6.0.0 and 5.0.0. I think 5.0.0 had the old syntax. I've tried several models from the library, and the Izhikevich tutorial.
Any thoughts about how to fix it?
-Chris
Hi,
I've been trying to read through the source code to understand this, but I'm still having trouble figuring it out.
From what I can see, the neurons are updated using a for loop, meaning each neuron is updated one at a time. The update function for each neuron can run for multiple timesteps, but I'm unclear on how its B_.input_buffer_ gets updated while the update function is running. If it doesn't get updated during this process, wouldn't it miss some spike events? Additionally, how does the code ensure that neurons updated one at a time for all simulation steps do not miss any spike events?
Thank you for your help!
Best regards,
Anh Phan
Hi!
After using some PyNEST functions and modifying the C++ implementation of DumpLayerConnections(), I was thinking on a possible further improvement of this function (or creating a new function). But since I do not know the design and architecture of C++ nestkernel code, I prefer to ask.
In my code I normalize the presynaptic connections of every neuron. To do this, I originally do something like
for i in range(len(target_layer))
conn[i] = nest.GetConnections(source_layer, target_layer, synapse_model)
normalize(conn)
Since I am using MPI and the loop iterates over all the neurons, I modified the previous code to
local_nodes = nest.GetLocalNodeCollection(target_layer)
local_nodes = nest.NodeCollection(local_nodes)
for i in range(len(local_nodes))
conn[i] = nest.GetConnections(source_layer, local_nodes, synapse_model)
normalize(conn)
This last code is faster that the previous one (I guess that local_nodes variable is local to every MPI process and, as a consequence, GetConnections() is more efficient because it only works with local nodes instead of with all of them).
Using the idea of the GetLocalNodeCollection(), I was thinking it could be used into the C++ implementation of DumpLayerConnections(). Presently, this function obtain all the connections between source and target layers. Could it be possible to call the equivalent C++ implementation of GetLocalCollection()? I understand that the problem is that, since DumpLayerConnections() needs the spatial information of the layers, the node collections obtained with GetLocalNodeCollection() (I guess similarly its C++ implementation) does not have this spatial information.
As a second possibility, I was thinking on adding a new method (GetSpatialInformation()) and enhancing DumpLayerConnections() (or add a new function). The GetSpatialInformation() function could return the spatial information of a collection of nodes (the ones obtained by GetLocalNodeCollection() ). The DumpLayerConnections() (or a new function) could be enhanced by changing the target layer parameter to a pair of parameters that contain the local nodes collection and their spatial information. Something like DumpLaterConnections(source_layer, local_nodes_collection, spatial_information, synapse_model). This way DumpLayerConnections() will only used local nodes and would be much faster.
Sorry for the technical email.
Xavier
Dear Colleagues,
This mail is mainly for those of you who contribute to NEST Simulator development.
NumPy 2.0, released last Sunday, has some minor changes that broke existing tests and examples. This has now been fixed in the master branch (PRs #3226, #3227). Please pull master into all your branches—otherwise, the testsuite will fail on Github and your contributions cannot be merged.
Best,
Hans Ekkehard
--
Prof. Dr. Hans Ekkehard Plesser
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(a)nmbu.no<mailto:hans.ekkehard.plesser@nmbu.no>
Home http://arken.nmbu.no/~plesser
Dear NEST Users & Developers!
I would like to invite you to our next fortnightly Open NEST Developer Video Conference today
*Monday June 3, at 11:30 CEST (UTC+0200).*
Despite many people attending conferences this week, we will briefly meet to offer attention also to smaller questions or more general topics that you may bring. The Project team round, might however be quite short today.
Feel free to join the meeting and bring your own quick questions for direct discussion or just to hear what's going on in and around NEST.
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/2024-06-03-Open-NEST-Developer-… <https://github.com/nest/nest-simulator/wiki/2024-06-03-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 Juelich GmbH
52425 Juelich
Sitz der Gesellschaft: Juelich
Eingetragen im Handelsregister des Amtsgerichts Dueren Nr. HR B 3498
Vorsitzender des Aufsichtsrats: MinDir Stefan Müller
Geschaeftsfuehrung: Prof. Dr. Astrid Lambrecht (Vorsitzende),
Karsten Beneke (stellv. Vorsitzender), Dr. Ir. Pieter Jansens
----------------------------------------------------------------------
Dear NEST Users,
We are looking forward to an exciting Virtual NEST Conference 2024 on Monday/Tuesday 17./18. June 2024.
This years program includes keynotes by
Tadashi Yamazaki, University of Electro-Communications, Japan
Diversity and inclusion: Distributed simulation of multiple brain and body models in multiple simulators on multiple computers across multiple organizations
Benedetta Gambosi, University of Pavia
A multiarea model predicts the changes in thalamocortical beta oscillations caused by dopamine depletion in basal ganglia and cerebellum
Tobias Gemmeke, RWTH Aachen
Accelerated Simulation of Biological Neural Networks
Behnam Ghazinouri, Ruhr-Universität Bochum
The attractor dynamics of behavioral flexibility in spatial and reversal learning
complemented by contributed talks, posters and a workshop Introducing Arbor.
For the full program an to register, please see https://nest-simulator.org/conference.
Registration deadline is this FRIDAY, 7 June 2024.
We are looking forward to seeing you at the NEST Conference 2024!
Hans Ekkehard Plesser
--
Prof. Dr. Hans Ekkehard Plesser
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(a)nmbu.no<mailto:hans.ekkehard.plesser@nmbu.no>
Home http://arken.nmbu.no/~plesser